Papers that used NIH HPC (Biowulf) resources

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2026 to date (32 papers)

Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach Alves, G; Hamaneh, MB; Ogurtsov, AY; Yu, YK; , J Am Soc Mass Spectrom, DOI://10.1021/jasms.5c00332 (2026)
An insight into the ovary and midgut transcriptome of Dermacentor nitens tick Lu, S; Bosio, CF; Andrade-Silva, V et al. Ticks Tick Borne Dis, DOI://10.1016/j.ttbdis.2025.102600 (2026)
Children's state anxiety before MRI scanning and resting state functional connectivity in large scale brain networks Qamar, P; Díaz, DE; Benson, BE et al. Sci Rep, DOI://10.1038/s41598-025-34410-8 (2026)
PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments Polash, AH; Hafner, M; , Nucleic Acids Res, DOI://10.1093/nar/gkag062 (2026)
Eos plays a critical role in Treg homeostasis and modulates the function of recirculating thymic Tregs in the control of Treg development Xie, X; Thornton, AM; Tanwar, S et al. Cell Rep, DOI://10.1016/j.celrep.2025.116838 (2026)
Imaging spatial transcriptomics reveals molecular patterns underlying accumulation of p-Ser129 α-synuclein in a transgenic mouse model Horan-Portelance, L; Iba, M; Acri, DJ et al. NPJ Parkinsons Dis, DOI://10.1038/s41531-025-01246-y (2026)
Early axonal degeneration linked to clinical decline in Alzheimer's disease progression revealed with diffusion MRI Gong, Z; Laporte, JP; Guo, AY et al. J Clin Invest, DOI://10.1172/JCI196638 (2026)
The key role of cheaters in the persistence of cooperation Babajanyan, SG; Wolf, YI; Koonin, EV; Rochman, ND; , BMC Biol, DOI://10.1186/s12915-025-02492-5 (2026)
Impact of Single Halogen Atom Substitutions on Antiviral Profile of Inhibitors Targeting SARS-CoV‑2 Main Protease Bulut, H; Higashi-Kuwata, N; Ogata-Aoki, H et al. ACS Omega, DOI://10.1021/acsomega.5c10895 (2026)
Forecasting drug resistant HIV protease evolution Aggarwal, M; Periwal, V; , PLoS Comput Biol, DOI://10.1371/journal.pcbi.1013913 (2026)
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis Liu, F; He, R; Sheeley, T et al. BMC Bioinformatics, DOI://10.1186/s12859-025-06339-2 (2026)
Linking subjective experience of anxiety to brain function using natural language processing Kirk, PA; Qamar, P; Lentz, J et al. Soc Cogn Affect Neurosci, DOI://10.1093/scan/nsaf099 (2026)
A quorum-sensing molecule from Pseudomonas aeruginosa induces defensive multicellularity in a coinfecting pathogen Katharios-Lanwermeyer, S; Zarrella, TM; Godsil, M et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2513122123 (2026)
Macrophages Mediate Mesoscale Brain Mechanical Homeostasis So, WY; Johnson, B; Gordon, PB et al. Adv Mater, DOI://10.1002/adma.202517493 (2026)
Mesoscopic analysis of GABAergic marker expression in acetylcholine neurons in the whole mouse brain Goral, RO; Roy, S; Co, CA et al. iScience, DOI://10.1016/j.isci.2025.114531 (2026)
Genetic contributions to Alzheimer's disease and frontotemporal dementia in admixed Latin American populations Acosta-Uribe, J; Piña-Escudero, SD; Cochran, JN et al. NPJ Dement, DOI://10.1038/s44400-025-00025-z (2026)
Heritability and Transcriptional Impact of JAK3, STAT5A and STAT6 Variants in a Tyrolean Family Lee, HK; Haikarainen, T; Caf, Y et al. Int J Mol Sci, DOI://10.3390/ijms27020913 (2026)
LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiation Kwon, H; Kim, J; Zhou, L; Dean, A; , Nucleic Acids Res, DOI://10.1093/nar/gkag064 (2026)
Sequential Event Rate Monitoring Kim, DY; Han, SM; , Stat Med, DOI://10.1002/sim.70359 (2026)
Multi-site harmonization for magnetoencephalography spectral power data Nugent, AC; Namyst, AM; Carver, FW et al. Imaging Neurosci (Camb), DOI://10.1162/IMAG.a.1099 (2026)
Contralateral breast cancer after radiotherapy and hormone therapy in two cohorts of US breast cancer survivors Veiga, LHS; Gierach, GL; Smith, SA et al. Br J Cancer, DOI://10.1038/s41416-025-03240-w (2026)
The relationship between the Ewald sphere and exit wave explored using focal series electron micrographs Heymann, JB IUCrJ, DOI://10.1107/S2052252525010796 (2026)
STAT3 SH2 Domain Aspartic Acid 661 Mutations Activate Immune Gene Programs Lee, HK; Cho, G; Chen, J et al. J Cell Mol Med, DOI://10.1111/jcmm.71015 (2026)
Impact of rare JAK/STAT germline mutations on vaccination-induced innate immune responses in a Tyrolian population Hennighausen, L; Cho, G; Lee, SG et al. Int J Biol Sci, DOI://10.7150/ijbs.124098 (2026)
Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells Hor, JL; Schrom, EC; Wong-Rolle, A et al. Nature, DOI://10.1038/s41586-025-09440-x (2026)
Modelling the effects of human SUR1 R1420H variation on insulin secretory function using isogenic iPSC-derived pancreatic islets Nair, AK; Barkho, K; Cheranda, KP et al. Diabetologia, DOI://10.1007/s00125-025-06605-1 (2026)
Enhancer Rewiring Orchestrates Inflammation and Loss of Cell Identity During Muscle Stem Cell Aging Shi, C; Yang, N; Pizano, E et al. Aging Cell, DOI://10.1111/acel.70289 (2026)
A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy Thayer, JA; Petersen, JD; Huang, X et al. EMBO J, DOI://10.1038/s44318-025-00604-z (2026)
Using large language models to detect outcomes in qualitative studies of adolescent depression Xin, AW; Nielson, DM; Krause, KR et al. J Am Med Inform Assoc, DOI://10.1093/jamia/ocae298 (2026)
The structural heterogeneity of AKT autoinhibition Xu, L; Eren, M; Weako, J et al. Protein Sci, DOI://10.1002/pro.70420 (2026)
Artificial intelligence-based models for quantification of intra-pancreatic fat deposition and their clinical relevance: a systematic review of imaging studies Joshi, T; Virostko, J; Petrov, MS; , Eur Radiol, DOI://10.1007/s00330-025-11808-6 (2026)
(N)-Methanocarba-adenosines as monoamine transporter allosteric inhibitors: Extended N6 groups for bitopic stabilization Tosh, DK; Pavan, M; Kozell, LB et al. Eur J Med Chem, DOI://10.1016/j.ejmech.2025.118167 (2026)

2025 (292 papers)

Molecular basis for the regulation of membrane proteins through preferential lipid solvation Bernhardt, N; Ozturk, TN; Zhang, S et al. Nat Chem Biol, DOI://10.1038/s41589-025-02032-w (2025)
The Time-Dependent Association Between Irritable Bowel Syndrome and All-Cause and Cause-Specific Mortality in the NIH-AARP Cohort Study Gutiérrez-Torres, DS; Li, F; Liao, LM et al. Am J Gastroenterol, DOI://10.14309/ajg.0000000000003861 (2025)
Spatial Analysis of Hereditary Diffuse Gastric Cancer Reveals Indolent Phenotype of Signet Ring Cell Precursors Gallanis, AF; Gamble, LA; Oguz, C et al. Mol Cancer Res, DOI://10.1158/1541-7786.MCR-24-1039 (2025)
Bitopic A3 Adenosine Receptor Molecular Probes: Positive Allosteric Modulation and Noncanonical Activation Kurma, SH; Pavan, M; Wan, TC et al. J Med Chem, DOI://10.1021/acs.jmedchem.5c01985 (2025)
Methylphenidate reorganizes cortical hierarchy through dopaminergic modulation Tomasi, D; Manza, P; Demiral, ŞB et al. Nat Commun, DOI://10.1038/s41467-025-67477-y (2025)
Age-related differences in choroid plexus structural integrity are associated with changes in cognition Gong, Z; de Rouen, A; Zhang, N et al. Fluids Barriers CNS, DOI://10.1186/s12987-025-00749-3 (2025)
A prognostic signature for lung adenocarcinoma in patients who have never smoked Zhao, W; Zhang, T; Hua, X et al. Cancer Discov, DOI://10.1158/2159-8290.CD-25-0581 (2025)
Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma Zhang, T; Zhao, W; Wirth, C et al. Nature, DOI://10.1038/s41586-025-09825-y (2025)
Single-cell RNA sequencing reveals genes relevant to periodontal therapy and periodontitis Sekiguchi, R; Martin, D; Yamada, KM; , Physiol Genomics, DOI://10.1152/physiolgenomics.00002.2025 (2025)
Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes Potapova, TA; Kostos, P; McKinney, S et al. Cell Genom, DOI://10.1016/j.xgen.2025.101031 (2025)
Ecological determinants of altruism in prokaryote antivirus defense Biba, DA; Makarova, KS; Wolf, YI et al. Biol Direct, DOI://10.1186/s13062-025-00699-8 (2025)
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones Hirsch, MG; Pal, S; Rashidi Mehrabadi, F et al. Cell Syst, DOI://10.1016/j.cels.2024.11.013 (2025)
In situ structural mechanism of epothilone-B-induced CNS axon regeneration Bodakuntla, S; Taira, K; Yamada, Y et al. Nature, DOI://10.1038/s41586-025-09654-z (2025)
SLICE (SMARTS and Logic In ChEmistry): fast generation of molecules using advanced chemical synthesis logic and modern coding style Ilemo, SN; Delannée, V; Grushin, O et al. J Cheminform, DOI://10.1186/s13321-025-01119-9 (2025)
Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations McElderry, JP; Zhang, T; Zhao, W et al. Nat Commun, DOI://10.1038/s41467-025-66780-y (2025)
Modulators of gene amplification alter evolution of antibiotic resistance in Staphylococcus aureus Silva, KPT; Martini, AM; Khare, A; , PLoS Genet, DOI://10.1371/journal.pgen.1012011 (2025)
Human O-GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains Nyenhuis, SB; Steenackers, A; Mukherjee, MM et al. Commun Chem, DOI://10.1038/s42004-025-01813-7 (2025)
Investigation of the transcriptional impact of rare germline JAK/STAT variants found in a Tyrolean alpine community Hennighausen, L; Haikarainen, T; Lee, SG et al. BMC Genomics, DOI://10.1186/s12864-025-12307-0 (2025)
Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets Thakur, R; Xu, M; Sowards, H et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2025.04.015 (2025)
Post-transplant G-CSF impedes engraftment of gene-edited human hematopoietic stem cells by exacerbating p53-mediated DNA damage response Araki, D; Chen, V; Redekar, N et al. Cell Stem Cell, DOI://10.1016/j.stem.2024.10.013 (2025)
Evolution of a fuzzy ribonucleoprotein complex in viral assembly Zhao, H; Li, T; Hassan, SA et al. Elife, DOI://10.7554/eLife.108922 (2025)
Enhancing chest X-ray datasets with privacy-preserving large language models and multi-type annotations: A data-driven approach for improved classification Bigolin Lanfredi, R; Mukherjee, P; Summers, RM; , Med Image Anal, DOI://10.1016/j.media.2024.103383 (2025)
X chromosome inactivation across primary human tissues is mostly complete, with significant implications for genetic and clinical studies Shriner, D; Doumatey, AP; Lei, L et al. BMC Genomics, DOI://10.1186/s12864-025-12352-9 (2025)
Dual-view microscopy of single-molecule dipole orientations Sun, Y; Wang, Q; , Biophys Rep (N Y), DOI://10.1016/j.bpr.2025.100234 (2025)
GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes Wheeler, W; Wang, D; Zhao, I et al. BMC Bioinformatics, DOI://10.1186/s12859-025-06294-y (2025)
A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology Bohrer, CH; Larson, DR; , PLoS Comput Biol, DOI://10.1371/journal.pcbi.1013796 (2025)
Rare germline JAK/STAT variants in a Korean cohort amplify innate immune responses to vaccination Lee, HK; Cho, G; Huh, JW et al. iScience, DOI://10.1016/j.isci.2025.114110 (2025)
The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A Diederichs, KA; Botos, I; Hayashi, S et al. Nat Commun, DOI://10.1038/s41467-025-66417-0 (2025)
UDP-glucose and MRS2905 agonist-bound states of the purinergic P2Y14 receptor Fay, JF; Kousouros, J; Gao, ZG et al. Commun Biol, DOI://10.1038/s42003-025-09174-6 (2025)
The H4K20-mono-methyltransferase SETD8 promotes global accessibility of infecting herpes simplex virus genomes Arbuckle, JH; Yanez, AA; Baksh, SS et al. J Virol, DOI://10.1128/jvi.01293-25 (2025)
A convenient single-cell assay for the newly synthesized transcriptome reveals FLI1 regulon downregulation during T cell activation Lyu, J; Xu, X; Chen, C; , Cell Rep Methods, DOI://10.1016/j.crmeth.2025.101252 (2025)
A CGG Repeat Expansion in CSNK1E Associated with Progressive Myoclonic Epilepsy with Incomplete Penetrance Akçimen, F; Alvarez Jerez, P; Guliyeva, U et al. Mov Disord, DOI://10.1002/mds.30326 (2025)
Excess CMS morbidity and FEMA declarations: Phenome Wide Association Study of Generalized Linear Model interactions between CMS diagnostic code utilization and FEMA Incident types, 1999-2020 Williams, N Inform Med Unlocked, DOI://10.1016/j.imu.2025.101716 (2025)
NAT10 promotes cancer metastasis by modulating p300/CBP activity through chromatin-associated tRNA Amin, R; Ha, NH; Qiu, T et al. Mol Cell, DOI://10.1016/j.molcel.2025.11.010 (2025)
Epigenetic dysregulation in aged muscle stem cells drives mesenchymal progenitor expansion via IL-6 and Spp1 signaling Riparini, G; Mackenzie, M; Naz, F et al. Nat Aging, DOI://10.1038/s43587-025-01002-0 (2025)
Response of iPSC-derived neurons from individuals with treatment-resistant depression to (2 R,6 R)-hydroxynorketamine and reelin: an exploratory study Johnston, JN; Yuan, P; Kadriu, B et al. Transl Psychiatry, DOI://10.1038/s41398-025-03724-6 (2025)
Interlocking host and viral cis-regulatory networks drive Merkel cell carcinoma Miao, L; Milewski, D; Coxon, A et al. J Clin Invest, DOI://10.1172/JCI188924 (2025)
Examination of HLA-DRB1*15-linked candidate antigens in Still's disease with and without lung disease and features of drug hypersensitivity Kobrin, DM; Brown, DG; Burbelo, PD et al. J Rheumatol, DOI://10.3899/jrheum.2025-0522 (2025)
Large-scale multiomic analysis identifies non-coding somatic driver mutations and nominates ZFP36L2 as a driver gene for pancreatic ductal adenocarcinoma Zhong, J; O'Brien, A; Patel, MB et al. Gut, DOI://10.1136/gutjnl-2025-335152 (2025)
Tissue tropism and functional adaptation of the SARS-CoV-2 spike protein in a fatal case of COVID-19 Johnson, KEE; Stein, S; Boateng, RA et al. J Virol, DOI://10.1128/jvi.00857-25 (2025)
Spatial Profiling Identifies Regionally Distinct Microenvironments and Targetable Immunosuppressive Mechanisms in Pediatric Osteosarcoma Pulmonary Metastases Eigenbrood, J; Wong, N; Mallory, P et al. Cancer Res, DOI://10.1158/0008-5472.CAN-24-3723 (2025)
Radiogenomic Profiling of Prostate Tumors prior to External Beam Radiotherapy Converges on a Transcriptomic Signature of TGF-β Activity Driving Tumor Recurrence Ku, AT; Shankavaram, U; Trostel, SY et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-25-2186 (2025)
Path2Omics Enhances Transcriptomic and Methylation Prediction Accuracy from Tumor Histopathology Hoang, DT; Shulman, ED; Dhruba, SR et al. Cancer Res, DOI://10.1158/0008-5472.CAN-25-4350 (2025)

RNA-RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA-mRNA pairing Luo, X; Zhang, A; Esnault, C et al. Nucleic Acids Res, DOI://10.1093/nar/gkaf1313 (2025)
SMARCAL1 is a new osteosarcoma predisposition gene Rafati, M; Guenther, LM; Egolf, LE et al. J Natl Cancer Inst, DOI://10.1093/jnci/djaf278 (2025)
De novo origin of numerous microproteins in enterobacteria Fesenko, I; Shabalina, SA; Storz, G; Koonin, EV; , Nucleic Acids Res, DOI://10.1093/nar/gkaf1319 (2025)
Tracing low-level structures in cryo-electron tomography Alvarez Brecht, P; Aguilar-Martínez, F; Biertümpfel, C et al. PLoS One, DOI://10.1371/journal.pone.0338502 (2025)
Localized high-risk prostate cancer harbors an androgen receptor activity-low subpopulation susceptible to HER2 inhibition Wilkinson, S; Ku, AT; Lis, RT et al. J Clin Invest, DOI://10.1172/JCI189900 (2025)
P-type ATPase magnesium transporter MgtA acts as a dimer Zeinert, R; Zhou, F; Franco, P et al. Nat Struct Mol Biol, DOI://10.1038/s41594-025-01593-7 (2025)
A 120-y time series of genomes reveals the consequences of closed breeding in German Shepherd Dogs Scarsbrook, L; Spatola, GJ; Dreger, DL et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2421755122 (2025)
Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation Hatton, GH; James, SR; Mason, AS et al. Sci Adv, DOI://10.1126/sciadv.aea6124 (2025)
Subcontinental genetic variation in the All of Us Research Program: Implications for biomedical research Gouveia, MH; Meeks, KAC; Borda, V et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2025.04.012 (2025)
M-Ras distinct activation scenarios: A mechanistic outlook and targeting Xu, L; Liu, Y; Jang, H; Nussinov, R; , Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2025.11.025 (2025)
KSR1 is a scaffold for the Hippo signaling pathway Sayedyahossein, S; Babu Sait, MR; Li, Z et al. Commun Biol, DOI://10.1038/s42003-025-09009-4 (2025)
A device for simultaneous neural recording and drug infusion in rodents Barbera, G; Beacher, NJ; Lin, DT; , HardwareX, DOI://10.1016/j.ohx.2025.e00721 (2025)
The formation and propagation of human Robertsonian chromosomes de Lima, LG; Guarracino, A; Koren, S et al. Nature, DOI://10.1038/s41586-025-09540-8 (2025)
Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways Kumar, R; Zhang, F; Niphadkar, S et al. Elife, DOI://10.7554/eLife.102287 (2025)
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets Raush, E; Totrov, M; Hoop, CL et al. J Chem Inf Model, DOI://10.1021/acs.jcim.5c01335 (2025)
Pig Taste Cell-derived Organoids Synthesize Insulin Premathilake, HU; Mazucanti, CH; Yao, Q et al. Endocrinology, DOI://10.1210/endocr/bqaf126 (2025)
Boosting reservoir computing with brain-inspired adaptive control of E-I balance Srinivasan, K; Plenz, D; Girvan, M; , Nat Commun, DOI://10.1038/s41467-025-64978-8 (2025)
Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry Li, S; Fatema, K; Sundarraj, N et al. Nat Commun, DOI://10.1038/s41467-025-64631-4 (2025)
Heritability, phenotypic, and genetic correlations across dimensional and categorical models of bipolar disorder in a family sample Arbona-Lampaya, A; Sung, H; D'Amico, A et al. J Affect Disord, DOI://10.1016/j.jad.2024.12.030 (2025)
The Hydractinia Genome Project Portal: multi-omic annotation and visualization of Hydractinia genomic datasets Moreland, RT; Schnitzler, CE; Zhang, S et al. Bioinform Adv, DOI://10.1093/bioadv/vbaf215 (2025)
Fold-Switching Proteins Chakravarty, D; Porter, LL; , Annu Rev Biophys, DOI://10.1146/annurev-biophys-022924-012038 (2025)
Structural basis for dual DNA and RNA specificity of the G-quadruplex-resolving DEAH-box helicase DHX36 Banco, MT; Paul, T; Jiang, J et al. Cell Rep, DOI://10.1016/j.celrep.2025.116136 (2025)
Loss of paired immunoglobin-like type 2 receptor B gene associated with age-related macular degeneration impairs photoreceptor function in mouse retina Dey, PN; Singh, N; Zelinger, L et al. Hum Mol Genet, DOI://10.1093/hmg/ddae161 (2025)
ANTXR1 blockade enhances cardiac function in preclinical models of heart failure Boccella, N; Yu, G; Seaman, S et al. Nat Cardiovasc Res, DOI://10.1038/s44161-025-00725-y (2025)

Single-fibril Förster resonance energy transfer imaging and deep learning reveal concentration dependence of amyloid β 42 aggregation pathways Sohail, SH; Yoo, J; Chung, HS; , PNAS Nexus, DOI://10.1093/pnasnexus/pgaf342 (2025)
Effective in vivo RNA base editing via engineered cytidine deaminase APOBECs fused with PUF proteins Han, W; Yuan, B; Fan, X et al. Nat Commun, DOI://10.1038/s41467-025-64748-6 (2025)
Adipocyte death promotes hepatic infiltration of S100A8+ macrophages and steatotic liver disease progression in mice Guan, Y; Kim, Y; Wang, Y et al. J Clin Invest, DOI://10.1172/JCI190635 (2025)
Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA Chen, Y; Kim, JH; Lee, HS et al. J Mol Evol, DOI://10.1007/s00239-025-10269-1 (2025)
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice Bruno, M; Farhana, SM; Mitra, A et al. Nat Commun, DOI://10.1038/s41467-025-64609-2 (2025)
Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Manzo, G; Borkowski, K; Ovcharenko, I; , Genes (Basel), DOI://10.3390/genes16101223 (2025)
GPC2-CAR T cells have potent preclinical activity against orthotopic medulloblastoma xenografts Okada, R; Fanuzzi, M; Rodriguez, C et al. Mol Ther Oncol, DOI://10.1016/j.omton.2025.201067 (2025)
Risk of clonal hematopoiesis in families exposed to radiation following the Chornobyl accident Machiela, MJ; Wong, WSW; Mai, JZ et al. Carcinogenesis, DOI://10.1093/carcin/bgaf056 (2025)
A powerful penalized multinomial logistic regression approach Fuetterer, C; Nalenz, M; Augustin, T; Pfeiffer, RM; , Comput Stat, DOI://10.1007/s00180-025-01635-0 (2025)
A plasma proteomics-based candidate biomarker panel predictive of amyotrophic lateral sclerosis Chia, R; Moaddel, R; Kwan, JY et al. Nat Med, DOI://10.1038/s41591-025-03890-6 (2025)
The homeobox transcription factor MNX1 regulates the expression of many non-MN-specific neuronal genes in motor neurons Sun, MA; Fan, H; Ralls, S et al. Nucleic Acids Res, DOI://10.1093/nar/gkaf1015 (2025)
Associations between fMRI signal amplitude, hemispheric asymmetry, and task performance Tomasi, D; Volkow, ND; , Commun Biol, DOI://10.1038/s42003-025-08843-w (2025)
Structural insights into Cir-mediated killing by the antimicrobial protein Microcin V Maurakis, SA; O'Donnell, AC; Botos, I et al. Commun Biol, DOI://10.1038/s42003-025-08846-7 (2025)
Brain region and cell type-specific DNA methylation profiles in association with ADHD Meijer, M; Sudre, G; Ahn, K et al. Sci Rep, DOI://10.1038/s41598-025-18724-1 (2025)
Elucidating molecularly stratified single agent, and combination, therapeutic strategies targeting MCL1 for lethal prostate cancer Jiménez-Vacas, JM; Westaby, D; Figueiredo, I et al. Nat Commun, DOI://10.1038/s41467-025-64042-5 (2025)
Transgene-Induced Chromosomal Rearrangement With Aberrant Human Vascular Endothelial Growth Factor at the Optic Fissure Leads to Uveal Coloboma in Mice Wang, YA; Alur, RP; Kalaskar, V et al. Invest Ophthalmol Vis Sci, DOI://10.1167/iovs.66.13.7 (2025)
Sensitivity Analyses for Missing in Repeatedly Measured Outcome Data Troendle, JF; Sur, A; Leifer, ES; Powell-Wiley, T; , Stat Med, DOI://10.1002/sim.70282 (2025)
Skeletal Maturity and Age-Related Changes in Immune Cells and Circulatory Factors Impair Large-Scale Bone Regeneration de Almeida, LY; Dietrich, C; Hanner, AS et al. Aging Cell, DOI://10.1111/acel.70177 (2025)
Paradoxical carbapenemase activity detected by modified carbapenemase inactivation (mCIM) method in Citrobacter sedlakii Brown, DG; Surette, M; Ray, S et al. J Clin Microbiol, DOI://10.1128/jcm.00589-25 (2025)
FastSpel: A Method for Fast Spectral Library Generation Hamaneh, MB; Yu, YK; , J Proteome Res, DOI://10.1021/acs.jproteome.5c00279 (2025)
Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics Babajanyan, SG; Garushyants, SK; Wolf, YI; Koonin, EV; , mBio, DOI://10.1128/mbio.02409-25 (2025)
Screening of Hidden Pathogenic Structural Variants in PRKN Daida, K; Cogan, G; Tesson, C et al. Mov Disord, DOI://10.1002/mds.30267 (2025)
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing Keskus, AG; Bryant, A; Ahmad, T et al. Nat Biotechnol, DOI://10.1038/s41587-025-02618-8 (2025)
CBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice Zhen, T; Cao, Y; Dou, T et al. J Clin Invest, DOI://10.1172/JCI192923 (2025)
Identification of Cembrane Diterpenoids from Sinularia sp. That Reduce the Viability of Diffuse Pleural Mesothelioma Cell Lines Orfanoudaki, M; Shaikh, AF; Wang, D et al. J Nat Prod, DOI://10.1021/acs.jnatprod.5c00786 (2025)
Infiltrating macrophages replace Kupffer cells and play diverse roles in severe alcohol-associated hepatitis Wang, Y; Guan, Y; Feng, D et al. Cell Mol Immunol, DOI://10.1038/s41423-025-01343-1 (2025)
Characterization of MAIT cells in glioblastoma reveals a potential immunosuppressive role through a MAIT-neutrophil axis Keretsu, S; Hana, T; Lee, A et al. Neurooncol Adv, DOI://10.1093/noajnl/vdaf173 (2025)
Improved muscle and fat segmentation for body composition measures on quantitative CT Liu, J; Balamuralikrishna, PTS; Tan, S et al. Int J Comput Assist Radiol Surg, DOI://10.1007/s11548-025-03466-2 (2025)
Structural basis of fast N-type inactivation in Kv channels Tan, XF; Fernández-Mariño, AI; Li, Y et al. Nature, DOI://10.1038/s41586-025-09339-7 (2025)
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Insights into the renal pathophysiology in Hermansky-Pudlak syndrome-1 from urinary extracellular vesicle proteomics and a new mouse model Maynard, DM; Gochuico, BR; Pri Chen, H et al. FEBS Lett, DOI://10.1002/1873-3468.15088 (2025)
Germline Pathogenic DROSHA Variants Are Linked to Pineoblastoma and Wilms Tumor Predisposition Fiorica, PN; Golmard, L; Kim, J et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-24-2785 (2025)
Diffuse astrocytoma, AYA-type, frequently MAPK-altered: report of 45 patients Singh, O; Dampier, C; Abdullaev, Z et al. Acta Neuropathol, DOI://10.1007/s00401-025-02873-8 (2025)
Investigating the association between human brainstem microstructural integrity and hypertension using magnetic resonance relaxometry Laporte, JP; Akhonda, MABS; Cortina, LE et al. Hypertens Res, DOI://10.1038/s41440-025-02114-1 (2025)
Role of charges in a dynamic disordered complex between an IDP and a folded domain Bugge, K; Sottini, A; Ivanović, MT et al. Nat Commun, DOI://10.1038/s41467-025-58374-5 (2025)
Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter Wang, L; Cui, CY; Lee, CT et al. Nat Commun, DOI://10.1038/s41467-025-58466-2 (2025)
Finding Multiple Optimal Solutions to an Integer Linear Program by Random Perturbations of Its Objective Function Schulhof, N; Sukprasert, P; Ruppin, E et al. Algorithms, DOI://10.3390/a18030140 (2025)
Fast and accurate peak skin dose estimation method for interventional fluoroscopy patients Han, H; Streitmatter, SW; Kitahara, CM; Lee, C; , Med Phys, DOI://10.1002/mp.17667 (2025)
Hot beverage intake and oesophageal cancer in the UK Biobank: prospective cohort study Inoue-Choi, M; Ramirez, Y; O'Connell, C et al. Br J Cancer, DOI://10.1038/s41416-025-02953-2 (2025)
Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Lee, HK; Jankowski, J; Liu, C; Hennighausen, L; , J Mammary Gland Biol Neoplasia, DOI://10.1007/s10911-025-09582-8 (2025)
Comparative phenotypic and genotypic antimicrobial susceptibility surveillance in Achromobacter spp. through whole genome sequencing Ray, S; Flemming, LK; Scudder, CJ et al. Microbiol Spectr, DOI://10.1128/spectrum.02527-24 (2025)
Cognitive predictors and genetic moderators of employment outcomes in people with schizophrenia Blackman, RK; Dickinson, D; Gregory, MD et al. Schizophr Res Cogn, DOI://10.1016/j.scog.2025.100356 (2025)
AlphaFold2's training set powers its predictions of some fold-switched conformations Schafer, JW; Porter, LL; , Protein Sci, DOI://10.1002/pro.70105 (2025)
Brain asymmetry and its association with inattention and heritability during neurodevelopment Tomasi, D; Volkow, ND; , Transl Psychiatry, DOI://10.1038/s41398-025-03327-1 (2025)
Regulatory Plasticity of the Human Genome Srivastava, J; Ovcharenko, I; , Mol Biol Evol, DOI://10.1093/molbev/msaf050 (2025)
A sequence-specific RNA acetylation catalyst Thalalla Gamage, S; Howpay Manage, S; Sas-Chen, A et al. Nucleic Acids Res, DOI://10.1093/nar/gkaf217 (2025)
Mutations in the Staphylococcus aureus Global Regulator CodY confer tolerance to an interspecies redox-active antimicrobial Martini, AM; Alexander, SA; Khare, A; , PLoS Genet, DOI://10.1371/journal.pgen.1011610 (2025)
Noncoding function of super enhancer derived Cpox pre-mRNA in modulating neighbouring gene expression and chromatin interactions Xie, B; Dean, A; , RNA Biol, DOI://10.1080/15476286.2025.2475421 (2025)
Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay Poonia, P; Valabhoju, V; Li, T et al. Nucleic Acids Res, DOI://10.1093/nar/gkaf143 (2025)
Retrospective assessment of clinical global impression of severity and change in GM1 gangliosidosis: a tool to score natural history data in rare disease cohorts Lewis, CJ; Johnston, JM; Zaragoza Domingo, S et al. Orphanet J Rare Dis, DOI://10.1186/s13023-025-03614-6 (2025)
Interleukin 35-producing B cells prolong the survival of GVHD mice by secreting exosomes with membrane-bound IL-35 and upregulating PD-1/LAG-3 checkpoint proteins Choi, JK; Mbanefo, EC; Yadav, MK et al. Theranostics, DOI://10.7150/thno.105069 (2025)
A statistical framework for analysis of trial-level temporal dynamics in fiber photometry experiments Loewinger, G; Cui, E; Lovinger, D; Pereira, F; , Elife, DOI://10.7554/eLife.95802 (2025)
A deep insight into the sialome of the house fly, Musca domestica, infected with the salivary gland hypertrophy virus (MdSGHV) Lu, S; Miller, N; Wilson, A et al. Sci Rep, DOI://10.1038/s41598-025-92569-6 (2025)
Molecular differences between young and mature stria vascularis from organotypic explants and transcriptomics Thulasiram, MR; Yamamoto, R; Olszewski, RT et al. iScience, DOI://10.1016/j.isci.2025.111832 (2025)
The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease Daida, K; Yoshino, H; Malik, L et al. Ann Neurol, DOI://10.1002/ana.27155 (2025)
The Relations Among Anxiety, Movie-Watching, and in-Scanner Motion Kirk, PA; Qamar, P; Zugman, A et al. Hum Brain Mapp, DOI://10.1002/hbm.70163 (2025)
Cross-species and mammal-to-mammal transmission of clade 2.3.4.4b highly pathogenic avian influenza A/H5N1 with PB2 adaptations Pardo-Roa, C; Nelson, MI; Ariyama, N et al. Nat Commun, DOI://10.1038/s41467-025-57338-z (2025)
Sequence clustering confounds AlphaFold2 Schafer, JW; Lee, M; Chakravarty, D et al. Nature, DOI://10.1038/s41586-024-08267-2 (2025)
Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution Ghosh, S; Wu, CJ; Moller, AG et al. Nat Commun, DOI://10.1038/s41467-025-57331-6 (2025)
CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer Xiang, RR; Lee, SA; Tyndall, CF et al. Cell Rep, DOI://10.1016/j.celrep.2025.115312 (2025)
Structure of blood cell-specific tubulin and demonstration of dimer spacing compaction in a single protofilament Montecinos, F; Eren, E; Watts, NR et al. J Biol Chem, DOI://10.1016/j.jbc.2024.108132 (2025)
N-terminal fragment shedding contributes to signaling of the full-length adhesion receptor ADGRL3 Perry-Hauser, NA; Du Rand, JR; Lee, KH et al. J Biol Chem, DOI://10.1016/j.jbc.2025.108174 (2025)
RNA Pol-II transcripts in nucleolar associated domains of cancer cell nucleoli Chowdhury, SR; Shilpi, A; Felsenfeld, G; , Nucleus, DOI://10.1080/19491034.2025.2468597 (2025)
The c.119-123dup5bp mutation in human γC-crystallin destabilizes the protein and activates the unfolded protein response to cause highly variable cataracts Shah, MH; Vendra, VPR; Ostrowski, C et al. Sci Rep, DOI://10.1038/s41598-025-90977-2 (2025)
Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome Palczewski, MB; Kuschman, HP; Hoffman, BM et al. Nat Commun, DOI://10.1038/s41467-025-56928-1 (2025)
Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential Akagbosu, CO; McCauley, KE; Namasivayam, S et al. Gut Microbes, DOI://10.1080/19490976.2025.2467833 (2025)
ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics Li, Z; Weller, CA; Shah, S et al. Genomics Proteomics Bioinformatics, DOI://10.1093/gpbjnl/qzae083 (2025)
Tumor and blood B-cell abundance outperforms established immune checkpoint blockade response prediction signatures in head and neck cancer Chang, TG; Spathis, A; Schäffer, AA et al. Ann Oncol, DOI://10.1016/j.annonc.2024.11.008 (2025)
Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region Zhou, W; Huang, WY; Freedman, ND; Machiela, M; , BMC Bioinformatics, DOI://10.1186/s12859-025-06076-6 (2025)
Exome sequencing in Asian populations identifies low-frequency and rare coding variation influencing Parkinson's disease risk Chew, EG; Liu, Z; Li, Z et al. Nat Aging, DOI://10.1038/s43587-024-00760-7 (2025)
The yeast genome is globally accessible in living cells Prajapati, HK; Eriksson, PR; Elizalde, PA et al. Nat Struct Mol Biol, DOI://10.1038/s41594-024-01318-2 (2025)
The ZFHX3 GGC Repeat Expansion Underlying Spinocerebellar Ataxia Type 4 has a Common Ancestral Founder Chen, Z; Alvarez Jerez, P; Anderson, C et al. Mov Disord, DOI://10.1002/mds.30077 (2025)
Next-Generation Sequencing-Based MSI Scoring Predicts Benefit in Mismatch Repair-Deficient Tumors Treated with Nivolumab: Follow-up on NCI-MATCH Arm Z1D Schoenfeld, JD; Azad, NS; Gross, J et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-24-0427 (2025)
Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential Florez-Vargas, O; Ho, M; Hogshead, MH et al. Nat Commun, DOI://10.1038/s41467-025-56947-y (2025)
Acanthamoeba Infection in a Hematopoietic Cell Transplant Recipient: Challenges in Diagnosis, Management, and Source Identification Banerjee, CT; Conlan, S; Mostaghim, A et al. Transpl Infect Dis, DOI://10.1111/tid.14425 (2025)
Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma Lee, OW; Karyadi, DM; Hartley, SW et al. Eur Thyroid J, DOI://10.1530/ETJ-24-0235 (2025)
The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency Chandrasekaran, P; Krausz, M; Han, Y et al. Microbiome, DOI://10.1186/s40168-025-02028-7 (2025)
Measurable residual FLT3 tyrosine kinase domain mutations before allogeneic transplant for acute myeloid leukemia Hegde, PS; Andrew, G; Gui, G et al. Bone Marrow Transplant, DOI://10.1038/s41409-024-02444-7 (2025)
Measurable residual mutated IDH2 before allogeneic transplant for acute myeloid leukemia Gui, G; Ravindra, N; Hegde, PS et al. Bone Marrow Transplant, DOI://10.1038/s41409-024-02449-2 (2025)
Realistic extension of partial-body pediatric CT for whole-body organ dose estimation in radiotherapy patients Rafet, SM; Lee, C; Griffin, KT et al. Radiat Phys Chem Oxf Engl 1993, DOI://10.1016/j.radphyschem.2024.112194 (2025)
Determining structures of RNA conformers using AFM and deep neural networks Degenhardt, MFS; Degenhardt, HF; Bhandari, YR et al. Nature, DOI://10.1038/s41586-024-07559-x (2025)
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction Chakravarty, D; Lee, M; Porter, LL; , Curr Opin Struct Biol, DOI://10.1016/j.sbi.2024.102973 (2025)
Cryo-electron tomography pipeline for plasma membranes Sun, WW; Michalak, DJ; Sochacki, KA et al. Nat Commun, DOI://10.1038/s41467-025-56045-z (2025)
Longitudinal maternal glycemia during pregnancy and placental epigenetic age acceleration Habtewold, TD; Wijesiriwardhana, P; Biedrzycki, RJ et al. Clin Epigenetics, DOI://10.1186/s13148-025-01825-z (2025)
Female germline expression of OVO transcription factor bridges Drosophila generations Benner, L; Muron, S; Wingfield, CL; Oliver, B; , G3 (Bethesda), DOI://10.1093/g3journal/jkae252 (2025)
Genome-first determination of the prevalence and penetrance of eight germline myeloid malignancy predisposition genes: a study of two population-based cohorts Hendricks, RM; Kim, J; Haley, JS et al. Leukemia, DOI://10.1038/s41375-024-02436-y (2025)
DNA methylation patterns are influenced by Pax3::Foxo1 expression and developmental lineage in rhabdomyosarcoma tumours forming in genetically engineered mouse models Sun, W; Hewitt, SM; Wright, H et al. J Pathol, DOI://10.1002/path.6386 (2025)
Nipah Virus-Associated Neuropathology in African Green Monkeys During Acute Disease and Convalescence Goldin, K; Liu, Y; Rosenke, R et al. J Infect Dis, DOI://10.1093/infdis/jiae300 (2025)
Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut Levy, S; Jiang, AK; Grant, MR et al. Nat Commun, DOI://10.1038/s41467-025-56332-9 (2025)
Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends Hickman, AB; Lannes, L; Furman, CM et al. Nat Commun, DOI://10.1038/s41467-024-55784-9 (2025)
Allosteric modulation of NF1 GAP: Differential distributions of catalytically competent populations in loss-of-function and gain-of-function mutants Xu, L; Jang, H; Nussinov, R; , Protein Sci, DOI://10.1002/pro.70042 (2025)
Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation Song, W; Ovcharenko, I; , iScience, DOI://10.1016/j.isci.2024.111658 (2025)
A Comparative Genomic Analysis of Parathyroid Adenomas and Carcinomas Harboring Heterozygous Germline CDC73 Mutations Li, Y; Simonds, WF; Chen, H; , J Clin Endocrinol Metab, DOI://10.1210/clinem/dgae506 (2025)
Sherlock-Genome: an R Shiny application for genomic analysis and visualization Klein, A; Zhong, J; Landi, MT; Zhang, T; , BMC Genomics, DOI://10.1186/s12864-024-11147-8 (2025)
An orally available P1'-5-fluorinated Mpro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier Higashi-Kuwata, N; Bulut, H; Hayashi, H et al. PNAS Nexus, DOI://10.1093/pnasnexus/pgae578 (2025)
High-resolution analysis of human centromeric chromatin Melters, DP; Bui, M; Rakshit, T et al. Life Sci Alliance, DOI://10.26508/lsa.202402819 (2025)
CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise Prajapat, MK; Maria, AG; Vidigal, JA; , Nucleic Acids Res, DOI://10.1093/nar/gkae1138 (2025)
Miniscope Imaging of Nucleus Accumbens Neural Activity in Freely Behaving Rats: Virus Injection, Gradient Index Lens Implantation, Recording Strategies, and Analytical Methods Beacher, NJ; Wang, MW; Broomer, MC et al. Curr Protoc, DOI://10.1002/cpz1.70090 (2025)
Hepatitis B virus genotypes A1 and A2 have distinct replication phenotypes due to polymorphisms in the HBx gene Zhang, M; Mouzannar, K; Zhang, Z et al. PLoS Pathog, DOI://10.1371/journal.ppat.1012803 (2025)
PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production Srivastav, MK; Folco, HD; Nathanailidou, P et al. Nat Commun, DOI://10.1038/s41467-024-55736-3 (2025)
Sickle Trait and Alpha Thalassemia Increase NOS-Dependent Vasodilation of Human Arteries Through Disruption of Endothelial Hemoglobin-eNOS Interactions Brooks, SD; Ruhl, AP; Zeng, X et al. Circulation, DOI://10.1161/CIRCULATIONAHA.123.066003 (2025)

2024 (533 papers)

Joint Modeling of Geometric Features of Longitudinal Process and Discrete Survival Time Measured on Nested Timescales: An Application to Fecundity Studies Saha, A; Ma, L; Biswas, A; Sundaram, R; , Stat Biosci, DOI://10.1007/s12561-023-09381-x (2024)
Assessing treatment efficacy for interval-censored endpoints using multistate semi-Markov models fit to multiple data streams Morsomme, R; Liang, CJ; Mateja, A et al. Biostatistics, DOI://10.1093/biostatistics/kxaf038 (2024)
Senescence suppresses the integrated stress response and activates a stress-remodeled secretory phenotype Payea, MJ; Dar, SA; Anerillas, C et al. Mol Cell, DOI://10.1016/j.molcel.2024.10.003 (2024)
Excessive MYC-topoisome activity triggers acute DNA damage, MYC degradation, and replacement by a p53-topoisome Das, SK; Karmakar, S; Venkatachalapathy, H et al. Mol Cell, DOI://10.1016/j.molcel.2024.10.006 (2024)
Expanded Functionality and Portability for the Colvars Library Fiorin, G; Marinelli, F; Forrest, LR et al. J Phys Chem B, DOI://10.1021/acs.jpcb.4c05604 (2024)
Genomic Analysis Identifies Risk Factors in Restless Legs Syndrome Akçimen, F; Chia, R; Saez-Atienzar, S et al. Ann Neurol, DOI://10.1002/ana.27040 (2024)
A bimodal taxonomy of adult human brain sulcal morphology related to timing of fetal sulcation and trans-sulcal gene expression gradients Snyder, WE; Vértes, PE; Kyriakopoulou, V et al. Neuron, DOI://10.1016/j.neuron.2024.07.023 (2024)
Single-Nucleus RNA Sequencing Reveals Loss of Distal Convoluted Tubule 1 Renal Tubules in HIV Viral Protein R Transgenic Mice Latt, KZ; Yoshida, T; Shrivastav, S et al. Am J Pathol, DOI://10.1016/j.ajpath.2024.06.006 (2024)
Organ-specific Biodosimetry Modeling Using Proteomic Biomarkers of Radiation Exposure Sproull, M; Fan, Y; Chen, Q et al. Radiat Res, DOI://10.1667/RADE-24-00092.1 (2024)
Reusability report: Leveraging supervised learning to uncover phenotype-relevant biology from single-cell RNA sequencing data Cao, Y; Chang, TG; Sahni, S; Ruppin, E; , Nat Mach Intell, DOI://10.1038/s42256-024-00804-y (2024)
QUANTILE REGRESSION DECOMPOSITION ANALYSIS OF DISPARITY RESEARCH USING COMPLEX SURVEY DATA: APPLICATION TO DISPARITIES IN BMI AND TELOMERE LENGTH BETWEEN U.S. MINORITY AND WHITE POPULATION GROUPS Hong, HG; Graubard, BI; Gastwirth, JL; Kim, MO; , Ann Appl Stat, DOI://10.1214/23-aoas1868 (2024)
Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic Tai, CH; Hinton, D; Yu, SH; , Methods Mol Biol, DOI://10.1007/978-1-0716-3565-0_4 (2024)
A deep intronic splice-altering AIRE variant causes APECED syndrome through antisense oligonucleotide-targetable pseudoexon inclusion Ochoa, S; Hsu, AP; Oler, AJ et al. Sci Transl Med, DOI://10.1126/scitranslmed.adk0845 (2024)
Investigating the Protective Role of the Mitochondrial 2158 T > C Variant in Parkinson's Disease Akçimen, F; van Midden, V; Akerman, SC et al. Mov Disord, DOI://10.1002/mds.29892 (2024)
Long-Read Sequencing Unravels the Complexity of Structural Variants in PRKN in Two Individuals with Early-Onset Parkinson's Disease Cogan, G; Daida, K; Billingsley, KJ et al. Mov Disord, DOI://10.1002/mds.29914 (2024)
Nucleosome remodeler exclusion by histone deacetylation enforces heterochromatic silencing and epigenetic inheritance Sahu, RK; Dhakshnamoorthy, J; Jain, S et al. Mol Cell, DOI://10.1016/j.molcel.2024.07.006 (2024)
Non-Invasive Tumor Grade Evaluation in Von Hippel-Lindau-Associated Clear Cell Renal Cell Carcinoma: A Magnetic Resonance Imaging-Based Study Zahergivar, A; Yazdian Anari, P; Mendhiratta, N et al. J Magn Reson Imaging, DOI://10.1002/jmri.29222 (2024)
NAD deficiency contributes to progressive kidney disease in HIV-nephropathy mice Yoshida, T; Myakala, K; Jones, BA et al. Am J Physiol Renal Physiol, DOI://10.1152/ajprenal.00061.2024 (2024)
DYNAMIC RISK PREDICTION FOR CERVICAL PRECANCER SCREENING WITH CONTINUOUS AND BINARY LONGITUDINAL BIOMARKERS Roy, S; Roy, A; Clarke, MA et al. Ann Appl Stat, DOI://10.1214/23-aoas1788 (2024)
Sentence-Aligned Simplification of Biomedical Abstracts Ondov, B; Demner-Fushman, D; , Artif Intell Med Conf Artif Intell Med (2005-), DOI://10.1007/978-3-031-66538-7_32 (2024)
Direct segmentation of cortical cytoarchitectonic domains using ultra-high-resolution whole-brain diffusion MRI Pas, KE; Saleem, KS; Basser, PJ; Avram, AV; , Imaging Neurosci (Camb), DOI://10.1162/imag_a_00393 (2024)
Single-Cell Transcriptional Signatures of Glomerular Disease in Transgenic Mice with APOL1 Variants Yoshida, T; Latt, KZ; Santo, BA et al. J Am Soc Nephrol, DOI://10.1681/ASN.0000000000000370 (2024)
Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4 Zhou, BR; Feng, H; Huang, F et al. Mol Cell, DOI://10.1016/j.molcel.2024.07.016 (2024)
Genome sequence analyses identify novel risk loci for multiple system atrophy Chia, R; Ray, A; Shah, Z et al. Neuron, DOI://10.1016/j.neuron.2024.04.002 (2024)
New Discorhabdin D Analogues from Latrunculia spp. Sponges Orfanoudaki, M; Dalilian, M; Du, L et al. J Nat Prod, DOI://10.1021/acs.jnatprod.4c01036 (2024)
PcdA promotes orthogonal division plane selection in Staphylococcus aureus Ramos-León, F; Anjuwon-Foster, BR; Anantharaman, V et al. Nat Microbiol, DOI://10.1038/s41564-024-01821-8 (2024)
Type VI Collagen Deficiency Causes Enhanced Periodontal Tissue Destruction Komori, T; Kram, V; Perry, S et al. J Dent Res, DOI://10.1177/00220345241256306 (2024)
Mutational analysis reveals the importance of residues of the access tunnel inhibitor site to human P-glycoprotein (ABCB1)-mediated transport Salazar, PB; Murakami, M; Ranganathan, N et al. Protein Sci, DOI://10.1002/pro.5155 (2024)
GBA1 rs3115534 Is Associated with REM Sleep Behavior Disorder in Parkinson's Disease in Nigerians Ojo, OO; Bandres-Ciga, S; Makarious, MB et al. Mov Disord, DOI://10.1002/mds.29753 (2024)
Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions Zhu, B; Tapinos, A; Koka, H et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2024.10.005 (2024)
Comparison of Novel Proteomic Expression Profiles for Radiation Exposure in Male and Female C57BL6 Mice Sproull, M; Fan, Y; Chen, Q et al. Radiat Res, DOI://10.1667/RADE-23-00180.1 (2024)
CD34+ cell yield among healthy donors: Large-scale model development and validation Alswied, A; Daniel, D; Chen, LN et al. J Clin Apher, DOI://10.1002/jca.22135 (2024)
MAPT H2 haplotype and risk of Pick's disease in the Pick's disease International Consortium: a genetic association study Valentino, RR; Scotton, WJ; Roemer, SF et al. Lancet Neurol, DOI://10.1016/S1474-4422(24)00083-8 (2024)
Prenatal exposure to air pollutant mixtures and birthweight in the upstate KIDS cohort Trees, IR; Saha, A; Putnick, DL et al. Environ Int, DOI://10.1016/j.envint.2024.108692 (2024)
Genome-Wide Analysis to Assess if Heavy Alcohol Consumption Modifies the Association between SNPs and Pancreatic Cancer Risk Ni, Z; Kundu, P; McKean, DF et al. Cancer Epidemiol Biomarkers Prev, DOI://10.1158/1055-9965.EPI-24-0096 (2024)
Schizophrenia risk-associated SNPs affect expression of microRNA 137 host gene: a postmortem study Feng, N; Mandal, A; Jambhale, A et al. Hum Mol Genet, DOI://10.1093/hmg/ddae130 (2024)
Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis Starrett, GJ; Baikie, BC; Stoff, BK et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-24-1327 (2024)
Comprehensive deletion scan of anti-CRISPR AcrIIA4 reveals essential and dispensable domains for Cas9 inhibition Iturralde, AB; Weller, CA; Giovanetti, SM; Sadhu, MJ; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2413743121 (2024)
Subcortico-Cortical Dysconnectivity in ADHD: A Voxel-Wise Mega-Analysis Across Multiple Cohorts Norman, LJ; Sudre, G; Price, J; Shaw, P; , Am J Psychiatry, DOI://10.1176/appi.ajp.20230026 (2024)
Toward Relieving Clinician Burden by Automatically Generating Progress Notes using Interim Hospital Data Soni, S; Demner-Fushman, D; , AMIA Annu Symp Proc, 1942-597X (2024)
Automating assignment of HIV+ patients into phenogroups from demography bound phenotype attack rates Williams, N AMIA Annu Symp Proc, 1942-597X (2024)
Capturing Autoinhibited PDK1 Reveals the Linker's Regulatory Role, Informing Innovative Inhibitor Design Xu, L; Jang, H; Nussinov, R; , J Chem Inf Model, DOI://10.1021/acs.jcim.4c01392 (2024)
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Koren, S; Bao, Z; Guarracino, A et al. Genome Res, DOI://10.1101/gr.279334.124 (2024)
Chromosome 7 Gain Compensates for Chromosome 10 Loss in Glioma Nair, NU; Schäffer, AA; Gertz, EM et al. Cancer Res, DOI://10.1158/0008-5472.CAN-24-1366 (2024)
Bacterial spore surface nanoenvironment requires a AAA+ ATPase to promote MurG function Delerue, T; Updegrove, TB; Chareyre, S et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2414737121 (2024)
Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa Warrell, DL; Zarrella, TM; Machalek, C; Khare, A; , J Bacteriol, DOI://10.1128/jb.00281-24 (2024)
Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors Lee, KH; Shi, L; , J Chem Inf Model, DOI://10.1021/acs.jcim.3c01956 (2024)
Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening Gao, P; Tambe, M; Chen, CZ et al. J Chem Inf Model, DOI://10.1021/acs.jcim.4c00530 (2024)
Evaluating large language models on medical, lay-language, and self-reported descriptions of genetic conditions Flaharty, KA; Hu, P; Hanchard, SL et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2024.07.011 (2024)
Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response Bou-Nader, C; Gaikwad, S; Bahmanjah, S et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2409628121 (2024)
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Electric Field Characteristics of Rotating Permanent Magnet Stimulation Robins, PL; Makaroff, SN; Dib, M et al. Bioengineering (Basel), DOI://10.3390/bioengineering11030258 (2024)
Clinical, behavioral, and electrophysiological profiles along a continuum of suicide risk: evidence from an implicit association task Lamontagne, SJ; Gilbert, JR; Zabala, PK et al. Psychol Med, DOI://10.1017/S0033291723003331 (2024)
Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution Gonzalez, P; Hauck, QC; Baxevanis, AD; , Genome Biol Evol, DOI://10.1093/gbe/evae052 (2024)
Questionnaire-based exposome-wide association studies for common diseases in the Personalized Environment and Genes Study Lloyd, D; House, JS; Akhtari, FS et al. Exposome, DOI://10.1093/exposome/osae002 (2024)
Nucleosome reorganisation in breast cancer tissues Jacob, DR; Guiblet, WM; Mamayusupova, H et al. Clin Epigenetics, DOI://10.1186/s13148-024-01656-4 (2024)
Flipped C-Terminal Ends of APOA1 Promote ABCA1-Dependent Cholesterol Efflux by Small HDLs He, Y; Pavanello, C; Hutchins, PM et al. Circulation, DOI://10.1161/CIRCULATIONAHA.123.065959 (2024)
Cox model inference for relative hazard and pure risk from stratified weight-calibrated case-cohort data Etievant, L; Gail, MH; , Lifetime Data Anal, DOI://10.1007/s10985-024-09621-2 (2024)
A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins Lu, X; Chandravanshi, M; Sabbasani, VR et al. Nat Commun, DOI://10.1038/s41467-024-46644-7 (2024)
Syntaxin1A overexpression and pain insensitivity in individuals with 7q11.23 duplication syndrome Iadarola, MJ; Sapio, MR; Loydpierson, AJ et al. JCI Insight, DOI://10.1172/jci.insight.176147 (2024)
Defining biology and recurrence risk in prostate cancers treated by neoadjuvant chemohormonal therapy Wilkinson, S; Sowalsky, AG; , J Natl Cancer Inst, DOI://10.1093/jnci/djad192 (2024)
Corrigendum: Glioblastoma survival is associated with distinct proteomic alteration signatures post chemoirradiation in a large-scale proteomic panel Krauze, AV; Sierk, M; Nguyen, T et al. Front Oncol, DOI://10.3389/fonc.2024.1348105 (2024)
Trial-by-trial variability in cortical responses exhibits scaling of spatial correlations predicted from critical dynamics Ribeiro, TL; Jendrichovsky, P; Yu, S et al. Cell Rep, DOI://10.1016/j.celrep.2024.113762 (2024)

Outcome differences by sex in oncology clinical trials Kammula, AV; Schäffer, AA; Rajagopal, PS et al. Nat Commun, DOI://10.1038/s41467-024-46945-x (2024)
Caspase-1 activates gasdermin A in non-mammals Billman, ZP; Kovacs, SB; Wei, B et al. Elife, DOI://10.7554/eLife.92362 (2024)
Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo Gaikwad, S; Ghobakhlou, F; Zhang, H; Hinnebusch, AG; , Elife, DOI://10.7554/eLife.92916 (2024)
Transcriptional control of leukemogenesis by the chromatin reader SGF29 Barbosa, K; Deshpande, A; Perales, M et al. Blood, DOI://10.1182/blood.2023021234 (2024)
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification Kim, J; Naqvi, AS; Corbett, RJ et al. Bioinformatics, DOI://10.1093/bioinformatics/btae114 (2024)
Recruitment and Maintenance of CX3CR1+CD4+ T Cells during Helminth Infection Loredan, DG; Devlin, JC; Khanna, KM; Loke, P; , J Immunol, DOI://10.4049/jimmunol.2300451 (2024)
Comparative neuroimaging of sex differences in human and mouse brain anatomy Guma, E; Beauchamp, A; Liu, S et al. Elife, DOI://10.7554/eLife.92200 (2024)
Leucine-rich repeat kinase 2 limits dopamine D1 receptor signaling in striatum and biases against heavy persistent alcohol drinking da Silva, D; Matsui, A; Murray, EM et al. Neuropsychopharmacology, DOI://10.1038/s41386-023-01731-z (2024)
Annotating microbial functions with ProkFunFind Dufault-Thompson, K; Jiang, X; , mSystems, DOI://10.1128/msystems.00036-24 (2024)
Molecular and clinicopathologic characteristics of CNS embryonal tumors with BRD4::LEUTX fusion Andreiuolo, F; Ferrone, CK; Rajan, S et al. Acta Neuropathol Commun, DOI://10.1186/s40478-024-01746-7 (2024)
A longitudinal transcriptomic analysis of Rhipicephalus microplus midgut upon feeding Lu, S; Waldman, J; Parizi, LF et al. Ticks Tick Borne Dis, DOI://10.1016/j.ttbdis.2023.102304 (2024)
Reprogramming of cardiac phosphoproteome, proteome, and transcriptome confers resilience to chronic adenylyl cyclase-driven stress Qu, JH; Chakir, K; Tarasov, KV et al. Elife, DOI://10.7554/eLife.88732 (2024)
Degradation and translation of maternal mRNA for embryogenesis Yang, G; Xin, Q; Dean, J; , Trends Genet, DOI://10.1016/j.tig.2023.12.008 (2024)
Comprehensive gene profiling of the metabolic landscape of humanized livers in mice Jiang, C; Li, P; Ma, Y et al. J Hepatol, DOI://10.1016/j.jhep.2023.11.020 (2024)
Developmental conversion of thymocyte-attracting cells into self-antigen-displaying cells in embryonic thymus medulla epithelium Ohigashi, I; White, AJ; Yang, MT et al. Elife, DOI://10.7554/eLife.92552 (2024)
QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration Advani, J; Mehta, PA; Hamel, AR et al. Nat Commun, DOI://10.1038/s41467-024-46063-8 (2024)
FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries Montepietra, D; Tesei, G; Martins, JM et al. Commun Biol, DOI://10.1038/s42003-024-05910-6 (2024)
Mycophenolate mofetil inhibits Merkel cell carcinoma growth Garman, KA; Thoreson, N; Strong, J et al. Br J Dermatol, DOI://10.1093/bjd/ljae018 (2024)
Author Correction: ATR inhibition augments the efficacy of lurbinectedin in small-cell lung cancer Schultz, CW; Zhang, Y; Elmeskini, R et al. EMBO Mol Med, DOI://10.1038/s44321-024-00029-x (2024)
Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection Dremel, SE; Tagawa, T; Koparde, VN et al. EMBO Rep, DOI://10.1038/s44319-023-00051-z (2024)
Regional centromere configuration in the fungal pathogens of the Pneumocystis genus Cissé, OH; Curran, SJ; Folco, HD et al. mBio, DOI://10.1128/mbio.03185-23 (2024)
Comparison of clinical geneticist and computer visual attention in assessing genetic conditions Duong, D; Johny, AR; Ledgister Hanchard, S et al. PLoS Genet, DOI://10.1371/journal.pgen.1011168 (2024)
Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago Blake, L; Phillips Savage, AC; Soto, E et al. Microbiol Resour Announc, DOI://10.1128/mra.00999-23 (2024)
Formation of Trideuteromethylated Artifacts of Pyrrole-Containing Natural Products Orfanoudaki, M; Akee, RK; Martínez-Fructuoso, L et al. J Nat Prod, DOI://10.1021/acs.jnatprod.3c01113 (2024)
A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling Kang, SWS; Cunningham, RP; Miller, CB et al. Nat Commun, DOI://10.1038/s41467-024-45751-9 (2024)
Neopetrotaurines A-C, Isoquinoline Alkaloids with an Unprecedented Taurine Bridge from the Sponge Neopetrosia sp Wang, D; Jiang, W; Churiwal, M et al. J Nat Prod, DOI://10.1021/acs.jnatprod.3c01041 (2024)
Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity Zhu, X; Joo, Y; Bossi, S et al. Prog Neurobiol, DOI://10.1016/j.pneurobio.2024.102568 (2024)
Biological aging markers in blood and brain tissue indicate age acceleration in alcohol use disorder Zillich, L; Cetin, M; Hummel, EM et al. Alcohol Clin Exp Res (Hoboken), DOI://10.1111/acer.15241 (2024)
Gut-liver axis calibrates intestinal stem cell fitness Kim, G; Chen, Z; Li, J et al. Cell, DOI://10.1016/j.cell.2024.01.001 (2024)
Actigraphy-derived measures of sleep and risk of prostate cancer in the UK Biobank Freeman, JR; Saint-Maurice, PF; Watts, EL et al. J Natl Cancer Inst, DOI://10.1093/jnci/djad210 (2024)
Geographic Distribution of Human Infections with Zoonotic Ancylostoma ceylanicum and Anthropophilic Hookworms in Ecuador: A Retrospective Analysis of Archived Stool Samples Aguilar-Rodríguez, D; Seco-Hidalgo, V; Lopez, A et al. Am J Trop Med Hyg, DOI://10.4269/ajtmh.23-0469 (2024)
Lineage and ecology define liver tumor evolution in response to treatment Revsine, M; Wang, L; Forgues, M et al. Cell Rep Med, DOI://10.1016/j.xcrm.2024.101394 (2024)
Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus Xin, Q; Feng, I; Yu, G; Dean, J; , J Clin Invest, DOI://10.1172/JCI174194 (2024)
Combined immune checkpoint inhibition with durvalumab and tremelimumab with and without radiofrequency ablation in patients with advanced biliary tract carcinoma Monge, C; Xie, C; Myojin, Y et al. Cancer Med, DOI://10.1002/cam4.6912 (2024)
Extrahelical Binding Site for a 1 H-Imidazo[4,5-c]quinolin-4-amine A3 Adenosine Receptor Positive Allosteric Modulator on Helix 8 and Distal Portions of Transmembrane Domains 1 and 7 Fisher, CL; Pavan, M; Salmaso, V et al. Mol Pharmacol, DOI://10.1124/molpharm.123.000784 (2024)
Interactive data sharing for multiple questionnaire-based exposome-wide association studies and exposome correlations in the Personalized Environment and Genes Study Lloyd, D; House, JS; Akhtari, FS et al. Exposome, DOI://10.1093/exposome/osae003 (2024)

The mineralocorticoid receptor forms higher order oligomers upon DNA binding Fettweis, G; Johnson, TA; Almeida-Prieto, B et al. Protein Sci, DOI://10.1002/pro.4890 (2024)
Long-term survivors of glioblastoma: Tumor molecular, clinical, and imaging findings Briceno, N; Vera, E; Komlodi-Pasztor, E et al. Neurooncol Adv, DOI://10.1093/noajnl/vdae019 (2024)
An unusual dual sugar-binding lectin domain controls the substrate specificity of a mucin-type O-glycosyltransferase Collette, AM; Hassan, SA; Schmidt, SI et al. Sci Adv, DOI://10.1126/sciadv.adj8829 (2024)
Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles Rhodes, CT; Asokumar, D; Sohn, M et al. Front Cell Neurosci, DOI://10.3389/fncel.2024.1334244 (2024)
B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage Park, EN; Mackens-Kiani, T; Berhane, R et al. EMBO J, DOI://10.1038/s44318-023-00010-3 (2024)
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity Folco, HD; Xiao, H; Wheeler, D et al. Nucleic Acids Res, DOI://10.1093/nar/gkad1182 (2024)
Identification of two novel heterodimeric ABC transporters in melanoma: ABCB5β/B6 and ABCB5β/B9 Gerard, L; Duvivier, L; Fourrez, M et al. J Biol Chem, DOI://10.1016/j.jbc.2023.105594 (2024)
ATOH1, TFAP2B, and CEACAM6 as Immunohistochemical Markers to Distinguish Merkel Cell Carcinoma and Small Cell Lung Cancer Vilasi, SM; Nguyen, J; Wang, CJ et al. Cancers (Basel), DOI://10.3390/cancers16040788 (2024)
Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study Ou, AH; Rosenthal, SB; Adli, M et al. Transl Psychiatry, DOI://10.1038/s41398-024-02811-4 (2024)
Mitochondrial Cytochrome bc1 Complex as Validated Drug Target: A Structural Perspective Esser, L; Xia, D; , Trop Med Infect Dis, DOI://10.3390/tropicalmed9020039 (2024)
Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species Trovão, NS; Khan, SM; Lemey, P et al. mBio, DOI://10.1128/mbio.02649-23 (2024)
Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome Walitt, B; Singh, K; LaMunion, SR et al. Nat Commun, DOI://10.1038/s41467-024-45107-3 (2024)
Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci Bayram, E; Reho, P; Litvan, I et al. NPJ Parkinsons Dis, DOI://10.1038/s41531-024-00649-7 (2024)
EXO1 protects BRCA1-deficient cells against toxic DNA lesions van de Kooij, B; Schreuder, A; Pavani, R et al. Mol Cell, DOI://10.1016/j.molcel.2023.12.039 (2024)
Multifaceted roles for STAT3 in gammaherpesvirus latency revealed through in vivo B cell knockout models Hogan, CH; Owens, SM; Reynoso, GV et al. mBio, DOI://10.1128/mbio.02998-23 (2024)
Association of cardiovascular disease management drugs with Lewy body dementia: a case-control study Scholz, SW; Moroz, BE; Saez-Atienzar, S et al. Brain Commun, DOI://10.1093/braincomms/fcad346 (2024)
Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway Azeroglu, B; Ozbun, L; Pegoraro, G; Lazzerini Denchi, E; , Methods Cell Biol, DOI://10.1016/bs.mcb.2022.10.010 (2024)
Transgenic Tg(Kcnj10-ZsGreen) fluorescent reporter mice allow visualization of intermediate cells in the stria vascularis Strepay, D; Olszewski, RT; Nixon, S et al. Sci Rep, DOI://10.1038/s41598-024-52663-7 (2024)
Trends in Patient Transfers From Overall and Caseload-Strained US Hospitals During the COVID-19 Pandemic Sarzynski, SH; Mancera, AG; Yek, C et al. JAMA Netw Open, DOI://10.1001/jamanetworkopen.2023.56174 (2024)
The Variegation of Human Brain Vulnerability to Rare Genetic Disorders and Convergence With Behaviorally Defined Disorders Levitis, E; Liu, S; Whitman, ET et al. Biol Psychiatry, DOI://10.1016/j.biopsych.2023.07.008 (2024)
Author Correction: Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex Hayne, CK; Butay, KJU; Stewart, ZD et al. Nat Struct Mol Biol, DOI://10.1038/s41594-024-01213-w (2024)
A deep learning adversarial autoencoder with dynamic batching displays high performance in denoising and ordering scRNA-seq data Ko, KD; Sartorelli, V; , iScience, DOI://10.1016/j.isci.2024.109027 (2024)
Diffuse Pediatric-type High-grade Glioma Arising in an Ovarian Mature Cystic Teratoma Elmuti, L; Amundson, J; Oberman, E et al. Int J Gynecol Pathol, DOI://10.1097/PGP.0000000000000954 (2024)
Identification of Fibroinflammatory and Fibrotic Transcriptomic Subsets of Human Cutaneous Sclerotic Chronic Graft-Versus-Host Disease Rosenstein, RK; Rose, JJ; Brooks, SR et al. JID Innov, DOI://10.1016/j.xjidi.2023.100246 (2024)
Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea Makarova, KS; Zhang, C; Wolf, YI et al. mBio, DOI://10.1128/mbio.03092-23 (2024)
Rapid anti-myeloma activity by T cells expressing an anti-BCMA CAR with a human heavy-chain-only antigen-binding domain Mikkilineni, L; Natrakul, DA; Lam, N et al. Mol Ther, DOI://10.1016/j.ymthe.2023.12.018 (2024)
Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems Rakesh, S; Aravind, L; Krishnan, A; , Nucleic Acids Res, DOI://10.1093/nar/gkad1213 (2024)
Observational and genetic associations between cardiorespiratory fitness and cancer: a UK Biobank and international consortia study Watts, EL; Gonzales, TI; Strain, T et al. Br J Cancer, DOI://10.1038/s41416-023-02489-3 (2024)
Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors Amin, M; Kaur, D; Brudvig, GW; Brooks, BR; , J Chem Theory Comput, DOI://10.1021/acs.jctc.3c00926 (2024)
CHCHD4-TRIAP1 regulation of innate immune signaling mediates skeletal muscle adaptation to exercise Ma, J; Wang, PY; Zhuang, J et al. Cell Rep, DOI://10.1016/j.celrep.2023.113626 (2024)
PancrESS - a meta-analysis resource for understanding cell-type specific expression in the human pancreas Sturgill, D; Wang, L; Arda, HE; , BMC Genomics, DOI://10.1186/s12864-024-09964-y (2024)
Selective transcriptomic dysregulation of metabolic pathways in liver and retina by short- and long-term dietary hyperglycemia Mondal, AK; Brock, DC; Rowan, S et al. iScience, DOI://10.1016/j.isci.2024.108979 (2024)
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma Fitzsimmons, CM; Mandler, MD; Lunger, JC et al. NAR Cancer, DOI://10.1093/narcan/zcae004 (2024)
Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation Accogli, A; Shakya, S; Yang, T et al. Nat Commun, DOI://10.1038/s41467-023-44611-2 (2024)
Multi-ancestry genome-wide association meta-analysis of Parkinson's disease Kim, JJ; Vitale, D; Otani, DV et al. Nat Genet, DOI://10.1038/s41588-023-01584-8 (2024)
The allosteric mechanism of mTOR activation can inform bitopic inhibitor optimization Liu, Y; Zhang, M; Jang, H; Nussinov, R; , Chem Sci, DOI://10.1039/d3sc04690g (2024)
Ongoing production of tissue-resident macrophages from hematopoietic stem cells in healthy adult macaques Rahmberg, AR; Wu, C; Shin, T et al. Blood Adv, DOI://10.1182/bloodadvances.2023011499 (2024)
Genomic landscape of patients with germline RUNX1 variants and familial platelet disorder with myeloid malignancy Yu, K; Deuitch, N; Merguerian, M et al. Blood Adv, DOI://10.1182/bloodadvances.2023011165 (2024)
Vasopressin V2 receptor, tolvaptan, and ERK1/2 phosphorylation in the renal collecting duct Khan, S; Raghuram, V; Chen, L et al. Am J Physiol Renal Physiol, DOI://10.1152/ajprenal.00124.2023 (2024)
TGFβ prevents IgE-mediated allergic disease by restraining T follicular helper 2 differentiation Haque, TT; Weissler, KA; Schmiechen, Z et al. Sci Immunol, DOI://10.1126/sciimmunol.adg8691 (2024)
Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration Kwong, A; Zawistowski, M; Fritsche, LG et al. Hum Mol Genet, DOI://10.1093/hmg/ddad189 (2024)
Evaluation of a deuterated triarylmethyl spin probe for in vivo R2 ∗-based EPR oximetric imaging with enhanced dynamic range Kishimoto, S; Devasahayam, N; Chandramouli, GVR et al. Magn Reson Med, DOI://10.1002/mrm.29811 (2024)
Changes in saliva protein profile throughout Rhipicephalus microplus blood feeding da Silva Vaz Junior, I; Lu, S; Pinto, AFM et al. Parasit Vectors, DOI://10.1186/s13071-024-06136-5 (2024)
From the fat body to the hemolymph: Profiling tick immune and storage proteins through transcriptomics and proteomics Urbanová, V; Lu, S; Kalinová, E et al. Insect Biochem Mol Biol, DOI://10.1016/j.ibmb.2024.104072 (2024)
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites Pugacheva, EM; Bhatt, DN; Rivero-Hinojosa, S et al. Genome Biol, DOI://10.1186/s13059-024-03175-0 (2024)
omicSynth: An open multi-omic community resource for identifying druggable targets across neurodegenerative diseases Alvarado, CX; Makarious, MB; Weller, CA et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2023.12.006 (2024)
RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames Zhang, T; Xue, Y; Su, S et al. Nucleic Acids Res, DOI://10.1093/nar/gkad1122 (2024)
TGF-β and BMP signaling are associated with the transformation of glioblastoma to gliosarcoma and then osteosarcoma Li, A; Hancock, JC; Quezado, M et al. Neurooncol Adv, DOI://10.1093/noajnl/vdad164 (2024)

Matrisome and Immune Pathways Contribute to Extreme Vascular Outcomes in Williams-Beuren Syndrome Liu, D; Billington, CJ; Raja, N et al. J Am Heart Assoc, DOI://10.1161/JAHA.123.031377 (2024)
Towards a structural and functional analysis of the immunoglobulin-fold proteome Tawfeeq, C; Song, J; Khaniya, U et al. Adv Protein Chem Struct Biol, DOI://10.1016/bs.apcsb.2023.11.002 (2024)
A systematic analysis of the landscape of synthetic lethality-driven precision oncology Schäffer, AA; Chung, Y; Kammula, AV et al. Med, DOI://10.1016/j.medj.2023.12.009 (2024)
Inhibition of vertebrate complement system by hematophagous arthropods: inhibitory molecules, mechanisms, physiological roles, and applications Sant'Anna, MRV; Pereira-Filho, AA; Mendes-Sousa, AF et al. Insect Sci, DOI://10.1111/1744-7917.13317 (2024)
Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines Valencia, EM; Maki, KA; Dootz, JN; Barb, JJ; , Sci Data, DOI://10.1038/s41597-023-02877-7 (2024)
Ultra-rare genetic variation in relapsing polychondritis: a whole-exome sequencing study Luo, Y; Ferrada, MA; Sikora, KA et al. Ann Rheum Dis, DOI://10.1136/ard-2023-224732 (2024)

GTax: improving de novo transcriptome assembly by removing foreign RNA contamination Alvarez, RV; Landsman, D; , Genome Biol, DOI://10.1186/s13059-023-03141-2 (2024)
Analysis of rare Parkinson's disease variants in millions of people Pitz, V; Makarious, MB; Bandres-Ciga, S et al. NPJ Parkinsons Dis, DOI://10.1038/s41531-023-00608-8 (2024)
BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen Hall, B; Levy, S; Dufault-Thompson, K et al. Nat Microbiol, DOI://10.1038/s41564-023-01549-x (2024)
Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies Reho, P; Saez-Atienzar, S; Ruffo, P et al. Commun Biol, DOI://10.1038/s42003-023-05725-x (2024)
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma Liu, Z; Luo, Y; Kirimunda, S et al. Commun Biol, DOI://10.1038/s42003-023-05701-5 (2024)
Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children Andargie, TE; Roznik, K; Redekar, N et al. J Clin Invest, DOI://10.1172/JCI178008 (2024)
C-DARL: Contrastive diffusion adversarial representation learning for label-free blood vessel segmentation Kim, B; Oh, Y; Wood, BJ et al. Med Image Anal, DOI://10.1016/j.media.2023.103022 (2024)
Brain Imaging and Registration in Larval Zebrafish Bhandiwad, AA; Gupta, T; Subedi, A et al. Methods Mol Biol, DOI://10.1007/978-1-0716-3401-1_9 (2024)

2023 (642 papers)

Microbial ligand-independent regulation of lymphopoiesis by NOD1 Iwamura, C; Ohnuki, H; Flomerfelt, FA et al. Nat Immunol, DOI://10.1038/s41590-023-01668-x (2023)
Improving the Interpretability of fMRI Decoding using Deep Neural Networks and Adversarial Robustness McClure, P; Moraczewski, D; Lam, KC et al. Apert Neuro, DOI://10.52294/001c.85074 (2023)
Predicting gene expression changes upon epigenomic drug treatment Agrawal, P; Gopalan, V; Rumi, MA; Hannenhalli, S; , F1000Res, DOI://10.12688/f1000research.140273.3 (2023)
Methods for Using Race and Ethnicity in Prediction Models for Lung Cancer Screening Eligibility Landy, R; Gomez, I; Caverly, TJ et al. JAMA Netw Open, DOI://10.1001/jamanetworkopen.2023.31155 (2023)
Excitation creates a distributed pattern of cortical suppression due to varied recurrent input O'Rawe, JF; Zhou, Z; Li, AJ et al. Neuron, DOI://10.1016/j.neuron.2023.09.010 (2023)
Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease Daida, K; Funayama, M; Billingsley, KJ et al. Mov Disord, DOI://10.1002/mds.29610 (2023)
Inter-subject correlation during long narratives reveals widespread neural correlates of reading ability Jangraw, DC; Finn, ES; Bandettini, PA et al. Neuroimage, DOI://10.1016/j.neuroimage.2023.120390 (2023)
Investigation of Two Zr-p-NO2Bn-DOTA Isomers via NMR and Quantum Chemical Studies Lee, YS; O'Connor, RD; Vasalatiy, O; , Eur J Inorg Chem, DOI://10.1002/ejic.202300439 (2023)
Monocyte-derived IL-6 programs microglia to rebuild damaged brain vasculature Choi, BR; Johnson, KR; Maric, D; McGavern, DB; , Nat Immunol, DOI://10.1038/s41590-023-01521-1 (2023)
A comparison of Illumina and PacBio methods to build tick salivary gland transcriptomes confirms large expression of lipocalins and other salivary protein families that are not represented in available tick genomes Guizzo, MG; Mans, B; Pienaar, R; Ribeiro, JMC; , Ticks Tick Borne Dis, DOI://10.1016/j.ttbdis.2023.102209 (2023)
U-shaped association between sleep duration and the risk of respiratory diseases mortality: a large prospective cohort study from UK Biobank Du, M; Liu, M; Liu, J; , J Clin Sleep Med, DOI://10.5664/jcsm.10732 (2023)
Identification of genetic risk loci and causal insights associated with Parkinson's disease in African and African admixed populations: a genome-wide association study Rizig, M; Bandres-Ciga, S; Makarious, MB et al. Lancet Neurol, DOI://10.1016/S1474-4422(23)00283-1 (2023)
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Investigating Determinants and Evaluating Deep Learning Training Approaches for Visual Acuity in Foveal Hypoplasia Malechka, VV; Duong, D; Bordonada, KD et al. Ophthalmol Sci, DOI://10.1016/j.xops.2022.100225 (2023)
An inducible amphipathic α-helix mediates subcellular targeting and membrane binding of RPE65 Uppal, S; Liu, T; Galvan, E et al. Life Sci Alliance, DOI://10.26508/lsa.202201546 (2023)
Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates Stagno, JR; Knoska, J; Chapman, HN; Wang, YX; , Methods Mol Biol, DOI://10.1007/978-1-0716-2687-0_16 (2023)
Combining Biophysical Methods for Structure-Function Analyses of RNA in Solution Lee, YT; Fan, L; Ding, J; Wang, YX; , Methods Mol Biol, DOI://10.1007/978-1-0716-2687-0_11 (2023)
Application of Molecular Dynamics to Expand Docking Program's Exploratory Capabilities and to Evaluate Its Predictions Kasprzak, WK; Shapiro, BA; , Methods Mol Biol, DOI://10.1007/978-1-0716-2687-0_6 (2023)

2022 (621 papers)

Clinical correlation but no elevation of striatal dopamine synthesis capacity in two independent cohorts of medication-free individuals with schizophrenia Eisenberg, DP; Kohn, PD; Hegarty, CE et al. Mol Psychiatry, DOI://10.1038/s41380-021-01337-1 (2022)
Circulating microRNAs in cellular and antibody-mediated heart transplant rejection Shah, P; Agbor-Enoh, S; Bagchi, P et al. J Heart Lung Transplant, DOI://10.1016/j.healun.2022.06.019 (2022)
Visual Field Sensitivity Prediction Using Optical Coherence Tomography Analysis in Hydroxychloroquine Toxicity Jayakar, G; De Silva, T; Cukras, CA; , Invest Ophthalmol Vis Sci, DOI://10.1167/iovs.63.1.15 (2022)
Fast intratumor heterogeneity inference from single-cell sequencing data Kızılkale, C; Rashidi Mehrabadi, F; Sadeqi Azer, E et al. Nat Comput Sci, DOI://10.1038/s43588-022-00298-x (2022)

A reference human induced pluripotent stem cell line for large-scale collaborative studies Pantazis, CB; Yang, A; Lara, E et al. Cell Stem Cell, DOI://10.1016/j.stem.2022.11.004 (2022)
Blocking CDK7-Mediated NOTCH1-cMYC Signaling Attenuates Cancer Stem Cell Activity in Anaplastic Thyroid Cancer Doolittle, WKL; Zhao, L; Cheng, SY; , Thyroid, DOI://10.1089/thy.2022.0087 (2022)
Opioid medication use and blood DNA methylation: epigenome-wide association meta-analysis Lee, M; Joehanes, R; McCartney, DL et al. Epigenomics, DOI://10.2217/epi-2022-0353 (2022)
Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade Palmer, DC; Webber, BR; Patel, Y et al. Med, DOI://10.1016/j.medj.2022.07.008 (2022)
Automated Assessment of Renal Calculi in Serial Computed Tomography Scans Mukherjee, P; Lee, S; Pickhardt, PJ; Summers, RM; , Appl Med Artif Intell (2022), DOI://10.1007/978-3-031-17721-7_5 (2022)
Protein pKa Prediction by Tree-Based Machine Learning Chen, AY; Lee, J; Damjanovic, A; Brooks, BR; , J Chem Theory Comput, DOI://10.1021/acs.jctc.1c01257 (2022)
Genetic association of IL17 and the importance of ABO blood group antigens in saliva to COVID-19 Nishida, N; Sugiyama, M; Kawai, Y et al. Sci Rep, DOI://10.1038/s41598-022-07856-3 (2022)
Noninvasive biomarkers in heart transplant: 2020-2021 year in review Qian, X; Shah, P; Agbor-Enoh, S; , Curr Opin Organ Transplant, DOI://10.1097/MOT.0000000000000945 (2022)
Metformin treatment rescues CD8+ T-cell response to immune checkpoint inhibitor therapy in mice with NAFLD Wabitsch, S; McCallen, JD; Kamenyeva, O et al. J Hepatol, DOI://10.1016/j.jhep.2022.03.010 (2022)
Magnetoencephalography biomarkers of suicide attempt history and antidepressant response to ketamine in treatment-resistant major depression Gilbert, JR; Gerner, JL; Burton, CR et al. J Affect Disord, DOI://10.1016/j.jad.2022.06.025 (2022)
Cardiovascular disease and all-cause mortality risk prediction from abdominal CT using deep learning Daniel C. Elton, Andy Chen, Perry J. Pickhardt, Ronald M. Summers Medical Imaging 2022, doi://10.1117/12.2612620 (2022)
Potential therapeutic response in a severe case of autosomal dominant osteopetrosis type I Jafri SM; Burke EA; et al . J Transl Genet Genom, doi://10.20517/jtgg.2021.63 (2022)
Molecular Genetic Analysis of Ukrainian Families with Congenital Cataracts Jiao, X; Viswanathan, M; Bobrova, NF et al. Children (Basel), DOI://10.3390/children10010051 (2022)
Heterogeneity of enhancers embodies shared and representative functional groups underlying developmental and cell type-specific gene regulation Song, W; Ovcharenko, I; , Gene, DOI://10.1016/j.gene.2022.146640 (2022)
Mediation of Healthy Behaviour on the Association of Frailty with Respiratory Diseases Mortality among 0.4 Million Participants: A Prospective Cohort Study from UK Biobank Du, M; Tao, L; Liu, M; Liu, J; , Nutrients, DOI://10.3390/nu14235046 (2022)
High-Throughput DNA FISH (hiFISH) Finn, E; Misteli, T; Pegoraro, G; , Methods Mol Biol, DOI://10.1007/978-1-0716-2497-5_12 (2022)
Middle age serum sodium levels in the upper part of normal range and risk of heart failure Dmitrieva, NI; Liu, D; Wu, CO; Boehm, M; , Eur Heart J, DOI://10.1093/eurheartj/ehac138 (2022)
Histone deacetylation primes self-propagation of heterochromatin domains to promote epigenetic inheritance Zofall, M; Sandhu, R; Holla, S et al. Nat Struct Mol Biol, DOI://10.1038/s41594-022-00830-7 (2022)

Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria Drummond, RA; Desai, JV; Ricotta, EE et al. Cell Host Microbe, DOI://10.1016/j.chom.2022.04.013 (2022)
Cytomegalovirus infection reduced CD70 expression, signaling and expansion of viral specific memory CD8+ T cells in healthy human adults Lu, J; Chen, G; Sorokina, A et al. Immun Ageing, DOI://10.1186/s12979-022-00307-7 (2022)
Multistate models for the natural history of cancer progression Cheung, LC; Albert, PS; Das, S; Cook, RJ; , Br J Cancer, DOI://10.1038/s41416-022-01904-5 (2022)
PD-1 combination therapy with IL-2 modifies CD8+ T cell exhaustion program Hashimoto, M; Araki, K; Cardenas, MA et al. Nature, DOI://10.1038/s41586-022-05257-0 (2022)
Higher levels of allograft injury in black patients early after heart transplantation Doshi, A; Shah, KB; Agbor-Enoh, S et al. J Heart Lung Transplant, DOI://10.1016/j.healun.2021.12.006 (2022)
Functional aspects of evolution in a cluster of salivary protein genes from mosquitoes Alvarenga, PH; Dias, DR; Xu, X et al. Insect Biochem Mol Biol, DOI://10.1016/j.ibmb.2022.103785 (2022)

Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina Liang, X; Brooks, MJ; Swaroop, A; , Hum Mol Genet, DOI://10.1093/hmg/ddac143 (2022)
Recreational physical activity before and during pregnancy and placental DNA methylation-an epigenome-wide association study Zhao, SK; Yeung, EH; Ouidir, M et al. Am J Clin Nutr, DOI://10.1093/ajcn/nqac111 (2022)
Hierarchical Voting-Based Feature Selection and Ensemble Learning Model Scheme for Glioma Grading with Clinical and Molecular Characteristics Tasci, E; Zhuge, Y; Kaur, H et al. Int J Mol Sci, DOI://10.3390/ijms232214155 (2022)
Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation Stubbs, FE; Flynn, BP; Rivers, CA et al. Oncogene, DOI://10.1038/s41388-022-02516-2 (2022)
Defining cellular population dynamics at single-cell resolution during prostate cancer progression Germanos, AA; Arora, S; Zheng, Y et al. Elife, DOI://10.7554/eLife.79076 (2022)
Logistic Regression-Based Model Is More Efficient Than U-Net Model for Reliable Whole Brain Magnetic Resonance Imaging Segmentation Dieckhaus, H; Meijboom, R; Okar, S et al. Top Magn Reson Imaging, DOI://10.1097/RMR.0000000000000296 (2022)
Mendelian randomization study reveals a causal relationship between adiponectin and LDL cholesterol in Africans Meeks, KAC; Bentley, AR; Doumatey, AP et al. Sci Rep, DOI://10.1038/s41598-022-21922-w (2022)
Baseline Microperimetry and OCT in the RUSH2A Study: Structure-Function Association and Correlation With Disease Severity Lad, EM; Duncan, JL; Liang, W et al. Am J Ophthalmol, DOI://10.1016/j.ajo.2022.08.013 (2022)
Rare germline deleterious variants increase susceptibility for lung cancer Sang, J; Zhang, T; Kim, J et al. Hum Mol Genet, DOI://10.1093/hmg/ddac123 (2022)
Nucleation causes an actin network to fragment into multiple high-density domains Chandrasekaran, A; Giniger, E; Papoian, GA; , Biophys J, DOI://10.1016/j.bpj.2022.07.035 (2022)
fast.adonis: a computationally efficient non-parametric multivariate analysis of microbiome data for large-scale studies Li, S; Vogtmann, E; Graubard, BI et al. Bioinform Adv, DOI://10.1093/bioadv/vbac044 (2022)
Early-Onset TIMP3-Related Retinopathy Associated With Impaired Signal Peptide Guan, B; Huryn, LA; Hughes, AB et al. JAMA Ophthalmol, DOI://10.1001/jamaophthalmol.2022.1822 (2022)
Cell-free DNA in lung transplantation: research tool or clinical workhorse? Keller, M; Agbor-Enoh, S; , Curr Opin Organ Transplant, DOI://10.1097/MOT.0000000000000979 (2022)
Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities Karz, A; Dimitrova, M; Kleffman, K et al. Pigment Cell Melanoma Res, DOI://10.1111/pcmr.13059 (2022)
Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation Jiang, J; Taylor, DK; Kim, EJ et al. Nat Commun, DOI://10.1038/s41467-022-33153-8 (2022)
Lysine methyltransferase Kmt2d regulates naive CD8+ T cell activation-induced survival Kim, J; Nguyen, T; Cifello, J et al. Front Immunol, DOI://10.3389/fimmu.2022.1095140 (2022)
Gene-Level Associations in Patients With and Without Pathogenic Germline Variants in CDKN2A and Pancreatic Cancer Astiazaran-Symonds, E; Graham, C; Kim, J et al. JCO Precis Oncol, DOI://10.1200/PO.22.00145 (2022)
Context-Dependent Function of Long Noncoding RNA PURPL in Transcriptome Regulation during p53 Activation Hartford, CCR; Shrestha, RL; Pongor, L et al. Mol Cell Biol, DOI://10.1128/mcb.00289-22 (2022)

Zfp503/Nlz2 Is Required for RPE Differentiation and Optic Fissure Closure Boobalan, E; Thompson, AH; Alur, RP et al. Invest Ophthalmol Vis Sci, DOI://10.1167/iovs.63.12.5 (2022)
A Graph-theoretic Algorithm for Small Bowel Path Tracking in CT Scans Shin, SY; Lee, S; Summers, RM; , Proc SPIE Int Soc Opt Eng, DOI://10.1117/12.2611878 (2022)
GRAPH-BASED SMALL BOWEL PATH TRACKING WITH CYLINDRICAL CONSTRAINTS Shin, SY; Lee, S; Summers, RM; , Proc IEEE Int Symp Biomed Imaging, DOI://10.1109/isbi52829.2022.9761423 (2022)
Deep Reinforcement Learning for Small Bowel Path Tracking using Different Types of Annotations Shin, SY; Summers, RM; , Med Image Comput Comput Assist Interv, DOI://10.1007/978-3-031-16443-9_53 (2022)
Identifying and predicting amyotrophic lateral sclerosis clinical subgroups: a population-based machine-learning study Faghri, F; Brunn, F; Dadu, A et al. Lancet Digit Health, DOI://10.1016/S2589-7500(21)00274-0 (2022)
An MRI-based radiomics model to predict clear cell renal cell carcinoma growth rate classes in patients with von Hippel-Lindau syndrome Anari, PY; Lay, N; Gopal, N et al. Abdom Radiol (NY), DOI://10.1007/s00261-022-03610-5 (2022)

Topoisomerase 3b is dispensable for replication of a positive-sense RNA virus--murine coronavirus Zhang, T; Su, S; Altouma, V et al. Antiviral Res, DOI://10.1016/j.antiviral.2022.105451 (2022)
Genetic Origins of the Two Canis lupus familiaris (Dog) Freight Dog Populations Ali, MB; Dreger, DL; Buckley, RM et al. J Hered, DOI://10.1093/jhered/esac002 (2022)
Differential regulation of transcription factor T-bet induction during NK cell development and T helper-1 cell differentiation Fang, D; Cui, K; Cao, Y et al. Immunity, DOI://10.1016/j.immuni.2022.03.005 (2022)
ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data Ford, MKB; Hari, A; Rodriguez, O et al. Cell Syst, DOI://10.1016/j.cels.2022.08.008 (2022)
Alcohol use disorder is associated with DNA methylation-based shortening of telomere length and regulated by TESPA1: implications for aging Jung, J; McCartney, DL; Wagner, J et al. Mol Psychiatry, DOI://10.1038/s41380-022-01624-5 (2022)
Discriminatory capacity of prenatal ultrasound measures for large-for-gestational-age birth: A Bayesian approach to ROC analysis using placement values Ghosal, S; Chen, Z; , Stat Biosci, DOI://10.1007/s12561-021-09311-9 (2022)

Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding Doyle, MT; Jimah, JR; Dowdy, T et al. Cell, DOI://10.1016/j.cell.2022.02.016 (2022)
Daily changes in light influence mood via inhibitory networks within the thalamic perihabenular nucleus Weil, T; Daly, KM; Yarur Castillo, H et al. Sci Adv, DOI://10.1126/sciadv.abn3567 (2022)
Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia Hall, HN; Bengani, H; Hufnagel, RB et al. PLoS One, DOI://10.1371/journal.pone.0268149 (2022)
Profiling the NOTCH2NLC GGC Repeat Expansion in Parkinson's Disease in the European Population Billingsley, KJ; Alvarez Jerez, P; Grenn, FP et al. Mov Disord, DOI://10.1002/mds.29155 (2022)
Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry White, JA; Kaninjing, ET; Adeniji, KA et al. Cancer Res Commun, DOI://10.1158/2767-9764.CRC-22-0136 (2022)
Evaluation of cutaneous immune response in a controlled human in vivo model of mosquito bites Guerrero, D; Vo, HTM; Lon, C et al. Nat Commun, DOI://10.1038/s41467-022-34534-9 (2022)
A novel role for GalNAc-T2 dependent glycosylation in energy homeostasis Verzijl, CRC; Oldoni, F; Loaiza, N et al. Mol Metab, DOI://10.1016/j.molmet.2022.101472 (2022)
Comorbidities and ethnic health disparities in the UK biobank Teagle, WL; Norris, ET; Rishishwar, L et al. JAMIA Open, DOI://10.1093/jamiaopen/ooac057 (2022)
Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase Klemm, BP; Singh, D; Smith, CE et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2123092119 (2022)
PUS7 deficiency in human patients causes profound neurodevelopmental phenotype by dysregulating protein translation Han, ST; Kim, AC; Garcia, K et al. Mol Genet Metab, DOI://10.1016/j.ymgme.2022.01.103 (2022)
Comparison of transcranial sonography and [18F]-fluorodopa PET imaging in GBA1 mutation carriers Eisenberg, DP; Lopez, G; Gregory, MD et al. Mov Disord, DOI://10.1002/mds.28852 (2022)
Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids Plassais, J; vonHoldt, BM; Parker, HG et al. Curr Biol, DOI://10.1016/j.cub.2021.12.036 (2022)

Quality control practices in FMRI analysis: Philosophy, methods and examples using AFNI Reynolds, RC; Taylor, PA; Glen, DR; , Front Neurosci, DOI://10.3389/fnins.2022.1073800 (2022)
Adverse childhood experiences and premature mortality through mid-adulthood: A five-decade prospective study Yu, J; Patel, RA; Haynie, DL et al. Lancet Reg Health Am, DOI://10.1016/j.lana.2022.100349 (2022)
Genetic testing in severe aplastic anemia is required for optimal hematopoietic cell transplant outcomes McReynolds, LJ; Rafati, M; Wang, Y et al. Blood, DOI://10.1182/blood.2022016508 (2022)
A filarial parasite-encoded human IL-10 receptor antagonist reveals a novel strategy to modulate host responses Ricciardi, A; Hassan, SA; Kamenyeva, O et al. PNAS Nexus, DOI://10.1093/pnasnexus/pgac184 (2022)
An Overview of D7 Protein Structure and Physiological Roles in Blood-Feeding Nematocera Alvarenga, PH; Andersen, JF; , Biology (Basel), DOI://10.3390/biology12010039 (2022)
The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities Jiménez-Panizo, A; Alegre-Martí, A; Tettey, TT et al. Nucleic Acids Res, DOI://10.1093/nar/gkac1119 (2022)

Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells Luo, W; Hickman, AB; Genzor, P et al. Nucleic Acids Res, DOI://10.1093/nar/gkac1191 (2022)
Domestic dog lineages reveal genetic drivers of behavioral diversification Dutrow, EV; Serpell, JA; Ostrander, EA; , Cell, DOI://10.1016/j.cell.2022.11.003 (2022)
Epidemiology of ICU-Onset Bloodstream Infection: Prevalence, Pathogens, and Risk Factors Among 150,948 ICU Patients at 85 U.S. Hospitals Gouel-Cheron, A; Swihart, BJ; Warner, S et al. Crit Care Med, DOI://10.1097/CCM.0000000000005662 (2022)
Mito-SiPE is a sequence-independent and PCR-free mtDNA enrichment method for accurate ultra-deep mitochondrial sequencing Walsh, DJ; Bernard, DJ; Pangilinan, F et al. Commun Biol, DOI://10.1038/s42003-022-04182-2 (2022)
Elevated cell-free DNA in respiratory viral infection and associated lung allograft dysfunction Bazemore, K; Permpalung, N; Mathew, J et al. Am J Transplant, DOI://10.1111/ajt.17125 (2022)
Plasma Cell-Free DNA Predicts Survival and Maps Specific Sources of Injury in Pulmonary Arterial Hypertension Brusca, SB; Elinoff, JM; Zou, Y et al. Circulation, DOI://10.1161/CIRCULATIONAHA.121.056719 (2022)

HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis Anibal, J; Day, AG; Bahadiroglu, E et al. PLoS Comput Biol, DOI://10.1371/journal.pcbi.1010349 (2022)
Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells Wu, C; Liang, JA; Brenchley, JM et al. Front Immunol, DOI://10.3389/fimmu.2022.994498 (2022)
Systemic Inflammation is Associated with Cardiometabolic Risk Factors and Clinical Outcomes Tejada, B; Joehanes, R; Hwang, SJ et al. J Inflamm Res, DOI://10.2147/JIR.S382620 (2022)
Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2 Wang, L; Candia, J; Ma, L et al. Int J Biol Sci, DOI://10.7150/ijbs.78002 (2022)
Kidney tumors associated with germline mutations of FH and SDHB show a CpG island methylator phenotype (CIMP) Ricketts, CJ; Killian, JK; Vocke, CD et al. PLoS One, DOI://10.1371/journal.pone.0278108 (2022)
A Mega-analytic Study of White Matter Microstructural Differences Across 5 Cohorts of Youths With Attention-Deficit/Hyperactivity Disorder Sudre, G; Norman, L; Bouyssi-Kobar, M et al. Biol Psychiatry, DOI://10.1016/j.biopsych.2022.09.021 (2022)
Acute worsening of CADASIL in a patient with COVID-19 infection: illustrative case Rosenblum, JS; Tunacao, JM; Nazari, MA et al. J Neurosurg Case Lessons, DOI://10.3171/CASE22413 (2022)
Evaluation of Cone- and Rod-Mediated Parameters in Dark Adaptation Testing as Outcome Measures in Age-Related Macular Degeneration Hess, K; de Silva, T; Grisso, P et al. Ophthalmol Retina, DOI://10.1016/j.oret.2022.05.018 (2022)
Protocol for base resolution mapping of ac4C using RedaC:T-seq Sturgill, D; Arango, D; Oberdoerffer, S; , STAR Protoc, DOI://10.1016/j.xpro.2022.101858 (2022)
COnstrained Reference frame diffusion TEnsor Correlation Spectroscopic (CORTECS) MRI: A practical framework for high-resolution diffusion tensor distribution imaging Avram, AV; Saleem, KS; Basser, PJ; , Front Neurosci, DOI://10.3389/fnins.2022.1054509 (2022)
Association between microbial composition, diversity, and function of the maternal gastrointestinal microbiome with impaired glucose tolerance on the glucose challenge test Dreisbach, C; Prescott, S; Alhusen, J et al. PLoS One, DOI://10.1371/journal.pone.0271261 (2022)
Identification and analysis of odorant receptors expressed in the two main olfactory organs, antennae and palps, of Schistocerca americana Boronat-Garcia, A; Iben, J; Dominguez-Martin, E; Stopfer, M; , Sci Rep, DOI://10.1038/s41598-022-27199-3 (2022)
Comparison of out-of-field normal tissue dose estimates for pencil beam scanning proton therapy: MCNP6, PHITS, and TOPAS Griffin, KT; Yeom, YS; Mille, MM et al. Biomed Phys Eng Express, DOI://10.1088/2057-1976/acaab1 (2022)
A Deeper Insight into the Tick Salivary Protein Families under the Light of Alphafold2 and Dali: Introducing the TickSialoFam 2.0 Database Mans, BJ; Andersen, JF; Ribeiro, JMC; , Int J Mol Sci, DOI://10.3390/ijms232415613 (2022)
The paradigm shift: Heartbeat initiation without "the pacemaker cell" Maltsev, VA; Stern, MD; , Front Physiol, DOI://10.3389/fphys.2022.1090162 (2022)
Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops Liu, S; Cao, Y; Cui, K et al. Nat Commun, DOI://10.1038/s41467-022-34276-8 (2022)
Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold Gordon, J; Chapus, FL; Viverette, EG et al. Nat Commun, DOI://10.1038/s41467-022-34610-0 (2022)
Cell type-specific changes in Wnt signaling and neuronal differentiation in the developing mouse cortex after prenatal alcohol exposure during neurogenesis Sambo, D; Gohel, C; Yuan, Q et al. Front Cell Dev Biol, DOI://10.3389/fcell.2022.1011974 (2022)

Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase Ziesel, A; Weng, Q; Ahuja, JS et al. PLoS Genet, DOI://10.1371/journal.pgen.1010407 (2022)
Adults with lysosomal storage diseases in the undiagnosed diseases network Xiao, C; Koziura, M; Cope, H et al. Mol Genet Genomic Med, DOI://10.1002/mgg3.2013 (2022)
Modeling Dinophysis in Western Andalucía using an autoregressive hidden Markov model Aron, J; Albert, PS; Gribble, MO; , Environ Ecol Stat, DOI://10.1007/s10651-022-00534-7 (2022)
Organ dose calculator for diagnostic nuclear medicine patients based on the ICRP reference voxel phantoms and biokinetic models Villoing, D; Kwon, TE; Pasqual, E et al. Biomed Phys Eng Express, DOI://10.1088/2057-1976/aca543 (2022)
Temporal Improvements in COVID-19 Outcomes for Hospitalized Adults: A Post Hoc Observational Study of Remdesivir Group Participants in the Adaptive COVID-19 Treatment Trial Potter, GE; Bonnett, T; Rubenstein, K et al. Ann Intern Med, DOI://10.7326/M22-2116 (2022)
Opposing functions of circadian protein DBP and atypical E2F family E2F8 in anti-tumor Th9 cell differentiation Park, SA; Lim, YJ; Ku, WL et al. Nat Commun, DOI://10.1038/s41467-022-33733-8 (2022)
Structural basis of 3'-end poly(A) RNA recognition by LARP1 Kozlov, G; Mattijssen, S; Jiang, J et al. Nucleic Acids Res, DOI://10.1093/nar/gkac696 (2022)
High-resolution cortical MAP-MRI reveals areal borders and laminar substructures observed with histological staining Avram, AV; Saleem, KS; Komlosh, ME et al. Neuroimage, DOI://10.1016/j.neuroimage.2022.119653 (2022)
Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways Mungale, A; McGaughey, DM; Zhang, C et al. Front Genet, DOI://10.3389/fgene.2022.949449 (2022)
A deep learning approach to identify missing is-a relations in SNOMED CT Abeysinghe, R; Zheng, F; Bernstam, EV et al. J Am Med Inform Assoc, DOI://10.1093/jamia/ocac248 (2022)
An imputation approach for a time-to-event analysis subject to missing outcomes due to noncoverage in disease registries Shih, JH; Albert, PS; Fine, J; Liu, D; , Biostatistics, DOI://10.1093/biostatistics/kxac049 (2022)
Insights into autoregulation of a membrane protein complex by its cytoplasmic domains Leone, V; Bradshaw, RT; Koshy, C et al. Biophys J, DOI://10.1016/j.bpj.2022.12.021 (2022)

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies Talsania, K; Shen, TW; Chen, X et al. Genome Biol, DOI://10.1186/s13059-022-02816-6 (2022)
Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity Long, E; Yin, J; Funderburk, KM et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2022.11.006 (2022)
Structural Determinants and Functional Significance of Dimerization for Osmosensing Transporter ProP in Escherichia coli Ozturk, TN; Coumoundouros, C; Culham, DE; Wood, JM; , Biochemistry, DOI://10.1021/acs.biochem.2c00393 (2022)
Rare copy number variants in males and females with childhood attention-deficit/hyperactivity disorder Jung, B; Ahn, K; Justice, C et al. Mol Psychiatry, DOI://10.1038/s41380-022-01906-y (2022)
Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer Mulenga, A; Radulovic, Z; Porter, L et al. Sci Rep, DOI://10.1038/s41598-022-24881-4 (2022)
TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks Jones, S; Beyers, M; Shukla, M et al. Cancer Inform, DOI://10.1177/11769351221139491 (2022)

Broad misappropriation of developmental splicing profile by cancer in multiple organs Singh, A; Rajeevan, A; Gopalan, V et al. Nat Commun, DOI://10.1038/s41467-022-35322-1 (2022)
Molecular models of multiple sclerosis severity identify heterogeneity of pathogenic mechanisms Kosa, P; Barbour, C; Varosanec, M et al. Nat Commun, DOI://10.1038/s41467-022-35357-4 (2022)
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Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers Lowery, FJ; Krishna, S; Yossef, R et al. Science, DOI://10.1126/science.abl5447 (2022)
Virtual Screening for the Discovery of Microbiome β-Glucuronidase Inhibitors to Alleviate Cancer Drug Toxicity Challa, AP; Hu, X; Zhang, YQ et al. J Chem Inf Model, DOI://10.1021/acs.jcim.1c01414 (2022)
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TMPRSS2-ERG promotes the initiation of prostate cancer by suppressing oncogene-induced senescence Fang, L; Li, D; Yin, J et al. Cancer Gene Ther, DOI://10.1038/s41417-022-00454-5 (2022)
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Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion Nussenblatt, V; Roder, AE; Das, S et al. J Infect Dis, DOI://10.1093/infdis/jiab622 (2022)

Imaging the immune system redux Germain, RN Immunol Rev, DOI://10.1111/imr.13063 (2022)
Structure of the Shaker Kv channel and mechanism of slow C-type inactivation Tan, XF; Bae, C; Stix, R et al. Sci Adv, DOI://10.1126/sciadv.abm7814 (2022)
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The complete sequence of a human genome Nurk, S; Koren, S; Rhie, A et al. Science, DOI://10.1126/science.abj6987 (2022)
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements Hoyt, SJ; Storer, JM; Hartley, GA et al. Science, DOI://10.1126/science.abk3112 (2022)
Epigenetic patterns in a complete human genome Gershman, A; Sauria, MEG; Guitart, X et al. Science, DOI://10.1126/science.abj5089 (2022)

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies McCartney AM, Shafin K, Alonge M et al Nat. Methods, 10.1038/s41592-022-01440-3 (2022)
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A complete reference genome improves analysis of human genetic variation Aganezov, S; Yan, SM; Soto, DC et al. Science, DOI://10.1126/science.abl3533 (2022)
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Transcriptomic analysis of human sensory neurons in painful diabetic neuropathy reveals inflammation and neuronal loss Hall, BE; Macdonald, E; Cassidy, M et al. Sci Rep, DOI://10.1038/s41598-022-08100-8 (2022)

The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol McCartney, MA; Auch, B; Kono, T et al. G3 (Bethesda), DOI://10.1093/g3journal/jkab423 (2022)
Epstein-Barr Virus in Burkitt Lymphoma in Africa Reveals a Limited Set of Whole Genome and LMP-1 Sequence Patterns: Analysis of Archival Datasets and Field Samples From Uganda, Tanzania, and Kenya Liao, HM; Liu, H; Chin, PJ et al. Front Oncol, DOI://10.3389/fonc.2022.812224 (2022)
The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective Ahmadi, S; Sukprasert, P; Vegesna, R et al. Nat Commun, DOI://10.1038/s41467-022-29154-2 (2022)
Complete Genome Sequence of Herpes Simplex Virus 2 Strain G Chang, W; Jiao, X; Sui, H et al. Viruses, DOI://10.3390/v14030536 (2022)
Single-molecule fluorescence imaging and deep learning reveal highly heterogeneous aggregation of amyloid-β 42 Meng, F; Yoo, J; Chung, HS; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2116736119 (2022)
Assessment of Aortoiliac Atherosclerotic Plaque on CT in Prostate Cancer Patients Undergoing Treatment Lee, S; Elton, DC; Gulley, JL et al. Tomography, DOI://10.3390/tomography8020050 (2022)

Lamina-specific immunohistochemical signatures in the olfactory bulb of healthy, Alzheimer's and Parkinson's disease patients Murray, HC; Johnson, K; Sedlock, A et al. Commun Biol, DOI://10.1038/s42003-022-03032-5 (2022)
Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival Ebrahimi, A; Korshunov, A; Reifenberger, G et al. Acta Neuropathol Commun, DOI://10.1186/s40478-021-01308-1 (2022)
Tuning Formation of Protein-DNA Coacervates by Sequence and Environment Lebold, KM; Best, RB; , J Phys Chem B, DOI://10.1021/acs.jpcb.2c00424 (2022)
Enhancer-silencer transitions in the human genome Huang, D; Ovcharenko, I; , Genome Res, DOI://10.1101/gr.275992.121 (2022)
Parallel functional subnetworks embedded in the macaque face patch system Park, SH; Koyano, KW; Russ, BE et al. Sci Adv, DOI://10.1126/sciadv.abm2054 (2022)
DNA methylation-based prognostic subtypes of chordoma tumors in tissue and plasma Zuccato, JA; Patil, V; Mansouri, S et al. Neuro Oncol, DOI://10.1093/neuonc/noab235 (2022)

Photoreceptor degeneration in ABCA4-associated retinopathy and its genetic correlates Pfau, M; Cukras, CA; Huryn, LA et al. JCI Insight, DOI://10.1172/jci.insight.155373 (2022)
Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma Hadrava Vanova, K; Pang, Y; Krobova, L et al. J Natl Cancer Inst, DOI://10.1093/jnci/djab158 (2022)
Preintubation Sequential Organ Failure Assessment Score for Predicting COVID-19 Mortality: External Validation Using Electronic Health Record From 86 U.S. Healthcare Systems to Appraise Current Ventilator Triage Algorithms Keller, MB; Wang, J; Nason, M et al. Crit Care Med, DOI://10.1097/CCM.0000000000005534 (2022)
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae Sim, CK; Kashaf, SS; Stacy, A et al. Microbiome, DOI://10.1186/s40168-021-01207-6 (2022)
Clinical Implications of Inter- and Intratumor Heterogeneity of Immune Cell Markers in Lung Cancer Zhao, W; Zhu, B; Hutchinson, A et al. J Natl Cancer Inst, DOI://10.1093/jnci/djab157 (2022)
Dual-function Spot 42 RNA encodes a 15-amino acid protein that regulates the CRP transcription factor Aoyama, JJ; Raina, M; Zhong, A; Storz, G; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2119866119 (2022)

Severe delayed hypersensitivity reactions to IL-1 and IL-6 inhibitors link to common HLA-DRB1*15 alleles Saper, VE; Ombrello, MJ; Tremoulet, AH et al. Ann Rheum Dis, DOI://10.1136/annrheumdis-2021-220578 (2022)
Ancestry-Matched and Cross-Ancestry Genetic Risk Scores of Type 2 Diabetes in Pregnant Women and Fetal Growth: A Study in an Ancestrally Diverse Cohort Ouidir, M; Zeng, X; Chatterjee, S et al. Diabetes, DOI://10.2337/db21-0655 (2022)
Taxonomic distribution and evolutionary analysis of the equol biosynthesis gene cluster Dufault-Thompson, K; Hall, B; Jiang, X; , BMC Genomics, DOI://10.1186/s12864-022-08426-7 (2022)
A year of COVID-19 GWAS results from the GRASP portal reveals potential genetic risk factors Thibord, F; Chan, MV; Chen, MH; Johnson, AD; , HGG Adv, DOI://10.1016/j.xhgg.2022.100095 (2022)
Quantification of cerebral blood volume changes caused by visual stimulation at 3 T using DANTE-prepared dual-echo EPI Li, L; Law, C; Marrett, S et al. Magn Reson Med, DOI://10.1002/mrm.29099 (2022)
Pembrolizumab and decitabine for refractory or relapsed acute myeloid leukemia Goswami, M; Gui, G; Dillon, LW et al. J Immunother Cancer, DOI://10.1136/jitc-2021-003392 (2022)

Mitochondria in cone photoreceptors act as microlenses to enhance photon delivery and confer directional sensitivity to light Ball, JM; Chen, S; Li, W; , Sci Adv, DOI://10.1126/sciadv.abn2070 (2022)
Topoisomerase VI is a chirally-selective, preferential DNA decatenase McKie, SJ; Desai, PR; Seol, Y et al. Elife, DOI://10.7554/eLife.67021 (2022)
Influence of network defects on the conformational structure of nanogel particles: From "closed compact" to "open fractal" nanogel particles Chremos, A; Horkay, F; Douglas, JF; , J Chem Phys, DOI://10.1063/5.0072274 (2022)
DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis Papanicolau-Sengos, A; Aldape, K; , Annu Rev Pathol, DOI://10.1146/annurev-pathol-042220-022304 (2022)
A systematic genome-wide account of binding sites for the model transcription factor Gcn4 Coey, CT; Clark, DJ; , Genome Res, DOI://10.1101/gr.276080.121 (2022)
Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase Lee, CJ; Stix, R; Rana, MS et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2022050119 (2022)

Interaction of A 3 adenosine receptor ligands with the human multidrug transporter ABCG2 Abel, B; Murakami, M; Tosh, DK et al. Eur J Med Chem, DOI://10.1016/j.ejmech.2022.114103 (2022)
Japanese pediatric and adult atomic bomb survivor dosimetry: potential improvements using the J45 phantom series and modern Monte Carlo transport Griffin, KT; Sato, T; Funamoto, S et al. Radiat Environ Biophys, DOI://10.1007/s00411-021-00946-2 (2022)
Activating NTRK2 and ALK receptor tyrosine kinase fusions extend the molecular spectrum of pleomorphic xanthoastrocytomas of early childhood: a diagnostic overlap with infant-type hemispheric glioma Lucas, CG; Abdullaev, Z; Bruggers, CS et al. Acta Neuropathol, DOI://10.1007/s00401-021-02396-y (2022)
Bridged Piperidine Analogues of a High Affinity Naphthalene-Based P2Y 14 R Antagonist Wen, Z; Salmaso, V; Jung, YH et al. J Med Chem, DOI://10.1021/acs.jmedchem.1c01964 (2022)
Immune cell gene expression signatures in diffuse glioma are associated with IDH mutation status, patient outcome and malignant cell state, and highlight the importance of specific cell subsets in glioma biology Mehani, B; Asanigari, S; Chung, HJ et al. Acta Neuropathol Commun, DOI://10.1186/s40478-022-01323-w (2022)
Evaluating treatment effects in group sequential multivariate longitudinal studies with covariate adjustment Jeffries, NO; Troendle, JF; Geller, NL; , Biometrics, DOI://10.1111/biom.13659 (2022)

Artificial Intelligence-based Tumor Segmentation in Mouse Models of Lung Adenocarcinoma Arlova, A; Jin, C; Wong-Rolle, A et al. J Pathol Inform, DOI://10.1016/j.jpi.2022.100007 (2022)
Periconception and Prenatal Exposure to Maternal Perceived Stress and Cord Blood DNA Methylation Polinski, KJ; Putnick, DL; Robinson, SL et al. Epigenet Insights, DOI://10.1177/25168657221082045 (2022)
DNA methylation cues in nucleosome geometry, stability and unwrapping Li, S; Peng, Y; Landsman, D; Panchenko, AR; , Nucleic Acids Res, DOI://10.1093/nar/gkac097 (2022)
Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module Lee, HK; Knabl, L; Knabl, L et al. Sci Rep, DOI://10.1038/s41598-022-06752-0 (2022)
Yap-Sox9 signaling determines hepatocyte plasticity and lineage-specific hepatocarcinogenesis Liu, Y; Zhuo, S; Zhou, Y et al. J Hepatol, DOI://10.1016/j.jhep.2021.11.010 (2022)
Layer-specific activation in human primary somatosensory cortex during tactile temporal prediction error processing Yu, Y; Huber, L; Yang, J et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.118867 (2022)
A 3 adenosine receptor agonists containing dopamine moieties for enhanced interspecies affinity Tosh, DK; Salmaso, V; Campbell, RG et al. Eur J Med Chem, DOI://10.1016/j.ejmech.2021.113983 (2022)
Structure-Activity Relationship of 3-Methylcytidine-5'-α,β-methylenediphosphates as CD73 Inhibitors Scortichini, M; Idris, RM; Moschütz, S et al. J Med Chem, DOI://10.1021/acs.jmedchem.1c01852 (2022)
MRP5 and MRP9 play a concerted role in male reproduction and mitochondrial function Chambers, IG; Kumar, P; Lichtenberg, J et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2111617119 (2022)
SARS-CoV-2 infection in free-ranging white-tailed deer Hale, VL; Dennis, PM; McBride, DS et al. Nature, DOI://10.1038/s41586-021-04353-x (2022)
An open-source tool for automated analysis of breathing behaviors in common marmosets and rodents Bishop, M; Weinhold, M; Turk, AZ et al. Elife, DOI://10.7554/eLife.71647 (2022)
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa Okoh, OS; Nii-Trebi, NI; Jakkari, A et al. iScience, DOI://10.1016/j.isci.2022.103880 (2022)

Identification of genetic risk loci and prioritization of genes and pathways for myasthenia gravis: a genome-wide association study Chia, R; Saez-Atienzar, S; Murphy, N et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2108672119 (2022)
The positive-negative mode link between brain connectivity, demographics and behaviour: a pre-registered replication of Smith et al. (2015) Goyal, N; Moraczewski, D; Bandettini, PA et al. R Soc Open Sci, DOI://10.1098/rsos.201090 (2022)
Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq Kavita, K; Zhang, A; Tai, CH et al. Nucleic Acids Res, DOI://10.1093/nar/gkac017 (2022)
MicroRNA-15a/16-1 Prevents Hepatocellular Carcinoma by Disrupting the Communication Between Kupffer Cells and Regulatory T Cells Liu, N; Chang, CW; Steer, CJ et al. Gastroenterology, DOI://10.1053/j.gastro.2021.10.015 (2022)
Synthesis, Biological Evaluation, and Molecular Modeling Studies of 3,4-Diarylpyrazoline Series of Compounds as Potent, Nonbrain Penetrant Antagonists of Cannabinoid-1 (CB1R) Receptor with Reduced Lipophilicity Iyer, MR; Cinar, R; Wood, CM et al. J Med Chem, DOI://10.1021/acs.jmedchem.1c01836 (2022)
MYC amplifies gene expression through global changes in transcription factor dynamics Patange, S; Ball, DA; Wan, Y et al. Cell Rep, DOI://10.1016/j.celrep.2021.110292 (2022)

Structural insights into the BRAF monomer-to-dimer transition mediated by RAS binding Martinez Fiesco, JA; Durrant, DE; Morrison, DK; Zhang, P; , Nat Commun, DOI://10.1038/s41467-022-28084-3 (2022)
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas Rudd, ML; Hansen, NF; Zhang, X et al. PLoS One, DOI://10.1371/journal.pone.0251286 (2022)
Prenatal origins of suicide mortality: A prospective cohort study in the United States Vidal-Ribas, P; Govender, T; Sundaram, R et al. Transl Psychiatry, DOI://10.1038/s41398-021-01777-x (2022)
Can AlphaFold2 predict the impact of missense mutations on structure? Buel, GR; Walters, KJ; , Nat Struct Mol Biol, DOI://10.1038/s41594-021-00714-2 (2022)
Hyperbolic trade-off: The importance of balancing trial and subject sample sizes in neuroimaging Chen, G; Pine, DS; Brotman, MA et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.118786 (2022)
Autonomic arousals contribute to brain fluid pulsations during sleep Picchioni, D; Özbay, PS; Mandelkow, H et al. Neuroimage, DOI://10.1016/j.neuroimage.2022.118888 (2022)
Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients Zhu, B; Joo, L; Zhang, T et al. HGG Adv, DOI://10.1016/j.xhgg.2021.100076 (2022)
Neural network classifiers for images of genetic conditions with cutaneous manifestations Duong, D; Waikel, RL; Hu, P et al. HGG Adv, DOI://10.1016/j.xhgg.2021.100053 (2022)
Central Vein Sign Profile of Newly Developing Lesions in Multiple Sclerosis: A 3-Year Longitudinal Study Al-Louzi, O; Letchuman, V; Manukyan, S et al. Neurol Neuroimmunol Neuroinflamm, DOI://10.1212/NXI.0000000000001120 (2022)
Evolution of influenza A virus in intensive and free-range swine farms in Spain Encinas, P; Del Real, G; Dutta, J et al. Virus Evol, DOI://10.1093/ve/veab099 (2022)
Artificial Intelligence in Medical Imaging and its Impact on the Rare Disease Community: Threats, Challenges and Opportunities Hasani, N; Farhadi, F; Morris, MA et al. PET Clin, DOI://10.1016/j.cpet.2021.09.009 (2022)
Functional variants in cytochrome b5 type A (CYB5A) are enriched in Southwest American Indian individuals and associate with obesity Day, SE; Traurig, M; Kumar, P et al. Obesity (Silver Spring), DOI://10.1002/oby.23359 (2022)

Threat imminence reveals links among unfolding of anticipatory physiological response, cortical-subcortical intrinsic functional connectivity, and anxiety Abend, R; Ruiz, SG; Bajaj, MA et al. Neurobiol Stress, DOI://10.1016/j.ynstr.2022.100428 (2022)
Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern Li, W; Chen, Y; Prévost, J et al. Cell Rep, DOI://10.1016/j.celrep.2021.110210 (2022)
Dose-dependent relationship between social drinking and brain aging Angebrandt, A; Abulseoud, OA; Kisner, M et al. Neurobiol Aging, DOI://10.1016/j.neurobiolaging.2021.11.008 (2022)
Integrated analysis of the sialotranscriptome and sialoproteome of the rat flea Xenopsylla cheopis Lu, S; Andersen, JF; Bosio, CF et al. J Proteomics, DOI://10.1016/j.jprot.2021.104476 (2022)
cLoops2: a full-stack comprehensive analytical tool for chromatin interactions Cao, Y; Liu, S; Ren, G et al. Nucleic Acids Res, DOI://10.1093/nar/gkab1233 (2022)
Fetal dose from proton pencil beam scanning craniospinal irradiation during pregnancy: a Monte Carlo study Yeom, YS; Griffin, KT; Mille, MM et al. Phys Med Biol, DOI://10.1088/1361-6560/ac4b38 (2022)

Viscoelastic parameterization of human skin cells characterize material behavior at multiple timescales Parvini, CH; Cartagena-Rivera, AX; Solares, SD; , Commun Biol, DOI://10.1038/s42003-021-02959-5 (2022)
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters Yan, W; Hall, AB; Jiang, X; , NPJ Biofilms Microbiomes, DOI://10.1038/s41522-021-00260-1 (2022)
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample Sahraeian, SME; Fang, LT; Karagiannis, K et al. Genome Biol, DOI://10.1186/s13059-021-02592-9 (2022)
Genomic analysis of childhood hearing loss in the Yoruba population of Nigeria Adeyemo, A; Faridi, R; Chattaraj, P et al. Eur J Hum Genet, DOI://10.1038/s41431-021-00984-w (2022)
Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein Heidarsson, PO; Mercadante, D; Sottini, A et al. Nat Chem, DOI://10.1038/s41557-021-00839-3 (2022)
Autocrine vitamin D signaling switches off pro-inflammatory programs of T H 1 cells Chauss, D; Freiwald, T; McGregor, R et al. Nat Immunol, DOI://10.1038/s41590-021-01080-3 (2022)
Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS stratifies melanoma patients to anti-PD-1 therapy Wang, K; Patkar, S; Lee, JS et al. Cancer Discov, DOI://10.1158/2159-8290.CD-21-0887 (2022)
Fluorine-Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier (BBB) Penetration Property of Novel Central Nervous System (CNS)-targeting HIV-1 Protease Inhibitors In Vitro Amano, M; Yedidi, RS; Salcedo-Gómez, PM et al. Antimicrob Agents Chemother, DOI://10.1128/AAC.01715-21 (2022)
Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market Kraberger, S; Austin, C; Farkas, K et al. Virology, DOI://10.1016/j.virol.2021.10.007 (2022)
Antipsychotic medication-mediated cognitive change in schizophrenia and polygenic score for cognitive ability Blackman, RK; Dickinson, D; Eisenberg, DP et al. Schizophr Res Cogn, DOI://10.1016/j.scog.2021.100223 (2022)
Artificial Intelligence in Vascular-PET:: Translational and Clinical Applications Paravastu, SS; Theng, EH; Morris, MA et al. PET Clin, DOI://10.1016/j.cpet.2021.09.003 (2022)

2021 (606 papers)

Basal ganglia activation localized in MEG using a reward task Sepe-Forrest, L; Carver, FW; Quentin, R et al. Neuroimage Rep, DOI://10.1016/j.ynirp.2021.100034 (2021)
B cell residency but not T cell-independent IgA switching in the gut requires innate lymphoid cells Zheng, M; Mao, K; Fang, D et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2106754118 (2021)
Phosphoproteomic Identification of Vasopressin/cAMP/Protein Kinase A-Dependent Signaling in Kidney Salhadar, K; Matthews, A; Raghuram, V et al. Mol Pharmacol, DOI://10.1124/mol.120.119602 (2021)
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SARS-CoV-2 infection of the oral cavity and saliva Huang, N; Pérez, P; Kato, T et al. Nat Med, DOI://10.1038/s41591-021-01296-8 (2021)
A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse Chen, L; Chou, CL; Knepper, MA; , J Am Soc Nephrol, DOI://10.1681/ASN.2020101406 (2021)
Integrative analysis of multiple case-control studies Zhang, H; Deng, L; Wheeler, W; Qin, J; Yu, K; , Biometrics, DOI://10.1111/biom.13461 (2021)
Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases Yao, C; Joehanes, R; Wilson, R et al. Clin Epigenetics, DOI://10.1186/s13148-021-01041-5 (2021)
Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis Kaczanowska, S; Beury, DW; Gopalan, V et al. Cell, DOI://10.1016/j.cell.2021.02.048 (2021)
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2 Ghorbani, M; Brooks, BR; Klauda, JB; , Biophys J, DOI://10.1016/j.bpj.2021.02.047 (2021)

Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area Thielen, PM; Wohl, S; Mehoke, T et al. JCI Insight, DOI://10.1172/jci.insight.144350 (2021)
Conformational Ensemble of Tte AdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition Ma, B; Bai, G; Nussinov, R; Ding, J; Wang, YX; , J Phys Chem B, DOI://10.1021/acs.jpcb.1c00038 (2021)
Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity Rouf Banday, A; Onabajo, OO; Lin, SH et al. Commun Biol, DOI://10.1038/s42003-021-01844-5 (2021)
Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation Guan, R; Lian, T; Zhou, BR et al. Nat Commun, DOI://10.1038/s41467-021-21985-9 (2021)
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma Hung, MH; Lee, JS; Ma, C et al. Nat Commun, DOI://10.1038/s41467-021-21804-1 (2021)
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Death agonist antibody against TRAILR2/DR5/TNFRSF10B enhances birinapant anti-tumor activity in HPV-positive head and neck squamous cell carcinomas An, Y; Jeon, J; Sun, L et al. Sci Rep, DOI://10.1038/s41598-021-85589-5 (2021)
Structure of membrane diacylglycerol kinase in lipid bilayers Li, J; Shen, Y; Chen, Y et al. Commun Biol, DOI://10.1038/s42003-021-01802-1 (2021)
Comparative engraftment and clonality of macaque HSPCs expanded on human umbilical vein endothelial cells versus non-expanded cells Srivastava, SK; Truitt, LL; Wu, C et al. Mol Ther Methods Clin Dev, DOI://10.1016/j.omtm.2021.02.009 (2021)
Genetically inferred telomere length and testicular germ cell tumor risk Brown, DW; Lan, Q; Rothman, N et al. Cancer Epidemiol Biomarkers Prev, DOI://10.1158/1055-9965.EPI-20-1775 (2021)
Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria Sun, Z; Yakhnin, AV; FitzGerald, PC et al. Nat Commun, DOI://10.1038/s41467-021-21150-2 (2021)
Tumor IsomiR Encyclopedia (TIE): a pancancer database of miRNA isoforms Bofill-De Ros, X; Luke, B; Guthridge, R et al. Bioinformatics, DOI://10.1093/bioinformatics/btab172 (2021)
Fully automated CT imaging biomarkers of bone, muscle, and fat: correcting for the effect of intravenous contrast Perez, AA; Pickhardt, PJ; Elton, DC; Sandfort, V; Summers, RM; , Abdom Radiol (NY), DOI://10.1007/s00261-020-02755-5 (2021)
Retroviral Elements in Human Evolution and Neural Development Wang, T; Doucet-O'Hare, TT; Henderson, L et al. J Exp Neurol, 2692-2819 (2021)
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Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord Nguyen, TH; Vicidomini, R; Choudhury, SD et al. Curr Protoc, DOI://10.1002/cpz1.38 (2021)
Dose conversion coefficients for neutron external exposures with five postures: walking, sitting, bending, kneeling, and squatting Yeom, YS; Griffin, K; Han, H et al. Radiat Environ Biophys, DOI://10.1007/s00411-021-00900-2 (2021)
Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells Gao, W; Ku, WL; Pan, L et al. Nucleic Acids Res, DOI://10.1093/nar/gkab102 (2021)
MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23 Mikami, Y; Philips, RL; Sciumè, G et al. Immunity, DOI://10.1016/j.immuni.2021.02.015 (2021)
Mitochondrial Ca 2+, redox environment and ROS emission in heart failure: Two sides of the same coin? Cortassa, S; Juhaszova, M; Aon, MA et al. J Mol Cell Cardiol, DOI://10.1016/j.yjmcc.2020.11.013 (2021)
CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids Yu, Y; Krämer, A; Venable, RM et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.0c01327 (2021)

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion Yu, Y; Krämer, A; Venable, RM et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.0c01326 (2021)
Midbrain activity shapes high-level visual properties in the primate temporal cortex Bogadhi, AR; Katz, LN; Bollimunta, A et al. Neuron, DOI://10.1016/j.neuron.2020.11.023 (2021)
Loop extrusion mediates physiological Igh locus contraction for RAG scanning Dai, HQ; Hu, H; Lou, J et al. Nature, DOI://10.1038/s41586-020-03121-7 (2021)
Mechanism of membrane-tethered mitochondrial protein synthesis Itoh, Y; Andréll, J; Choi, A et al. Science, DOI://10.1126/science.abe0763 (2021)
Gene-based analysis of bi-variate survival traits via functional regressions with applications to eye diseases Zhang, B; Chiu, CY; Yuan, F et al. Genet Epidemiol, DOI://10.1002/gepi.22381 (2021)
BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8 + T cells Yao, C; Lou, G; Sun, HW et al. Nat Immunol, DOI://10.1038/s41590-021-00868-7 (2021)

Lysosome-associated membrane protein 3 misexpression in salivary glands induces a Sjögren's syndrome-like phenotype in mice Nakamura, H; Tanaka, T; Pranzatelli, T et al. Ann Rheum Dis, DOI://10.1136/annrheumdis-2020-219649 (2021)
Structure of an activated DNA-PK and its implications for NHEJ Chen, X; Xu, X; Chen, Y et al. Mol Cell, DOI://10.1016/j.molcel.2020.12.015 (2021)
Does the ATP-bound EQ mutant reflect the pre- or post-ATP hydrolysis state in the catalytic cycle of human P-glycoprotein (ABCB1)? Lusvarghi, S; Durell, SR; Ambudkar, SV; , FEBS Lett, DOI://10.1002/1873-3468.14054 (2021)
Audiovisual integration in macaque face patch neurons Khandhadia, AP; Murphy, AP; Romanski, LM; Bizley, JK; Leopold, DA; , Curr Biol, DOI://10.1016/j.cub.2021.01.102 (2021)
A Genome-First Approach to Characterize DICER1 Pathogenic Variant Prevalence, Penetrance, and Phenotype Mirshahi, UL; Kim, J; Best, AF et al. JAMA Netw Open, DOI://10.1001/jamanetworkopen.2021.0112 (2021)
The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization Xiao, T; Li, X; Felsenfeld, G; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2023127118 (2021)
Trans-ethnic meta-analysis identifies new loci associated with longitudinal blood pressure traits Gouveia, MH; Bentley, AR; Leonard, H et al. Sci Rep, DOI://10.1038/s41598-021-83450-3 (2021)
Deep-learning based multi-modal retinal image registration for the longitudinal analysis of patients with age-related macular degeneration De Silva, T; Chew, EY; Hotaling, N; Cukras, CA; , Biomed Opt Express, DOI://10.1364/BOE.408573 (2021)
TRF2-mediated telomere protection is dispensable in pluripotent stem cells Markiewicz-Potoczny, M; Lobanova, A; Loeb, AM et al. Nature, DOI://10.1038/s41586-020-2959-4 (2021)
The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution Eriksson, PR; Clark, DJ; , Sci Rep, DOI://10.1038/s41598-021-82842-9 (2021)
Smoking modifies pancreatic cancer risk loci on 2q21.3 Mocci, E; Kundu, P; Wheeler, W et al. Cancer Res, DOI://10.1158/0008-5472.CAN-20-3267 (2021)
Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival Bai, J; Shi, J; Li, C et al. Nat Commun, DOI://10.1038/s41467-021-21026-5 (2021)

Exome Sequencing of 21 Bardet-Biedl Syndrome (BBS) Genes to Identify Obesity Variants in 6,851 American Indians Day, SE; Muller, YL; Koroglu, C et al. Obesity (Silver Spring), DOI://10.1002/oby.23115 (2021)
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community Lee, HK; Knabl, L; Pipperger, L et al. Sci Rep, DOI://10.1038/s41598-021-83110-6 (2021)
The NF-κB regulator Bcl-3 restricts terminal differentiation and promotes memory cell formation of CD8+ T cells during viral infection Jaiswal, H; Ciucci, T; Wang, H et al. PLoS Pathog, DOI://10.1371/journal.ppat.1009249 (2021)
Gene Therapy of Dominant CRX-Leber Congenital Amaurosis using Patient Stem Cell-Derived Retinal Organoids Kruczek, K; Qu, Z; Gentry, J et al. Stem Cell Reports, DOI://10.1016/j.stemcr.2020.12.018 (2021)
Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes Maruyama, SR; Rogerio, LA; Freitas, PD; Teixeira, MMG; Ribeiro, JMC; , Sci Rep, DOI://10.1038/s41598-021-81926-w (2021)
Dynamic sex chromosome expression in Drosophila male germ cells Mahadevaraju, S; Fear, JM; Akeju, M et al. Nat Commun, DOI://10.1038/s41467-021-20897-y (2021)

Admixture mapping identifies African and Amerindigenous local ancestry loci associated with fetal growth Tekola-Ayele, F; Ouidir, M; Shrestha, D et al. Hum Genet, DOI://10.1007/s00439-021-02265-4 (2021)
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture Chia, R; Sabir, MS; Bandres-Ciga, S et al. Nat Genet, DOI://10.1038/s41588-021-00785-3 (2021)
Genome-wide transcriptome study using deep RNA sequencing for myocardial infarction and coronary artery calcification Zhang, X; van Rooij, JGJ; Wakabayashi, Y et al. BMC Med Genomics, DOI://10.1186/s12920-020-00838-2 (2021)
Assessment of assumptions underlying models of prokaryotic pangenome evolution Sela, I; Wolf, YI; Koonin, EV; , BMC Biol, DOI://10.1186/s12915-021-00960-2 (2021)
Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets Kia, DA; Zhang, D; Guelfi, S et al. JAMA Neurol, DOI://10.1001/jamaneurol.2020.5257 (2021)
Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue Ghosh, U; Thurber, KR; Yau, WM; Tycko, R; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2023089118 (2021)

An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing Montemayor, C; Simone, A; Long, J et al. Vox Sang, DOI://10.1111/vox.13035 (2021)
On the Role of a Conserved Methionine in the Na+-Coupling Mechanism of a Neurotransmitter Transporter Homolog Zhou, W; Trinco, G; Slotboom, DJ; Forrest, LR; Faraldo-Gómez, JD; , Neurochem Res, DOI://10.1007/s11064-021-03253-w (2021)
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning Kim, JH; Noskov, VN; Ogurtsov, AY et al. Sci Rep, DOI://10.1038/s41598-021-82565-x (2021)
Deep transcriptome sequencing of subgenual anterior cingulate cortex reveals cross-diagnostic and diagnosis-specific RNA expression changes in major psychiatric disorders Akula, N; Marenco, S; Johnson, K et al. Neuropsychopharmacology, DOI://10.1038/s41386-020-00949-5 (2021)
An examination of the relationships between attention/deficit hyperactivity disorder symptoms and functional connectivity over time Norman, LJ; Sudre, G; Bouyssi-Kobar, M; Sharp, W; Shaw, P; , Neuropsychopharmacology, DOI://10.1038/s41386-021-00958-y (2021)
Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers Zhao, J; Mohan, N; Nussinov, R; Ma, B; Wu, WJ; , Antibodies (Basel), DOI://10.3390/antib10010007 (2021)

Infection trains the host for microbiota-enhanced resistance to pathogens Stacy, A; Andrade-Oliveira, V; McCulloch, JA et al. Cell, DOI://10.1016/j.cell.2020.12.011 (2021)
Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics Haspel, N; Jang, H; Nussinov, R; , Biophys J, DOI://10.1016/j.bpj.2020.12.007 (2021)
Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation Beck, DB; Basar, MA; Asmar, AJ et al. Sci Adv, DOI://10.1126/sciadv.abe2116 (2021)
Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity Cheng, K; Nair, NU; Lee, JS; Ruppin, E; , Sci Adv, DOI://10.1126/sciadv.abc2100 (2021)
Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types Saez-Atienzar, S; Bandres-Ciga, S; Langston, RG et al. Sci Adv, DOI://10.1126/sciadv.abd9036 (2021)
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements Eicher, T; Chan, J; Luu, H; Machiraju, R; Mathé, EA; , BMC Bioinformatics, DOI://10.1186/s12859-021-03976-1 (2021)

Associations of maternal blood pressure-raising polygenic risk scores with fetal weight Workalemahu, T; Rahman, ML; Ouidir, M; Wu, J; Zhang, C; Tekola-Ayele, F; , J Hum Hypertens, DOI://10.1038/s41371-021-00483-x (2021)
Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics Pillon, MC; Frazier, MN; Dillard, LB et al. Nat Commun, DOI://10.1038/s41467-020-20608-z (2021)
Dense cellular segmentation for EM using 2D-3D neural network ensembles Guay, MD; Emam, ZAS; Anderson, AB et al. Sci Rep, DOI://10.1038/s41598-021-81590-0 (2021)
An optimized protocol for acquiring and processing cryo-EM data of human 26S proteasome with M1-Ub6 Chen, X; Shi, D; Zhang, P; Walters, KJ; , STAR Protoc, DOI://10.1016/j.xpro.2020.100278 (2021)
A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication Hattori, SI; Higashi-Kuwata, N; Hayashi, H et al. Nat Commun, DOI://10.1038/s41467-021-20900-6 (2021)
Whole-exome sequencing reveals germline-mutated small cell lung cancer subtype with favorable response to DNA repair-targeted therapies Tlemsani, C; Takahashi, N; Pongor, L et al. Sci Transl Med, DOI://10.1126/scitranslmed.abc7488 (2021)

Cenote-Taker 2 democratizes virus discovery and sequence annotation Tisza, MJ; Belford, AK; Domínguez-Huerta, G; Bolduc, B; Buck, CB; , Virus Evol, DOI://10.1093/ve/veaa100 (2021)
Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma Pomella, S; Sreenivas, P; Gryder, BE et al. Nat Commun, DOI://10.1038/s41467-020-20386-8 (2021)
Glycolytic metabolism of pathogenic T cells enables early detection of GVHD by 13C-MRI Assmann, JC; Farthing, DE; Saito, K et al. Blood, DOI://10.1182/blood.2020005770 (2021)
TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization Brown, MA; Dotson, GA; Ronquist, S; Emons, G; Rajapakse, I; Ried, T; , Neoplasia, DOI://10.1016/j.neo.2020.12.010 (2021)
Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA Patterson-West, J; Tai, CH; Son, B; Hsieh, ML; Iben, JR; Hinton, DM; , Viruses, DOI://10.3390/v13010084 (2021)
Regulatory roles of Escherichia coli 5'UTR and ORF-internal RNAs detected by 3'end mapping Adams, PP; Baniulyte, G; Esnault, C et al. Elife, DOI://10.7554/eLife.62438 (2021)

Survivin Expression is Differentially Regulated by a Selective Crosstalk between Rbm38 and miRNAs let-7b or miR-203a Lucchesi, CA; Zhang, J; Ma, B; Nussinov, R; Chen, X; , Cancer Res, DOI://10.1158/0008-5472.CAN-20-3157 (2021)
Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes Kanfer, G; Sarraf, SA; Maman, Y et al. J Cell Biol, DOI://10.1083/jcb.202006180 (2021)
A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia Tottone, L; Lancho, O; Loh, JW et al. Blood Cancer Discov, DOI://10.1158/2643-3230.BCD-20-0201 (2021)
A high-throughput predictive method for sequence-similar fold switchers Kim, AK; Looger, LL; Porter, LL; , Biopolymers, DOI://10.1002/bip.23416 (2021)
Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates Liu, C; Yen, CC; Szczupak, D; Tian, X; Glen, D; Silva, AC; , Neuroimage, DOI://10.1016/j.neuroimage.2020.117620 (2021)
A collaborative resource platform for non-human primate neuroimaging Messinger, A; Sirmpilatze, N; Heuer, K et al. Neuroimage, DOI://10.1016/j.neuroimage.2020.117519 (2021)

Thymic stromal lymphopoietin limits primary and recall CD8 + T-cell anti-viral responses Ebina-Shibuya, R; West, EE; Spolski, R et al. Elife, DOI://10.7554/eLife.61912 (2021)
Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes Rodrigues, RR; Gurung, M; Li, Z et al. Nat Commun, DOI://10.1038/s41467-020-20313-x (2021)
Ambulatory Assessment Methods to Examine Momentary State-Based Predictors of Opioid Use Behaviors Burgess-Hull, A; Epstein, DH; , Curr Addict Rep, DOI://10.1007/s40429-020-00351-7 (2021)
Pleiotropic genetic influence on birth weight and childhood obesity Chatterjee, S; Ouidir, M; Tekola-Ayele, F; , Sci Rep, DOI://10.1038/s41598-020-80084-9 (2021)
A population scale analysis of rare SNCA variation in the UK Biobank Blauwendraat, C; Makarious, MB; Leonard, HL et al. Neurobiol Dis, DOI://10.1016/j.nbd.2020.105182 (2021)
Platypus and echidna genomes reveal mammalian biology and evolution Zhou, Y; Shearwin-Whyatt, L; Li, J et al. Nature, DOI://10.1038/s41586-020-03039-0 (2021)

Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux Castellano, S; Claxton, DP; Ficici, E et al. J Biol Chem, DOI://10.1074/jbc.RA120.016792 (2021)
Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake Schureck, MA; Darling, JE; Merk, A et al. Elife, DOI://10.7554/eLife.65282 (2021)
Automated assessment of longitudinal biomarker changes at abdominal CT: correlation with subsequent cardiovascular events in an asymptomatic adult screening cohort Graffy, PM; Summers, RM; Perez, AA; Sandfort, V; Zea, R; Pickhardt, PJ; , Abdom Radiol (NY), DOI://10.1007/s00261-020-02885-w (2021)
Great Expectations: A Critical Review of and Suggestions for the Study of Reward Processing as a Cause and Predictor of Depression Nielson, DM; Keren, H; O'Callaghan, G et al. Biol Psychiatry, DOI://10.1016/j.biopsych.2020.06.012 (2021)
END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells Wong, N; John, S; Nussenzweig, A; Canela, A; , Methods Mol Biol, DOI://10.1007/978-1-0716-0644-5_2 (2021)

2020 (521 papers)

Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers Hennighausen, L; Lee, HK; , SSRN, DOI://10.2139/ssrn.3601827 (2020)
Genomic profiling of primary histiocytic sarcoma reveals two molecular subgroups Egan, C; Nicolae, A; Lack, J et al. Haematologica, DOI://10.3324/haematol.2019.230375 (2020)
Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans Sinha, S; Mitchell, KA; Zingone, A et al. Nat Cancer, DOI://10.1038/s43018-019-0009-7 (2020)
Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study Alcon-Giner, C; Dalby, MJ; Caim, S et al. Cell Rep Med, DOI://10.1016/j.xcrm.2020.100077 (2020)
Virome diversity analysis reveals novel enteroviruses and a human picobirnavirus in stool samples from African green monkeys with diarrhea Li, W; Qiang, X; Qin, S et al. Infect Genet Evol, DOI://10.1016/j.meegid.2020.104279 (2020)
Incorporation of α-methylated amino acids into Apolipoprotein A-I mimetic peptides improves their helicity and cholesterol efflux potential Islam, R; Sviridov, DO; Drake, SK et al. Biochem Biophys Res Commun, DOI://10.1016/j.bbrc.2020.03.070 (2020)
Phenotypic profiling with a living biobank of primary rhabdomyosarcoma unravels disease heterogeneity and AKT sensitivity Manzella, G; Schreck, LD; Breunis, WB et al. Nat Commun, DOI://10.1038/s41467-020-18388-7 (2020)

Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells Dai, L; Hallmark, L; Bofill De Ros, X et al. RNA Biol, DOI://10.1080/15476286.2020.1813439 (2020)
Identification and functional validation of genetic variants in potential miRNA target sites of established BMI genes Kumar, P; Traurig, M; Baier, LJ; , Int J Obes (Lond), DOI://10.1038/s41366-019-0488-8 (2020)
Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations Chen, MH; Raffield, LM; Mousas, A et al. Cell, DOI://10.1016/j.cell.2020.06.045 (2020)
The genomic landscape of Mongolian hepatocellular carcinoma Candia, J; Bayarsaikhan, E; Tandon, M et al. Nat Commun, DOI://10.1038/s41467-020-18186-1 (2020)
Author Correction: Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq) Carter, B; Ku, WL; Kang, JY et al. Nat Commun, DOI://10.1038/s41467-020-18309-8 (2020)
The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases Auslander, N; Ramos, DM; Zelaya, I et al. Mol Syst Biol, DOI://10.15252/msb.20209701 (2020)

Exome Sequencing Identifies A Nonsense Variant in DAO Associated With Reduced Energy Expenditure in American Indians Piaggi, P; Köroğlu, Ç; Nair, AK et al. J Clin Endocrinol Metab, DOI://10.1210/clinem/dgaa548 (2020)
Retinal ganglion cell defects cause decision shifts in visually evoked defense responses Lees, RN; Akbar, AF; Badea, TC; , J Neurophysiol, DOI://10.1152/jn.00474.2019 (2020)
In vitro model of perimenopausal depression implicates steroid metabolic and proinflammatory genes Rudzinskas, S; Hoffman, JF; Martinez, P et al. Mol Psychiatry, DOI://10.1038/s41380-020-00860-x (2020)
NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor Yakhnin, AV; Kashlev, M; Babitzke, P; , Crit Rev Biochem Mol Biol, DOI://10.1080/10409238.2020.1828261 (2020)
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Abl Signaling Directs Growth of a Pioneer Axon in Drosophila by Shaping the Intrinsic Fluctuations of Actin Clarke, A; McQueen, PG; Fang, HY et al. Mol. Biol. Cell, DOI://10.1091/mbc.E19-10-0564 (2020)
Information-limiting correlations in large neural populations Bartolo, R; Saunders, RC; Mitz, AR; Averbeck, BB; J. Neurosci., DOI://10.1523/JNEUROSCI.2072-19.2019 (2020)

Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos Lee, HK; Smith, HE; Liu, C; Willi, M; Hennighausen, L; Commun Biol, DOI://10.1038/s42003-019-0745-3 (2020)
A Transcriptome-Wide Association Study (TWAS) Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer Zhong, J; Jermusyk, A; Wu, L et al. J. Natl. Cancer Inst., DOI://10.1093/jnci/djz246 (2020)
Mutations that prevent caspase cleavage of RIPK1 cause autoinflammatory disease Lalaoui, N; Boyden, SE; Oda, H et al. Nature, DOI://10.1038/s41586-019-1828-5 (2020)
Endogenous oxidized phospholipids reprogram cellular metabolism and boost hyperinflammation Di Gioia, M; Spreafico, R; Springstead, JR et al. Nat. Immunol., DOI://10.1038/s41590-019-0539-2 (2020)

2019 (520 papers)

Emerging consensus on the mechanism of polyspecific substrate recognition by the multidrug transporter P-glycoprotein Xia, D; Zhou, F; Esser, L; , Cancer Drug Resist, DOI://10.20517/cdr.2019.22 (2019)
Renal-Tubule Epithelial Cell Nomenclature for Single-Cell RNA-Sequencing Studies Chen, L; Clark, JZ; Nelson, JW et al. J Am Soc Nephrol, DOI://10.1681/ASN.2019040415 (2019)
Probing the Structural Organization of Virions and Genomic Ribonucleoprotein Complexes from Type B Influenza Virus by Cryo-electron Microscopy Gulati, NM; Gallagher, JR; McCraw, DM; Harris, AK; , Microsc Microanal, DOI://10.1017/S1431927619007244 (2019)
A novel HIV-1 protease inhibitor, GRL-044, has potent activity against various HIV-1s with an extremely high genetic barrier to the emergence of HIV-1 drug resistance Aoki, M; Chang, SB; Das, D et al. Glob Health Med, DOI://10.35772/ghm.2019.01003 (2019)
MAIT cells are imprinted by the microbiota in early life and promote tissue repair Constantinides, MG; Link, VM; Tamoutounour, S et al. Science, DOI://10.1126/science.aax6624 (2019)
Amphetamines signal through intracellular TAAR1 receptors coupled to Gα13 and GαS in discrete subcellular domains Underhill, SM; Hullihen, PD; Chen, J et al. Mol. Psychiatry, DOI://10.1038/s41380-019-0469-2 (2019)
GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia Belver, L; Yang, AY; Albero, R et al. Cancer Discov, DOI://10.1158/2159-8290.CD-19-0471 (2019)
Sptlc1 is essential for myeloid differentiation and hematopoietic homeostasis Parthibane, V; Acharya, D; Srideshikan, SM et al. Blood Adv, DOI://10.1182/bloodadvances.2019000729 (2019)
Genome-Wide Association Study in Irradiated Childhood Cancer Survivors Identifies HTR2A for Subsequent Basal Cell Carcinoma Sapkota, Y; Turcotte, LM; Ehrhardt, MJ et al. J. Invest. Dermatol., DOI://10.1016/j.jid.2019.02.029 (2019)
Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq) Carter, B; Ku, WL; Kang, JY et al. Nat Commun, DOI://10.1038/s41467-019-11559-1 (2019)
Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex Pillon, MC; Hsu, AL; Krahn, JM et al. Nat. Struct. Mol. Biol., DOI://10.1038/s41594-019-0289-8 (2019)
Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer Magen, A; Das Sahu, A; Lee, JS et al. Cell Rep, DOI://10.1016/j.celrep.2019.06.067 (2019)
ATP-dependent thermostabilization of human P-glycoprotein (ABCB1) is blocked by modulators Lusvarghi, S; Ambudkar, SV; , Biochem. J., DOI://10.1042/BCJ20190736 (2019)
Organ Doses from Chest Radiographs in Tuberculosis Patients in Canada and Their Uncertainties in Periods from 1930 to 1969 Kocher, DC; Apostoaei, AI; Thomas, BA; Borrego, D; Lee, C; Zablotska, LB; , Health Phys, DOI://10.1097/HP.0000000000001171 (2019)
Association of dietary folate and vitamin B-12 intake with genome-wide DNA methylation in blood: a large-scale epigenome-wide association analysis in 5841 individuals Mandaviya, PR; Joehanes, R; Brody, J et al. Am. J. Clin. Nutr., DOI://10.1093/ajcn/nqz031 (2019)
PARP1 inhibition alleviates injury in ARH3-deficient mice and human cells Mashimo, M; Bu, X; Aoyama, K et al. JCI Insight, DOI://10.1172/jci.insight.124519 (2019)
Placental malaria vaccine candidate antigen VAR2CSA displays atypical domain architecture in some Plasmodium falciparum strains Doritchamou, JYA; Morrison, R; Renn, JP et al. Commun Biol, DOI://10.1038/s42003-019-0704-z (2019)
The Selective Class IIa Histone Deacetylase Inhibitor TMP195 Resensitizes ABCB1- and ABCG2-Overexpressing Multidrug-Resistant Cancer Cells to Cytotoxic Anticancer Drugs Wu, CP; Lusvarghi, S; Wang, JC et al. Int J Mol Sci, DOI://10.3390/ijms21010238 (2019)
Assessment of APOE in atypical parkinsonism syndromes Sabir, MS; Blauwendraat, C; Ahmed, S et al. Neurobiol. Dis., DOI://10.1016/j.nbd.2019.02.016 (2019)
SLC35A2-CDG: Functional characterization, expanded molecular, clinical, and biochemical phenotypes of 30 unreported Individuals Ng, BG; Sosicka, P; Agadi, S et al. Hum. Mutat., DOI://10.1002/humu.23731 (2019)
Association between epigenetic age acceleration and depressive symptoms in a prospective cohort study of urban-dwelling adults Beydoun, MA; Hossain, S; Chitrala, KN et al. J Affect Disord, DOI://10.1016/j.jad.2019.06.032 (2019)
Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons Sheng, C; Javed, U; Rosenthal, J; Yin, J; Qin, B; Yuan, Q; J Vis Exp, DOI://10.3791/60287 (2019)
The Genetic Architecture of Parkinson Disease in Spain: Characterizing Population-Specific Risk, Differential Haplotype Structures, and Providing Etiologic Insight Bandres-Ciga, S; Ahmed, S; Sabir, MS et al. Mov. Disord., DOI://10.1002/mds.27864 (2019)
Anoctamin 8 tethers endoplasmic reticulum and plasma membrane for assembly of Ca2+ signaling complexes at the ER/PM compartment Jha, A; Chung, WY; Vachel, L et al. EMBO J, DOI://10.15252/embj.2018101452 (2019)
Gene signature predictive of hepatocellular carcinoma patient response to transarterial chemoembolization Fako, V; Martin, SP; Pomyen, Y et al. Int. J. Biol. Sci., DOI://10.7150/ijbs.39534 (2019)
Assessment of the Association of D2 Dopamine Receptor Gene and Reported Allele Frequencies With Alcohol Use Disorders: A Systematic Review and Meta-analysis Jung, Y; Montel, RA; Shen, PH; Mash, DC; Goldman, D; JAMA Netw Open, DOI://10.1001/jamanetworkopen.2019.14940 (2019)

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies Nalls, MA; Blauwendraat, C; Vallerga, CL et al. Lancet Neurol, DOI://10.1016/S1474-4422(19)30320-5 (2019)
Resistin-like Molecule α Provides Vitamin-A-Dependent Antimicrobial Protection in the Skin Harris, TA; Gattu, S; Propheter, DC et al. Cell Host Microbe, DOI://10.1016/j.chom.2019.04.004 (2019)
Complementary Task Structure Representations in Hippocampus and Orbitofrontal Cortex during an Odor Sequence Task Zhou, J; Montesinos-Cartagena, M; Wikenheiser, AM; Gardner, MPH; Niv, Y; Schoenbaum, G; Curr. Biol., DOI://10.1016/j.cub.2019.08.040 (2019)
Negative-Stain Transmission Electron Microscopy of Molecular Complexes for Image Analysis by 2D Class Averaging Gallagher, JR; Kim, AJ; Gulati, NM; Harris, AK; Curr Protoc Microbiol, DOI://10.1002/cpmc.90 (2019)
NAA10 polyadenylation signal variants cause syndromic microphthalmia Johnston, JJ; Williamson, KA; Chou, CM et al. J. Med. Genet., DOI://10.1136/jmedgenet-2018-105836 (2019)
Immunoelectron Microscopy of Viral Antigens Gulati, NM; Torian, U; Gallagher, JR; Harris, AK; Curr Protoc Microbiol, DOI://10.1002/cpmc.86 (2019)

The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity Jevtić, P; Schibler, AC; Wesley, CC; Pegoraro, G; Misteli, T; Levy, DL; , EMBO Rep., DOI://10.15252/embr.201847283 (2019)
Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma Gryder, BE; Pomella, S; Sayers, C et al. Nat. Genet., DOI://10.1038/s41588-019-0534-4 (2019)
Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma Yeung, C; Gibson, AE; Issaq, SH et al. Cancer Res., DOI://10.1158/0008-5472.CAN-19-0217 (2019)
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire Shinoda, K; Maman, Y; Canela, A; Schatz, DG; Livak, F; Nussenzweig, A; , Cell Rep, DOI://10.1016/j.celrep.2019.11.088 (2019)
Targeting the Chromosomal Passenger Complex Subunit INCENP Induces Polyploidization, Apoptosis, and Senescence in Neuroblastoma Sun, M; Veschi, V; Bagchi, S et al. Cancer Res., DOI://10.1158/0008-5472.CAN-19-0695 (2019)
Meta-analysis of Chromatin Programming by Steroid Receptors Paakinaho, V; Swinstead, EE; Presman, DM; Grøntved, L; Hager, GL; , Cell Rep, DOI://10.1016/j.celrep.2019.08.039 (2019)

Sympathetic activity contributes to the fMRI signal Özbay, PS; Chang, C; Picchioni, D et al. Commun Biol, DOI://10.1038/s42003-019-0659-0 (2019)
Evidence for a Causal Role of the SH2B3-β 2 M Axis in Blood Pressure Regulation Keefe, JA; Hwang, SJ; Huan, T et al. Hypertension, DOI://10.1161/HYPERTENSIONAHA.118.12094 (2019)
Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus Mistry, P; Nakabo, S; O'Neil, L et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1908576116 (2019)
The Bone Marrow Protects and Optimizes Immunological Memory during Dietary Restriction Collins, N; Han, SJ; Enamorado, M et al. Cell, DOI://10.1016/j.cell.2019.07.049 (2019)
Relationship between human leukocyte antigen alleles and risk of Kaposi's sarcoma in Cameroon Cornejo Castro, EM; Morrison, BJ; Marshall, VA et al. Genes Immun., DOI://10.1038/s41435-019-0077-9 (2019)
Integration of TGF-β-induced Smad signaling in the insulin-induced transcriptional response in endothelial cells Budi, EH; Hoffman, S; Gao, S; Zhang, YE; Derynck, R; , Sci Rep, DOI://10.1038/s41598-019-53490-x (2019)
Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling Adikaram, PR; Zhang, JH; Kittock, CM et al. Commun Biol, DOI://10.1038/s42003-019-0585-1 (2019)
Differential expression and subcellular localization of Copines in mouse retina Goel, M; Li, T; Badea, TC; J. Comp. Neurol., DOI://10.1002/cne.24684 (2019)
Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1 Martin, KB; Williams, IM; Cluzeau, CV et al. Int J Mol Sci, DOI://10.3390/ijms21010292 (2019)
A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers El Khattabi, L; Zhao, H; Kalchschmidt, J et al. Cell, DOI://10.1016/j.cell.2019.07.011 (2019)
Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae Kulkarni, SD; Zhou, F; Sen, ND; Zhang, H; Hinnebusch, AG; Lorsch, JR; BMC Biol., DOI://10.1186/s12915-019-0718-5 (2019)
A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity Bradfield, JP; Vogelezang, S; Felix, JF et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddz161 (2019)

Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in mice Wang, Z; Xu, X; Li, JL; Palmer, C; Maric, D; Dean, J; Nat Commun, DOI://10.1038/s41467-019-13193-3 (2019)
A Peripheral Blood DNA Methylation Signature of Hepatic Fat Reveals a Potential Causal Pathway for Nonalcoholic Fatty Liver Disease Ma, J; Nano, J; Ding, J et al. Diabetes, DOI://10.2337/DB18-1193 (2019)
Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival Tang, W; Putluri, V; Ambati, CR; Dorsey, TH; Putluri, N; Ambs, S; , Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-19-0094 (2019)
ARSA variants in α-synucleinopathies Makarious, MB; Diez-Fairen, M; Krohn, L et al. Brain, DOI://10.1093/brain/awz340 (2019)
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands Farrer, RA; Chang, M; Davis, MJ et al. mBio, DOI://10.1128/mBio.02306-19 (2019)
Contribution of SLC22A12 on hypouricemia and its clinical significance for screening purposes Cha, DH; Gee, HY; Cachau, R et al. Sci Rep, DOI://10.1038/s41598-019-50798-6 (2019)

Dose coefficients of mesh-type ICRP reference computational phantoms for external exposures of neutrons, protons, and helium ions Yeom YS, Choi C, et al. Nuc. Engg. Tech., doi://10.1016/j.net.2019.12.020 (2019)
White Blood Cell Count and Risk of Incident Lung Cancer in the UK Biobank Wong JYY, Bassig BA et al. JNCI Cancer Spectrum, doi://10.1093/jncics/pkz102 (2019)
Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery Botos I, Lountos GT et al. Cur. Res. Struct. Biol. , doi://0.1016/j.crstbi.2019.10.001 (2019)
Dosimetric impact of voxel resolutions of computational human phantoms for external photon exposure Choonsik Lee, Andreu Badal, Yeon Soo Yeom, Keith T Griffin and Dayton McMillan Biomed. Phys. Engg. Exp. , doi://10.1088/2057-1976/ab2850 (2019)
Joint modelling of competing risks and current status data: an application to a spontaneous labour study Youjin Lee Mei; Cheng Wang; Katherine L. Grantz; Rajeshwari Sundaram Royal Statistical Society, doi://10.1111/rssc.12351 (2019)
Keratinocyte-intrinsic MHCII expression controls microbiota-induced Th1 cell responses Tamoutounour, S; Han, SJ; Deckers, J et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1912432116 (2019)
Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women Jones, GS; Spencer Feigelson, H; Falk, RT et al. PLoS ONE, DOI://10.1371/journal.pone.0216114 (2019)
NMR Analysis of Apo Glutamine-Binding Protein Exposes Challenges in the Study of Interdomain Dynamics Kooshapur, H; Ma, J; Tjandra, N; Bermejo, GA; Angew. Chem. Int. Ed. Engl., DOI://10.1002/anie.201911015 (2019)
Proteomics Pipeline for Identifying Variant Proteins in Plasmodium falciparum Parasites Isolated from Children Presenting with Malaria Gonzales Hurtado, PA; Morrison, R; Ribeiro, JMC et al. J. Proteome Res., DOI://10.1021/acs.jproteome.9b00169 (2019)
Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry Guven-Maiorov, E; Tsai, CJ; Nussinov, R; , Front Oncol, DOI://10.3389/fonc.2019.01236 (2019)
Rat Orbitofrontal Ensemble Activity Contains Multiplexed but Dissociable Representations of Value and Task Structure in an Odor Sequence Task Zhou, J; Gardner, MPH; Stalnaker, TA et al. Curr. Biol., DOI://10.1016/j.cub.2019.01.048 (2019)
Non-Leishmania Parasite in Fatal Visceral Leishmaniasis-Like Disease, Brazil Maruyama, SR; de Santana, AKM; Takamiya, NT et al. Emerging Infect. Dis., DOI://10.3201/eid2511.181548 (2019)

A Phase II Study of Tumor-infiltrating Lymphocyte Therapy for Human Papillomavirus-associated Epithelial Cancers Stevanovic, S; Helman, SR; Wunderlich, JR et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-18-2722 (2019)
Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans Mitchell, KA; Nichols, N; Tang, W et al. Nat Commun, DOI://10.1038/s41467-019-13732-y (2019)
The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease Bandres-Ciga, S; Saez-Atienzar, S; Bonet-Ponce, L et al. Mov. Disord., DOI://10.1002/mds.27614 (2019)
The GATOR complex regulates an essential response to meiotic double-stranded breaks in Drosophila Wei, Y; Bettedi, L; Ting, CY et al. Elife, DOI://10.7554/eLife.42149 (2019)
Next generation sequencing and the classical HLA loci in full heritage Pima Indians of Arizona: Defining the core HLA variation for North American Paleo-Indians Williams, RC; Knowler, WC; Shuldiner, AR et al. Hum Immunol, DOI://10.1016/j.humimm.2019.10.002 (2019)
Autosomal recessive congenital cataracts linked to HSF4 in a consanguineous Pakistani family Jiao, X; Khan, SY; Kaul, H et al. PLoS ONE, DOI://10.1371/journal.pone.0225010 (2019)
White Matter Microstructure in Pediatric Bipolar Disorder and Disruptive Mood Dysregulation Disorder Linke, JO; Adleman, NE; Sarlls, J et al. J Am Acad Child Adolesc Psychiatry, DOI://10.1016/j.jaac.2019.05.035 (2019)
DENND5B Regulates Intestinal Triglyceride Absorption and Body Mass Gordon, SM; Neufeld, EB; Yang, Z et al. Sci Rep, DOI://10.1038/s41598-019-40296-0 (2019)
Reply to Spreng et al.: Multiecho fMRI denoising does not remove global motion-associated respiratory signals Power, JD; Lynch, CJ; Gilmore, AW; Gotts, SJ; Martin, A; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1909852116 (2019)
HiPLA: High-throughput imaging proximity ligation assay Serebryannyy, LA; Misteli, T; , Methods, DOI://10.1016/j.ymeth.2018.11.004 (2019)
Single molecule analysis of lamin dynamics Serebryannyy, LA; Ball, DA; Karpova, TS; Misteli, T; , Methods, DOI://10.1016/j.ymeth.2018.08.009 (2019)
HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction Neckles, C; Boer, RE; Aboreden, N et al. RNA, DOI://10.1261/rna.072454.119 (2019)
Correction to: ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference Pranzatelli, TJF; Michae, DG; Chiorini, JA; , BMC Genomics, DOI://10.1186/s12864-019-5441-7 (2019)
Head and Neck Cancers Promote an Inflammatory Transcriptome Through Coactivation of Classic and Alternative NF-κB Pathways Yang, X; Cheng, H; Chen, J et al. Cancer Immunol Res, DOI://10.1158/2326-6066.CIR-18-0832 (2019)
Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3 Wang, S; Chim, B; Su, Y et al. Genes Dev., DOI://10.1101/gad.325100.119 (2019)
Genome-Wide Profiling of Cervical RNA-Binding Proteins Identifies Human Papillomavirus Regulation of RNASEH2A Expression by Viral E7 and E2F1 Xu, J; Liu, H; Yang, Y et al. mBio, DOI://10.1128/mBio.02687-18 (2019)
Classification of GBA Variants and Their Effects in Synucleinopathies Gan-Or, Z; Alcalay, RN; Makarious, MB; Scholz, SW; Blauwendraat, C; , ; Mov. Disord., DOI://10.1002/mds.27803 (2019)
H3.3K4M destabilizes enhancer H3K4 methyltransferases MLL3/MLL4 and impairs adipose tissue development Jang, Y; Broun, A; Wang, C et al. Nucleic Acids Res., DOI://10.1093/nar/gky982 (2019)
MicroRNA-mediated control of developmental lymphangiogenesis Jung, HM; Hu, CT; Fister, AM et al. Elife, DOI://10.7554/eLife.46007 (2019)
Immunoprecipitation and Sequencing of Acetylated RNA Arango, D; Sturgill, D; Oberdoerffer, S; , Bio Protoc, DOI://10.21769/BioProtoc.3278 (2019)
Correction: Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo Zeidan, Q; He, F; Zhang, F; Zhang, H; Jacobson, A; Hinnebusch, AG; PLoS Genet., DOI://10.1371/journal.pgen.1008299 (2019)
Understanding Cancer Through the Lens of Epigenetic Inheritance, Allele-Specific Gene Expression, and High-Throughput Technology Lee, MP Front Oncol, DOI://10.3389/fonc.2019.00794 (2019)
A deconvolution algorithm for multi-echo functional MRI: Multi-echo Sparse Paradigm Free Mapping Caballero-Gaudes, C; Moia, S; Panwar, P; Bandettini, PA; Gonzalez-Castillo, J; Neuroimage, DOI://10.1016/j.neuroimage.2019.116081 (2019)
A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests Chen, G; Cox, RW; Glen, DR; Rajendra, JK; Reynolds, RC; Taylor, PA; Hum Brain Mapp, DOI://10.1002/hbm.24399 (2019)
Association of Maternal Exposure to Persistent Organic Pollutants in Early Pregnancy With Fetal Growth Ouidir, M; Buck Louis, GM; Kanner, J et al. JAMA Pediatr, DOI://10.1001/jamapediatrics.2019.5104 (2019)
Modeling ligand docking to RNA in the design of RNA-based nanostructures Kasprzak, WK; Ahmed, NA; Shapiro, BA; Curr. Opin. Biotechnol., DOI://10.1016/j.copbio.2019.10.010 (2019)
Integrating Hi-C links with assembly graphs for chromosome-scale assembly Ghurye, J; Rhie, A; Walenz, BP et al. PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1007273 (2019)
Magnetoencephalographic Correlates of Suicidal Ideation in Major Depression Gilbert, JR; Ballard, ED; Galiano, CS; Nugent, AC; Zarate, CA; Biol Psychiatry Cogn Neurosci Neuroimaging, DOI://10.1016/j.bpsc.2019.11.011 (2019)
Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis Korrapati, S; Taukulis, I; Olszewski, R et al. Front Mol Neurosci, DOI://10.3389/fnmol.2019.00316 (2019)
Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods Hu, X; Compton, JR; Legler, PM; J Vis Exp, DOI://10.3791/60421 (2019)

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells Magen, A; Nie, J; Ciucci, T et al. Cell Rep, DOI://10.1016/j.celrep.2019.10.131 (2019)
Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal Kaya KD, Chen HY, Brooks MJ et al Mol Vis (2019)
Novel Protease Inhibitors Containing C-5-Modified bis-Tetrahydrofuranylurethane and Aminobenzothiazole as P2 and P2' Ligands That Exert Potent Antiviral Activity against Highly Multidrug-Resistant HIV-1 with a High Genetic Barrier against the Emergence of Drug Resistance Takamatsu, Y; Aoki, M; Bulut, H et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.00372-19 (2019)
Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores Shao, Y; Mei, Y; Sundholm, D; Kaila, VRI; J Chem Theory Comput, DOI://10.1021/acs.jctc.9b00823 (2019)
Novel Central Nervous System (CNS)-Targeting Protease Inhibitors for Drug-Resistant HIV Infection and HIV-Associated CNS Complications Amano, M; Salcedo-Gómez, PM; Yedidi, RS et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.00466-19 (2019)
HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry Gourh, P; Safran, SA; Alexander, T et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1906593116 (2019)
Maternal fatty acid concentrations and newborn DNA methylation Robinson, SL; Mumford, SL; Guan, W et al. Am. J. Clin. Nutr., DOI://10.1093/ajcn/nqz311 (2019)
DHHC20 Palmitoyl-Transferase Reshapes the Membrane to Foster Catalysis Stix, R; Song, J; Banerjee, A; Faraldo-Gómez, JD; Biophys. J., DOI://10.1016/j.bpj.2019.11.003 (2019)
Analysis of ordered composite endpoints Follmann, D; Fay, MP; Hamasaki, T; Evans, S; Stat Med, DOI://10.1002/sim.8431 (2019)
Large-scale state-dependent membrane remodeling by a transporter protein Zhou, W; Fiorin, G; Anselmi, C et al. Elife, DOI://10.7554/eLife.50576 (2019)
CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes Dalgleish, JL; Wang, Y; Zhu, J; Meltzer, PS; Cancer Inform, DOI://10.1177/1176935119890290 (2019)
Identification of 102 Correlations between Serum Metabolites and Habitual Diet in a Metabolomics Study of the Prostate, Lung, Colorectal, and Ovarian Cancer Trial Mazzilli, KM; McClain, KM; Lipworth, L et al. J. Nutr., DOI://10.1093/jn/nxz300 (2019)

Permeability of membranes in the liquid ordered and liquid disordered phases Ghysels, A; Krämer, A; Venable, RM et al. Nat Commun, DOI://10.1038/s41467-019-13432-7 (2019)
A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation Vacchio, MS; Ciucci, T; Gao, Y et al. Immunity, DOI://10.1016/j.immuni.2019.06.023 (2019)
SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics Song, L; Liu, A; Shi, J; , ; Bioinformatics, DOI://10.1093/bioinformatics/btz176 (2019)
Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates Rawi, R; Mall, R; Shen, CH et al. Sci Rep, DOI://10.1038/s41598-019-50635-w (2019)
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Antimicrobial Chrysophaentin Analogs Identified from Laboratory Cultures of the Marine Microalga Chrysophaeum taylorii Davison, JR; Bewley, CA; J. Nat. Prod., DOI://10.1021/acs.jnatprod.8b00858 (2019)
Distinct Clinical and Pathological Features of Melorheostosis Associated With Somatic MAP2K1 Mutations Jha, S; Fratzl-Zelman, N; Roschger, P et al. J. Bone Miner. Res., DOI://10.1002/jbmr.3577 (2019)
The prevalence of germline DICER1 pathogenic variation in cancer populations Kim, J; Schultz, KAP; Hill, DA; Stewart, DR; Mol Genet Genomic Med, DOI://10.1002/mgg3.555 (2019)
Sequence Variation Associated with SLC12A5 Gene Expression Is Linked to Brain Structure and Function in Healthy Adults Gregory, MD; Kippenhan, JS; Callicott, JH et al. Cereb. Cortex, DOI://10.1093/cercor/bhy344 (2019)
Structure and function of an ectopic Polycomb chromatin domain De, S; Cheng, Y; Sun, MA; Gehred, ND; Kassis, JA; Sci Adv, DOI://10.1126/sciadv.aau9739 (2019)
A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing Xie, G; Vo, TV; Thillainadesan, G et al. Nat Commun, DOI://10.1038/s41467-018-08273-9 (2019)

Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology Schwartz, DM; Farley, TK; Richoz, N et al. Immunity, DOI://10.1016/j.immuni.2018.12.014 (2019)
The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok Ciucci, T; Vacchio, MS; Gao, Y et al. Immunity, DOI://10.1016/j.immuni.2018.12.019 (2019)
Next-Generation Sequencing to Diagnose Suspected Genetic Disorders Adams, DR; Eng, CM; N. Engl. J. Med., DOI://10.1056/NEJMc1814955 (2019)
Effect of amino acids on transcription and translation of key genes in E. coli K and B grown at a steady state in minimal medium Baez, A; Kumar, A; Sharma, AK; Anderson, ED; Shiloach, J; N Biotechnol, DOI://10.1016/j.nbt.2018.10.004 (2019)
The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis Baechler, SA; Factor, VM; Dalla Rosa, I et al. Nat Commun, DOI://10.1038/s41467-018-07922-3 (2019)
Secondary Metabolites from the Fungus Dictyosporium sp. and Their MALT1 Inhibitory Activities Tran, TD; Wilson, BAP; Henrich, CJ et al. J. Nat. Prod., DOI://10.1021/acs.jnatprod.8b00871 (2019)

The phenotypic landscape of a Tbc1d24 mutant mouse includes convulsive seizures resembling human early infantile epileptic encephalopathy Tona, R; Chen, W; Nakano, Y et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy445 (2019)
Hydrogen-bond dependent conformational switching: a computational challenge from experimental thermochemistry Luccarelli, J; Paton, RS; J. Org. Chem., DOI://10.1021/acs.joc.8b02436 (2019)
Early infantile-onset epileptic encephalopathy 28 due to a homozygous microdeletion involving the WWOX gene in a region of uniparental disomy Davids, M; Markello, T; Wolfe, LA et al. Hum. Mutat., DOI://10.1002/humu.23675 (2019)
A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics Bachu, M; Tamura, T; Chen, C et al. J. Biol. Chem., DOI://10.1074/jbc.RA118.005550 (2019)
Genetic analysis of neurodegenerative diseases in a pathology cohort Blauwendraat C, Pletnikova O, Geiger, JT et al Neurobiology of Aging, 10.1016/j.neurobiolaging.2018.11.007 (2019)
Conformational stability and dynamics of the cancer-associated isoform δ133p53β are modulated by p53 peptides and p53-specific DNA Lei, J; Qi, R; Tang, Y et al. FASEB J., DOI://10.1096/fj.201801973R (2019)

hnRNP L-dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma Kishor, A; Ge, Z; Hogg, JR; EMBO J., DOI://10.15252/embj.201899128 (2019)
Linear mixed models for association analysis of quantitative traits with next-generation sequencing data Chiu, CY; Yuan, F; Zhang, BS et al. Genet. Epidemiol., DOI://10.1002/gepi.22177 (2019)
Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements Marinelli, F; Fiorin, G; Structure, DOI://10.1016/j.str.2018.10.013 (2019)
Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury Harrison, OJ; Linehan, JL; Shih, HY et al. Science, DOI://10.1126/science.aat6280 (2019)
Mosaic Y loss is moderately associated with solid tumor risk Loftfield, E; Zhou, W; Yeager, M; Chanock, SJ; Freedman, ND; Machiela, MJ; Cancer Res., DOI://10.1158/0008-5472.CAN-18-2566 (2019)
Targeted deletion of an NRL- and CRX-regulated alternative promoter specifically silences FERM and PDZ domain containing 1 (Frmpd1) in rod photoreceptors Campla, CK; Mast, H; Dong, L et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy388 (2019)

Practical issues in using generalized estimating equations for inference on transitions in longitudinal data: What is being estimated Bible, J; Albert, PS; Simons-Morton, BG; Liu, D; Stat Med, DOI://10.1002/sim.8014 (2019)
Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation Michael, DG; Pranzatelli, TJF; Warner, BM; Yin, H; Chiorini, JA; J. Dent. Res., DOI://10.1177/0022034518806518 (2019)
Organ Dose Estimation accounting for uncertainty for pediatric and young adult CT scans in the United Kingdom Lee, C; Journy, N; Moroz, BE et al. Radiat Prot Dosimetry, DOI://10.1093/rpd/ncy184 (2019)
Optimizing and evaluating biomarker combinations as trial-level general surrogates Gabriel, EE; Sachs, MC; Daniels, MJ; Halloran, ME; Stat Med, DOI://10.1002/sim.7996 (2019)
Interface-Based Structural Prediction of Novel Host-Pathogen Interactions Guven-Maiorov, E; Tsai, CJ; Ma, B; Nussinov, R; Methods Mol. Biol., DOI://10.1007/978-1-4939-8736-8_18 (2019)
QuagmiR: A Cloud-based Application for IsomiR Big Data Analytics Bofill-De Ros, X; Chen, K; Chen, S et al. Bioinformatics, DOI://10.1093/bioinformatics/bty843 (2019)
Early life disadvantage and adult adiposity: tests of sensitive periods during childhood and behavioural mediation in adulthood Gilman, SE; Huang, YT; Jimenez, MP et al. Int J Epidemiol, DOI://10.1093/ije/dyy199 (2019)
A Bayesian multi-dimensional couple-based latent risk model with an application to infertility Hwang, BS; Chen, Z; Louis, GMB; Albert, PS; Biometrics, DOI://10.1111/biom.12972 (2019)
Half blind superiority tests for clinical trials of anti-infective drugs Follmann, D; Brittain, E; Lumbard, K; Stat Med, DOI://10.1002/sim.7954 (2019)
Time-varying whole-brain functional network connectivity coupled to task engagement Xie H, Gonzalez-Castillo J, Handwerker D, Bandettini P Network Neuro Science, doi://10.1162/netn_a_00051 (2019)
Neurophysiological Changes Associated with Antidepressant Response to Ketamine Not Observed in a Negative Trial of Scopolamine in Major Depressive Disorder Park, L; Furey, M; Nugent, AC et al. Int. J. Neuropsychopharmacol., DOI://10.1093/ijnp/pyy051 (2019)
Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia Dillon, LW; Hayati, S; Roloff, GW et al. Haematologica, DOI://10.3324/haematol.2018.203133 (2019)

Whole Blood Gene Expression Associated with Clinical Biological Age Lin, H; Lunetta, KL; Zhao, Q et al. J. Gerontol. A Biol. Sci. Med. Sci., DOI://10.1093/gerona/gly164 (2019)
Deep-learning-assisted Volume Visualization Cheng, HC; Cardone, A; Jain, S et al. IEEE Trans Vis Comput Graph, DOI://10.1109/TVCG.2018.2796085 (2019)
A feasibility study to reduce misclassification error in occupational dose estimates for epidemiological studies using body size-dependent computational phantoms Sarah Kim, Lienard Chang, Elizabeth Mosher, Choonik Lee, and Choonsik IEEE Transactions on Radiation and Plasma Medical Sciences, 0.1109/TRPMS.2018.2847227 (2019)
Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium Merino, J; Dashti, HS; Li, SX et al. Mol. Psychiatry, DOI://10.1038/s41380-018-0079-4 (2019)
Tightly Integrated Genomic and Epigenomic Data Mining Using Tensor Decomposition Fang, J Bioinformatics, DOI://10.1093/bioinformatics/bty513 (2019)
Mapping the neuroanatomic substrates of cognition in familial attention deficit hyperactivity disorder Muster, R; Choudhury, S; Sharp, W; Kasparek, S; Sudre, G; Shaw, P; Psychol Med, DOI://10.1017/S0033291718001241 (2019)

A joint spatial factor analysis model to accommodate data from misaligned areal units with application to Louisiana social vulnerability Nethery, RC; Sandler, DP; Zhao, S; Engel, LS; Kwok, RK; Biostatistics, DOI://10.1093/biostatistics/kxy016 (2019)
Ketamine has distinct electrophysiological and behavioral effects in depressed and healthy subjects Nugent, AC; Ballard, ED; Gould, TD et al. Mol. Psychiatry, DOI://10.1038/s41380-018-0028-2 (2019)

2018 (482 papers)

BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome Hoffman, JA; Trotter, KW; Ward, JM; Archer, TK; , Elife, DOI://10.7554/eLife.35073 (2018)
Collecting duct principal, but not intercalated, cell prorenin receptor regulates renal sodium and water excretion Ramkumar, N; Stuart, D; Mironova, E et al. Am J Physiol Renal Physiol, DOI://10.1152/ajprenal.00122.2018 (2018)
Whole genome sequencing data for two individuals of Pakistani descent Khan, SY; Kabir, F; M'Hamdi, O et al. Sci Data, DOI://10.1038/sdata.2018.174 (2018)
An approximate joint model for multiple paired longitudinal outcomes and time-to-event data Elmi, AF; Grantz, KL; Albert, PS; , Biometrics, DOI://10.1111/biom.12862 (2018)
Methylomic profiling and replication implicates deregulation of PCSK9 in alcohol use disorder Lohoff, FW; Sorcher, JL; Rosen, AD et al. Mol. Psychiatry, DOI://10.1038/mp.2017.168 (2018)
Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates Zhang, M; Zheng, J; Nussinov, R; Ma, B; Antibodies (Basel), DOI://10.3390/antib7030025 (2018)
Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water" Best, RB; Zheng, W; Borgia, A et al. Science, DOI://10.1126/science.aar7101 (2018)
Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA Tagawa, T; Gao, S; Koparde, VN et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1816183115 (2018)
Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism Burke, EA; Frucht, SJ; Thompson, K et al. Clin. Genet., DOI://10.1111/cge.13172 (2018)
Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures Lee, JS; Adler, L; Karathia, H et al. Cell, DOI://10.1016/j.cell.2018.07.019 (2018)

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells Bodogai, M; O'Connell, J; Kim, K et al. Sci Transl Med, DOI://10.1126/scitranslmed.aat4271 (2018)
Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits Evangelou, E; Warren, HR; Mosen-Ansorena, D et al. Nat. Genet., DOI://10.1038/s41588-018-0205-x (2018)
Fully automated segmentation and quantification of visceral and subcutaneous fat at abdominal CT: application to a longitudinal adult screening cohort Lee, SJ; Liu, J; Yao, J; Kanarek, A; Summers, RM; Pickhardt, PJ; Br J Radiol, DOI://10.1259/bjr.20170968 (2018)
Analysis of type 2 diabetes and obesity genetic variants in Mexican Pima Indians: Marked allelic differentiation among Amerindians at HLA Hsueh, WC; Bennett, PH; Esparza-Romero, J et al. Ann. Hum. Genet., DOI://10.1111/ahg.12252 (2018)
A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation Ferreira, CR; Xia, ZJ; Clément, A et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.09.003 (2018)
Reservoir pH replica exchange Damjanovic, A; Miller, BT; Okur, A; Brooks, BR; J Chem Phys, DOI://10.1063/1.5027413 (2018)

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides Narayan, B; Herbert, C; Yuan, Y; Rodriguez, BJ; Brooks, BR; Buchete, NV; J Chem Phys, DOI://10.1063/1.5027580 (2018)
EXP2 is a nutrient-permeable channel in the vacuolar membrane of Plasmodium and is essential for protein export via PTEX Garten, M; Nasamu, AS; Niles, JC; Zimmerberg, J; Goldberg, DE; Beck, JR; Nat Microbiol, DOI://10.1038/s41564-018-0222-7 (2018)
Non-classical monocytes as mediators of tissue destruction in arthritis Puchner, A; Saferding, V; Bonelli, M et al. Ann. Rheum. Dis., DOI://10.1136/annrheumdis-2018-213250 (2018)
Abruptio placentae risk and genetic variations in mitochondrial biogenesis and oxidative phosphorylation: replication of a candidate gene association study Workalemahu, T; Enquobahrie, DA; Gelaye, B et al. Am. J. Obstet. Gynecol., DOI://10.1016/j.ajog.2018.08.042 (2018)
Activation of Th1 Immunity within the Tumor Microenvironment Is Associated with Clinical Response to Lenalidomide in Chronic Lymphocytic Leukemia Aue, G; Sun, C; Liu, D et al. J. Immunol., DOI://10.4049/jimmunol.1800570 (2018)
Comparison of normal tissue dose calculation methods for epidemiological studies of radiotherapy patients Mille, MM; Jung, JW; Lee, C; Kuzmin, GA; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aabd4f (2018)

Novel variants in SPTAN1 without epilepsy: An expansion of the phenotype Gartner, V; Markello, TC; Macnamara, E et al. Am. J. Med. Genet. A, DOI://10.1002/ajmg.a.40628 (2018)
Novel truncating mutation in TENM3 in siblings with motor developmental delay, ocular coloboma, oval cornea, without microphthalmia Stephen, J; Nampoothiri, S; Kuppa, S et al. Am. J. Med. Genet. A, DOI://10.1002/ajmg.a.40658 (2018)
Exogenous ghrelin administration increases alcohol self-administration and modulates brain functional activity in heavy-drinking alcohol-dependent individuals Farokhnia, M; Grodin, EN; Lee, MR et al. Mol. Psychiatry, DOI://10.1038/mp.2017.226 (2018)
Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase Hickman, AB; Voth, AR; Ewis, H; Li, X; Craig, NL; Dyda, F; Nucleic Acids Res., DOI://10.1093/nar/gky838 (2018)
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila Wang, Y; Cho, DY; Lee, H; Fear, J; Oliver, B; Przytycka, TM; Nat Commun, DOI://10.1038/s41467-018-06382-z (2018)
High density lipoprotein proteome is associated with cardiovascular risk factors and atherosclerosis burden as evaluated by coronary CT angiography Gordon, SM; Chung, JH; Playford, MP et al. Atherosclerosis, DOI://10.1016/j.atherosclerosis.2018.09.032 (2018)

Agreement in Histological Assessment of Mitotic Activity Between Microscopy and Digital Whole Slide Images Informs Conversion for Clinical Diagnosis Wei, BR; Halsey, CH; Hoover, SB et al. Acad Pathol, DOI://10.1177/2374289519859841 (2018)
Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy Norouzi, D; Zhurkin, VB; Biophys. J., DOI://10.1016/j.bpj.2018.06.032 (2018)
GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking Wu, K; Wang, L; Chen, Y et al. J. Cell. Sci., DOI://10.1242/jcs.221036 (2018)
Sequential loss of tumor surface antigens following chimeric antigen receptor T-cell therapies in diffuse large B-cell lymphoma Shalabi, H; Kraft, IL; Wang, HW et al. Haematologica, DOI://10.3324/haematol.2017.183459 (2018)
GATA2 deficiency and human hematopoietic development modeled using induced pluripotent stem cells Jung, M; Cordes, S; Zou, J et al. Blood Adv, DOI://10.1182/bloodadvances.2018017137 (2018)
Interdomain Stabilization Impairs CD4 Binding and Improves Immunogenicity of the HIV-1 Envelope Trimer Zhang, P; Gorman, J; Geng, H et al. Cell Host Microbe, DOI://10.1016/j.chom.2018.05.002 (2018)

Genetic variations and risk of placental abruption: A genome-wide association study and meta-analysis of genome-wide association studies Workalemahu, T; Enquobahrie, DA; Gelaye, B et al. Placenta, DOI://10.1016/j.placenta.2018.04.008 (2018)
Role of humoral immunity against hepatitis B virus core antigen in the pathogenesis of acute liver failure Chen, Z; Diaz, G; Pollicino, T et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1809028115 (2018)
Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism Stephen, J; Maddirevula, S; Nampoothiri, S et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.11.001 (2018)
Using Devices to Assess Physical Activity and Sedentary Behavior in a Large Cohort Study, the Women's Health Study Lee, IM; Shiroma, EJ; Evenson, KR; Kamada, M; LaCroix, AZ; Buring, JE; J Meas Phys Behav, DOI://10.1123/jmpb.2018-0005 (2018)
Co-activation patterns in resting-state fMRI signals Liu, X; Zhang, N; Chang, C; Duyn, JH; Neuroimage, DOI://10.1016/j.neuroimage.2018.01.041 (2018)
Using mobile location data in biomedical research while preserving privacy Goldenholz, DM; Goldenholz, SR; Krishnamurthy, KB et al. J Am Med Inform Assoc, DOI://10.1093/jamia/ocy071 (2018)
Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease Splinter, K; Adams, DR; Bacino, CA et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1714458 (2018)
GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes Franceschini, N; Giambartolomei, C; de Vries, PS et al. Nat Commun, DOI://10.1038/s41467-018-07340-5 (2018)
Hallmarks of primate lentiviral immunodeficiency infection recapitulate loss of innate lymphoid cells Mudd, JC; Busman-Sahay, K; DiNapoli, SR et al. Nat Commun, DOI://10.1038/s41467-018-05528-3 (2018)
The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage Brady, OA; Jeong, E; Martina, JA; Pirooznia, M; Tunc, I; Puertollano, R; Elife, DOI://10.7554/eLife.40856 (2018)
Tenectin recruits integrin to stabilize bouton architecture and regulate vesicle release at the Drosophila neuromuscular junction Wang, Q; Han, TH; Nguyen, P; Jarnik, M; Serpe, M; Elife, DOI://10.7554/eLife.35518 (2018)
CD22-targeted CAR T cells induce remission in B-ALL that is naive or resistant to CD19-targeted CAR immunotherapy Fry, TJ; Shah, NN; Orentas, RJ et al. Nat. Med., DOI://10.1038/nm.4441 (2018)

Mutant IL-7Rα and mutant NRas are sufficient to induce murine T cell acute lymphoblastic leukemia Cramer, SD; Hixon, JA; Andrews, C et al. Leukemia, DOI://10.1038/s41375-017-0001-0 (2018)
Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay Morimoto, M; Waller-Evans, H; Ammous, Z et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.09.014 (2018)
De Novo Missense Variants in TRAF7 Cause Developmental Delay, Congenital Anomalies, and Dysmorphic Features Tokita, MJ; Chen, CA; Chitayat, D et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.06.005 (2018)
Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot Sapp, JC; Johnston, JJ; Driscoll, K et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.07.018 (2018)
Exploratory genome-wide association analysis of response to ketamine and a polygenic analysis of response to scopolamine in depression Guo, W; Machado-Vieira, R; Mathew, S et al. Transl Psychiatry, DOI://10.1038/s41398-018-0311-7 (2018)
IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages John, SP; Sun, J; Carlson, RJ et al. Cell Rep, DOI://10.1016/j.celrep.2018.09.002 (2018)

GWAS of epigenetic aging rates in blood reveals a critical role for TERT Lu, AT; Xue, L; Salfati, EL et al. Nat Commun, DOI://10.1038/s41467-017-02697-5 (2018)
Identification of seven novel loci associated with amino acid levels using single-variant and gene-based tests in 8545 Finnish men from the METSIM study Teslovich, TM; Kim, DS; Yin, X et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy067 (2018)
Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel Martin, C; Cho, YE; Kim, H et al. Biol Res Nurs, DOI://10.1177/1099800418758951 (2018)
Human retinoic acid-regulated CD161+ regulatory T cells support wound repair in intestinal mucosa Povoleri, GAM; Nova-Lamperti, E; Scottà, C et al. Nat. Immunol., DOI://10.1038/s41590-018-0230-z (2018)
Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length Dunn-Fletcher, CE; Muglia, LM; Pavlicev, M et al. PLoS Biol., DOI://10.1371/journal.pbio.2006337 (2018)
Interactions between genetic variation and cellular environment in skeletal muscle gene expression Taylor, DL; Knowles, DA; Scott, LJ et al. PLoS ONE, DOI://10.1371/journal.pone.0195788 (2018)
Analysis of Meiotic Double-Strand Break Initiation in Mammals Brick, K; Pratto, F; Sun, CY; Camerini-Otero, RD; Petukhova, G; Meth. Enzymol., DOI://10.1016/bs.mie.2017.11.037 (2018)
Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition Shastri, N; Tsai, YC; Hile, S et al. Mol. Cell, DOI://10.1016/j.molcel.2018.08.047 (2018)
Automated Cervical Screening and Triage, Based on HPV Testing and Computer-Interpreted Cytology Yu, K; Hyun, N; Fetterman, B et al. J. Natl. Cancer Inst., DOI://10.1093/jnci/djy044 (2018)
Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation Teumer, A; Chaker, L; Groeneweg, S et al. Nat Commun, DOI://10.1038/s41467-018-06356-1 (2018)
Molecular basis of Mitomycin C enhanced corneal sensory nerve repair after debridement wounding Stepp, MA; Pal-Ghosh, S; Tadvalkar, G; Li, L; Brooks, SR; Morasso, MI; Sci Rep, DOI://10.1038/s41598-018-35090-3 (2018)
MAVS deficiency induces gut dysbiotic microbiota conferring a proallergic phenotype Plantamura, E; Dzutsev, A; Chamaillard, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1722372115 (2018)
Subcutaneous adipose tissue imaging of human obesity reveals two types of adipocyte membranes: Insulin-responsive and -nonresponsive McCormick, CD; Waters, HN; Bezrukov, L et al. J. Biol. Chem., DOI://10.1074/jbc.RA118.003751 (2018)
SPT6 interacts with NSD2 and facilitates interferon-induced transcription Ouda, R; Sarai, N; Nehru, V et al. FEBS Lett., DOI://10.1002/1873-3468.13069 (2018)
Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing Matson, KJE; Sathyamurthy, A; Johnson, KR; Kelly, MC; Kelley, MW; Levine, AJ; J Vis Exp, DOI://10.3791/58413 (2018)
Generation of Tumor Antigen-Specific iPSC-Derived Thymic Emigrants Using a 3D Thymic Culture System Vizcardo, R; Klemen, ND; Islam, SMR et al. Cell Rep, DOI://10.1016/j.celrep.2018.02.087 (2018)
Transcriptional profiling reveals gland-specific differential expression in the three major salivary glands of the adult mouse Gao, X; Oei, MS; Ovitt, CE; Sincan, M; Melvin, JE; Physiol. Genomics, DOI://10.1152/physiolgenomics.00124.2017 (2018)
Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA Ray, S; Tillo, D; Assad, N et al. Biochem. Biophys. Res. Commun., DOI://10.1016/j.bbrc.2018.05.080 (2018)

Interferon stimulation creates chromatin marks and establishes transcriptional memory Kamada, R; Yang, W; Zhang, Y et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1720930115 (2018)
Lipid-dependence of target membrane stability during influenza viral fusion Haldar, S; Mekhedov, E; McCormick, CD; Blank, PS; Zimmerberg, J; J. Cell. Sci., DOI://10.1242/jcs.218321 (2018)
Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry Oetjen, KA; Lindblad, KE; Goswami, M et al. JCI Insight, DOI://10.1172/jci.insight.124928 (2018)
Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms Weismiller, HA; Murphy, R; Wei, G; Ma, B; Nussinov, R; Margittai, M; J. Biol. Chem., DOI://10.1074/jbc.RA118.005316 (2018)
Enhanced detection of neoantigen-reactive T cells targeting unique and shared oncogenes for personalized cancer immunotherapy Yossef, R; Tran, E; Deniger, DC et al. JCI Insight, DOI://10.1172/jci.insight.122467 (2018)
Dynamic analysis of human tyrosinase intra-melanosomal domain and mutant variants to further understand oculocutaneous albinism type 1 Farney, SK; Dolinska, MB; Sergeev, YV; J Anal Pharm Res, DOI://10.15406/japlr.2018.07.00293 (2018)

Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation Guzzo, C; Zhang, P; Liu, Q et al. MBio, DOI://10.1128/mBio.00955-18 (2018)
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An insight into the salivary gland and fat body transcriptome of Panstrongylus lignarius (Hemiptera: Heteroptera), the main vector of Chagas disease in Peru Nevoa, JC; Mendes, MT; da Silva, MV; Soares, SC; Oliveira, CJF; Ribeiro, JMC; PLoS Negl Trop Dis, DOI://10.1371/journal.pntd.0006243 (2018)
Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation Meng, F; Bellaiche, MMJ; Kim, JY; Zerze, GH; Best, RB; Chung, HS; Biophys. J., DOI://10.1016/j.bpj.2017.12.025 (2018)

Identification of Casz1 as a Regulatory Protein Controlling T Helper Cell Differentiation, Inflammation, and Immunity Bhaskaran, N; Liu, Z; Saravanamuthu, SS et al. Front Immunol, DOI://10.3389/fimmu.2018.00184 (2018)
GRL-079, a Novel HIV-1 Protease Inhibitor, Is Extremely Potent against Multidrug-Resistant HIV-1 Variants and Has a High Genetic Barrier against the Emergence of Resistant Variants Delino NS, Aoki M, Hayashi H, Hattori SI, Chang SB, Takamatsu Y, Martyr CD, Das D, Ghosh AK, Mitsuya H Antimicrob Agents Chemother. , doi: 10.1128/AAC.02060-17 (2018)
Design and statistical considerations for studies evaluating the efficacy of a single dose of the human papillomavirus (HPV) vaccine Sampson, JN; Hildesheim, A; Herrero, R; Gonzalez, P; Kreimer, A; Gail, MH; Contemp Clin Trials, DOI://10.1016/j.cct.2018.02.010 (2018)
Transcriptional regulation by NR5A2 links differentiation and inflammation in the pancreas Cobo, I; Martinelli, P; Flández, M et al. Nature, DOI://10.1038/nature25751 (2018)
Estimating recurrence and incidence of preterm birth subject to measurement error in gestational age: A hidden Markov modeling approach Albert, PS Stat Med, DOI://10.1002/sim.7624 (2018)
Extreme disorder in an ultrahigh-affinity protein complex Borgia, A; Borgia, MB; Bugge, K et al. Nature, DOI://10.1038/nature25762 (2018)

Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology Howard, BH; Hirai, TH; Russanova, VR; PLoS ONE, DOI://10.1371/journal.pone.0191033 (2018)
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells Hu, G; Cui, K; Fang, D et al. Immunity, DOI://10.1016/j.immuni.2018.01.013 (2018)
Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations Tofoleanu, F; Yuan, Y; Pickard, FC; Tywoniuk, B; Brooks, BR; Buchete, NV; J Phys Chem B, DOI://10.1021/acs.jpcb.7b12083 (2018)
Assessment of PCXMC for patients with different body size in chest and abdominal x ray examinations: a Monte Carlo simulation study Borrego, D; Lowe, EM; Kitahara, CM; Lee, C; Phys Med Biol, DOI://10.1088/1361-6560/aab13e (2018)
Dose coefficients for children and young adolescents exposed to external neutron fields Griffin, KT; Mille, M; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aab126 (2018)
CD63, MHC class 1, and CD47 identify subsets of extracellular vesicles containing distinct populations of noncoding RNAs Kaur, S; Elkahloun, AG; Arakelyan, A et al. Sci Rep, DOI://10.1038/s41598-018-20936-7 (2018)

Transient Receptor Potential Channels TRPM4 and TRPC3 Critically Contribute to Respiratory Motor Pattern Formation but not Rhythmogenesis in Rodent Brainstem Circuits Koizumi, H; John, TT; Chia, JX et al. eNeuro, DOI://10.1523/ENEURO.0332-17.2018 (2018)
Ridding fMRI data of motion-related influences: Removal of signals with distinct spatial and physical bases in multiecho data Power, JD; Plitt, M; Gotts, SJ et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1720985115 (2018)
The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance Yoshimura, T; McLean, MH; Dzutsev, AK et al. J. Immunol., DOI://10.4049/jimmunol.1602073 (2018)
Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance Weingarten, RA; Johnson, RC; Conlan, S et al. MBio, DOI://10.1128/mBio.02011-17 (2018)
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox Müller, F; Cunningham, T; Stookey, S et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1714512115 (2018)
Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling Li, S; Jang, H; Zhang, J; Nussinov, R; Structure, DOI://10.1016/j.str.2018.01.011 (2018)

Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho Brown, JL; Sun, MA; Kassis, JA; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1716299115 (2018)
Precise genome-wide mapping of single nucleosomes and linkers in vivo Chereji, RV; Ramachandran, S; Bryson, TD; Henikoff, S; Genome Biol., DOI://10.1186/s13059-018-1398-0 (2018)
Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer Klein, AP; Wolpin, BM; Risch, HA et al. Nat Commun, DOI://10.1038/s41467-018-02942-5 (2018)
The klotho-related protein KLPH (lctl) has preferred expression in lens and is essential for expression of clic5 and normal lens suture formation Fan, J; Lerner, J; Wyatt, MK et al. Exp. Eye Res., DOI://10.1016/j.exer.2018.02.001 (2018)
Self-reported executive function and hoarding in adults with obsessive-compulsive disorder Samuels, J; Bienvenu, OJ; Krasnow, J et al. Compr Psychiatry, DOI://10.1016/j.comppsych.2017.11.009 (2018)
Sequence determinants of protein phase behavior from a coarse-grained model Dignon, GL; Zheng, W; Kim, YC; Best, RB; Mittal, J; PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1005941 (2018)

Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy VanderWeele, DJ; Finney, R; Katayama, K et al. Eur Urol Focus, DOI://10.1016/j.euf.2018.01.006 (2018)
Extended amygdala connectivity changes during sustained shock anticipation Torrisi, S; Gorka, AX; Gonzalez-Castillo, J et al. Transl Psychiatry, DOI://10.1038/s41398-017-0074-6 (2018)
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2 Ozdemir, ES; Jang, H; Gursoy, A et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001596 (2018)
Binding kinetics of ultrasmall gold nanoparticles with proteins André Lira, Rodrigo Ferreira, Ricardo Torquato, Huaying Zhao, Maria Luiza Oliva, Sergio A. Hassan, Peter Schuck and Alioscka A Sousa Nanoscale, DOI: 10.1039/C7NR06810G (2018)
Cleavage of TL1A Differentially Regulates Its Effects on Innate and Adaptive Immune Cells Ferdinand, JR; Richard, AC; Meylan, F; Al-Shamkhani, A; Siegel, RM; J. Immunol., DOI://10.4049/jimmunol.1700891 (2018)
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads Eccles, D; Chandler, J; Camberis, M et al. BMC Biol., DOI://10.1186/s12915-017-0473-4 (2018)
Accelerometer-Measured Physical Activity and Sedentary Behavior in Relation to All-Cause Mortality: The Women's Health Study Lee, IM; Shiroma, EJ; Evenson, KR; Kamada, M; LaCroix, AZ; Buring, JE; Circulation, DOI://10.1161/CIRCULATIONAHA.117.031300 (2018)
Altered avalanche dynamics in a developmental NMDAR hypofunction model of cognitive impairment Seshadri, S; Klaus, A; Winkowski, DE; Kanold, PO; Plenz, D; Transl Psychiatry, DOI://10.1038/s41398-017-0060-z (2018)
Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma Zheng, H; Pomyen, Y; Hernandez, MO et al. Hepatology, DOI://10.1002/hep.29778 (2018)
Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis Gill, T; Asquith, M; Brooks, SR; Rosenbaum, JT; Colbert, RA; Arthritis Rheumatol., DOI://10.1002/art.40405 (2018)

2017 (403 papers)

Performing Skin Microbiome Research: A Method to the Madness Kong, HH; Andersson, B; Clavel, T et al. J Invest Dermatol, DOI://10.1016/j.jid.2016.10.033 (2017)
Genome-wide siRNA screen of genes regulating the LPS-induced TNF-α response in human macrophages Sun, J; Katz, S; Dutta, B et al. Sci Data, DOI://10.1038/sdata.2017.7 (2017)

Functionalized non-viral cationic vectors for effective siRNA induced cancer therapy Gupta, K; Puri, A; Shapiro, BA; , DNA RNA Nanotechnol, DOI://10.1515/rnan-2017-0001 (2017)
APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast Saini, N; Roberts, SA; Sterling, JF et al. DNA Repair (Amst), DOI://10.1016/j.dnarep.2017.03.003 (2017)
Flexible risk prediction models for left or interval-censored data from electronic health records Hyun, N; Cheung, LC; Pan, Q; Schiffman, M; Katki, HA; , Ann Appl Stat, DOI://10.1214/17-AOAS1036 (2017)
Phantoms models to characterize influenza hemagglutinin-based vaccines McCraw, DM; Harris, AK; , Microsc. Microanal., DOI://10.1017/S1431927617007279 (2017)
Inhibitors of the Histone Methyltransferases EZH2/1 Induce a Potent Antiviral State and Suppress Infection by Diverse Viral Pathogens Arbuckle, JH; Gardina, PJ; Gordon, DN et al. mBio, DOI://10.1128/mBio.01141-17 (2017)
Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage Iantorno, SA; Durrant, C; Khan, A et al. mBio, DOI://10.1128/mBio.01393-17 (2017)
Social influence on 5-year survival in a longitudinal chemotherapy ward co-presence network Lienert, J; Marcum, CS; Finney, J; Reed-Tsochas, F; Koehly, L; , Netw Sci (Camb Univ Press), DOI://10.1017/nws.2017.16 (2017)
SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches Gudla, PR; Nakayama, K; Pegoraro, G; Misteli, T; Cold Spring Harb. Symp. Quant. Biol., DOI://10.1101/sqb.2017.82.033761 (2017)
Systematic Investigation of Multi-TLR Sensing Identifies Regulators of Sustained Gene Activation in Macrophages Lin, B; Dutta, B; Fraser, IDC; , Cell Syst, DOI://10.1016/j.cels.2017.06.014 (2017)
The C-terminal multimerization domain is essential for leukemia development by CBFβ-SMMHC in a mouse knockin model Zhao, L; Alkadi, H; Kwon, EM et al. Leukemia, DOI://10.1038/leu.2017.262 (2017)
Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs vonHoldt, BM; Shuldiner, E; Koch, IJ et al. Sci Adv, DOI://10.1126/sciadv.1700398 (2017)
Secretory Expression and Characterization of Chinese Narcissus GNA-Like Lectin in Pichia pastoris Li, X; Zhang, P; Zhang, N et al. Appl Biochem Biotechnol, DOI://10.1007/s12010-017-2408-5 (2017)
Structural deficits in salience network regions are associated with increased impulsivity and compulsivity in alcohol dependence Grodin, EN; Cortes, CR; Spagnolo, PA; Momenan, R; , Drug Alcohol Depend, DOI://10.1016/j.drugalcdep.2017.06.014 (2017)
Regulation of chromatin folding by conformational variations of nucleosome linker DNA Buckwalter, JM; Norouzi, D; Harutyunyan, A; Zhurkin, VB; Grigoryev, SA; , Nucleic Acids Res., DOI://10.1093/nar/gkx562 (2017)
La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis Blewett, NH; Iben, JR; Gaidamakov, S; Maraia, RJ; , Mol. Cell. Biol., DOI://10.1128/MCB.00588-16 (2017)
Genome-wide siRNA screen of genes regulating the LPS-induced NF-κB and TNF-α responses in mouse macrophages Li, N; Katz, S; Dutta, B et al. Sci Data, DOI://10.1038/sdata.2017.8 (2017)
The emerging importance and challenges of the human mycobiome Kong, HH; Morris, A; , Virulence, DOI://10.1080/21505594.2017.1279780 (2017)
Effects of spatial fMRI resolution on the classification of naturalistic movies Mandelkow, H; de Zwart, JA; Duyn, JH; Neuroimage, DOI://10.1016/j.neuroimage.2017.08.053 (2017)

Automatic magnetic resonance prostate segmentation by deep learning with holistically nested networks Cheng, R; Roth, HR; Lay, N et al. J Med Imaging (Bellingham), DOI://10.1117/1.JMI.4.4.041302 (2017)
Critical functions for STAT5 tetramers in the maturation and survival of natural killer cells Lin, JX; Du, N; Li, P et al. Nat Commun, DOI://10.1038/s41467-017-01477-5 (2017)
BRD4 facilitates DNA damage response and represses CBX5/Heterochromatin protein 1 (HP1) Pongas, G; Kim, MK; Min, DJ et al. Oncotarget, DOI://10.18632/oncotarget.17572 (2017)
Bitopic fluorescent antagonists of the A2A adenosine receptor based on pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-amine functionalized congeners Duroux, R; Ciancetta, A; Mannes, P et al. Medchemcomm, DOI://10.1039/C7MD00247E (2017)
Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay Weiss, K; Wigby, K; Fannemel, M et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2017.86 (2017)
Longitudinal Structural and Functional Differences Between Proportional and Poor Motor Recovery After Stroke Guggisberg, AG; Nicolo, P; Cohen, LG; Schnider, A; Buch, ER; Neurorehabil Neural Repair, DOI://10.1177/1545968317740634 (2017)
The Molecular Revolution in Cutaneous Biology: Investigating the Skin Microbiome Kong, HH; Segre, JA; , J Invest Dermatol, DOI://10.1016/j.jid.2016.07.045 (2017)
STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus Li, P; Mitra, S; Spolski, R et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1714019114 (2017)
Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis van Rooij, FJA; Qayyum, R; Smith, AV et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2016.11.016 (2017)
Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans Mitchell, KA; Zingone, A; Toulabi, L; Boeckelman, J; Ryan, BM; , Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-17-0527 (2017)
Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells Rivero-Hinojosa, S; Kang, S; Lobanenkov, VV; Zentner, GE; Sci Rep, DOI://10.1038/srep41279 (2017)
Preparation of a Conditional RNA Switch Zakrevsky, P; Parlea, L; Viard, M; Bindewald, E; Afonin, KA; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_20 (2017)
Computational Generation of RNA Nanorings Sharan, R; Bindewald, E; Kasprzak, WK; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_2 (2017)
Protocols for Molecular Dynamics Simulations of RNA Nanostructures Kim, T; Kasprzak, WK; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_3 (2017)
Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma Chaisaingmongkol, J; Budhu, A; Dang, H et al. Cancer Cell, DOI://10.1016/j.ccell.2017.05.009 (2017)
Visualizing abnormalities in chest radiographs through salient network activations in Deep Learning Rajaraman S, Antani SK, Xue Z, Candemir S, Jaeger S, Thoma GR Proc. IEEE Life Sciences Conference (LSC), Sydney, Australia, 10.1109/LSC.2017.826814 (2017)
PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability Gryder, BE; Yohe, ME; Chou, HC et al. Cancer Discov, DOI://10.1158/2159-8290.CD-16-1297 (2017)
Parental bonding and hoarding in obsessive-compulsive disorder Chen, D; Bienvenu, OJ; Krasnow, J et al. Compr Psychiatry, DOI://10.1016/j.comppsych.2016.11.004 (2017)
Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer Assadipour, Y; Zacharakis, N; Crystal, JS et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-16-1423 (2017)
Systems-level identification of PKA-dependent signaling in epithelial cells Isobe, K; Jung, HJ; Yang, CR et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1709123114 (2017)
Association of red cell distribution width with all-cause and cardiovascular-specific mortality in African American and white adults: a prospective cohort study Tajuddin, SM; Nalls, MA; Zonderman, AB; Evans, MK; J Transl Med, DOI://10.1186/s12967-017-1313-6 (2017)
Sieve analysis using the number of infecting pathogens Follmann, D; Huang, CY; Biometrics, DOI://10.1111/biom.12833 (2017)
Meat Consumption During Pregnancy and Substance Misuse Among Adolescent Offspring: Stratification of TCN2 Genetic Variants Hibbeln, JR; SanGiovanni, JP; Golding, J et al. Alcohol. Clin. Exp. Res., DOI://10.1111/acer.13494 (2017)
A Systems Biology Approach to Investigating Sex Differences in Cardiac Hypertrophy Harrington, J; Fillmore, N; Gao, S et al. J Am Heart Assoc, DOI://10.1161/JAHA.117.005838 (2017)

Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation Agbor-Enoh, S; Tunc, I; De Vlaminck, I et al. J. Heart Lung Transplant., DOI://10.1016/j.healun.2017.05.026 (2017)
Broadly protective murine monoclonal antibodies against influenza B virus target highly conserved neuraminidase epitopes Wohlbold, TJ; Podolsky, KA; Chromikova, V et al. Nat Microbiol, DOI://10.1038/s41564-017-0011-8 (2017)
Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts Mozaffarian, D; Dashti, HS; Wojczynski, MK et al. PLoS ONE, DOI://10.1371/journal.pone.0186456 (2017)
Amygdala Contributions to Stimulus-Reward Encoding in the Macaque Medial and Orbital Frontal Cortex during Learning Rudebeck, PH; Ripple, JA; Mitz, AR; Averbeck, BB; Murray, EA; J. Neurosci., DOI://10.1523/JNEUROSCI.0933-16.2017 (2017)
Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq Zhang, Y; Ku, WL; Liu, S et al. Cell Res., DOI://10.1038/cr.2017.112 (2017)
Deciphering the olfactory repertoire of the tiger mosquito Aedes albopictus Lombardo, F; Salvemini, M; Fiorillo, C et al. BMC Genomics, DOI://10.1186/s12864-017-4144-1 (2017)

Susceptible genes and disease mechanisms identified in frontotemporal dementia and frontotemporal dementia with Amyotrophic Lateral Sclerosis by DNA-methylation and GWAS Taskesen, E; Mishra, A; van der Sluis, S et al. Sci Rep, DOI://10.1038/s41598-017-09320-z (2017)
Shelterin components mediate genome reorganization in response to replication stress Mizuguchi, T; Taneja, N; Matsuda, E et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1705527114 (2017)
The Interplay between Long- and Short-Range Temporal Correlations Shapes Cortex Dynamics across Vigilance States Meisel, C; Klaus, A; Vyazovskiy, VV; Plenz, D; J. Neurosci., DOI://10.1523/JNEUROSCI.0448-17.2017 (2017)
Insights Into Onchocerca volvulus Population Biology Through Multilocus Immunophenotyping Norice-Tra, CT; Ribeiro, J; Bennuru, S et al. J. Infect. Dis., DOI://10.1093/infdis/jix394 (2017)
Dynamic landscape of alternative polyadenylation during retinal development Hu, W; Li, S; Park, JY et al. Cell. Mol. Life Sci., DOI://10.1007/s00018-016-2429-1 (2017)
An Analysis of Two Genome-wide Association Meta-analyses Identifies a New Locus for Broad Depression Phenotype Direk, N; Williams, S; Smith, JA et al. Biol. Psychiatry, DOI://10.1016/j.biopsych.2016.11.013 (2017)

The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins Wang, AH; Juan, AH; Ko, KD et al. Mol. Cell, DOI://10.1016/j.molcel.2017.09.016 (2017)
Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy Folco, HD; Chalamcharla, VR; Sugiyama, T et al. Nature, DOI://10.1038/nature21372 (2017)
Pyrimidine Nucleotides Containing a (S)-Methanocarba Ring as P2Y6 Receptor Agonists Toti, KS; Jain, S; Ciancetta, A et al. Medchemcomm, DOI://10.1039/C7MD00397H (2017)
NFκB Promotes Ovarian Tumorigenesis via Classical Pathways That Support Proliferative Cancer Cells and Alternative Pathways That Support ALDH+ Cancer Stem-like Cells House, CD; Jordan, E; Hernandez, L et al. Cancer Res., DOI://10.1158/0008-5472.CAN-17-0366 (2017)
ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer Shukla, V; Rao, M; Zhang, H et al. Cancer Res., DOI://10.1158/0008-5472.CAN-17-0570 (2017)
SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication Taneja, N; Zofall, M; Balachandran, V et al. Mol. Cell, DOI://10.1016/j.molcel.2017.02.006 (2017)

High-Resolution CBV-fMRI Allows Mapping of Laminar Activity and Connectivity of Cortical Input and Output in Human M1 Huber, L; Handwerker, DA; Jangraw, DC et al. Neuron, DOI://10.1016/j.neuron.2017.11.005 (2017)
KLF4-dependent perivascular cell plasticity mediates pre-metastatic niche formation and metastasis Murgai, M; Ju, W; Eason, M et al. Nat. Med., DOI://10.1038/nm.4400 (2017)
CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression Ren, G; Jin, W; Cui, K et al. Mol. Cell, DOI://10.1016/j.molcel.2017.08.026 (2017)
Bromodomain and Extraterminal Protein Inhibitor JQ1 Suppresses Thyroid Tumor Growth in a Mouse Model Zhu, X; Enomoto, K; Zhao, L et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-16-0914 (2017)
Molecular-based diagnosis of multiple sclerosis and its progressive stage Barbour, C; Kosa, P; Komori, M et al. Ann. Neurol., DOI://10.1002/ana.25083 (2017)
Serum starvation of ARPE-19 changes the cellular distribution of cholesterol and Fibulin3 in patterns reminiscent of age-related macular degeneration Rajapakse, D; Peterson, K; Mishra, S; Wistow, G; Exp. Cell Res., DOI://10.1016/j.yexcr.2017.10.036 (2017)

Crystal Structures of Diaryliodonium Fluorides and Their Implications for Fluorination Mechanisms Lee, YS; Chun, JH; Hodošček, M; Pike, VW; Chemistry, DOI://10.1002/chem.201604803 (2017)
Loci associated with skin pigmentation identified in African populations Crawford, NG; Kelly, DE; Hansen, MEB et al. Science, DOI://10.1126/science.aan8433 (2017)
eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast Martin-Marcos, P; Zhou, F; Karunasiri, C et al. Elife, DOI://10.7554/eLife.31250 (2017)
Polygenic risk score and heritability estimates reveals a genetic relationship between ASD and OCD Guo, W; Samuels, JF; Wang, Y et al. Eur Neuropsychopharmacol, DOI://10.1016/j.euroneuro.2017.03.011 (2017)
Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres Xiao, H; Wang, F; Wisniewski, J et al. Genes Dev., DOI://10.1101/gad.304782.117 (2017)
T-Cell Transfer Therapy Targeting Mutant KRAS Rosenberg, SA; Tran, E; Robbins, PF; N. Engl. J. Med., DOI://10.1056/NEJMc1616637 (2017)
Correction: The complex genetics of gait speed: genome-wide meta-analysis approach Ben-Avraham, D; Karasik, D; Verghese, J et al. Aging (Albany NY), DOI://10.18632/aging.101260 (2017)
Effect of Threat on Right dlPFC Activity during Behavioral Pattern Separation Balderston, NL; Hsiung, A; Ernst, M; Grillon, C; J. Neurosci., DOI://10.1523/JNEUROSCI.0717-17.2017 (2017)
GATE: an efficient procedure in study of pleiotropic genetic associations Zhang, W; Yang, L; Tang, LL et al. BMC Genomics, DOI://10.1186/s12864-017-3928-7 (2017)
Progressive and Multi-path Holistically Nested Neural Networks for Pathological Lung Segmentation from CT Images Harrison A.P., Xu Z., George K., Lu L., Summers R.M., Mollura D.J. In: Descoteaux M., Maier-Hein L., Franz A., Jannin P., Colli, 10.1007/978-3-319-66179-7-71 (2017)
Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease Warren, CR; O'Sullivan, JF; Friesen, M et al. Cell Stem Cell, DOI://10.1016/j.stem.2017.01.010 (2017)
An Adult Mouse Thyroid Side Population Cell Line that Exhibits Enriched Epithelial-Mesenchymal Transition Murata, T; Iwadate, M; Takizawa, Y et al. Thyroid, DOI://10.1089/thy.2016.0130 (2017)
NRF1 coordinates with DNA methylation to regulate spermatogenesis Wang, J; Tang, C; Wang, Q et al. FASEB J., DOI://10.1096/fj.201700093R (2017)
Two Distinct Actin Networks Mediate Traction Oscillations to Confer Focal Adhesion Mechanosensing Wu, Z; Plotnikov, SV; Moalim, AY; Waterman, CM; Liu, J; Biophys. J., DOI://10.1016/j.bpj.2016.12.035 (2017)
'Final common pathway' of human cancer immunotherapy: targeting random somatic mutations Tran, E; Robbins, PF; Rosenberg, SA; Nat. Immunol., DOI://10.1038/ni.3682 (2017)
Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression Parkhurst, M; Gros, A; Pasetto, A et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-16-2680 (2017)
The Distinct Transcriptional Response of the Midgut of Amblyomma sculptum and Amblyomma aureolatum Ticks to Rickettsia rickettsii Correlates to Their Differences in Susceptibility to Infection Martins, LA; Galletti, MFBM; Ribeiro, JM et al. Front Cell Infect Microbiol, DOI://10.3389/fcimb.2017.00129 (2017)
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Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome Bickhart, DM; Rosen, BD; Koren, S et al. Nat. Genet., DOI://10.1038/ng.3802 (2017)
Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness Plassais, J; Rimbault, M; Williams, FJ; Davis, BW; Schoenebeck, JJ; Ostrander, EA; PLoS Genet., DOI://10.1371/journal.pgen.1006661 (2017)
SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation Kidder, BL; Hu, G; Cui, K; Zhao, K; Epigenetics Chromatin, DOI://10.1186/s13072-017-0115-7 (2017)
Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome Kouzine, F; Wojtowicz, D; Baranello, L et al. Cell Syst, DOI://10.1016/j.cels.2017.01.013 (2017)

Circulating tumor cells capture disease evolution in advanced prostate cancer Lack, J; Gillard, M; Cam, M; Paner, GP; VanderWeele, DJ; J Transl Med, DOI://10.1186/s12967-017-1138-3 (2017)
Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer Liu, Q; Acharya, P; Dolan, MA et al. Nat. Struct. Mol. Biol., DOI://10.1038/nsmb.3382 (2017)
The effects of shared information on semantic calculations in the gene ontology Bible, PW; Sun, HW; Morasso, MI; Loganantharaj, R; Wei, L; Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2017.01.009 (2017)
Ultra-High-Field fMRI Reveals a Role for the Subiculum in Scene Perceptual Discrimination Hodgetts, CJ; Voets, NL; Thomas, AG; Clare, S; Lawrence, AD; Graham, KS; J. Neurosci., DOI://10.1523/JNEUROSCI.3225-16.2017 (2017)
Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies Hedman, ÅK; Mendelson, MM; Marioni, RE et al. Circ Cardiovasc Genet, DOI://10.1161/CIRCGENETICS.116.001487 (2017)
Circulating miRNA Associated with Posttraumatic Stress Disorder in a Cohort of Military Combat Veterans Christiana G. Martin, Hyungsuk Kim, Sijung Yun, Whitney Livingston, Joseph Fetta, Vincent Mysliwiec, Tristin Baxter, Jessica M. Gill Psychiatry Research, doi://10.1016/j.psychres.2017.01.081 (2017)

The dynamic mechanism of RASSF5 and MST kinase activation by Ras Liao, TJ; Jang, H; Tsai, CJ; Fushman, D; Nussinov, R; Phys Chem Chem Phys, DOI://10.1039/c6cp08596b (2017)
Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus Pooley, JR; Flynn, BP; Grøntved, L et al. Endocrinology, DOI://10.1210/en.2016-1929 (2017)
Somatic mutations in murine models of leukemia and lymphoma: Disease specificity and clinical relevance Goldberg, L; Gough, SM; Lee, F et al. Genes Chromosomes Cancer, DOI://10.1002/gcc.22451 (2017)
Multivariate meta-analysis with an increasing number of parameters Boca, SM; Pfeiffer, RM; Sampson, JN; Biom J, DOI://10.1002/bimj.201600013 (2017)
Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species Arcà, B; Lombardo, F; Struchiner, CJ; Ribeiro, JM; BMC Genomics, DOI://10.1186/s12864-017-3579-8 (2017)
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes Varshney, A; Scott, LJ; Welch, RP et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1621192114 (2017)

A novel DLX3-PKC integrated signaling network drives keratinocyte differentiation Palazzo, E; Kellett, MD; Cataisson, C et al. Cell Death Differ., DOI://10.1038/cdd.2017.5 (2017)
Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch Le, MT; Kasprzak, WK; Kim, T et al. Elife, DOI://10.7554/eLife.22883 (2017)
Thiazole-valine peptidomimetic (TTT-28) antagonizes multidrug resistance in vitro and in vivo by selectively inhibiting the efflux activity of ABCB1 Wang, YJ; Patel, BA; Anreddy, N et al. Sci Rep, DOI://10.1038/srep42106 (2017)
Messenger RNA and MicroRNA transcriptomic signatures of cardiometabolic risk factors McManus, DD; Rong, J; Huan, T et al. BMC Genomics, DOI://10.1186/s12864-017-3533-9 (2017)
iPSCs and fibroblast subclones from the same fibroblast population contain comparable levels of sequence variations Kwon, EM; Connelly, JP; Hansen, NF et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1616035114 (2017)
Dense genotyping of immune-related loci implicates host responses to microbial exposure in Behçet's disease susceptibility Takeuchi, M; Mizuki, N; Meguro, A et al. Nat. Genet., DOI://10.1038/ng.3786 (2017)

Insights from NMR Spectroscopy into the Conformational Properties of Man-9 and Its Recognition by Two HIV Binding Proteins Shahzad-Ul-Hussan, S; Sastry, M; Lemmin, T et al. Chembiochem, DOI://10.1002/cbic.201600665 (2017)
MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers Chereji, RV; Ocampo, J; Clark, DJ; Mol. Cell, DOI://10.1016/j.molcel.2016.12.009 (2017)
Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts Lee, J; Kim, YH; T Arce, F et al. ACS Chem Neurosci, DOI://10.1021/acschemneuro.7b00006 (2017)
Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing Jansen, IE; Ye, H; Heetveld, S et al. Genome Biol., DOI://10.1186/s13059-017-1147-9 (2017)
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm Zimin, AV; Puiu, D; Luo, MC et al. Genome Res., DOI://10.1101/gr.213405.116 (2017)
Hedgehog Signaling Inhibitors Fail to Reduce Merkel Cell Carcinoma Viability Carroll, TM; Williams, JS; Daily, K et al. J. Invest. Dermatol., DOI://10.1016/j.jid.2017.01.008 (2017)

Differential methylation of genes in individuals exposed to maternal diabetes in utero Chen, P; Piaggi, P; Traurig, M et al. Diabetologia, DOI://10.1007/s00125-016-4203-1 (2017)
ERBIN deficiency links STAT3 and TGF-β pathway defects with atopy in humans Lyons, JJ; Liu, Y; Ma, CA et al. J. Exp. Med., DOI://10.1084/jem.20161435 (2017)
Frequent inactivating germline mutations in DNA repair genes in patients with Ewing sarcoma Brohl, AS; Patidar, R; Turner, CE et al. Genet. Med., DOI://10.1038/gim.2016.206 (2017)
Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies Joehanes, R; Zhang, X; Huan, T et al. Genome Biol., DOI://10.1186/s13059-016-1142-6 (2017)
Gleason Score 7 Prostate Cancers Emerge through Branched Evolution of Clonal Gleason Pattern 3 and 4 Sowalsky, AG; Kissick, HT; Gerrin, SJ et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-16-2414 (2017)
Dose coefficients for ICRP reference pediatric phantoms exposed to idealised external gamma fields Chang, LA; Simon, SL; Jorgensen, TJ; Schauer, DA; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aa559e (2017)

Actin dynamics and competition for myosin monomer govern the sequential amplification of myosin filaments Beach, JR; Bruun, KS; Shao, L et al. Nat. Cell Biol., DOI://10.1038/ncb3463 (2017)
Functionally-interdependent shape-switching nanoparticles with controllable properties Halman, JR; Satterwhite, E; Roark, B et al. Nucleic Acids Res., DOI://10.1093/nar/gkx008 (2017)
SDHD promoter mutations ablate GABP transcription factor binding in melanoma Zhang, T; Xu, M; Makowski, MM et al. Cancer Res., DOI://10.1158/0008-5472.CAN-16-0919 (2017)
Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity Parra, GI; Squires, RB; Karangwa, CK et al. PLoS Pathog., DOI://10.1371/journal.ppat.1006136 (2017)
Novel genetic loci associated with hippocampal volume Hibar, DP; Adams, HH; Jahanshad, N et al. Nat Commun, DOI://10.1038/ncomms13624 (2017)
Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach Mendelson, MM; Marioni, RE; Joehanes, R et al. PLoS Med., DOI://10.1371/journal.pmed.1002215 (2017)

Quantitative stability of hematopoietic stem and progenitor cell clonal output in rhesus macaques receiving transplants Koelle, SJ; Espinoza, DA; Wu, C et al. Blood, DOI://10.1182/blood-2016-07-728691 (2017)
Sequence of Reston Virus Isolate AZ-1435, an Ebolavirus Isolate Obtained during the 1989-1990 Reston Virus Epizootic in the United States Cornish, JP; Diaz, L; Ricklefs, SM et al. Genome Announc, DOI://10.1128/genomeA.01448-16 (2017)
An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches Huang, J; Mei, Y; König, G et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.6b01125 (2017)
Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils Xu, L; Ma, B; Nussinov, R; Thompson, D; ACS Chem Neurosci, DOI://10.1021/acschemneuro.6b00406 (2017)
Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices Hua, X; Goedert, JJ; Landi, MT; Shi, J; Hum. Hered., DOI://10.1159/000448733 (2017)
High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss Siersbæk, M; Varticovski, L; Yang, S et al. Sci Rep, DOI://10.1038/srep40220 (2017)

The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas Pemov, A; Li, H; Patidar, R et al. Oncogene, DOI://10.1038/onc.2016.464 (2017)
Characterization of the disassembly and reassembly of the HBV glycoprotein surface antigen, a pliable nanoparticle vaccine platform Gallagher, JR; Torian, U; McCraw, DM; Harris, AK; Virology, DOI://10.1016/j.virol.2016.12.025 (2017)
The Papillomavirus Episteme: a major update to the papillomavirus sequence database Van Doorslaer, K; Li, Z; Xirasagar, S et al. Nucleic Acids Res., DOI://10.1093/nar/gkw879 (2017)
Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure Le Nouën, C; McCarty, T; Brown, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1619242114 (2017)
Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting Doria-Rose, NA; Altae-Tran, HR; Roark, RS et al. PLoS Pathog., DOI://10.1371/journal.ppat.1006148 (2017)
An insight into the sialome of Hyalomma excavatum Ribeiro, JM; Slovák, M; Francischetti, IM; Ticks Tick Borne Dis, DOI://10.1016/j.ttbdis.2016.08.011 (2017)

Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct Xue, Z; Chen, JX; Zhao, Y; Medvar, B; Knepper, MA; Physiol. Genomics, DOI://10.1152/physiolgenomics.00120.2016 (2017)
Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity Gong, Y; Zhu, Y; Zou, Y; Ma, B; Nussinov, R; Zhang, Q; J Phys Chem B, DOI://10.1021/acs.jpcb.6b11094 (2017)
Computational models of the neural control of breathing Molkov, YI; Rubin, JE; Rybak, IA; Smith, JC; Wiley Interdiscip Rev Syst Biol Med, DOI://10.1002/wsbm.1371 (2017)
Structural studies of influenza virus RNPs by electron microscopy indicate molecular contortions within NP supra-structures Gallagher, JR; Torian, U; McCraw, DM; Harris, AK; J. Struct. Biol., DOI://10.1016/j.jsb.2016.12.007 (2017)
EBI2 overexpression in mice leads to B1 B-cell expansion and chronic lymphocytic leukemia-like B-cell malignancies Niss Arfelt, K; Barington, L; Benned-Jensen, T et al. Blood, DOI://10.1182/blood-2016-02-697185 (2017)
The cell cycle restricts activation-induced cytidine deaminase activity to early G1 Wang, Q; Kieffer-Kwon, KR; Oliveira, TY et al. J. Exp. Med., DOI://10.1084/jem.20161649 (2017)

Neural Markers in Pediatric Bipolar Disorder and Familial Risk for Bipolar Disorder Wiggins, JL; Brotman, MA; Adleman, NE et al. J Am Acad Child Adolesc Psychiatry, DOI://10.1016/j.jaac.2016.10.009 (2017)
The bald and the beautiful: hairlessness in domestic dog breeds Parker, HG; Harris, A; Dreger, DL; Davis, BW; Ostrander, EA; Philos. Trans. R. Soc. Lond., B, Biol. Sci., DOI://10.1098/rstb.2015.0488 (2017)
ADORA1 mutations are not a common cause of Parkinson's disease and dementia with Lewy bodies Blauwendraat, C; Nalls, MA; Federoff, M et al. Mov. Disord., DOI://10.1002/mds.26886 (2017)
Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization Wang, Y; Khan, A; Marks, AB et al. Nucleic Acids Res., DOI://10.1093/nar/gkw1211 (2017)
Acquired somatic mutations in PNH reveal long-term maintenance of adaptive NK cells independent of HSPCs Corat, MA; Schlums, H; Wu, C et al. Blood, DOI://10.1182/blood-2016-08-734285 (2017)
Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes Karyadi, DM; Geybels, MS; Karlins, E et al. Oncotarget, DOI://10.18632/oncotarget.13646 (2017)

Long-term monitoring of cardiorespiratory patterns in drug-resistant epilepsy Goldenholz, DM; Kuhn, A; Austermuehle, A et al. Epilepsia, DOI://10.1111/epi.13606 (2017)
Assessing variation across 8 established East Asian loci for type 2 diabetes mellitus in American Indians: Suggestive evidence for new sex-specific diabetes signals in GLIS3 and ZFAND3 Muller, YL; Piaggi, P; Chen, P et al. Diabetes Metab. Res. Rev., DOI://10.1002/dmrr.2869 (2017)
Estimating the Heritability of Structural and Functional Brain Connectivity in Families Affected by Attention-Deficit/Hyperactivity Disorder Sudre, G; Choudhuri, S; Szekely, E et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2016.3072 (2017)
Oculocutaneous albinism type 1: link between mutations, tyrosinase conformational stability, and enzymatic activity Dolinska, MB; Kus, NJ; Farney, SK; Wingfield, PT; Brooks, BP; Sergeev, YV; Pigment Cell Melanoma Res, DOI://10.1111/pcmr.12546 (2017)
DLX3-Dependent Regulation of Ion Transporters and Carbonic Anhydrases is Crucial for Enamel Mineralization Duverger, O; Ohara, T; Bible, PW; Zah, A; Morasso, MI; J. Bone Miner. Res., DOI://10.1002/jbmr.3022 (2017)
Untangling the relatedness among correlations, Part II: Inter-subject correlation group analysis through linear mixed-effects modeling Chen, G; Taylor, PA; Shin, YW; Reynolds, RC; Cox, RW; Neuroimage, DOI://10.1016/j.neuroimage.2016.08.029 (2017)

Topographical and physiological differences of the skin mycobiome in health and disease Jo, JH; Kennedy, EA; Kong, HH; Virulence, DOI://10.1080/21505594.2016.1249093 (2017)
Empirically derived patterns of psychiatric symptoms in youth: A latent profile analysis Kircanski, K; Zhang, S; Stringaris, A et al. J Affect Disord, DOI://10.1016/j.jad.2016.09.016 (2017)
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge Lee, J; Tofoleanu, F; Pickard, FC et al. J. Comput. Aided Mol. Des., DOI://10.1007/s10822-016-9968-2 (2017)
Perfluoroalkyl Chemicals, Menstrual Cycle Length, and Fecundity: Findings from a Prospective Pregnancy Study Lum, KJ; Sundaram, R; Barr, DB; Louis, TA; Buck Louis, GM; Epidemiology, DOI://10.1097/EDE.0000000000000552 (2017)
Anxiety Patients Show Reduced Working Memory Related dlPFC Activation During Safety and Threat Balderston, NL; Vytal, KE; O'Connell, K et al. Depress Anxiety, DOI://10.1002/da.22518 (2017)

2016 (394 papers)

landsman Duplat-Bermúdez, L; Ruiz-Medrano, R; Landsman, D et al. Data Brief, DOI://10.1016/j.dib.2016.06.002 (2016)
DNA Breaks and End Resection Measured Genome-wide by End Sequencing Canela, A; Sridharan, S; Sciascia, N et al. Mol Cell, DOI://10.1016/j.molcel.2016.06.034 (2016)
Can dielectric spheres accurately model atomic-scale interactions Obolensky, OI; Doerr, TP; Ogurtsov, AY; Yu, YK; Europhys Lett, DOI://10.1209/0295-5075/116/24003 (2016)
Transcriptomic analysis of Arabidopsis overexpressing flowering locus T driven by a meristem-specific promoter that induces early flowering Duplat-Bermúdez, L; Ruiz-Medrano, R; Landsman, D et al. Gene, DOI://10.1016/j.gene.2016.04.060 (2016)
BIG: a large-scale data integration tool for renal physiology Zhao, Y; Yang, CR; Raghuram, V et al. Am J Physiol Renal Physiol, DOI://10.1152/ajprenal.00249.2016 (2016)
Direct Regulation of Alternative Splicing by SMAD3 through PCBP1 Is Essential to the Tumor-Promoting Role of TGF-β Tripathi, V; Sixt, KM; Gao, S et al. Mol. Cell, DOI://10.1016/j.molcel.2016.09.013 (2016)
Functional connectivity during masked and unmasked face emotion processing in bipolar disorder Tseng, WL; Thomas, LA; Harkins, E et al. Psychiatry Res Neuroimaging, DOI://10.1016/j.pscychresns.2016.10.006 (2016)

Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase Puppala, AK; French, RL; Matthies, D; Baxa, U; Subramaniam, S; Simonović, M; Sci Rep, DOI://10.1038/srep32563 (2016)
Ionic immune suppression within the tumour microenvironment limits T cell effector function Eil, R; Vodnala, SK; Clever, D et al. Nature, DOI://10.1038/nature19364 (2016)
Oxygen Sensing by T Cells Establishes an Immunologically Tolerant Metastatic Niche Clever, D; Roychoudhuri, R; Constantinides, MG et al. Cell, DOI://10.1016/j.cell.2016.07.032 (2016)
The transcription factor BACH2 promotes tumor immunosuppression Roychoudhuri, R; Eil, RL; Clever, D et al. J. Clin. Invest., DOI://10.1172/JCI82884 (2016)
BACH2 regulates CD8(+) T cell differentiation by controlling access of AP-1 factors to enhancers Roychoudhuri, R; Clever, D; Li, P et al. Nat. Immunol., DOI://10.1038/ni.3441 (2016)
Memory T cell-driven differentiation of naive cells impairs adoptive immunotherapy Klebanoff, CA; Scott, CD; Leonardi, AJ et al. J. Clin. Invest., DOI://10.1172/JCI81217 (2016)

Human-Mouse Chimeras with Normal Expression and Function Reveal That Major Domain Swapping Is Tolerated by P-Glycoprotein (ABCB1) Pluchino, KM; Hall, MD; Moen, JK et al. Biochemistry, DOI://10.1021/acs.biochem.5b01064 (2016)
Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view Lu, S; Jang, H; Gu, S; Zhang, J; Nussinov, R; Chem Soc Rev, DOI://10.1039/c5cs00911a (2016)
Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective: Multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factors Swinstead, EE; Paakinaho, V; Presman, DM; Hager, GL; Bioessays, DOI://10.1002/bies.201600137 (2016)
Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant Li, J; Woods, SL; Healey, S et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2016.03.001 (2016)
Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations Doran, AG; Wong, K; Flint, J; Adams, DJ; Hunter, KW; Keane, TM; Genome Biol., DOI://10.1186/s13059-016-1024-y (2016)
A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome Zhou, BR; Feng, H; Ghirlando, R; Li, S; Schwieters, CD; Bai, Y; J. Mol. Biol., DOI://10.1016/j.jmb.2016.08.016 (2016)
Comparing Brain Morphometry Across Multiple Childhood Psychiatric Disorders Gold, AL; Brotman, MA; Adleman, NE et al. J Am Acad Child Adolesc Psychiatry, DOI://10.1016/j.jaac.2016.08.008 (2016)
Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation Wen, H; Qin, F; Zheng, W; Proteins, DOI://10.1002/prot.25177 (2016)
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections Pickard, FC; König, G; Tofoleanu, F et al. J. Comput. Aided Mol. Des., DOI://10.1007/s10822-016-9955-7 (2016)
Identification of therapeutic targets applicable to clinical strategies in ovarian cancer Kim, MK; Caplen, N; Chakka, S et al. BMC Cancer, DOI://10.1186/s12885-016-2675-5 (2016)
Childhood peer network characteristics: genetic influences and links with early mental health trajectories Szekely, E; Pappa, I; Wilson, JD et al. J Child Psychol Psychiatry, DOI://10.1111/jcpp.12493 (2016)
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop Adams, PD; Aertgeerts, K; Bauer, C et al. Structure, DOI://10.1016/j.str.2016.02.017 (2016)
Partition coefficients for the SAMPL5 challenge using transfer free energies Jones, MR; Brooks, BR; Wilson, AK; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-016-9964-6 (2016)
Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III Esser, L; Zhou, F; Zhou, Y et al. J. Biol. Chem., DOI://10.1074/jbc.M116.744391 (2016)
An Open Pilot Study of Training Hostile Interpretation Bias to Treat Disruptive Mood Dysregulation Disorder Stoddard, J; Sharif-Askary, B; Harkins, EA et al. J Child Adolesc Psychopharmacol, DOI://10.1089/cap.2015.0100 (2016)
Estimation of FST and the Impact of de novo Mutation Shriner, D; Chen, G; Adeyemo, A; Rotimi, CN; Hum. Hered., DOI://10.1159/000477782 (2016)
Neuroendocrine Tumor of the Pancreas as a Manifestation of Cowden Syndrome: A Case Report Neychev, V; Sadowski, SM; Zhu, J et al. J. Clin. Endocrinol. Metab., DOI://10.1210/jc.2015-3684 (2016)
Light induced structural changes of the photoprotein mnemiopsin: Characterization and contribution in photoinactivation Pashandi, Z; Molakarimi, M; Sajedi, RH et al. J Photochem Photobiol B, DOI://10.1016/j.jphotobiol.2016.10.018 (2016)
Robust spike sorting of retinal ganglion cells tuned to spot stimuli Ghahari, A; Badea, TC; Conf Proc IEEE Eng Med Biol Soc, DOI://10.1109/EMBC.2016.7591054 (2016)
Assessing the reproducibility of exome copy number variations predictions Hong, CS; Singh, LN; Mullikin, JC; Biesecker, LG; Genome Med, DOI://10.1186/s13073-016-0336-6 (2016)
Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method König, G; Mei, Y; Pickard, FC et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.5b00874 (2016)
Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G>A) in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion Sorber, R; Teper, Y; Abisoye-Ogunniyan, A et al. PLoS ONE, DOI://10.1371/journal.pone.0149833 (2016)
Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data Shi, J; Park, JH; Duan, J et al. PLoS Genet., DOI://10.1371/journal.pgen.1006493 (2016)
Block network mapping approach to quantitative trait locus analysis Shreif, ZZ; Gatti, DM; Periwal, V; BMC Bioinformatics, DOI://10.1186/s12859-016-1351-8 (2016)
Lineage-Specific and Non-specific Cytokine-Sensing Genes Respond Differentially to the Master Regulator STAT5 Zeng, X; Willi, M; Shin, HY; Hennighausen, L; Wang, C; Cell Rep, DOI://10.1016/j.celrep.2016.11.079 (2016)
Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models Chiu, CY; Jung, J; Chen, W et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2016.170 (2016)
Towards understanding the structural basis of partial agonism at the dopamine D3 receptor Michino, M; Boateng, CA; Donthamsetti, P et al. J. Med. Chem., DOI://10.1021/acs.jmedchem.6b01148 (2016)
Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data Holzinger, ER; Szymczak, S; Malley, J et al. BMC Proc, DOI://10.1186/s12919-016-0021-1 (2016)
From 20th Century Metabolic Wall Charts to 21st Century Systems Biology: Database of Mammalian Metabolic Enzymes Corcoran, CC; Grady, CR; Pisitkun, T; Parulekar, J; Knepper, MA; Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00601.2016 (2016)
Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions Venable, RM; Ingólfsson, HI; Lerner, MG et al. J Phys Chem B, DOI://10.1021/acs.jpcb.6b09111 (2016)

DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases Ligthart, S; Marzi, C; Aslibekyan, S et al. Genome Biol., DOI://10.1186/s13059-016-1119-5 (2016)
Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT2B/5HT2C Serotonin Receptor Antagonists Tosh, DK; Ciancetta, A; Warnick, E; Crane, S; Gao, ZG; Jacobson, KA; J. Med. Chem., DOI://10.1021/acs.jmedchem.6b01183 (2016)
Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications Ombrello, MJ; Arthur, VL; Remmers, EF et al. Ann. Rheum. Dis., DOI://10.1136/annrheumdis-2016-210324 (2016)
Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids He, S; Chandler, M; Varani, AM; Hickman, AB; Dekker, JP; Dyda, F; MBio, DOI://10.1128/mBio.01987-16 (2016)
Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study Shi, J; Hua, X; Zhu, B et al. PLoS Med., DOI://10.1371/journal.pmed.1002162 (2016)
Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer Winter, JM; Gildea, DE; Andreas, JP et al. Cell Syst, DOI://10.1016/j.cels.2016.10.018 (2016)

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Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain Tang WK, Xia D Sci Rep, DOI://10.1038/srep20037 (2016)
Epigenetic regulation of hematopoiesis by DNA methylation Gore, AV; Athans, B; Iben, JR et al. Elife, DOI://10.7554/eLife.11813 (2016)

The TRAIL receptor agonist drozitumab targets basal B triple-negative breast cancer cells that express vimentin and Axl Dine, JL; O'Sullivan, CC; Voeller, D et al. Breast Cancer Res. Treat., DOI://10.1007/s10549-015-3673-z (2016)
Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7 Faraji, F; Hu, Y; Yang, HH et al. PLoS Genet., DOI://10.1371/journal.pgen.1005820 (2016)
Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study Liping Hou, Urs Heilbronner et al. Lancet, doi:10.1016/S0140-6736(16)00143-4 (2016)
Autosomal-Recessive Hearing Impairment due to Rare Missense Variants within S1PR2 Regie Lyn P. Santos-Cortez, Rabia Faridi, Atteeq U. Rehman et al. American Journal of Human Genetics, doi://10.1016/j.ajhg.2015.12.004 (2016)
Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool Thomas Hoenen, Allison Groseth, Kyle Rosenke et al. Emerging Infectious Diseases, doi: 10.3201/eid2202.151796. (2016)
Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment Zhong, C; Cui, K; Wilhelm, C et al. Nat. Immunol., DOI://10.1038/ni.3318 (2016)

Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy Sukumar, M; Liu, J; Mehta, GU et al. Cell Metab., DOI://10.1016/j.cmet.2015.11.002 (2016)
Reliability of 7T (1) H-MRS measured human prefrontal cortex glutamate, glutamine, and glutathione signals using an adapted echo time optimized PRESS sequence: A between- and within-sessions investigation Lally, N; An, L; Banerjee, D et al. J Magn Reson Imaging, DOI://10.1002/jmri.24970 (2016)
A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration de Vries, PS; Chasman, DI; Sabater-Lleal, M et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddv454 (2016)
PubChem Substance and Compound databases Kim, S; Thiessen, PA; Bolton, EE et al. Nucleic Acids Res., DOI://10.1093/nar/gkv951 (2016)
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes Lorenzi, H; Khan, A; Behnke, MS et al. Nat Commun, DOI://10.1038/ncomms10147 (2016)
SBR-Blood: systems biology repository for hematopoietic cells Lichtenberg, J; Heuston, EF; Mishra, T; Keller, CA; Hardison, RC; Bodine, DM; Nucleic Acids Res., DOI://10.1093/nar/gkv1263 (2016)

GABBR1 and SLC6A1, Two Genes Involved in Modulation of GABA Synaptic Transmission, Influence Risk for Alcoholism: Results from Three Ethnically Diverse Populations Enoch, MA; Hodgkinson, CA; Shen, PH et al. Alcohol. Clin. Exp. Res., DOI://10.1111/acer.12929 (2016)
SDHB-Deficient Cancers: The Role of Mutations That Impair Iron Sulfur Cluster Delivery Saxena, N; Maio, N; Crooks, DR et al. J. Natl. Cancer Inst., DOI://10.1093/jnci/djv287 (2016)
Evolutionary Dynamics of Influenza A Viruses in US Exhibition Swine Nelson, MI; Wentworth, DE; Das, SR et al. J. Infect. Dis., DOI://10.1093/infdis/jiv399 (2016)

2015 (317 papers)

Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences Hoenen, T; Safronetz, D; Groseth, A et al. Science, DOI://10.1126/science.aaa5646 (2015)
RNA sequencing of the nephron transcriptome: a technical note Lee, JW Kidney Res Clin Pract, DOI://10.1016/j.krcp.2015.08.008 (2015)
miR-501-3p mediates the activity-dependent regulation of the expression of AMPA receptor subunit GluA1 Hu, Z; Zhao, J; Hu, T; Luo, Y; Zhu, J; Li, Z; J. Cell Biol., DOI://10.1083/jcb.201404092 (2015)

Bayesian dose-response analysis for epidemiological studies with complex uncertainty in dose estimation Deukwoo Kwon, F. Owen Hoffman, Brian E. Moroz, Steven L. Simon Statistics in Medicine, DOI: 10.1002/sim.6635 (2015)
Augmented trial designs for evaluation of principal surrogates Erin E. Gabriel and Dean Follmann Biostatistics, 10.1093/biostatistics/kxv055 (2015)
Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly Datta, SA; Clark, PK; Fan, L et al. J. Virol., DOI://10.1128/JVI.02061-15 (2015)
Multivariate classification of smokers and nonsmokers using SVM-RFE on structural MRI images Ding X, Yang Y, Stein EA, Ross TJ Hum Brain Mapp, DOI://10.1002/hbm.22956 (2015)
The higher level of complexity of K-Ras4B activation at the membrane Hyunbum Jang, Avik Banerjee, Tanmay S. Chavan, Shaoyong Lu, Jian Zhang, Vadim Gaponenko and Ruth Nussinov FASEB J. , doi: 10.1096/fj.15-279091 (2015)
Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness Shyh-Ching Lo, Guo-Chiuan Hung, Bing jie Li, Haiyan Lei, Tianwei Li, Kenjiro Nagamine, Shien Tsai, Mark J Zucker, Ludmilla Olesnicky Int J Clin Exp Patho, 8(11), 13834-13852. (2015)

Meta-analysis of Complex Diseases at Gene Level by Generalized Functional Linear Models Ruzong Fan, Yifan Wang, Chi-yang Chiu, Wei Chen, Haobo Ren, Yun Li, Michael Boehnke, Christopher I. Amos, Jason H. Moore, Momiao Xiong Genetics, DOI: 10.1534/genetics.115.180869 (2015)
TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing Ryan J Marina, David Sturgill, Marc A Bailly, Morgan Thenoz, Garima Varma, Maria F Prigge, Kyster K Nanan, Sanjeev Shukla, Nazmul Haque, Shalini Oberdoerffer EMBO J., DOI 10.15252/embj.201593235 (2015)
RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification Arimbasseri, AG; Blewett, NH; Iben, JR et al. PLoS Genet., DOI://10.1371/journal.pgen.1005671 (2015)
Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design Jason Gorman, Cinque Soto, Max M Yang, et al. Nature Structural and Molecular Biology, doi:10.1038/nsmb.3144 (2015)
ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo Allissa A. Dillman, Mark R. Cookson & Dagmar Galter RNA Biology, DOI://10.1080/15476286.2015.1110675 (2015)
Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability Jeongkyu Kim, David Sturgill, Andy D. Tran, David A. Sinclair and Philipp Oberdoerffer Nucleic Acids Research, doi: 10.1093/nar/gkv1482 (2015)

Distributed acoustic cues for caller identity in macaque vocalization Makoto Fukushima, Alex M. Doyle, Matthew P. Mullarkey, Mortimer Mishkin, Bruno B. Averbeck Royal Society Open Science, DOI: 10.1098/rsos.150432 (2015)
Socioeconomic disadvantage and neural development from infancy through early childhood Chin-Lun Hung, G; Hahn, J; Alamiri, B et al. Int J Epidemiol, DOI://10.1093/ije/dyv303 (2015)
Directed and persistent movement arises from mechanochemistry of the ParA/ParB system Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1505147112 (2015)
Assessment of established HDL-C loci for association with HDL-C levels and type 2 diabetes in Pima Indians Anup K. Nair, Paolo Piaggi, Nellie A. McLean, Manmeet Kaur, Sayuko Kobes, William C. Knowler, Clifton Bogardus, Robert L. Hanson, Leslie J. Baier Diabetologia, doi://10.1007/s00125-015-3835-x (2015)
Genome-wide association study identifies African-ancestry specific variants for metabolic syndrome Tekola-Ayele, F; Doumatey, AP; Shriner, D et al. Mol. Genet. Metab., DOI://10.1016/j.ymgme.2015.10.008 (2015)
Evolutionary context for the association of γ-globin, serum uric acid, and hypertension in African Americans Shriner, D; Kumkhaek, C; Doumatey, AP et al. BMC Med. Genet., DOI://10.1186/s12881-015-0249-z (2015)

High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site Tanmay S. Chavan, Hyunbum Jang, Lyuba Khavrutskii, Sherwin J. Abraham, Avik Banerjee, Benjamin C. Freed, Liv Johannessen, Sergey G. Tarasov, Vadim Gaponenko, Ruth Nussinov4, Nadya I. Tarasova Biophys. J. , doi:10.1016/j.bpj.2015.09.034 (2015)
Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions Alexey K. Shaytan, Grigoriy A. Armeev, Alexander Goncearenco, Victor B. Zhurkin, David Landsman, Anna R. Panchenko J. Mol. Biol., doi:10.1016/j.jmb.2015.12.004 (2015)
Drug-Protein Hydrogen Bonds Govern the Inhibition of the ATP Hydrolysis of the Multidrug Transporter P-glycoprotein Eduardo E. Chufan, Khyati Kapoor, Suresh V. Ambudkar Biochemical Pharmacology, doi:10.1016/j.bcp.2015.12.007 (2015)
MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma Shile Zhang, Jun S. Wei1 , Samuel Q. Li , Tom C. Badgett , Young K. Song , Saurabh Agarwal , Cristian Coarfa , Catherine Tolman , Laura Hurd , Hongling Liao , Jianbin He , Xinyu Wen , Zhihui Liu , Carol J. Thiele , Frank Westermann , Shahab Asgharzadeh , Robert C. Seeger , John M. Maris , Jamie M. Guidry Auvil , Malcolm A. Smith , Eric D. Kolaczyk , Jason Shohet , Javed Khan Cancer Letters, doi://10.1016/j.canlet.2015.11.045 (2015)
Multi-modal characterization of rapid anterior hippocampal volume increase associated with aerobic exercise Adam G. Thomas, Andrea Dennis, Nancy B. Rawlings, Charlotte J. Stagg, Lucy Matthews, Martyn Morris, Shannon H. Kolind, Sean Foxley, Mark Jenkinson, Thomas E. Nichols, Helen Dawes, Peter A. Bandettini, Heidi Johansen-Berg NeuroImage, doi:10.1016/j.neuroimage.2015.10.090 (2015)
Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal Liang Xu , Ruth Nussinov and Buyong Ma Chem. Commun., DOI: 10.1039/C5CC08107F (2015)

Intrinsic excitability measures track antiepileptic drug action and uncover increasing/decreasing excitability over the wake/sleep cycle Christian Meisel, Andreas Schulze-Bonhage, Dean Freestone, Mark James Cook, Peter Achermann, Dietmar Plenz PNAS, doi: 10.1073/pnas.1513716112 (2015)
Transcriptional and Chromatin Regulation during Fasting - The Genomic Era Goldstein I, Hager GL Trends Endocrinol. Metab., DOI://10.1016/j.tem.2015.09.005 (2015)
Evaluation of Genome Wide Association Study Associated Type 2 Diabetes Susceptibility Loci in Sub Saharan Africans Adeyemo, AA; Tekola-Ayele, F; Doumatey, AP et al. Front Genet, DOI://10.3389/fgene.2015.00335 (2015)
Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006 Rocío M. Gamez, Fernando Rodríguez, Johan F. Bernal, Richa Agarwala, David Landsman, Leonardo Mariño-Ramírez Genome Announc., doi: 10.1128/genomeA.01391-15 (2015)
HIV Therapeutics and Methods of Making and Using Same Paolo Lusso and Raffaelo Cimbro Patent, United States Patent Application 20150313990 (2015)
NCICT: a computational solution to estimate organ doses for pediatric and adult patients undergoing CT scans Choonsik Lee, Kwang Pyo Kim, Wesley E Bolch, Brian E Moroz and Les Folio J. Radiological Protection, doi:10.1088/0952-4746/35/4/891 (2015)

Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion Wenwei Zheng and Robert B. Best J. Phys. Chem. , DOI: 10.1021/acs.jpcb.5b09741 (2015)
Transient misfolding dominates multidomain protein folding Alessandro Borgia, Katherine R. Kemplen, Madeleine B. Borgia, Andrea Soranno, Sarah Shammas, Bengt Wunderlich, Daniel Nettels, Robert B. Best, Jane Clarke & Benjamin Schuler Nature Communications, doi:10.1038/ncomms9861 (2015)
Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data Praveen F. Cherukuri, Valerie Maduro, Karin V. Fuentes-Fajardo, Kevin Lam, David R. Adams, Cynthia J. Tifft, James C. Mullikin, William A. Gahl, Cornelius F. Boerkoel and NISC Comparative Sequencing Program BMC Genomics, doi:10.1186/s12864-015-2107-y (2015)
HLA-DRB1*11 and variants of the MHC class II locus are strong risk factors for systemic juvenile idiopathic arthritis Michael J. Ombrello, Elaine F. Remmers, Ioanna Tachmazidou et al and the International Childhood Arthritis Genetics (INCHARGE) Consortium PNAS, doi: 10.1073/pnas.1520779112 (2015)
Estimation of interaction effects using pooled biospecimens in a case-control study Michelle R. Danaher, Paul S. Albert, Aninyda Roy and Enrique F. Schisterman Statistics in Medicine, DOI: 10.1002/sim.6798 (2015)
Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations Lei H, Li T, Li B, Tsai S, Biggar RJ, Nkrumah F, Neequaye J, Gutierrez M, Epelman S, Mbulaiteye SM, Bhatia K, Lo SC Sci Rep., doi: 10.1038/srep16706 (2015)

A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies Gregory D. Marquart, Kathryn M. Tabor, Mary Brown, Jennifer L. Strykowski, Gaurav K. Varshney, Matthew C. LaFave, Thomas Mueller, Shawn M. Burgess, Shin-ichi Higashijima and Harold A. Burgess Frontiers in Neural Circuits, doi://10.3389/fncir.2015.00078 (2015)
GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site Lu S, Banerjee A, Jang H, Zhang J, Gaponenko V, Nussinov R J. Biol. Chem., DOI://10.1074/jbc.M115.664755 (2015)
A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR Sgourakis NG, May NA, Boyd LF, Ying J, Bax A, Margulies DH J. Biol. Chem., DOI://10.1074/jbc.M115.689661 (2015)
Epidermal devices for noninvasive, precise, and continuous mapping of macrovascular and microvascular blood flow Webb, RC; Ma, Y; Krishnan, S et al. Sci Adv, DOI://10.1126/sciadv.1500701 (2015)
Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure Alexandru V. Avram, Joelle E. Sarlls, Alan S. Barnett, Evren Özarslan, Cibu Thomas, M. Okan Irfanoglu, Elizabeth Hutchinson, Carlo Pierpaoli, Peter J. Basser NeuroImage, doi:10.1016/j.neuroimage.2015.11.027 (2015)
Aurora B kinase is a potent and selective target in MYCN-driven neuroblastoma Bogen, D; Wei, JS; Azorsa, DO et al. Oncotarget, DOI://10.18632/oncotarget.6208 (2015)

Phenotypic variance explained by local ancestry in admixed African Americans Shriner, D; Bentley, AR; Doumatey, AP et al. Front Genet, DOI://10.3389/fgene.2015.00324 (2015)
Selectivity in the Use of Gi/o Proteins Is Determined by the DRF Motif in CXCR6 and Is Cell-Type Specific Satya P. Singh, John F. Foley, Hongwei H. Zhang, Darrell E. Hurt, Jennifer L. Richards, Craig S. Smith, Fang Liao, and Joshua M. Farber Molecular Pharmacology, doi: 10.1124/mol.115.099960 (2015)
The Structural Basis of Actin Organization by Vinculin and Metavinculin Laura Y. Kim, Peter M. Thompson, Hyunna T. Lee, Mihir Pershad, Sharon L. Campbell, Gregory M. Alushin J. Mol. Biol. , doi:10.1016/j.jmb.2015.09.031 (2015)
Analysis of SLC16A11 variants in 12,811 American Indians: genotype-obesity interaction for type 2 diabetes and an association with RNASEK expression Michael Traurig, Robert L. Hanson, Alejandra Marinelarena, Sayuko Kobes, Paolo Piaggi, Shelley Cole, Joanne E. Curran, John Blangero, Harald Göring, Satish Kumar, Robert G. Nelson, Barbara V. Howard, William C. Knowler, Leslie J. Baier and Clifton Bogardus Diabetes, doi: 10.2337/db15-0571 (2015)
In Search of a Cure for Proteostasis-Addicted Cancer: A AAA Target Revealed Xia D, Ye Y Cancer Cell, DOI://10.1016/j.ccell.2015.10.006 (2015)
Genome-wide estimate of the heritability of Multiple System Atrophy M. Federoff, T.R. Price, A. Sailer, S. Scholz, D. Hernandez, A. Nicolas, A.B. Singleton, M. Nalls, H. Houlden Parkinsonism and Related Disorders, doi:10.1016/j.parkreldis.2015.11.005 (2015)

Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l Chryssa Kanellopoulou, Timothy Gilpatrick, Gokhul Kilaru, Patrick Burr, Cuong K. Nguyen, Aaron Morawski, Michael J. Lenardo, Stefan A. Muljo Stem Cell Reports, doi:10.1016/j.stemcr.2015.10.001 (2015)
Resting-state functional connectivity and presynaptic monoamine signaling in Alcohol Dependence Zhu X, Dutta N, Helton SG, Schwandt M, Yan J, Hodgkinson CA, Cortes CR, Kerich M, Hall S, Sun H, Phillips M, Momenan R, Lohoff FW Hum Brain Mapp., doi: 10.1002/hbm.22951 (2015)
Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein Zhu, Y; Yang, S; Qi, R et al. J Phys Chem B, DOI://10.1021/acs.jpcb.5b07962 (2015)
ColoWeb: a resource for analysis of colocalization of genomic features Kim R, Smith OK, Wong WC, Ryan AM, Ryan MC, Aladjem MI BMC genomics, doi: 10.1186/s12864-015-1345-3. (2015)
Methylated cytosines mutate to transcription factor binding sites that drive tetrapod evolution Ximiao He, Desiree Tillo, Jeff Vierstra, Khund-Sayeed Syed, Callie Deng, Jordan G. Ray, John Stamatoyannopoulos, Peter C. Fitzgerald and Charles Vinson Genome Biol. and Evol. , doi: 10.1093/gbe/evv205 (2015)
Sequence-and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations Gül H. Zerze, Robert B Best, and Jeetain Mittal J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.5b08619 (2015)

Proteomic Profiling of Nuclear Fractions from Native Renal Inner Medullary Collecting Duct Cells Christina M. Pickering, Cameron R. Grady, Barbara Medvar, Milad Emamian, Pablo Concha Sandoval, Yue Zhao, Chin-Rang Yang, Hyun Jun Jung, Chung-Lin Chou, Mark A. Knepper Physiol Genomics., DOI: 10.1152/physiolgenomics.00090.2015 (2015)
Structure dependent hydrophobic and hydrophilic interactions between nickel(II) Schiff base complexes and serum albumins: Spectroscopic and docking studies Banabithi Koley Seth, Aurkie Ray, Mousumi Banerjee, Teerna Bhattacharyya, Dhananjay Bhattacharyya, Samita Basu J. Luminescence, doi:10.1016/j.jlumin.2015.11.009 (2015)
Integrated genome-wide analysis of genomic changes and gene regulation in human adrenocortical tissue samples Gara, SK; Wang, Y; Patel, D et al. Nucleic Acids Res., DOI://10.1093/nar/gkv908 (2015)
An insight into the sialome of the horse fly, Tabanus bromius Ribeiro JM, Kazimirova M, Takac P, Andersen JF, Francischetti IM Insect Biochem. Mol. Biol., DOI://10.1016/j.ibmb.2015.09.002 (2015)
TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney Saskia L. Gooskens, Samantha Gadd, Jaime M. Guidry Auvil, Daniela S. Gerhard, Javed Khan, Rajesh Patidar, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Charles G. Mullighan, Jing Ma, Lawrence J. Jennings, Ronald R. de Krijger, Marry M. van den Heuvel-Eibrink, Malcolm A. Smith, Nicole Ross, Julie M. Gastier-Foster, Elizabeth J. Perlman Oncotarget 6(18):15828-15841 (2015)
Molecular mechanisms in genetically defined autoinflammatory diseases: disorders of amplified danger signaling de Jesus AA, Canna SW, Liu Y, Goldbach-Mansky R. Annu Rev Immunol., doi: 10.1146/annurev-immunol-032414-112227 (2015)

Functional connectivity classification of autism identifies highly predictive brain features but falls short of biomarker standards Plitt M, Barnes KA, Martin A Neuroimage Clin., doi: 10.1016/j.nicl.2014.12.013. (2015)
Effects of the Mu opioid receptor polymorphism (OPRM1 A118G) on pain regulation, placebo effects and associated personality trait measures Peciña M, Love T, Stohler CS, Goldman D, Zubieta JK Neuropsychopharmacology, doi: 10.1038/npp.2014.272 (2015)
Calculation of Organ Doses for a Large Number of Patients Undergoing CT Examinations Amir Bahadori, Diana Miglioretti, Randell Kruger, Michael Flynn, Sheila Weinmann, Rebecca Smith-Bindman and Choonsik Lee Medical Physics and Informatics, DOI:10.2214/AJR.14.14135 (2015)
Survival of human lymphoma cells requires B-cell receptor engagement by self-antigens Ryan M. Young, Tianyi Wu, Roland Schmitz, Moez Dawood, Wenming Xiao, James D. Phelan, Weihong Xu, Laurence Menard, Eric Meffre, Wing-Chung C. Chan, Elaine S. Jaffe, Randy D. Gascoyne, Elìas Campo, Andreas Rosenwald, German Ott, Jan Delabie, Lisa M. Rimsza, and Louis M. Staudt PNAS, doi: 10.1073/pnas.1514944112 (2015)
Shifts in connectivity during procedural learning after motor cortex stimulation; a combined transcranial magnetic stimulation /functional magnetic resonance imaging study Adam Steel, Sunbin Song, Devin Bageac, Kristine M. Knutson, Ziad S. Saad, Stephen J. Gotts, Eric M. Wassermann, Leonora Wilkinson Cortex, doi:10.1016/j.cortex.2015.10.004 (2015)
Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain Pilar Donado-Godoy, Johan F. Bernal, Fernando Rodrìguez, Yolanda Gomez, Richa Agarwala, David Landsman, Leonardo Mariño-Ramìrez Genome Announc., doi: 10.1128/genomeA.01265-15 (2015)

The transcriptional landscape of age in human peripheral blood Peters, MJ; Joehanes, R; Pilling, LC et al. Nat Commun, DOI://10.1038/ncomms9570 (2015)
Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations Wenwei Zheng, Alessandro Borgia, Madeleine B. Borgia, Benjamin Schuler, and Robert B. Best J. Chem. Theory and Computation, DOI: 10.1021/acs.jctc.5b00778 (2015)
Characterization of the metastatic phenotype of a panel of established osteosarcoma cells Ren, L; Mendoza, A; Zhu, J et al. Oncotarget, DOI://10.18632/oncotarget.5177 (2015)
Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels Hyunbum Jang, Fernando Teran Arce, Joon Lee, Alan L. Gillman, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal, Ruth Nussinov Protein Amyloid Aggregation, doi://10.1007/978-1-4939-2978-8-16 (2015)
Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear Burns JC, Kelly MC, Hoa M, Morell RJ, Kelley MW Nature Communications, doi: 10.1038/ncomms9557. (2015)
Interleaved Text/Image Deep Mining on a Large-Scale Radiology Database for Automated Image Interpretation Hoo-Chang Shin, Le Lu, Lauren Kim, Ari Seff, Jianhua Yao, Ronald M. Summers IEEE CVPR , p. 1090-1099 (2015)

Longitudinal clinical trials with adaptive choice of follow-up time Jeffries N, Geller NL Biometrics, doi: 10.1111/biom.12287. E (2015)
Effects of Neural Morphology and Input Distribution on Synaptic Processing by Global and Focal NMDA-Spikes Poleg-Polsky, A PLoS ONE, DOI://10.1371/journal.pone.0140254 (2015)
Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks Morgun, A; Dzutsev, A; Dong, X et al. Gut, DOI://10.1136/gutjnl-2014-308820 (2015)
MST2-RASSF protein-protein interactions through SARAH domains Goar Sànchez-Sanz, David Matallanas, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch and Nicolae-Viorel Buchete Briefings in Bioinformatics, doi://10.1093/bib/bbv070 (2015)
Subassemblies and asymmetry in assembly of herpes simplex virus procapsid Aksyuk, AA; Newcomb, WW; Cheng, N et al. MBio, DOI://10.1128/mBio.01525-15 (2015)
GNL3 and SKA3 are novel prostate cancer metastasis susceptibility genes Minnkyong Lee, Kendra A. Williams, Ying Hu, Jonathan Andreas, Shashank J. Patel, Suiyuan Zhang, Nigel P. S. Crawford Clin Exp Metastasis, DOI 10.1007/s10585-015-9745-y (2015)

Putative Prostate Cancer Risk SNP in an Androgen Receptor-Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites Huajie Bu, Narisu Narisu, Bettina Schlick, Johannes Rainer, Thomas Manke, Georg Schäfer, Lorenza Pasqualini, Peter Chines, Michal R. Schweiger, Christian Fuchsberger and Helmut Klocker Human Mutation, DOI: 10.1002/humu.22909 (2015)
Asymmetric Action of STAT Transcription Factors Drives Transcriptional Outputs and Cytokine Specificity Hirahara K, Onodera A, Villarino AV, Bonelli M, Sciumè G, Laurence A3 Sun HW, Brooks SR, Vahedi, Shih HY, Gutierrez-Cruz, Iwata S, Suzuki, Mikami Y, Okamoto Y, Nakayama T, Holland SM, Hunter CA, Kanno Y, O'Shea JJ Immunity, doi: 10.1016/j.immuni.2015.04.014. (2015)
Efficient test for nonlinear dependence of two continuous variables Wang Y, Li Y, Cao H, Xiong M, Shugart YY, Jin L BMC Bioinformatics, doi: 10.1186/s12859-015-0697-7 (2015)
Whole-genome association analysis of treatment response in obsessive-compulsive disorder Qin H, Samuels JF, Wang Y et al. Mol. Psychiatr., doi: 10.1038/mp.2015.32 (2015)
The CENP-A N-tail confers epigenetic stability to centromeres via the CENP-T branch of the CCAN in fission yeast Folco HD, Campbell CS, May KM, Espinoza C, Oegema K, Hardwick KG, Grewal SI, Desai A Curr. Biology, doi: 10.1016/j.cub.2014.11.060 (2015)
Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing Manes, NP; Angermann, BR; Koppenol-Raab, M et al. Mol. Cell Proteomics, DOI://10.1074/mcp.M115.048918 (2015)

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster Razvan V. Chereji, Tsung-Wai Kan, Magda K. Grudniewska, Alexander V. Romashchenko, Eugene Berezikov, Igor F. Zhimulev, Victor Guryev, Alexandre V. Morozov and Yuri M. Moshkin Nucleic Acids Research, doi: 10.1093/nar/gkv978 (2015)
Deep Proteomic Profiling of Vasopressin-Sensitive Collecting Duct Cells. II. Bioinformatic Analysis of Vasopressin Signaling Chin-Rang Yang, Viswanathan Raghuram, Milad Emamian, Pablo Concha Sandoval, Mark A. Knepper Am. J. Physiol. - Cell Physiol. , DOI: 10.1152/ajpcell.00214.2015 (2015)
Exposure of chick embryos to cadmium changes the extra-embryonic vascular branching pattern and alters expression of VEGF-A and VEGF-R2 Anna Kaskova Gheorghescu, Bartlomiej Tywoniuk, Johannes Duess, Nicolae-Viorel Buchete, Jennifer Thompson Toxicology & Applied Pharmacology, doi://10.1016/j.taap.2015.09.004 (2015)
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Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells Golnaz Vahedi, Yuka Kanno, Yasuko Furumoto, Kan Jiang, Stephen C. J. Parker, Michael R. Erdos, Sean R. Davis, Rahul Roychoudhuri, Nicholas P. Restifo, Massimo Gadina, Zhonghui Tang, Yijun Ruan, Francis S. Collins, Vittorio Sartorelli & John J. O'Shea Nature, doi:10.1038/nature14154 (2015)
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD. Fetics SK, Guterres H, Kearney BM, Buhrman G, Ma B, Nussinov R, Mattos C Structure, doi: 10.1016/j.str.2014.12.017 (2015)
Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL Genome Res. , doi: 10.1101/gr.184168.114 (2015)

Role of contingency in striatal response to incentive in adolescents with anxiety Benson BE, Guyer AE, Nelson EE, Pine DS, Ernst M Cogn Affect Behav Neurosci, DOI://10.3758/s13415-014-0307-6 (2015)
The NAD(+)-dependent SIRT1 deacetylase translates a metabolic switch into regulatory epigenetics in skeletal muscle stem cells Ryall, JG; Dell'Orso, S; Derfoul, A et al. Cell Stem Cell, DOI://10.1016/j.stem.2014.12.004 (2015)
Efficient Data Mining for Local Binary Pattern in Texture Image Analysis Jin Tae Kwak, , Sheng Xu , Bradford J. Wood Expert Systems with Applications, doi:10.1016/j.eswa.2015.01.055 (2015)
What's Next for Next-Gen Sequencing? MaryAnn Labant Genetic Engineering and Biotechnology News, doi:10.1089/gen.35.03.02. (2015)
Transcriptional profiles reveal a stepwise developmental program of memory CD8(+) T cell differentiation Roychoudhuri, R; Lefebvre, F; Honda, M et al. Vaccine, DOI://10.1016/j.vaccine.2014.10.007 (2015)
Myosin II controls cellular branching morphogenesis and migration in three dimensions by minimizing cell-surface curvature Elliott, H; Fischer, RS; Myers, KA et al. Nat. Cell Biol., DOI://10.1038/ncb3092 (2015)

Optimizing the order of hypotheses in serial testing of multiple endpoints in clinical trials. Zhang Z, Wang C, Troendle JF. Stat. Med., doi: 10.1002/sim.6425. (2015)
CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells Rajbir K Athwal, Marcin P Walkiewicz, Songjoon Baek, Song Fu, Minh Bui, Jordi Camps, Thomas Ried, Myong-Hee Sung and Yamini Dalal Epigenetics and Chromatin, doi:10.1186/1756-8935-8-2 (2015)
Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach Robert Send , Carl-Mikael Suomivuori , Ville R. I. Kaila , and Dage Sundholm J. Phys. Chem. B, DOI: 10.1021/jp5120898 (2015)
Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma Shakhova, O; Cheng, P; Mishra, PJ et al. PLoS Genet., DOI://10.1371/journal.pgen.1004877 (2015)
Withdrawal from long-term methamphetamine self-administration 'normalizes' neurometabolites in rhesus monkeys: a (1) H MR spectroscopy study Yang S, Belcher AM, Chefer S, Vaupel DB, Schindler CW, Stein EA, Yang Y. Addict Biol., doi: 10.1111/adb.12078. (2015)
Molecular basis of the polyspecificity of P-glycoprotein (ABCB1): recent biochemical and structural studies Chufan EE, Sim HM, Ambudkar SV Adv Cancer Res, doi: 10.1016/bs.acr.2014.10.003 (2015)

fMRI functional connectivity applied to adolescent neurodevelopment Ernst M, Torrisi S, Balderston N, Grillon C, Hale EA. Annu Rev Clin Psychol., doi: 10.1146/annurev-clinpsy-032814-112753 (2015)
A systematic heritability analysis of the human whole blood transcriptome. Huan T, Liu C, Joehanes R, Zhang X, Chen BH, Johnson AD, Yao C, Courchesne P, O'Donnell CJ, Munson PJ, Levy D. Human Genetics (2015)
Detecting Functional Connectivity during Audiovisual Integration with MEG: a Comparison of Connectivity Metrics. Ard TD, Carver F, Holroyd T, Horwitz B, Coppola R. Brain Connect. (2015)
Cerebro-cerebellar connectivity is increased in primary lateral sclerosis Meoded A, Morrissette AE, Katipally R, Schanz O, Gotts SJ, Floeter MK Neuroimage Clin, DOI://10.1016/j.nicl.2014.12.009 (2015)
Functional mapping of face-selective regions in the extrastriate visual cortex of the marmoset Hung, CC; Yen, CC; Ciuchta, JL et al. J. Neurosci., DOI://10.1523/JNEUROSCI.2659-14.2015 (2015)
Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups. Tofoleanu F, Brooks BR, Buchete NV. ACS Chem Neurosci., doi://abs/10.1021/cn500277f (2015)

Insights into the Mechanism of Inhibition of CXCR4: Identification of Piperidinylethanamine Analogs as Anti-HIV-1 Inhibitors Das D, Maeda K, Hayashi Y, Gavande N, Desai DV, Chang SB, Ghosh AK, Mitsuya H Antimicrob Agents Chemother., pii: AAC.04654-14. (2015)
Variable selection method for the identification of epistatic models Holzinger ER, Szymczak S, Dasgupta A, Malley J, Li Q, Bailey-Wilson JE Pac Symp Biocomput, 2335-6936 (2015)
CDD: NCBI's conserved domain database Marchler-Bauer, A; Derbyshire, MK; Gonzales, NR et al. Nucleic Acids Res., DOI://10.1093/nar/gku1221 (2015)
NRG1, ERBB4 and AKT1 Epistasis Increases Schizophrenia Risk and is Biologically Validated via Functional Neuroimaging in Healthy Controls Nicodemus KK, Law AJ, Radulescu E, Luna A, Kolachana B, Vakkalanka R, Rujescu D, Giegling I, Straub RE, McGee K, Gold B, Dean M, Muglia P, Callicott JH, Tan HY, Weinberger DR. Arch Gen Psychiatry, doi: 10.1001/archgenpsychiatry.2010.117 (2015)
Maturation of the HIV-1 core by a non-diffusional phase transition Frank GA, Narayan K, Bess JW Jr, Del Prete GQ, Wu X, Moran A, Hartnell LM, Earl LA, Lifson JD, Subramaniam S Nature Communications, doi: 10.1038/ncomms6854 (2015)
Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension Xiaofeng Zhu, Tao Feng, Bamidele O. Tayo et al. Am J Hum Genet., doi: 10.1016/j.ajhg.2014.11.011. (2015)

Protein structural information derived from NMR chemical shift with the neural network program TALOS-N Shen Y, Bax A Methods Mol. Biol., DOI://10.1007/978-1-4939-2239-0_2 (2015)
BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O'Shea JJ, Ozato K Nat Struct Mol Biol., doi: 10.1038/nsmb.2912 (2015)

2014 (267 papers)

Teneurin-4 promotes cellular protrusion formation and neurite outgrowth through focal adhesion kinase signaling Suzuki, N; Numakawa, T; Chou, J et al. FASEB J., DOI://10.1096/fj.13-241034 (2014)
Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure Guertin, MJ; Zhang, X; Anguish, L et al. PLoS Genet., DOI://10.1371/journal.pgen.1004613 (2014)
Loss of signalling via Gα13 in germinal centre B-cell-derived lymphoma Muppidi, JR; Schmitz, R; Green, JA et al. Nature, DOI://10.1038/nature13765 (2014)
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences Chuang, GY; Liou, D; Kwong, PD; Georgiev, IS; Nucleic Acids Res., DOI://10.1093/nar/gku318 (2014)

Structural basis of resistance to anti-cytochrome bc₁ complex inhibitors: implication for drug improvement Esser, L; Yu, CA; Xia, D; Curr. Pharm. Des., DOI://10.2174/138161282005140214163327 (2014)
Concurrent alterations in TERT, KDM6A, and the BRCA pathway in bladder cancer Nickerson, ML; Dancik, GM; Im, KM et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-14-0330 (2014)
Ciliopathy-associated gene Cc2d2a promotes assembly of subdistal appendages on the mother centriole during cilia biogenesis Veleri, S; Manjunath, SH; Fariss, RN et al. Nat Commun, DOI://10.1038/ncomms5207 (2014)
A new approach to radial basis function approximation and its application to QSAR Zakharov, AV; Peach, ML; Sitzmann, M; Nicklaus, MC; J Chem Inf Model, DOI://10.1021/ci400704f (2014)
Applications of multivariate modeling to neuroimaging group analysis: a comprehensive alternative to univariate general linear model Chen, G; Adleman, NE; Saad, ZS; Leibenluft, E; Cox, RW; Neuroimage, DOI://10.1016/j.neuroimage.2014.06.027 (2014)
An electrocorticographic electrode array for simultaneous recording from medial, lateral, and intrasulcal surface of the cortex in macaque monkeys Fukushima, M; Saunders, RC; Mullarkey, M; Doyle, AM; Mishkin, M; Fujii, N; J. Neurosci. Methods, DOI://10.1016/j.jneumeth.2014.06.022 (2014)
Towards a mechanistic understanding of pathological anxiety: the dorsal medial prefrontal-amygdala 'aversive amplification' circuit in unmedicated generalized and social anxiety disorders Robinson, OJ; Krimsky, M; Lieberman, L; Allen, P; Vytal, K; Grillon, C; Lancet Psychiatry, DOI://10.1016/S2215-0366(14)70305-0 (2014)
Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen Gladney, LM; Katz, LS; Knipe, KM et al. Genome Announc, DOI://10.1128/genomeA.01188-14 (2014)
Perlecan is required for FGF-2 signaling in the neural stem cell niche Kerever, A; Mercier, F; Nonaka, R et al. Stem Cell Res, DOI://10.1016/j.scr.2013.12.009 (2014)
Molecular architecture of transcription factor hotspots in early adipogenesis Siersbæk, R; Baek, S; Rabiee, A et al. Cell Rep, DOI://10.1016/j.celrep.2014.04.043 (2014)
A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors Petrini, I; Meltzer, PS; Kim, IK et al. Nat. Genet., DOI://10.1038/ng.3016 (2014)
Clonal tracking of rhesus macaque hematopoiesis highlights a distinct lineage origin for natural killer cells Wu, C; Li, B; Lu, R et al. Cell Stem Cell, DOI://10.1016/j.stem.2014.01.020 (2014)
Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions Morris, SA; Baek, S; Sung, MH et al. Nat. Struct. Mol. Biol., DOI://10.1038/nsmb.2718 (2014)
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae Conlan, S; Thomas, PJ; Deming, C et al. Sci Transl Med, DOI://10.1126/scitranslmed.3009845 (2014)
Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function Tang, W; Kowgier, M; Loth, DW et al. PLoS ONE, DOI://10.1371/journal.pone.0100776 (2014)
Role of myelin plasticity in oscillations and synchrony of neuronal activity Pajevic, S; Basser, PJ; Fields, RD; Neuroscience, DOI://10.1016/j.neuroscience.2013.11.007 (2014)
High-resolution traction force microscopy Plotnikov, SV; Sabass, B; Schwarz, US; Waterman, CM; Methods Cell Biol., DOI://10.1016/B978-0-12-420138-5.00020-3 (2014)
Elucidation of the structural basis of interaction of the BCR-ABL kinase inhibitor, nilotinib (Tasigna) with the human ABC drug transporter P-glycoprotein Shukla, S; Chufan, EE; Singh, S et al. Leukemia, DOI://10.1038/leu.2014.21 (2014)

miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression Escobar, TM; Kanellopoulou, C; Kugler, DG et al. Immunity, DOI://10.1016/j.immuni.2014.03.014 (2014)
Transcriptional and epigenetic networks of helper T and innate lymphoid cells Shih, HY; Sciumè, G; Poholek, AC et al. Immunol. Rev., DOI://10.1111/imr.12208 (2014)
High rate of disease-related copy number variations in childhood onset schizophrenia Ahn, K; Gotay, N; Andersen, TM et al. Mol. Psychiatry, DOI://10.1038/mp.2013.59 (2014)
Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 loci Simpson, CL; Wojciechowski, R; Oexle, K et al. PLoS ONE, DOI://10.1371/journal.pone.0107110 (2014)
A C-terminal fragment of fibulin-7 interacts with endothelial cells and inhibits their tube formation in culture de Vega, S; Suzuki, N; Nonaka, R et al. Arch. Biochem. Biophys., DOI://10.1016/j.abb.2014.01.013 (2014)
High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias Waterfall, JJ; Arons, E; Walker, RL et al. Nat. Genet., DOI://10.1038/ng.2828 (2014)

Structure and immune recognition of trimeric pre-fusion HIV-1 Env Pancera, M; Zhou, T; Druz, A et al. Nature, DOI://10.1038/nature13808 (2014)
Synthesis, biological, and biophysical studies of DAG-indololactones designed as selective activators of RasGRP Garcia, LC; Donadío, LG; Mann, E et al. Bioorg. Med. Chem., DOI://10.1016/j.bmc.2014.04.024 (2014)
Neonatal health of infants born to mothers with asthma Mendola, P; Männistö, TI; Leishear, K; Reddy, UM; Chen, Z; Laughon, SK; J. Allergy Clin. Immunol., DOI://10.1016/j.jaci.2013.06.012 (2014)
Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer Qi, R; Luo, Y; Ma, B; Nussinov, R; Wei, G; Biomacromolecules, DOI://10.1021/bm401406e (2014)
Dipeptide analysis of p53 mutations and evolution of p53 family proteins Huang, Q; Yu, L; Levine, AJ; Nussinov, R; Ma, B; Biochim. Biophys. Acta, DOI://10.1016/j.bbapap.2013.04.002 (2014)
Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma Hysi, PG; Cheng, CY; Springelkamp, H et al. Nat. Genet., DOI://10.1038/ng.3087 (2014)
Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy Cui, F; Chen, L; LoVerso, PR; Zhurkin, VB; BMC Bioinformatics, DOI://10.1186/1471-2105-15-313 (2014)
Design and synthesis of human ABCB1 (P-glycoprotein) inhibitors by peptide coupling of diverse chemical scaffolds on carboxyl and amino termini of (S)-valine-derived thiazole amino acid Singh, S; Prasad, NR; Chufan, EE et al. J. Med. Chem., DOI://10.1021/jm401966m (2014)
Building through breaking: the development of cancer neochromosomes Waterfall, JJ; Meltzer, PS; Cancer Cell, DOI://10.1016/j.ccell.2014.10.013 (2014)
Mutant ADA2 in vasculopathies Kastner, DL; Zhou, Q; Aksentijevich, I; N. Engl. J. Med., DOI://10.1056/NEJMc1405506 (2014)
Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes Guertin, MJ; Zhang, X; Coonrod, SA; Hager, GL; Mol. Endocrinol., DOI://10.1210/me.2014-1130 (2014)
RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast Ganguli, D; Chereji, RV; Iben, JR; Cole, HA; Clark, DJ; Genome Res., DOI://10.1101/gr.177014.114 (2014)
Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2-V3 interaction and modulates neutralization sensitivity Cimbro, R; Gallant, TR; Dolan, MA et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1314718111 (2014)
Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest Cui, F; Zhurkin, VB; Nucleic Acids Res., DOI://10.1093/nar/gkt943 (2014)
Mutations of epigenetic regulatory genes are common in thymic carcinomas Wang, Y; Thomas, A; Lau, C et al. Sci Rep, DOI://10.1038/srep07336 (2014)
A closed-loop model of the respiratory system: focus on hypercapnia and active expiration Molkov, YI; Shevtsova, NA; Park, C et al. PLoS ONE, DOI://10.1371/journal.pone.0109894 (2014)
Laminin α1 regulates age-related mesangial cell proliferation and mesangial matrix accumulation through the TGF-β pathway Ning, L; Kurihara, H; de Vega, S et al. Am. J. Pathol., DOI://10.1016/j.ajpath.2014.02.006 (2014)
Family-based tests applied to extended pedigrees identify rare variants related to hypertension Xu, M; Wang, HZ; Guo, W; Qin, H; Shugart, YY; BMC Proc, DOI://10.1186/1753-6561-8-S1-S31 (2014)

Genome sequencing highlights the dynamic early history of dogs Freedman, AH; Gronau, I; Schweizer, RM et al. PLoS Genet., DOI://10.1371/journal.pgen.1004016 (2014)
Independence of familial transmission of mania and depression: results of the NIMH family study of affective spectrum disorders Merikangas, KR; Cui, L; Heaton, L et al. Mol. Psychiatry, DOI://10.1038/mp.2013.116 (2014)
pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3) Yamazaki, F; Kim, HH; Lau, P et al. PLoS ONE, DOI://10.1371/journal.pone.0088217 (2014)
Sex- and age-interacting eQTLs in human complex diseases Yao, C; Joehanes, R; Johnson, AD et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddt582 (2014)
Experimental basis for a new allosteric model for multisubunit proteins Viappiani, C; Abbruzzetti, S; Ronda, L et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1413566111 (2014)
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation Richard, AC; Lyons, PA; Peters, JE et al. BMC Genomics, DOI://10.1186/1471-2164-15-649 (2014)
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation Kidder, BL; Hu, G; Zhao, K; Genome Biol., DOI://10.1186/gb-2014-15-2-r32 (2014)
Genomics of CpG methylation in developing and developed zebrafish McGaughey, DM; Abaan, HO; Miller, RM; Kropp, PA; Brody, LC; G3 (Bethesda), DOI://10.1534/g3.113.009514 (2014)
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes Dowen, JM; Fan, ZP; Hnisz, D et al. Cell, DOI://10.1016/j.cell.2014.09.030 (2014)
The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees Guo, W; Shugart, YY; BMC Genomics, DOI://10.1186/1471-2164-15-632 (2014)
Gain-of-function CCR4 mutations in adult T cell leukemia/lymphoma Nakagawa, M; Schmitz, R; Xiao, W et al. J. Exp. Med., DOI://10.1084/jem.20140987 (2014)
A mouse model of HIES reveals pro- and anti-inflammatory functions of STAT3 Steward-Tharp, SM; Laurence, A; Kanno, Y et al. Blood, DOI://10.1182/blood-2013-09-523167 (2014)
Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes Zhang, X; Johnson, AD; Hendricks, AE et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddt461 (2014)
Sparse representation based biomarker selection for schizophrenia with integrated analysis of fMRI and SNPs Cao, H; Duan, J; Lin, D; Shugart, YY; Calhoun, V; Wang, YP; Neuroimage, DOI://10.1016/j.neuroimage.2014.01.021 (2014)
Transcriptional profiling of Wnt3a mutants identifies Sp transcription factors as essential effectors of the Wnt/β-catenin pathway in neuromesodermal stem cells Dunty, WC; Kennedy, MW; Chalamalasetty, RB; Campbell, K; Yamaguchi, TP; PLoS ONE, DOI://10.1371/journal.pone.0087018 (2014)
Interleukin-1 and interferon-γ orchestrate β-glucan-activated human dendritic cell programming via IκB-ζ modulation Cardone, M; Dzutsev, AK; Li, H et al. PLoS ONE, DOI://10.1371/journal.pone.0114516 (2014)
Dimerization of HIV-1 protease occurs through two steps relating to the mechanism of protease dimerization inhibition by darunavir Hayashi, H; Takamune, N; Nirasawa, T et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1400027111 (2014)
Whole blood gene expression and interleukin-6 levels Lin, H; Joehanes, R; Pilling, LC et al. Genomics, DOI://10.1016/j.ygeno.2014.10.003 (2014)
Single mutations in tau modulate the populations of fibril conformers through seed selection Meyer, V; Dinkel, PD; Luo, Y et al. Angew. Chem. Int. Ed. Engl., DOI://10.1002/anie.201308473 (2014)
Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci Conlan, S; Deming, C; Tsai, YC et al. Genome Announc, DOI://10.1128/genomeA.01332-14 (2014)
Mutations in TBC1D24, a gene associated with epilepsy, also cause nonsyndromic deafness DFNB86 Rehman, AU; Santos-Cortez, RL; Morell, RJ et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2013.12.004 (2014)
Synthesis of a des-B-ring bryostatin analogue leads to an unexpected ring expansion of the bryolactone core Kraft, MB; Poudel, YB; Kedei, N et al. J. Am. Chem. Soc., DOI://10.1021/ja5078188 (2014)
QSAR modeling of imbalanced high-throughput screening data in PubChem Zakharov, AV; Peach, ML; Sitzmann, M; Nicklaus, MC; J Chem Inf Model, DOI://10.1021/ci400737s (2014)
Modulation of miR-29 expression by α-fetoprotein is linked to the hepatocellular carcinoma epigenome Parpart, S; Roessler, S; Dong, F et al. Hepatology, DOI://10.1002/hep.27200 (2014)

Diacylglycerol lactones targeting the structural features that distinguish the atypical C1 domains of protein kinase C ζ and ι from typical C1 domains Pu, Y; Kang, JH; Sigano, DM et al. J. Med. Chem., DOI://10.1021/jm500165n (2014)
Pharmacophore modeling of nilotinib as an inhibitor of ATP-binding cassette drug transporters and BCR-ABL kinase using a three-dimensional quantitative structure-activity relationship approach Shukla, S; Kouanda, A; Silverton, L; Talele, TT; Ambudkar, SV; Mol. Pharm., DOI://10.1021/mp400762h (2014)
Synthesis of seco-B-ring bryostatin analogue WN-1 via C-C bond-forming hydrogenation: critical contribution of the B-ring in determining bryostatin-like and phorbol 12-myristate 13-acetate-like properties Andrews, IP; Ketcham, JM; Blumberg, PM et al. J. Am. Chem. Soc., DOI://10.1021/ja507825s (2014)
Enumeration of ring-chain tautomers based on SMIRKS rules Guasch, L; Sitzmann, M; Nicklaus, MC; J Chem Inf Model, DOI://10.1021/ci500363p (2014)
Type I IFN induces binding of STAT1 to Bcl6: divergent roles of STAT family transcription factors in the T follicular helper cell genetic program Nakayamada, S; Poholek, AC; Lu, KT et al. J. Immunol., DOI://10.4049/jimmunol.1300675 (2014)
Promoter-bound p300 complexes facilitate post-mitotic transmission of transcriptional memory Wong, MM; Byun, JS; Sacta, M; Jin, Q; Baek, S; Gardner, K; PLoS ONE, DOI://10.1371/journal.pone.0099989 (2014)

Telomere attrition and candidate gene mutations preceding monosomy 7 in aplastic anemia. Dumitriu B, Feng X, Townsley DM, Ueda Y, Yoshizato T, Calado RT, Yang Y, Wakabayashi Y, Kajigaya S, Ogawa S, Zhu J, Young NS Blood, doi://10.1182/blood-2014-10-607572 (2014)
Polymorphism in Self-Assembly of Peptide-Based β-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity Yifat Miller, Buyong Ma, and Ruth Nussinov J. Phys. Chem. B, DOI: 10.1021/jp511485n (2014)
Prospective Associations of Coronary Heart Disease Loci in African Americans Using the MetaboChip: The PAGE Study Nora Franceschini, Yijuan Hu, Alex P. Reiner, et al. PLoS One, DOI: 10.1371/journal.pone.0113203 (2014)
Behçet disease-associated MHC class I residues implicate antigen binding and regulation of cell-mediated cytotoxicity. Ombrello MJ, Kirino Y, de Bakker PI, Gül A, Kastner DL, Remmers EF PNAS, doi: 10.1073/pnas.1406575111 (2014)
Integrated transcriptome analysis of mouse spermatogenesis Margolin G, Khil PP, Kim J, Bellani MA, Camerini-Otero RD BMC Genomics, doi: 10.1186/1471-2164-15-39 (2014)
Integromic Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes Chen Yao, Brian H. Chen, Roby Joehanes, et al. Circulation, doi: 10.1161/CIRCULATIONAHA.114.010696 (2014)

Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B Dev. Cell, doi: 10.1016/j.devcel.2014.11.021 (2014)
Leveraging Local identity-by-descent increases the power of Case/Control GWAS with Related Individuals Joshua N Sampson, Bill Wheeler, Peng Li, Jianxin Shi Ann Appl Stat. 8(2):974-998. (2014)
Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58 Wang X, Li Y, Ni T, Xie X, Zhu J, Zheng ZM Cell Biosci. , doi: 10.1186/2045-3701-4-5 (2014)
Complex interactions of transcription factors in mediating cytokine biology in T cells Li P, Spolski R, Liao W, Leonard WJ. Immunol Rev, doi: 10.1111/imr.12199. (2014)
Opposing actions of IL-2 and IL-21 on Th9 differentiation correlate with their differential regulation of BCL6 expression Liao W, Spolski R, Li P, Du N, West EE, Ren M, Mitra S, Leonard WJ. PNAS, doi: 10.1073/pnas.1301138111 (2014)
Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. Rudicell RS1, Kwon YD, Ko SY et al. Journal of Virology, doi: 10.1128/JVI.02213-14 (2014)

High Accuracy of Karplus Equations for Relating Three-Bond J Couplings to Protein Backbone Torsion Angles Fang Li, Jung Ho Lee, Alexander Grishaev, Jinfa Ying and Ad Bax Eur. J. Chem. Phys. Chem. , DOI: 10.1002/cphc.201402704 (2014)
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Common genetic variation in the glucokinase gene (GCK) is associated with type 2 diabetes and rates of carbohydrate oxidation and energy expenditure Muller YL, Piaggi P, Hoffman D, Huang K, Gene B, Kobes S, Thearle MS, Knowler WC, Hanson RL, Baier LJ, Bogardus C Diabetologia, doi: 10.1007/s00125-014-3234-8 (2014)
Task Dependence, Tissue Specificity, and Spatial Distribution of Widespread Activations in Large Single-Subject Functional MRI Datasets at 7T Javier Gonzalez-Castillo, Colin W. Hoy, Daniel A. Handwerker, Vinai Roopchansingh, Souheil J. Inati, Ziad S. Saad, Robert W. Cox and Peter A. Bandettini Cerebral Cortex, doi://10.1093/cercor/bhu148 (2014)

Corpus Callosum Size Is Highly Heritable in Humans, and May Reflect Distinct Genetic Influences on Ventral and Rostral Regions Girma Woldehawariat, Pedro E. Martinez, Peter Hauser, David M. Hoover, Wayne W. C. Drevets, Francis J. McMahon PLoS One, DOI: 10.1371/journal.pone.0099980 (2014)
Thermodynamic, Dynamic and Solvational Properties of PDEδ Binding to Farnesylated Cystein: A Model Study for Uncovering the Molecular Mechanism of PDEδ Interaction with Prenylated Proteins S. Suladze, S. Ismail, and R. Winter J. Phys. Chem. B, DOI: 10.1021/jp411466r (2014)
Inhibition of Paracoccidioides lutzii Pb01 Isocitrate Lyase by the Natural Compound Argentilactone and Its Semi-Synthetic Derivatives Renata Silva do Prado, Ricardo Justino Alves et al PLoS One, DOI: 10.1371/journal.pone.0094832 (2014)
Genome-wide association analysis identifies six new loci associated with forced vital capacity Loth DW, Artigas MS, Gharib SA et al. Nat Genet., doi: 10.1038/ng.3011. (2014)
Introductions and evolution of human-origin seasonal influenza A viruses in multinational swine populations Martha I. Nelson, David E. Wentworth, Marie R. Culhane, Amy L. Vincent, Cecile Viboud, Matthew P. LaPointe, Xudong Lin, Edward C. Holmes and Susan E. Detmer J. Virology, doi: 10.1128/JVI.01080-14 (2014)
The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua Martha I. Nelson, Angel Balmaseda, Guillermina Kuan, Saira Saborio, Xudong Lin, Rebecca A. Halpin, Timothy B. Stockwell, David E. Wentworth, Eva Harris, Aubree Gordon Virology, DOI: 10.1016/j.virol.2014.05.025 (2014)
Highly efficient production of peptides: N-glycosidase F for N-glycomics analysis Ling Hua, b, Xin Gao, Xiaopan Yang, Deyou Wan, Chunpeng He, Jiyue Cao, Haifeng Song Protein Expression and Purification, DOI: 10.1016/j.pep.2014.02.004 (2014)
Approaches to retrospective sampling for longitudinal transition regression models Sally Hunsberger, Paul S. Albert, and Marie Thoma Statistics and Its Interface 7:75-85, doi://10.4310/SII.2014.v7.n1.a9 (2014)
Identification and Characterization of Seminal Fluid Proteins in the Asian Tiger Mosquito, Aedes albopictus Kathryn E. Boes, José M. C. Ribeiro, Alex Wong, Laura C. Harrington, Mariana F. Wolfner, and Laura K. Sirot PLoS Neglected Tropical Diseases, doi: 10.1371/journal.pntd.0002946 (2014)
Marginal analysis of measurement agreement among multiple raters with non-ignorable missing ratings Zhen Chen and Yunlong Xie Statistics and Its Interface 7:113-120, doiL//10.4310/SII.2014.v7.n1.a12 (2014)
Linear mixed models for multiple outcomes using extended multivariate skew-t distributions Binbing Yu, A. James O'Malley, and Pulak Ghosh Statistics and Its Interface 7:101-111, doi://10.4310/SII.2014.v7.n1.a11 (2014)
Matched longitudinal analysis of biomarkers associated with survival Lori E. Dodd, Reed F. Johnson, Joseph E. Blaney and Dean Follmann Clinical & Vaccine Immunology, doi: 10.1128/CVI.00252-14 (2014)

Frontotemporal dementia and its subtypes: a genome-wide association study Ferrari R, Hernandez D, Nalls M et al. The Lancet Neurology, DOI: 10.1016/S1474-4422(14)70065-1 (2014)
Activity and Architecture of Pyroglutamate Modified Amyloid-β (AβpE3-42) Pores Alan L Gillman , Hyunbum Jang , Joon Lee , Srinivasan Ramachandran , Bruce L. Kagan , Ruth Nussinov , and Fernando Teran Arce J. Phys. Chem. B, DOI: 10.1021/jp5040954 (2014)
Computational Tools and Algorithms for Designing Customized Synthetic Genes Nathan Gould, Oliver Hendy, and Dimitris Papamichail Front Bioeng Biotechnol, doi: 10.3389/fbioe.2014.00041 (2014)
Role of LDB1 in the transition from chromatin looping to transcription activation. Krivega I, Dale RK, Dean A. Genes Dev., doi: 10.1101/gad.239749.114 (2014)
Implicit treatment of solvent dispersion forces in protein simulations Sergio A Hassan Journal of Computational Chemistry, DOI: 10.1002/jcc.23655 (2014)
Conscious recall of different aspects of skill memory Sunbin Song & Leonardo G Cohen Frontiers in Behavioural Neuroscience, doi:10.3389/fnbeh.2014.00233 (2014)

A novel role of CDX1 in embryonic epicardial development Chu M, Wang L, Wang H, Shen T, Yang Y, Sun Y, Tang N, Ni T, Zhu J, Mailman RB, Wang Y PLoS One, doi: 10.1371/journal.pone.0103271 (2014)
Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy Alberto Bartesaghi, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam Nat Struct Mol Biol., doi: 10.1038/nsmb.2711 (2014)
Clinical correlates and genetic linkage of social and communication difficulties in families with obsessive-compulsive disorder: Results from the OCD Collaborative Genetics Study Samuels, J; Shugart, YY; Wang, Y et al. Am. J. Med. Genet. B Neuropsychiatr. Genet., DOI://10.1002/ajmg.b.32235 (2014)
The spatial structure of resting state connectivity stability on the scale of minutes Javier Gonzalez-Castillo, Daniel A Handwerker, Meghan E. Robinson, Colin Wier Hoy, Laura Cathleen Buchanan, Ziad S Saad and Peter A Bandettini Frontiers in Neuroscience, DOI://10.3389/fnins.2014.00138 (2014)
The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. King MR, Matzat LH, Dale RK, Lim SJ, Lei EP J. Cell. Sci., doi: 10.1242/jcs.151126 (2014)
Use of LC-MS/MS and Bayes' Theorem to Identify Protein Kinases That Phosphorylate Aquaporin-2 at Ser256 Davis Bradford, Viswanathan Raghuram, Justin L.L. Wilson, Chung-Lin Chou, Jason D. Hoffert, Mark A. Knepper, Trairak Pisitkun Am. J. Physiol. - Cell Physiol. , DOI: 10.1152/ajpcell.00377.2012 (2014)
Nill-Schiff base complex as an enzyme inhibitor of hen egg white lysozyme: a crystallographic and spectroscopic study Banabithi Koley Seth, Aurkie Ray, Sampa Biswas and Samita Basu Metallomics, DOI: 10.1039/C4MT00098F (2014)
Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing Yun Ji, Natalie Abrams, Wei Zhu, Eddie Salinas, Zhiya Yu, Douglas C. Palmer, Parthav Jailwala, Zulmarie Franco, Rahul Roychoudhuri, Eric Stahlberg, Luca Gattinoni, Nicholas P. Restifo PLoS One, DOI: 10.1371/journal.pone.0096650 (2014)
Combination of longitudinal biomarkers in predicting binary events Danping Liu and Paul S Albert Biostatistics, doi: 10.1093/biostatistics/kxu020 (2014)
Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma Shi J, Yang XR, Ballew B Nature Genetics, doi: 10.1038/ng.2941 (2014)
Pleiotropic genes for metabolic syndrome and inflammation Kraja AT, Chasman DI, North KE et al. Molecular Genetics & Metabolism, doi://10.1016/j.ymgme.2014.04.007 (2014)
Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves Kent R. Thurber and Robert Tycko J. Chem. Phys. , DOI: 10.1063/1.4874341 (2014)
Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome Yudkin, D; Hayward, BE; Aladjem, MI; Kumari, D; Usdin, K; Hum. Mol. Genet., DOI://10.1093/hmg/ddu006 (2014)
Rhythmic Bursting in the Pre-Bötzinger Complex: Mechanisms and Models Ilya A. Rybak, Yaroslav I. Molkov, Patrick E. Jasinski, Natalia A. Shevtsova, Jeffrey C. Smith Progress in Brain Research, doi://10.1016/B978-0-444-63274-6.00001-1 (2014)
Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2 Francesco Trepiccione, Trairak Pisitkun, Jason D Hoffert, Søren B Poulsen, Giovambattista Capasso, Søren Nielsen, Mark A Knepper, Robert A Fenton and Birgitte M Christensen Kidney International, doi: 10.1038/ki.2014.107 (2014)
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I Ville R. I. Kaila, Mârten Wikström and Gerhard Hummer PNAS, doi: 10.1073/pnas.1319156111 (2014)
Hierarchical clustering of ryanodine receptors enables emergence of a calcium clock in sinoatrial node cells Michael D. Stern, Larissa A. Maltseva, Magdalena Juhaszova, Steven J. Sollott, Edward G. Lakatta, and Victor A. Maltsev J. Gen. Physiol. , doi: 10.1085/jgp.201311123 (2014)
Conserved hydrogen-bonding network of P2 bis-tetrahydrofuran containing HIV-1 protease inhibitors (PI) with protease active site amino acid-backbone aid in their activity against PI-resistant HIV Ravikiran S. Yedidi, Harisha Garimella, Manabu Aoki, Hiromi Aoki, Darshan V. Desai, Simon B. Chang, David A. Davis, W. Sean Fyvie, Joshua D. Kaufman, David W. Smith, Debananda Das, Paul T. Wingfield, Kenji Maeda, Arun K. Ghosh and Hiroaki Mitsuya Antimicrob Agents Chemother., doi://10.1128/AAC.00107-14 (2014)

Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer Ewy A Mathe, Andrew D Patterson, Majda Haznadar, Soumen K Manna, Kristopher W. Krausz, Elise D Bowman, Peter G. Shields, Jeffrey R. Idle, Philip B Smith, Katsuhiro Anami, Dickran Kazandjian, Emmanuel Hatzakis, Frank J Gonzalez, and Curtis C. Harris Cancer Res., doi:10.1158/0008-5472.CAN-14-0109 (2014)
Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin J.-H. Kang, S.A. Hassan, 1, P. Zhao, C.H. Tsai-Morris, M.L. Dufau Biochim. et Biophys. Acta, doi://10.1016/j.bbagen.2014.04.006 (2014)
A Fast and Powerful Tree-Based Association Test for Detecting Complex Joint Effects in Case-Control Studies Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor and Kai Yu Bioinformatics, doi://10.1093/bioinformatics/btu186 (2014)
Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain David N. Hauser, Allissa A. Dillman, Jinhui Ding, Yan Li, Mark R. Cookson PLoS One, DOI: 10.1371/journal.pone.0094646 (2014)
Studies on Inhibition of Respiratory Cytochrome bc1 Complex by the Fungicide Pyrimorph Suggest a Novel Inhibitory Mechanism Yu-Mei Xiao, Lothar Esser, Fei Zhou, Chang Li, Yi-Hui Zhou, Chang-An Yu, Zhao-Hai Qin, Di Xia PLoS One, DOI: 10.1371/journal.pone.0093765 (2014)
Regulation of a novel isoform of Receptor Expression Enhancing Protein REEP6 in rod photoreceptors by bZIP transcription factor NRL Hong Hao, Shobi Veleri, Bo Sun, Douglas S. Kim, Patrick W. Keeley, Jung-Woong Kim, Hyun-Jin Yang, Sharda P. Yadav, Souparnika H. Manjunath, Raman Sood, Paul Liu, Benjamin E. Reese and Anand Swaroop Human Molecular Genetics, doi: 10.1093/hmg/ddu143 (2014)

Distributed MRI reconstruction using gadgetron-based cloud computing Hui Xue, Souheil Inati, Thomas Sangild Sørensen, Peter Kellman and Michael S. Hansen Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25213 (2014)
Hemoglobinopathic erythrocytes affect the intraerythrocytic multiplication of Plasmodium falciparum in vitro Svetlana Glushakova, Amanda Balaban, Philip G. McQueen, Rosane Coutinho, Jeffery L. Miller, Ralph Nossal, Rick M. Fairhurst, Joshua Zimmerberg J. Infectious Diseases, doi:10.1093/infdis/jiu203 (2014)
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface Guntur Fibriansah, Joanne L Tan,Scott A Smith, Adamberage R Alwis, Thiam-Seng Ng, Victor A Kostyuchenko, Kristie D Ibarra, Jiaqi Wang, Eva Harris, Aravinda Silva, James E Crowe, and Shee-Mei Lok EMBO Molecular Medicine, doi: 10.1002/emmm.201303404 (2014)
A mixture of transition models for heterogeneous longitudinal ordinal data: with applications to longitudinal bacterial vaginosis data Kyeongmi Cheon, Marie E. Thoma, Xiangrong Kong and Paul S. Albert Statistics in Medicine, DOI: 10.1002/sim.6151 (2014)
Abdominal lymphadenopathy detection using random forest Kevin M. Cherry, Shijun Wang, Evrim B. Turkbey, Ronald M. Summers SPIE Proceedings, Volume 9035, Lung, Chest, and Abdomen II, doi:10.1117/12.2043837 (2014)
VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions Jianxin Shi, Xiaohong R. Yang, Neil E. Caporaso, Maria T. Landi, and Peng Li Frontiers in Genetics, doi://10.3389/fgene.2014.00053 (2014)

Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values Gelio Alves and Yi-Kuo Yu PLoS One, doi: 10.1371/journal.pone.0091225 (2014)
Differential Coding of Conspecific Vocalizations in the Ventral Auditory Cortical Stream Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck J. Neuroscience, doi: 10.1523/JNEUROSCI.3969-13.2014 (2014)
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein Ville R. I. Kaila, Friedrich Schotte, Hyun Sun Cho, Gerhard Hummer & Philip A. Anfinrud Nature Chemistry, doi:10.1038/nchem.1898 (2014)
Practice and sleep form different aspects of skill Sunbin Song & Leonardo G. Cohen Nature Communications, doi:10.1038/ncomms4407 (2014)
Temperature-dependent solvation modulates the dimensions of disordered proteins René Wuttke, Hagen Hofmann, Daniel Nettels, Madeleine B. Borgia, Jeetain Mittal, Robert B. Best, and Benjamin Schuler PNAS, doi: 10.1073/pnas.1313006111 (2014)
Hypoosmotic Expression of Dunaliella bardawil ζ-Carotene Desaturase Is Attributed to a Hypoosmolarity-Responsive Element Different from Other Key Carotenogenic Genes Yong-Min Lao, Lan Xiao, Li-Xin Luo and Jian-Guo Jiang Plant Physiology, doi://10.1104/pp.114.235390 (2014)

Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Jianxin Shi, Crystal N. Marconett, Jubao Duan et al. Nature Communications, doi:10.1038/ncomms4365 (2014)
Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal and Ruth Nussinov Chem. Soc. Rev., doi://10.1039/C3CS60459D (2014)
Abnormal cortical growth in schizophrenia targets normative modules of synchronized development Aaron F. Alexander-Bloch, Philip T. Reiss, Judith Rapoport, Harry McAdams, Jay N. Giedd, Ed T. Bullmore, Nitin Gogtay Biological Psychiatry, doi://10.1016/j.biopsych.2014.02.010 (2014)
Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis Edina Rosta, Wei Yang, and Gerhard Hummer JACS, DOI: 10.1021/ja411408x (2014)
Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes Gerhard König, Phillip Stephen Hudson, Stefan Boresch, and H. Lee Woodcock J. Chem. Theory & Computation, DOI: 10.1021/ct401118k (2014)
A Network Characteristic That Correlates Environmental and Genetic Robustness Zeina Shreif, Vipul Periwal PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1003474 (2014)

A GCH1 haplotype confers sex-specific susceptibility to pain crises and altered endothelial function in adults with sickle cell anemia Inna Belfer, Victoria Youngblood et al. Am. J. Hematology, DOI: 10.1002/ajh.23613 (2014)
Meta-analysis of Loci Associated with Age at Natural Menopause in African-American Women CTL Chen, C-T Liu, GK Chen, et al Human Molecular Genetics, doi: 10.1093/hmg/ddu041 (2014)
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks J. Computer-Aided Molecular Design, doi://10.1007/s10822-014-9708-4 (2014)
Predicting Stroke Through Genetic Risk Functions CA Ibrahim-Verbaas,M Fornage, JC Bis, et al Stroke, doi: 10.1161/STROKEAHA.113.003044 (2014)
Multilocus Genetic Risk Score Associates With Ischemic Stroke in Case-Control and Prospective Cohort Studies R Malik, S Bevan, M Nalls et al Stroke, doi: 10.1161/STROKEAHA.113.002938 (2014)
Reverse regression: A method for joint analysis of multiple endpoints in randomized clinical trials Zhiwei Zhang Statistica Sinica, doi://10.5705/ss.2010.111 (2014)

Using single cell sequencing data to model the evolutionary history of a tumor Kyung In Kim and Richard Simon BMC Bioinformatics :27, doi: 10.1186/1471-2105-15-27 (2014)
Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors Jack F. Shern, Li Chen, Juliann Chmielecki, et al. Cancer Discovery, doi:10.1158/2159-8290.CD-13-0639 (2014)
Fluorescence excitation and ultraviolet absorption spectra and theoretical calculations for benzocyclobutane: Vibrations and structure of its excited S1(π,π*) electronic state Hee Won Shin, Esther J. Ocola, Sunghwan Kim and Jaan Laane J. Chem. Phys., doi://10.1063/1.4858412 (2014)
Spectral Tuning of Rhodopsin and Visual Cone Pigments Xiuwen Zhou , Dage Sundholm , Tomasz Adam Wesolowski , and Ville R. I. Kaila J.Am.Chem.Soc., DOI: 10.1021/ja411864m (2014)
RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder N Akula, J Barb, X Jiang, J R Wendland, K H Choi, S K Sen, L Hou, D T W Chen, G Laje, K Johnson, B K Lipska, J E Kleinman, H Corrada-Bravo, S Detera-Wadleigh, P J Munson and F J McMahon Molecular Psychiatry, doi: 10.1038/mp.2013.170 (2014)

2013 (180 papers)

Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains Chuang, GY; Acharya, P; Schmidt, SD et al. J. Virol., DOI://10.1128/JVI.00984-13 (2013)
Integrated strategy for improving functional connectivity mapping using multiecho fMRI Kundu, P; Brenowitz, ND; Voon, V et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301725110 (2013)
Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia Wang, E; Kawaoka, S; Yu, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301045110 (2013)
Correlated biomarker measurement error: an important threat to inference in environmental epidemiology Pollack, AZ; Perkins, NJ; Mumford, SL; Ye, A; Schisterman, EF; Am. J. Epidemiol., DOI://10.1093/aje/kws209 (2013)
Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies Zhou, T; Zhu, J; Wu, X et al. Immunity, DOI://10.1016/j.immuni.2013.04.012 (2013)
Effective Preprocessing Procedures Virtually Eliminate Distance-Dependent Motion Artifacts in Resting State FMRI Jo, HJ; Gotts, SJ; Reynolds, RC et al. J Appl Math, DOI://10.1155/2013/935154 (2013)
A structural and molecular dynamics approach to understanding the peptide-receptive transition state of MHC-I molecules Mage, MG; Dolan, MA; Wang, R et al. Mol. Immunol., DOI://10.1016/j.molimm.2012.10.021 (2013)
PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum Jiang, L; Mu, J; Zhang, Q et al. Nature, DOI://10.1038/nature12361 (2013)
Subconjunctival Palomid 529 in the treatment of neovascular age-related macular degeneration Dalal, M; Jacobs-El, N; Nicholson, B et al. Graefes Arch. Clin. Exp. Ophthalmol., DOI://10.1007/s00417-013-2375-7 (2013)
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment Rietveld, CA; Medland, SE; Derringer, J et al. Science, DOI://10.1126/science.1235488 (2013)
Multivariate normally distributed biomarkers subject to limits of detection and receiver operating characteristic curve inference Perkins, NJ; Schisterman, EF; Vexler, A; Acad Radiol, DOI://10.1016/j.acra.2013.04.001 (2013)
Genome-wide association study of retinopathy in individuals without diabetes Jensen, RA; Sim, X; Li, X et al. PLoS ONE, DOI://10.1371/journal.pone.0054232 (2013)
Topographic diversity of fungal and bacterial communities in human skin Findley, K; Oh, J; Yang, J et al. Nature, DOI://10.1038/nature12171 (2013)
Accuracy loss due to selection bias in cohort studies with left truncation Schisterman, EF; Cole, SR; Ye, A; Platt, RW; Paediatr Perinat Epidemiol, DOI://10.1111/ppe.12073 (2013)
Age-dependent regulation of synaptic connections by dopamine D2 receptors Jia, JM; Zhao, J; Hu, Z; Lindberg, D; Li, Z; Nat. Neurosci., DOI://10.1038/nn.3542 (2013)
Instant super-resolution imaging in live cells and embryos via analog image processing York, AG; Chandris, P; Nogare, DD et al. Nat. Methods, DOI://10.1038/nmeth.2687 (2013)
Obstetric complications among US women with asthma Mendola, P; Laughon, SK; Männistö, TI et al. Am. J. Obstet. Gynecol., DOI://10.1016/j.ajog.2012.11.007 (2013)
Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error Stambolian, D; Wojciechowski, R; Oexle, K et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddt116 (2013)
A systems biology framework identifies molecular underpinnings of coronary heart disease Huan, T; Zhang, B; Wang, Z et al. Arterioscler. Thromb. Vasc. Biol., DOI://10.1161/ATVBAHA.112.300112 (2013)
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia Verhoeven, VJ; Hysi, PG; Wojciechowski, R et al. Nat. Genet., DOI://10.1038/ng.2554 (2013)
The altered landscape of the human skin microbiome in patients with primary immunodeficiencies Oh, J; Freeman, AF; , et al. Genome Res., DOI://10.1101/gr.159467.113 (2013)
Identification of an ABCB1 (P-glycoprotein)-positive carfilzomib-resistant myeloma subpopulation by the pluripotent stem cell fluorescent dye CDy1 Hawley, TS; Riz, I; Yang, W et al. Am. J. Hematol., DOI://10.1002/ajh.23387 (2013)
Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics Li, M; Shoemaker, BA; Thangudu, RR; Ferraris, JD; Burg, MB; Panchenko, AR; J Phys Chem B, DOI://10.1021/jp403310a (2013)
Severe painful vaso-occlusive crises and mortality in a contemporary adult sickle cell anemia cohort study Darbari, DS; Wang, Z; Kwak, M et al. PLoS ONE, DOI://10.1371/journal.pone.0079923 (2013)
Association of adiposity genetic variants with menarche timing in 92,105 women of European descent Fernández-Rhodes, L; Demerath, EW; Cousminer, DL et al. Am. J. Epidemiol., DOI://10.1093/aje/kws473 (2013)

TGF-ß regulates enamel mineralization and maturation through KLK4 expression Cho, A; Haruyama, N; Hall, B et al. PLoS ONE, DOI://10.1371/journal.pone.0082267 (2013)
Race, genetic ancestry and response to antidepressant treatment for major depression Murphy, E; Hou, L; Maher, BS et al. Neuropsychopharmacology, DOI://10.1038/npp.2013.166 (2013)
Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment Snitkin, ES; Zelazny, AM; Gupta, J et al. Genome Res., DOI://10.1101/gr.154328.112 (2013)
53BP1 alters the landscape of DNA rearrangements and suppresses AID-induced B cell lymphoma Jankovic, M; Feldhahn, N; Oliveira, TY et al. Mol. Cell, DOI://10.1016/j.molcel.2012.11.029 (2013)
Building a fission machine--structural insights into dynamin assembly and activation Chappie, JS; Dyda, F; J. Cell. Sci., DOI://10.1242/jcs.108845 (2013)
Global 'bootprinting' reveals the elastic architecture of the yeast TFIIIB-TFIIIC transcription complex in vivo Nagarajavel, V; Iben, JR; Howard, BH; Maraia, RJ; Clark, DJ; Nucleic Acids Res., DOI://10.1093/nar/gkt611 (2013)

Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation Wood, AR; Perry, JR; Tanaka, T et al. PLoS ONE, DOI://10.1371/journal.pone.0064343 (2013)
Human papillomavirus type 58 genome variations and RNA expression in cervical lesions Li, Y; Wang, X; Ni, T et al. J. Virol., DOI://10.1128/JVI.01154-13 (2013)
De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts Zhu, J; Wu, X; Zhang, B et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1306262110 (2013)
The role of macrophage class a scavenger receptors in a laser-induced murine choroidal neovascularization model Jawad, S; Liu, B; Li, Z et al. Invest. Ophthalmol. Vis. Sci., DOI://10.1167/iovs.12-11380 (2013)
Suppression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic Spo11 allele Smagulova, F; Brick, K; Pu, Y; Sengupta, U; Camerini-Otero, RD; Petukhova, GV; BMC Genomics, DOI://10.1186/1471-2164-14-493 (2013)
Regional replication of association with refractive error on 15q14 and 15q25 in the Age-Related Eye Disease Study cohort Simpson, CL; Wojciechowski, R; Yee, SS; Soni, P; Bailey-Wilson, JE; Stambolian, D; Mol. Vis., 1090-0535 (2013)

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis Van Doorslaer, K; Tan, Q; Xirasagar, S et al. Nucleic Acids Res., DOI://10.1093/nar/gks984 (2013)
The origin of B cell recurrent chromosomal translocations: proximity versus DNA damage Casellas, R; Resch, W; Hakim, O; Nussenzweig, MC; Mol. Cell, DOI://10.1016/j.molcel.2013.07.020 (2013)
NGSPE: A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms Huang, K; Yellapantula, V; Baier, L; Dinu, V; Comput. Biol. Med., DOI://10.1016/j.compbiomed.2013.05.025 (2013)
Genetic associations with valvular calcification and aortic stenosis Thanassoulis, G; Campbell, CY; Owens, DS et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1109034 (2013)
Transforming growth factor-β3 (TGF-β3) knock-in ameliorates inflammation due to TGF-β1 deficiency while promoting glucose tolerance Hall, BE; Wankhade, UD; Konkel, JE et al. J. Biol. Chem., DOI://10.1074/jbc.M113.480764 (2013)
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Effects of pre-existing anti-carrier immunity and antigenic element multiplicity on efficacy of a modular virus-like particle vaccine Yap P. Chuan, Tania Rivera-Hernandez, Nani Wibowo, Natalie K. Connors, Yang Wu, Fiona K. Hughes, Linda H. L. Lua, Anton P. J. Middelberg Biotech. & Bioengg. , DOI: 10.1002/bit.24907 (2013)

Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans Panpan Yu, Trairak Pisitkun, Guanghui Wang, Rong Wang, Yasuhiro Katagiri, Marjan Gucek, Mark A. Knepper, Herbert M. Geller PLoS One, doi:10.1371/journal.pone.0059285 (2013)
The alkaline pectate lyase PEL168 of Bacillus subtilis heterologously expressed in Pichia pastoris is more stable and efficient for degumming ramie fiber Chengjie Zhang, Jia Yao,Cheng Zhou,Liangwei Mao, Guimin Zhang, Yanhe Ma BMC Biotechnology, doi:10.1186/1472-6750-13-26 (2013)
In Silico, In Vitro, and In Vivo Studies Indicate the Potential Use of Bolaamphiphiles for Therapeutic siRNAs Delivery Taejin Kim, Kirill A. Afonin, Mathias Viard, Alexey Y Koyfman, Selene Sparks, Eliahu Heldman, Sarina Grinberg, Charles Linder, Robert P Blumenthal and Bruce A Shapiro Mol. Therapy - Nuc. Acids, doi:10.1038/mtna.2013.5 (2013)
RNAi triggered by specialized machinery silences developmental genes and retrotransposons Soichiro Yamanaka, Sameet Mehta, Francisca E. Reyes-Turcu, Fanglei Zhuang, Ryan T. Fuchs, Yikang Rong, Gregory B. Robb & Shiv I. S. Grewal Nature, doi:10.1038/nature11716 (2013)
Transcription-dependent dynamic supercoiling is a short-range genomic force Fedor Kouzine, Ashutosh Gupta, Laura Baranello, Damian Wojtowicz, Khadija Ben-Aissa, Juhong Liu, Teresa M Przytycka & David Levens Nature Structural & Molecular Biology, doi:10.1038/nsmb.2517 (2013)
X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications Nitika Mukhi, Sonali Dhindwal, Sheetal Uppal, Pravindra Kumar, Jagreet Kaur, Suman Kundu Biochim. et Biophys. Acta, doi://10.1016/j.bbapap.2013.02.024 (2013)

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing David Zanuy, Francisco J. Sayago, Guillem Revilla-López, Gema Ballano, Lilach Agemy, Venkata Ramana Kotamraju, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, April M. Sawvel, Galen Stucky, Erkki Ruoslahti, Carlos Alemán J. Computer-Aided Mol. Design, doi:10.1007/s10822-012-9623-5 (2013)
A novel taurocyamine kinase found in the protist Phytophthora infestans Kouji Uda, Michihiro Hoshijima, Tomohiko Suzuki Comp. Biochem. Phys. Part B: Biochem & Mol. Bio. , doi://10.1016/j.cbpb.2013.03.003 (2013)
Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies AK Harris, JR Meyerson, Y Matsuoka, O Kuybeda, A Moran, D Bliss, SR Das, JW Yewdell, G Sapiro, K Subbarao, and S Subramaniam PNAS, doi: 10.1073/pnas.1214913110 (2013)
Gene Synthesis by Assembly of Deoxyuridine-Containing Oligonucleotides Romualdas Vaisvila, Jurate Bitinaite Methods in Molecular Biology, doi: 10.1007/978-1-62703-293-3_12 (2013)
The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin Simina Grigoriu, Rachel Bond, Pilar Cossio, Jennifer A. Chen, Nina Ly, Gerhard Hummer, Rebecca Page, Martha S. Cyert, Wolfgang Peti PLoS Biology, doi:10.1371/journal.pbio.1001492 (2013)
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network Z Chen, H Tang, R Qayyum, UM Schick, MA Nalls et al. Human Molecular Genetics, doi: 10.1093/hmg/ddt087 (2013)

Common Variants Within Oxidative Phosphorylation Genes Influence Risk of Ischemic Stroke and Intracerebral Hemorrhage CD Anderson, A Biffi, MA Nalls, et al. & the International Stroke Genetics Consortium Stroke, doi: 10.1161/STROKEAHA.112.672089 (2013)
Antedependence models for nonstationary categorical longitudinal data with ignorable missingness likelihood-based inference Yunlong Xie, Dale Zimmerman Statistics in Medicine, DOI: 10.1002/sim.5763 (2013)
Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor David Zanuy, Rohith Kotla, Ruth Nussinov, Tambet Teesalu, Kazuki N. Sugahara, Carlos Alemán, Nurit Haspel J. Struct. Biol. , doi://10.1016/j.jsb.2013.02.006 (2013)
Electrostatic spectral tuning mechanism of the green fluorescent protein Ville R. I. Kaila , Robert Send and Dage Sundholm Phys. Chem. Chem. Phys., DOI: 10.1039/C3CP00058C (2013)
Alzheimer's disease: Which type of amyloid-preventing drug agents to employ? Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , Bruce L Kagan and Ruth Nussinov Phys. Chem. Chem. Phys., DOI: 10.1039/C3CP00017F (2013)
Control of breathing by interacting pontine and pulmonary feedback loops Yaroslav I. Molkov, Bartholomew J. Bacak, Thomas E. Dick, and Ilya A. Rybak Frontiers in Neural Circuits, doi: 10.3389/fncir.2013.00016 (2013)

Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome Yu Xu, Hong Wang, Ruth Nussinov, Buyong Ma Proteomics, DOI: 10.1002/pmic.201100540 (2013)
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly C Park, X Chen, J-R Yang, J Zhang PNAS, doi: 10.1073/pnas.1218066110 (2013)
The Val158Met COMT polymorphism is a modifier of the age at onset in Parkinson's disease with a sexual dimorphism S Klebe, J-L Golmard, MA Nalls et al, French Parkinson's Disease Genetics Study Group and the International Parkinson's Disease Genomics Consortium J Neurol Neurosurg Psychiatry , doi:10.1136/jnnp-2012-304475 (2013)
The Convergence of Maturational Change and Structural Covariance in Human Cortical Networks Aaron Alexander-Bloch, Armin Raznahan, Ed Bullmore, and Jay Giedd J. Neuroscience , doi: 10.1523/JNEUROSCI.3554-12.2013 (2013)
Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer Li-Jun Di, Jung S. Byun, Madeline M. Wong, Clay Wakano, Tara Taylor, Sven Bilke, Songjoon Baek, Kent Hunter, Howard Yang, Maxwell Lee, Cecilia Zvosec, Galina Khramtsova, Fan Cheng, Charles M. Perou, C. Ryan Miller, Rachel Raab, Olufunmilayo I. Olopade & Kevin Gardner Nature Communications, doi:10.1038/ncomms2438 (2013)
Ischemic stroke is associated with the ABO locus: The EuroCLOT study FMK Williams, AM Carter, PG Hysi et al and EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2, MORGAM, MetaStroke and the International Stroke Genetics Consortium Annals of Neurology, DOI: 10.1002/ana.23838 (2013)

Initial Assessment of the Pathogenic Mechanisms of the Recently Identified Alzheimer Risk Loci P Holton, M Ryten, MA Nalls et al. Annals of Human Genetics, DOI: 10.1111/ahg.12000 (2013)
Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin Erica L.W. Majumder, Jeremy D. King, Robert E. Blankenship Biochim. et Biophys. Acta - Bioenergetics, doi://10.1016/j.bbabio.2013.01.008 (2013)
Identification of Early Replicating Fragile Sites that Contribute to Genome Instability JH Barlow, RB Faryabi, E Callen, N Wong, A Malhowski, H Tang Chen, G Gutierrez-Cruz, H-W Sun, P McKinnon, G Wright, R Casellas, DF Robbiani, L Staudt, O Fernandez-Capetillo, A Nussenzweig Cell, doi://10.1016/j.cell.2013.01.006 (2013)
Genetic variation associated with circulating monocyte count in the eMERGE Network DR Crosslin, A McDavid, N Weston et al Hum. Mol. Genetics, doi: 10.1093/hmg/ddt010 (2013)
PI(4,5)P2-Mediated Cell Signaling: Emerging Principles and PTEN as a Paradigm for Regulatory Mechanism Arne Gericke, Nicholas R. Leslie, Mathias Lösche, Alonzo H. Ross Adv Exp Med Biol, doi: 10.1007/978-94-007-6331-9_6 (2013)

2012 (144 papers)

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids Mittal, J; Hummer, G; , J Chem Phys, DOI://10.1063/1.4732515 (2012)
An efficient algorithm for clustering of large-scale mass spectrometry data Saeed F, Pisitkun T, Knepper MA, Hoffert JD Proceedings (IEEE Int Conf Bioinformatics Biomed), doi://10.1109/BIBM.2012.6392738 (2012)
A Dual Polybasic Motif Determines Phosphoinositide Binding and Regulation in the P2X Channel Family Louis-Philippe Bernier, Dominique Blais, É ́ric Boué-Grabot, Philippe Séguéla PLoS One 7:1-9, doi: 10.1371/journal.pone.0040595 (2012)
Estimating Diagnostic Accuracy of Raters Without a Gold Standard by Exploiting a Group of Experts Zhang B, Chen Z, Albert PS. Biometrics, doi: 10.1111/j.1541-0420.2012.01789.x (2012)
Entropy of single-file water in (6,6) carbon nanotubes Aparna Waghe, Jayendran C. Rasaiah, and Gerhard Hummer J. Chem. Phys. , doi://10.1063/1.4737842 (2012)
Assessment of the Effect of 24-Hour Aldosterone Administration on Protein Abundance in Fluorescence-Sorted Mouse Distal Renal Tubules by Mass Spectrometry Jensen T.B., Pisitkun T., Hoffert J.D., Jensen U.B., Fenton R.A, Praetorius H.A, Knepper M.A, Praetorius J. Nephron Physiology, DOI:10.1159/000346832 (2012)
On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions Edina Rosta and Arieh Warshal J Chem Theory Comput. , doi: 10.1021/ct2009329 (2012)

An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data Fahad Saeed, Trairak Pisitkun, Jason D. Hoffert, Guanghui Wang, Marjan Gucek, and Mark A. Knepper Proceedings of IEEE Int Conf Bioinformatics Biomed, doi://10.1109/BIBMW.2012.6470210 (2012)
Cell population-specific expression analysis of human cerebellum A Kuhn, A Kumar, A Beilina, A Dillman, MR Cookson, AB Singleton BMC Genomics, doi:10.1186/1471-2164-13-610 (2012)
Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus Olivier Escaffre, Cyril Le Nouën, Michel Amelot, Xavier Ambroggio, Kristen M. Ogden, Olivier Guionie, Didier Toquin, Hermann Müller, Mohammed R. Islam and Nicolas Eterradossi J. Virology, doi: 10.1128/JVI.02360-12 (2012)
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. in Mass. Spec., DOI: 10.1002/rcm.6451 (2012)
Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site Deep Sankar Rudra, Uttam Pal, Nakul Chandra Maiti, Russel J. Reiter, Snehasikta Swarnakar J. Pineal Research, DOI: 10.1111/jpi.12034 (2012)
RPA Accumulation during Class Switch Recombination Represents 5'-3' DNA-End Resection during the S-G2/M Phase of the Cell Cycle Arito Yamane, Davide F. Robbiani, Wolfgang Resch, Anne Bothmer, Hirotaka Nakahashi, Thiago Oliveira, Philipp C. Rommel, Eric J. Brown, Andre Nussenzweig, Michel C. Nussenzweig, Rafael Casellas Cell Reports, doi://10.1016/j.celrep.2012.12.006, (2012)

Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives Joel R. Meyerson, Erin E. H. Tran, Oleg Kuybeda, Weizao Chen, Dimiter S. Dimitrov, Andrea Gorlani, Theo Verrips, Jeffrey D. Lifson, and Sriram Subramaniam PNAS, doi:10.1073/pnas.1214810110 (2012)
Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase H. Sepasi Tehrani, A.A. Moosavi-Movahedia, H. Ghourchian, F. Ahmad, A. Kiany, M.S. Atri, Sh Ariaeenejad, K. Kavousi & A.A. Sabourya J. Biomol. Struct. Dynamics, DOI:10.1080/07391102.2012.742460 (2012)
RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells MA Alhoot, SM Wang, SD Sekaran PLoS One, RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells (2012)
On the edge of web-based multiple sequence alignment services Nguyen, Ken D. Tsinghua Science and Technology 17(6):629-637 (2012)
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. in Mass. Spec., DOI: 10.1002/rcm.6451 (2012)
Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Bruce L. Kagan , Ratnesh Lal , and Ruth Nussinov J. Chem. Theory Compt. , DOI: 10.1021/ct300916f (2012)

Structural Ensemble of an Intrinsically Disordered Polypeptide Jeetain Mittal , Tae Hyeon Yoo , George Georgiou , and Thomas Michael Truskett J. Phys. Chem. B, DOI: 10.1021/jp308984e (2012)
STATs Shape the Active Enhancer Landscape of T Cell Populations Golnaz Vahedi, Hayato Takahashi, Shingo Nakayamada, Hong-wei Sun, Vittorio Sartorelli, Yuka Kanno, John J. O'Shea Cell, doi://10.1016/j.cell.2012.09.044, (2012)
Screening system for orthogonal suppressor tRNAs based on the species-specific toxicity of suppressor tRNAs Hong Tian, Danni Deng, Jie Huang, Dongning Yao, Xiaowei Xu, Xiangdong Gao Biochimie, doi://10.1016/j.biochi.2012.12.010 (2012)
Structural and Mechanistic Investigations of Phosphothreonine Lyase Class of Enzymes Alok Gopalkrishna Shenoy Graduate Thesis, Utah State University (2012)
Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery Sapna Kumari, Jeff Nie, Huann-Sheng Chen, Hao Ma, Ron Stewart, Xiang Li, Meng-Zhu Lu, William M. Taylor, Hairong Wei PLoS One, doi:10.1371/journal.pone.0050411 (2012)
Common genetic variation near the Connexin-43 gene is associated with resting heart rate in African Americans: A Genome-wide Association Study of 13,372 participants R Deo, MA Nalls, CL Avery, JG Smith et al. Heart Rhythm, doi://10.1016/j.hrthm.2012.11.014 (2012)

Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography Alberto Bartesaghi, Federico Lecumberry, Guillermo Sapiro, Sriram Subramaniam Structure 20(12):2003-2013 (2012)
A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons Eugene Paulechka , Kenneth Kroenlein , Andrei Kazakov , and Michael Frenkel J. Phys. Chem. B, DOI: 10.1021/jp309119h (2012)
The Impact of Ancestry and Common Genetic Variants on QT Interval in African Americans JG Smith, CL Avery, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/CIRCGENETICS.112.962787 (2012)
The effect of spatial smoothing on fMRI decoding of columnar-level organization with linear support vector machine Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini J. Neuroscience Methods, doi://10.1016/j.jneumeth.2012.11.004 (2012)
Candidate Gene Association Study of BMI-Related Loci, Weight, and Adiposity in Old Age Rachel A. Murphy, Michael A. Nalls, Margaux Keller, Melissa Garcia, Stephen B. Kritchevsky, Frances A. Tylavsky, Anne B. Newman, Gregory J. Tranah, Gudny Eiriksdottir, Vilmundur Gudnason and Tamara B. Harris J. Gerontology A, doi: 10.1093/gerona/gls227 (2012)
Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities as Self-Aggregating Materials Nurit Haspel, Adéle D. Laurent, David Zanuy , Ruth Nussinov, Carlos Aleman, Jordi Puiggali, and Guillermo Revilla-López J. Phys. Chem. B, DOI: 10.1021/jp3043363 (2012)

Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography F Schotte, HS Cho, VRI Kaila, H Kamikubo, N Dashdorj, ER Henry, TJ Graber, R Henning, M Wulff, G Hummer, M Kataoka, and PA Anfinrud PNAS, doi: 10.1073/pnas.1210938109 (2012)
Effects of the BDNF Val66Met Polymorphism on White Matter Microstructure in Healthy Adults H Tost, T Alam, M Geramita, C Rebsch, B Kolachana, D Dickinson, BA Verchinski, H Lemaitre, AS Barnett, JW Trampush, DR Weinberger and S Marenco Neuropsychopharmacology , doi: 10.1038/npp.2012.214 (2012)
Sodium and calcium mechanisms of rhythmic bursting in excitatory neural networks of the pre-Bötzinger complex: a computational modelling study Patrick E. Jasinski, Yaroslav I. Molkov, Natalia A. Shevtsova, Jeffrey C. Smith, Ilya A. Rybak Eur. J. Neuroscience, DOI: 10.1111/ejn.12042 (2012)
Effects of image contrast on functional MRI image registration Javier Gonzalez-Castillo, Kristen N. Duthie, Ziad S. Saad, Carlton Chu, Peter A. Bandettini, Wen-Ming Luh NeuroImage, doi://10.1016/j.neuroimage.2012.10.076 (2012)
Accurate decoding of sub-TR timing differences in stimulations of sub-voxel regions from multi-voxel response patterns Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini NeuroImage, doi://10.1016/j.neuroimage.2012.10.069, (2012)
Novel Loci Associated with PR Interval in a Genome-Wide Association Study of Ten African American Cohorts AM Butler, X Yin, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/CIRCGENETICS.112.963991 (2012)
Response of the Mitochondrial Proteome of Rat Renal Proximal Convoluted Tubules to Chronic Metabolic Acidosis D Freund, JE Prenni, NP Curthoys Renal Physiology, ,doi: 10.1152/ajprenal.00526.2012 (2012)
PTEN: An Intercellular Peacekeeper? Nick R. Leslie Science Signaling, DOI: 10.1126/scisignal.2003685 (2012)
Gene Silencing Mediated by siRNA-binding Fusion Proteins Is Attenuated by Double-stranded RNA-binding Domain Structure James C Geoghegan, Brian L Gilmore and Beverly L Davidson Molecular Therapy Nucleic Acids, doi:10.1038/mtna.2012.43 (2012)
A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography Oleg Kuybeda, Gabriel A. Frank, Alberto Bartesaghi, Mario Borgnia, Sriram Subramaniam , Guillermo Sapiro J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.010 (2012)
Novel inhibitors of a Grb2 SH3C domain interaction identified by a virtual screen Philip C. Simister, James Luccarelli, Sam Thompson, Daniel H. Appella, Stephan M. Feller , Andrew D. Hamilton Bioorganic & Medicinal Chemistry, doi://10.1016/j.bmc.2012.10.023 (2012)
Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation John Ferguson, William Wheeler, YiPing Fu, Ludmila Prokunina-Olsson, Hongyu Zhao and Joshua Sampson Eur. J. Hum. Genetics, doi: 10.1038/ejhg.2012.220 (2012)

Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project Paul L. Auer, Jill M. Johnsen, Andrew D. Johnson et al. Am. J. Hum. Genet., doi://10.1016/j.ajhg.2012.08.031 (2012)
SHAVE: shrinkage estimator measured for multiple visits increases power in GWAS of quantitative traits Osorio D Meirelles, Jun Ding, Toshiko Tanaka, Serena Sanna, Hsih-Te Yang, Dawood B Dudekula, Francesco Cucca, Luigi Ferrucci, Goncalo Abecasis and David Schlessinger European J. Hum. Genetics, doi: 10.1038/ejhg.2012.215 (2012)
Membrane Association of the PTEN Tumor Suppressor: Electrostatic Interaction with Phosphatidylserine-Containing Bilayers and Regulatory Role of the C-Terminal Tail Siddharth S. Shenoy, Hirsh Nanda, c, Mathias Lösche J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.003, (2012)
Characterization of synonymous codon usage bias in the pseudorabies virus US1 gene Meili Li, Zhiyao Zhao, Jianhong Chen, Bingyun Wang, Zi Li, Jian Li and Mingsheng Cai Virologica Sinica, DOI: 10.1007/s12250-012-3270-9 (2012)
Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins Raghunath Chatterjee, Jianfei Zhao, Ximiao He, Andrey Shlyakhtenko, Ishminder Mann, Joshua J. Waterfall, Paul Meltzer, B. K. Sathyanarayana, Peter C. FitzGerald, Charles Vinson Genes | Genomes | Genetics, doi://10.1534/g3.112.004002 (2012)
Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE Collaboration): a meta-analysis of genome-wide association studies M Traylor, M Farrall, EG Holliday et al & International Stroke Genetics Consortium The Lancet Neurology, doi://10.1016/S1474-4422(12)70234-X, (2012)

Siblings with Ischemic Stroke Study (SWISS): Results of a Genome-wide Scan for Stroke Loci JF. Meschia, M Nalls, M Matarin, TG. Brott, RD. Brown, Jr., J Hardy, B Kissela, SS. Rich, A Singleton, D Hernandez, L Ferrucci, K Pearce, M Keller, BB. Worrall, for the Siblings with Ischemic Stroke Study (SWISS) Investigators Stroke, doi: 10.1161/STROKEAHA.111.620484 (2012)
Effect of Complement CR1 on Brain Amyloid Burden During Aging and Its Modification by APOE Genotype M Thambisetty, Y An, M Nalls et al for the Baltimore Longitudinal Study of Aging and the Alzheimer's Disease Neuroimaging Initiative Biological Psychiatry, doi://10.1016/j.biopsych.2012.08.015 (2012)
CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, Fahad Saeed Proteomics, DOI: 10.1002/pmic.201200189 (2012)
Quantitative Phosphoproteomics in Nuclei of Vasopressin-Sensitive Renal Collecting Duct Cells Steven J. Bolger, Patricia A. Gonzales Hurtado, Jason D. Hoffert, Fahad Saeed, Trairak Pisitkun, and Mark A. Knepper Am J Physiol Cell Physiol, doi:10.1152/ajpcell.00260.2012 (2012)
Are Myocardial Infarction-Associated Single-Nucleotide Polymorphisms Associated With Ischemic Stroke? Cheng YC, Anderson CD, Bione S et al Stroke, doi: 10.1161/STROKEAHA.111.632075 (2012)
Lin28b Reprograms Adult Bone Marrow Hematopoietic Progenitors to Mediate Fetal-Like Lymphopoiesis Joan Yuan, Cuong K. Nguyen, Xiuhuai Liu, Chrysi Kanellopoulou, Stefan A. Muljo Science 335 (6073):1195-1200 (2012)

Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation AL Kovalchuk, C Ansarah-Sobrinho, O Hakim, W Resch, Helena Tolarová, W Dubois, A Yamane, M Takizawa, IKlein, GL Hager, HC Morse III, M Potter, MC Nussenzweig, and R Casellas PNAS, doi: 10.1073/pnas.1200106109 (2012)
Testing associations of copy number variations in genome-wide association studies Jianxin Shi and Peng Li Statistica Sinica, doi://10.5705/ss.2012.071s (2012)
Systems Biology in Physiology: The Vasopressin Signaling Network in Kidney Mark A. Knepper Am. J. Physiol. - Cell Physiol. , doi: 10.1152/ajpcell.00270.2012 (2012)
Comparing the Expected Misclassification Cost for Two Classifiers Based on Estimates From the Same Sample James F. Troendle, Kai F. Yu, Peter H. Westfall, Gene Pennello & Enrique F. Schisterman Statistics in Biopharmaceutical Research, DOI:10.1080/19466315.2012.695263 (2012)
Theory for cross effect dynamic nuclear polarization under magic-angle spinning in solid state nuclear magnetic resonance: The importance of level crossings Kent Thurber and Robert Tycko J. Chem. Phys. , doi://10.1063/1.4747449 (2012)
Prediction of variable translation rate effects on cotranslational protein folding Edward P. O'Brien, Michele Vendruscolo & Christopher M. Dobson Nature Communications, doi:10.1038/ncomms1850 (2012)
Directed evolution reveals requisite sequence elements in the functional expression of P450 2F1 in Escherichia coli JBYH Behrendorff, CD Moore, K-H Kim, D-H Kim, CA Smith, WA Johnston, C-H Yun, GS Yost, and EMJ Gillam Chemical Research in Toxicology, DOI: 10.1021/tx300281g (2012)
Using Genome-wide Complex Trait Analysis to quantify 'missing heritability' in Parkinson's disease MF Keller, M Saad, et al and International Parkinson's Disease Genomics Consortium and the Wellcome Trust Case Control Consortium 2 Human Molecular Genetics, doi: 10.1093/hmg/dds335 (2012)
Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics R Schmitz, RM Young et al Nature, doi:10.1038/nature11378 (2012)
Automated subcortical segmentation using FIRST: Test-retest reliability, interscanner reliability, and comparison to manual segmentation Allison C. Nugent, David A. Luckenbaugh, Suzanne E. Wood, Wendy Bogers, Carlos A. Zarate Jr., Wayne C Drevets Human Brain Mapping, DOI: 10.1002/hbm.22068 (2012)
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, Jeetain Mittal, Michael Feig, and Alexander D. MacKerell, Jr. J. Chem. Theory Comput., DOI: 10.1021/ct300400x (2012)
Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis Patrizia Farci, Kurt Wollenberg, Giacomo Diaz, Ronald E. Engle, Maria Eliana Lai, Paul Klenerman, Robert H. Purcell, Oliver G. Pybus, and Harvey J. Alter PNAS, doi: 10.1073/pnas.1210592109 (2012)

Multiple Testing of Composite Null Hypotheses in Heteroscedastic Models Wenguang Sun & Alexander C. McLain Journal of the American Statistical Association 107(498):637-687 (2012)
Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities F Mittag, F Büchel, M Saad, A Jahn, C Schulte, Z Bochdanovits, J Simón-Sánchez, MA Nalls, M Keller, DG Hernandez, JR Gibbs, S Lesage, A Brice, P Heutink, M Martinez, NW Wood, J Hardy, AB Singleton, A Zell, T Gasser, M Sharma for the International Parkinson's Disease Genomics Consortium (IPDGC) Human Mutation, DOI: 10.1002/humu.22161 (2012)
Drying Transition in the Hydrophobic Gate of the GLIC Channel Blocks Ion Conduction Fangqiang Zhu and Gerhard Hummer Biophys. J. 103(2):219-227, doi://10.1016/j.bpj.2012.06.003 (2012)
Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation Erin E. H. Tran, Mario J. Borgnia, Oleg Kuybeda, David M. Schauder, Alberto Bartesaghi, Gabriel A. Frank, Guillermo Sapiro, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1002797 (2012)
The impact of random-effect misspecification on percentile estimation for longitudinal growth data Kyeongmi Cheon, Paul S. Albert, Zhiwei Zhang Statistics in Medicine, DOI: 10.1002/sim.5437 (2012)
Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly Tranah GJ, Nalls MA, Katzman SM, Yokoyama JS, Lam ET, Zhao Y, Mooney S, Thomas F, Newman AB, Liu Y, Cummings SR, Harris TB, Yaffe K J. Alzheimer's Disease, doi://10.3233/JAD-2012-120466 (2012)
Weighted logrank tests for interval censored data when assessment times depend on treatment Michael P. Fay, Joanna H. Shih Statistics in Medicine, DOI: 10.1002/sim.5447 (2012)
Genetic Contributions to Individual Differences in Vulnerability to Addiction and Abilities to Quit George R. Uhl and Tomas Drgon in Drug Abuse and Addiction in Mental Illness, DOI: 10.1007/978-1-4614-3375-0-7 (2012)
Design and Assembly of Large Synthetic DNA Constructs Aleksandr E. Miklos, Randall A. Hughes, Andrew D. Ellington Current Protocols in Molecular Biology, DOI: 10.1002/0471142727.mb0323s99 (2012)
Leptin regulates dopamine responses to sustained stress in humans Paul R Burghardt, Tiffany M Love, Christian S. Stohler, Colin Hodgkinson, Pei-Hong Shen, Mary Ann Enoch, David Goldman, Jon-Kar Zubieta J. Neurosci. , doi: 10.1523/JNEUROSCI.2521-12.2012 (2012)
Estimating ancestral proportions in a multi-ethnic US sample: implications for studies of admixed populations Orna Levran, Olaoluwakitan Awolesi, Pei-Hong Shen, Miriam Adelson, and Mary Jeanne Kreek Human Genomics, doi: 10.1186/1479-7364-6-2 (2012)
The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics Michael G. Mage, Michael A. Dolan, Rui Wang, Lisa F. Boyd, Maria Jamela Revilleza, Howard Robinson, Kannan Natarajan, Nancy B. Myers, Ted H. Hansen and David H. Margulies J. Immunol. , doi: 10.4049/jimmunol.1200831 (2012)

The Folliculin-FNIP1 pathway deleted in human Birt-Hogg-Dubé syndrome is required for B cell development Baba M, Keller JR, Sun HW, Resch W, Kuchen S, Suh HC, Hasumi H, Hasumi Y, Kieffer-Kwon KR, Gonzalez CG, Hughes RM, Klein ME, Oh HF, Bible P, Southon E, Tessarollo L, Schmidt LS, Linehan WM, Casellas R. Blood, DOI 10.1182/blood-2012-02-410407 (2012)
Identifying Protein Kinase Target Preferences Using Mass Spectrometry Jacqueline Douglass, Ruwan Gunaratne, Davis Bradford, Fahad Saeed, Jason D. Hoffert, Peter J. Steinbach, Mark A. Knepper, and Trairak Pisitkun Cell Physiol., doi: 10.1152/ajpcell.00166.2012 (2012)
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im J. Phys. Chem. B, DOI: 10.1021/jp304056p (2012)
Crystal structure of a plectonemic RNA supercoil Jason R. Stagno, Buyong Ma, Jess Li, Amanda S. Altieri, R. Andrew Byrd & Xinhua Ji Nature Communications, doi:10.1038/ncomms1903 (2012)
Codon optimization for high level expression of human bone morphogenetic protein-2 in Escherichia coli Debbie S. Retnoningruma, H.T. Pramestia, P.Y. Santikaa, O. Valeriusb, S. Asjariea, T. Suciatia Prot. Expr. and Pur., doi://10.1016/j.pep.2012.05.010 (2012)
Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases Sarah Baxter, Abigail R. Lambert, Ryan Kuhar, Jordan Jarjour, Nadia Kulshina, Fabio Parmeggiani, Patrick Danaher, Jacob Gano, David Baker, Barry L. Stoddard and Andrew M. Scharenberg Nucleic Acids Research, doi: 10.1093/nar/gks502 (2012)

Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions Edward P O'Brien, John Christodoulou, Michele Vendruscolo, and Christopher M. Dobson J. Am. Chem. Soc. , DOI: 10.1021/ja302305u (2012)
Genomic Analysis of Immune Response against Vibrio cholerae Hemolysin in Caenorhabditis elegans Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Joseph E. LeClerc, and Hediye Nese Cinar PLoS One, doi: 10.1371/journal.pone.0038200 (2012)
Spontaneous High-Gamma Band Activity Reflects Functional Organization of Auditory Cortex in the Awake Macaque Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck Neuron, DOI 10.1016/j.neuron.2012.04.014 (2012)
Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly Gregory J. Tranah, Ernest T. Lam, Shana M. Katzman, Michael A. Nalls, Yiqiang Zhao, Daniel S. Evans, Jennifer S. Yokoyama, Ludmila Pawlikowska, Pui-Yan Kwok, Sean Mooney, Stephen Kritchevsky, Bret H. Goodpaster, Anne B. Newman, Tamara B. Harris, Todd M. Manini, Steven R. Cummings, For the Health, Aging and Body Composition Study Biochim. et Biophys. Acta - Bioenergetics, doi://10.1016/j.bbabio.2012.05.012 (2012)
An online tool for calculation of free-energy balance for the renal inner medulla Ryan L. Vilbig, Abhijit Sarkar, Joseph Zischkau, Mark A. Knepper, and Trairak Pisitkun Am. J. Physiol. , doi: 10.1152/ajprenal.00147.2012 (2012)
Application of systems biology principles to protein biomarker discovery: Urinary exosomal proteome in renal transplantation Trairak Pisitkun, Maria T. Gandolfo, Samarjit Das, Mark A. Knepper, Serena M. Bagnasco Proteomics -- Clinical Applications, doi://10.1002/prca.201100108 (2012)

Methods of adjusted comparison of medians James F. Troendle, Zhiwei Zhang, Megan E. Mathews, Junchi Guo Biometrical Journal, DOI: 10.1002/bimj.201100220 (2012)
Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions Margaret E. Johnson and Gerhard Hummer J. Phys. Chem. B, DOI: 10.1021/jp212611k (2012)
Tissue-Specific Regulation of Chromatin Insulator Function Leah H. Matzat, Ryan K. Dale, Nellie Moshkovich, and Elissa P. Lei PLoS Genetics, doi: 10.1371/journal.pgen.1003069 (2012)
A Subset-Based Approach Improves Power and Interpretation for the Combined Analysis of Genetic Association Studies of Heterogeneous Traits Samsiddhi Bhattacharjee, Preetha Rajaraman, Kevin B. Jacobs, William A. Wheeler, Beatrice S. Melin, Patricia Hartge, GliomaScan Consortium, Meredith Yeager, Charles C. Chung, Stephen J. Chanock, Nilanjan Chatterjee Am. J. Hum. Genet., doi:/10.1016/j.ajhg.2012.03.015 (2012)
Seeing is believing: video classification for computed tomographic colonography using multiple-instance learning. Shijun Wang, Matthew T McKenna, Tan B Nguyen, Joseph E Burns, Nicholas Petrick, Berkman Sahiner, Ronald M Summers IEEE Transactions on Medical Imaging 31 (5):1141 (2012)
Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins Xiang Yu, Yin Luo, Paul Dinkel, Jie Zheng, Guanghong Wei, Martin Margittai, Ruth Nussinov, Buyong Ma J. Biol. Chem., doi: 10.1074/jbc.M112.340794 (2012)

An Integrative Segmentation Method for Detecting Germline Copy Number Variations in SNP Arrays Jianxin Shi, Peng Li Genetic Epidemiology 36(4):373-383, DOI: 10.1002/gepi.21631 (2012)
Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP Yu Xu, Buyong Ma, and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp300307u (2012)
Imino Hydrogen Positions in Nucleic Acids from Density Functional Theory Validated by NMR Residual Dipolar Couplings Alexander Grishaev, Jinfa Ying, Ad Bax J. Am. Chem. Soc., doi: 10.1021/ja301775j (2012)
The transcriptome of Spodoptera exigua larvae exposed to different types of microbes Laura Pascual, Agata K. Jakubowska, Jose M. Blanca, Joaquin Cañizares, Juan Ferré, Gernot Gloeckner, Heiko Vogel, Salvador Herrero Insect Biochem. Mol. Bio. , doi://10.1016/j.ibmb.2012.04.003 (2012)
A Two-Platform Design for Next Generation Genome-Wide Association Studies Joshua N. Sampson, Kevin Jacobs, Zhaoming Wang, Meredith Yeager, Stephen Chanock, Nilanjan Chatterjee Genetic Epidemiology, doi: 10.1002/gepi.21634 (2012)
Postnatal development-and age-related changes in DNA-methylation patterns in the human genome Paraskevi Salpea, Valya R. Russanova, Tazuko H. Hirai, Thomae G. Sourlingas, Kalliope E. Sekeri-Pataryas, Roberto Romero, Jonathan Epstein and Bruce H. Howard Nucleic Acids Research, doi: 10.1093/nar/gks312 (2012)

Restraints on backbone conformations in solid state NMR studies of uniformly labeled proteins from quantitative amide¹⁵N-¹⁵N and carbonyl ¹³C-¹³C dipolar recoupling data Kan-Nian Hua, Wei Qiang, Guillermo A. Bermejo, Charles D. Schwieters, Robert Tycko J. Magnetic Resonance, doi:10.1016/j.jmr.2012.03.001 (2012)
The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis The Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium Lancet, doi: 10.1016/S0140-6736(12)60110-X (2012)
Distinct contributions of human hippocampal theta to spatial cognition and anxiety Brian R. Cornwell, Nicole Arkin, Cassie Overstreet, Frederick W. Carver, Christian Grillon Hippocampus, doi: 10.1002/hipo.22019 (2012)
Simple models of human brain functional networks Petra E. Vértes, Aaron F. Alexander-Bloch, Nitin Gogtay, Jay N. Giedd, Judith L. Rapoport, and Edward T. Bullmore PNAS, doi: 10.1073/pnas.1111738109 (2012)
Computational tools for metabolic engineering Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro Metabolic Engineering, doi:10.1016/j.ymben.2012.03.001 (2012)
Nickel (II)-Schiff base complex recognizing domain II of bovine and human serum albumin: Spectroscopic and docking studies Aurkie Ray, Banabithi Koley Seth, Uttam Pal, Samita Basu Spectrochimica Acta Part A: Molecular and Biomolecular Spect, doi:10.1016/j.saa.2012.02.060 (2012)
Modular engineering of a microbially-produced viral capsomere vaccine for influenza Nani Wibowo, Yap P. Chuan, Linda H.L. Lua, Anton P.J. Middelberg Chemical Engineering Science, doi:10.1016/j.ces.2012.04.001 (2012)
Predicting kinase-substrate interactions in the era of proteomics. Focus on “Identifying protein kinase target preferences using mass spectrometry” Ewout J. Hoorn and Marcel E. Meima Am J. Phyiol. Cell Physiol., 10.1152/ajpcell.00232.2012 (2012)
Search and Analysis of Identical Reverse Octapeptides in Unrelated Proteins Konda Mani Saravanan, Samuel Selvaraj Genomics, Proteomics & Bioinformatics, doi://10.1016/j.gpb.2012.11.005 (2012)
Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields Sergio A Hassan J. Chem. Phys. , doi://10.1063/1.4742910 (2012)
Effects of Point Substitutions on the Structure of Toxic Alzheimer's β-Amyloid Channels: Atomic Force Microscopy and Molecular Dynamics Simulations Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. Biochemistry, doi: 10.1021/bi300257e (2012)
Quantitative Proteomics Identifies Vasopressin-Responsive Nuclear Proteins in Collecting Duct Cells. Laura K. Schenk, Steven J. Bolger, Kelli Luginbuhl, Patricia A. Gonzales, Markus M. Rinschen, Ming-Jiun Yu, Jason D. Hoffert, Trairak Pisitkun and Mark A. Knepper J. Am. Soc. Nephrology, doi: 10.1681/ASN.2011070738 (2012)

Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis Javier Gonzalez-Castillo, Ziad S. Saad, Daniel A. Handwerker, Souheil J. Inati, Noah Brenowitz, and Peter A. Bandettini PNAS, doi: 10.1073/pnas.1121049109 (2012)
Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database Lill CM , Roehr JT , McQueen MB , Kavvoura FK , Bagade S , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002548 (2012)
Unraveling the ORE1 Regulon in Arabidopsis thaliana: Molecular and Functional Characterization of Up- and Down-stream Components von Lilian Paola Matallana-Ramírez PhD Thesis, University of Potsdam (2012)
SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome BA Liu, BW Engelmann, K Jablonowski, K Higginbotham, AB Stergachis and PD Nash Cell Communication and Signaling 10:27 (2012)
Optimization and Modeling of Protein Refolding Conditions Bernd Rainer Kurt Anselment PhD Thesis, Institute of Biochemical Engineering of the Technische Universit�t M�nchen (2012)
Cooperative Genome-Wide Analysis Shows Increased Homozygosity in Early Onset Parkinson's Disease Simón-Sánchez J , Kilarski LL , Nalls MA , Martinez M , Schulte C , et al. PLoS One, doi:10.1371/journal.pone.0028787 (2012)

Stochastic Modeling for the Expression of a Gene Regulated by Competing Transcription Factors Hsih-Te Yang, Minoru S. H. Ko PLoS One, doi:10.1371/journal.pone.0032376 (2012)
Marginal analysis of longitudinal count data in long sequences: Methods and applications to a driving study Zhiwei Zhang, Paul S. Albert, and Bruce Simons-Morton Ann.Appl.Stat. 6(1):27-54 (2012)
Theory and simulation of ion conduction in the pentameric GLIC channel Fangqiang Zhu and Gerhard Hummer J. Chem. Theory and Computation, doi: 10.1021/ct2009279 (2012)
A Meta-Analysis and Genome-Wide Association Study of Platelet Count and Mean Platelet Volume in African Americans Qayyum R , Snively BM , Ziv E , Nalls MA , Liu Y , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002491 (2012)
Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells Mangmang Li, Yunlong He, Wendy Dubois, Xiaolin Wu, Jianxin Shi, Jing Huang Molecular Cell, doi:10.1016/j.molcel.2012.01.020 (2012)
Modeling fecundity in the presence of a sterile fraction using a semi-parametric transformation model for grouped survival data Alexander McLain, Rajeshwari Sundaram, Germaine Buck Louis Stat. Meth. in Med. Res. , doi: 10.1177/0962280212438646 (2012)

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA Pavel P Khil, Fatima Smagulova, Kevin M Brick, R. Daniel Camerini-Otero and Galina V Petukhova Genome Res., doi:10.1101/gr.130583.111 (2012)
A Bayesian approach to mixture cure models with spatial frailties for population-based cancer relative survival data Binbing Yu, Ram C. Tiwari Canadian Journal of Statistics, doi: 10.1002/cjs.10135 (2012)
Using DNAWorks in Designing Oligonucleotides for PCR-Based Gene Synthesis. David Hoover Methods in Molecular Biology 852(3):215-223 (2012)
Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments. Michael A. Dolan, James W. Noah and Darrell Hurt Methods in Molecular Biology 857:399-414 (2012)
The elusive phosphotyrosine: pinning down a rare species. Focus on “Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination Carolyn M. Ecelbarger Am J Physiol Cell Physiol January 302:C16-C17 (2012)
Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging Gabriel A. Frank, Alberto Bartesaghi, Oleg Kuybeda, Mario J. Borgnia, Tommi A. White, Guillermo Sapiro, Sriram Subramaniam J. Struct. Biol. , doi:/10.1016/j.jsb.2012.01.004 (2012)

A Joint Mixed Effects Dispersion Model for Menstrual Cycle Length and Time-to-Pregnancy Alexander C. McLain, Kirsten J. Lum, Rajeshwari Sundaram Biometrics, doi: 10.1111/j.1541-0420.2011.01711.x (2012)
PDB Ligand Conformational Energies Calculated Quantum-Mechanically Markus Sitzmann, Iwona Wedlich, Igor V Filippov, Chenzhong Liao, Megan L. Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G Karki, Yulia V Borodina, Raul E Cachau, and Marc C Nicklaus J. Chem. Inf. Model. , doi: 10.1021/ci200595n (2012)
Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke The International Stroke Genetics Consortium (ISGC), the Wellcome Trust Case Control Consortium et al. Nature Genetics, doi:10.1038/ng.1081 (2012)
A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs Alexander Zawaira and Youtaro Shibayama J. Struct. Funct. Genomics, doi://10.1007/s10969-012-9141-7 (2012)
DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes Ofir Hakim, Wolfgang Resch, Arito Yamane, Isaac Klein, Kyong-Rim Kieffer-Kwon, Mila Jankovic, Thiago Oliveira, Anne Bothmer, Ty C. Voss, Camilo Ansarah-Sobrinho, Ewy Mathe, Genqing Liang, Jesse Cobell, Hirotaka Nakahashi, Davide F. Robbiani, Andre Nussenzweig, Gordon L. Hager, Michel C. Nussenzweig & Rafael Casellas Nature, doi:10.1038/nature10909 (2012)
Bubblegrams Reveal the Inner Body of Bacteriophage φKZ Weimin Wu, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, Alasdair C. Steven Science 335 (6065):182 (2012)

Integrated cross-species transcriptional network analysis of metastatic susceptibility Ying Hu, Gang Wu, Michael Rusch, Luanne Lukes, Kenneth H. Buetow, Jinghui Zhang, and Kent W. Hunter PNAS, doi: 10.1073/pnas.1117872109 (2012)
All-D-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Laura S Connelly, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Chem. Theory and Computation, doi: 10.1021/ct200885r (2012)
Inositol phosphate-induced stabilization of inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase and its role in substrate specificity Varin Gosein, Ting-Fung Leung, Oren Krajden, Gregory J. Miller Protein Science, doi: 10.1002/pro.2049 (2012)
Probing Structural Features of Alzheimer's β-Amyloid Pores in Bilayers Using Site-Specific Amino Acid Substitutions Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/bi2017427 (2012)
Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's β-Amyloid Peptide: Relevance to the Ion Channel Laura S Connelly, Fernando Teran Arce, Hyunbum Jang, Ricardo Capone, Samuel A Kotler, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/jp2108126 (2012)

2011 (131 papers)

Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies International Parkinson Disease Genomics Consortium Lancet, doi: 10.1016/S0140-6736(10)62345-8 (2011)

Comparing statistical methods for removing seasonal variation from vitamin D measurements in case-control studies Hong Zhang, Jiyoung Ahn, and Kai Yu Statistics and its Interface 3:85-93 (2011)
Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link Hyunbum Jang, Fernando Teran Arce, Mirela Mustata, Srinivasan Ramachandran, Ricardo Capone, Ruth Nussinov, Ratnesh Lal Biophys. J., doi: 10.1016/j.bpj.2011.01.072 (2011)
Quantifying Protein-Protein Interactions Within Noncovalent Complexes Using Electrospray Ionization Mass Spectrometry Elisabetta Boeri Erba, Konstantin Barylyuk, Yang Yang, and Renato Zenobi Anal. Chem. 83(24):9251-9259 (2011)
Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC. Cell 147(1):95-106 (2011)
Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering Thomas C. Markello, Ted Han, Hannah Carlson-Donohoe, Chidi Ahaghotu, Ursula Harper, MaryPat Jones, Settara Chandrasekharappa, Yair Anikster, David R. Adams, NISC Comparative Sequencing Program, William A. Gahl, Cornelius F. Boerkoel Mol. Genetics & Metabolism, doi:10.1016/j.ymgme.2011.12.014 (2011)
Independent component analysis of resting brain activity reveals transient modulation of local cortical processing by transcranial direct current stimulation. Venkatakrishnan A, Contreras-Vidal JL, Sandrini M, Cohen LG. Conf Proc IEEE Eng Med Biol Soc. Aug:8102-5 (2011)

The Anatomical Distance of Functional Connections Predicts Brain Network Topology in Health and Schizophrenia Aaron F. Alexander-Bloch, Petra E. Vértes, Reva Stidd, François Lalonde, Liv Clasen, Judith Rapoport, Jay Giedd, Edward T. Bullmore and Nitin Gogtay Cerebral Cortex, doi:10.1093/cercor/bhr388 (2011)
Parietofrontal integrity determines neural modulation associated with grasping imagery after stroke Ethan R. Buch, Amirali Modir Shanechi, Alissa D. Fourkas, Cornelia Weber, Niels Birbaumer and Leonardo G. Cohen Brain, doi:10.1093/brain/awr331 (2011)
Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman PLoS One, doi:10.1371/journal.pone.0029711 (2011)
Tryptic y++ Fragment Ion Distributions Are Guided by Coulombic Repulsion Karl K. Irikura, John K. Merle and Yamil Sim´n-Manso J. Am. Soc. Mass Spec., doi:10.1007/s13361-011-0293-7 (2011)
Structural models of TREK channels and their gating mechanism Adina L Milac, Andriy Anishkin, Sarosh N Fatakia, Carson C Chow, Sergei Sukharev, and H Robert Guy Channels, doi: 10.4161/chan.5.1.13905 (2011)
Overproduction of recombinant proteins in plants Erin Egelkrout, Vidya Rajan, John A. Howard Plant Science, doi:10.1016/j.plantsci.2011.12.005 (2011)
Expression, purification and characterization of recombinant human serine proteinase inhibitor Kazal-type 6 (SPINK6) in Pichia pastoris Hairong Lu, Jinjiang Huang, Guodong Li, Kuikui Ge, Hongyu Wu, Qingshan Huang Protein Expression and Purification, doi:10.1016/j.pep.2011.12.004 (2011)
Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions Alexander Samoshkin, Stanimir Dulev, Dmitry Loukinov, Jeffrey A. Rosenfeld and Alexander V. Strunnikov Chromosoma Biology of the Nucleus, doi: 10.1007/s00412-011-0353-6 (2011)
Effects of pH on proteins: Predictions for ensemble and single molecule pulling experiments Edward P O'Brien , Bernard R. Brooks , and Devarajan Thirumalai JACS, doi: 10.1021/ja206557y (2011)
Inherited Variation at Chromosome 12p13. 33, Including RAD52, Influences the Risk of Squamous Cell Lung Carcinoma Jianxin Shi, Nilanjan Chatterjee, Melissa Rotunno, Yufei Wang, Angela C. Pesatori, Dario Consonni, Peng Li, William Wheeler, Peter Broderick, Marc Henrion, Timothy Eisen, Zhaoming Wang, Wei Chen, Qiong Dong, Demetrius Albanes, Michael Thun, Margaret R. Spitz, Pier Alberto Bertazzi, Neil E. Caporaso, Stephen J. Chanock, Christopher I. Amos, Richard S. Houlston and Maria Teresa Landi Cancer Discovery, doi: 10.1158/2159-8290.CD-11-024 (2011)
Causal Inference on Quantiles with an Obstetric Application Zhiwei Zhang, Zhen Chen, James F. Troendle, and Jun Zhang Biometrics, doi: 10.1111/j.1541-0420.2011.01712.x (2011)
Does feature selection improve classification accuracy? Impact of sample size and feature selection on classification using anatomical magnetic resonance images Carlton Chu, Ai-Ling Hsu, Kun-Hsien Chou, Peter Bandettini, Ching-Po Lin, , and the Alzheimer's Disease Neuroimaging Initiative NeuroImage, doi:10.1016/j.neuroimage.2011.11.066 (2011)

Structural basis of anthrax edema factor neutralization by a neutralizing antibody Michelle Makiya, Michael Dolan, Liane Agulto, Robert Purcell, Zhaochun Chen Biochem. Biophys. Res. Comm., doi:10.1016/j.bbrc.2011.11.108 (2011)
High-level expression and characterization of a highly thermostable chitosanase from Aspergillus fumigatus in Pichia pastoris Xiaomei Chen, Chao Zhai, Lixin Kang, Chunhua Li, Hong Yan, Yuling Zhou, Xiaolan Yu and Lixin Ma Biotech. Letters, doi: 10.1007/s10529-011-0816-0 (2011)
Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging. Joel R. Meyerson, Tommi A. White et al J. Visualized Experiments, doi: 10.3791/2770 (2011)
Interaction of Merocyanine 540 with Serum Albumins: Photophysical and Binding Studies Mousumi Banerjee, Uttam Pal, Arijita Subudhhi, Abhijit Chakrabarti, Samita Basu J. Photochemistry and Photobiology B, doi:10.1016/j.jphotobiol.2011.12.005 (2011)
Gene Expression Databases for Kidney Epithelial Cells Jennifer C. Huling, Trairak Pisitkun, Jae H. Song, Ming-Jiun Yu, Jason D. Hoffert, and Mark A. Knepper Am. J. Physiol. - Renal Physiol., doi: 10.?1152/?ajprenal.?00457.?2011 doi: 10.?1152/?ajprenal.?00457.?2011 (2011)
Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics Jason D. Hoffert, Trairak Pisitkun, Fahad Saeed, Jae V. Song, Chung-Lin Chou and Mark A. Knepper Mol. Cell Proteomics, doi: 10.1074/mcp.M111.014613 (2011)
Standard reactions for comparative rate studies: Experiments on the dehydrochlorination reactions of 2-chloropropane, chlorocyclopentane, and chlorocyclohexane Iftikhar A. Awan, Donald R. Burgess Jr., Wing Tsang, Jeffrey A. Manion Int. J. Chem. Kinetics, doi: 10.1002/kin.20566 (2011)
Convergence and error estimation in free energy calculations using the weighted histogram analysis method Fangqiang Zhu, Gerhard Hummer J. Comp. Chem. , doi: 10.1002/jcc.21989 (2011)
The discovery of population differences in network community structure: New methods and applications to brain functional networks in schizophrenia Aaron Alexander-Bloch, Renaud Lambiotte, Ben Roberts, Jay Giedd, Nitin Gogtay, Ed Bullmore NeuroImage, doi:10.1016/j.neuroimage.2011.11.035 (2011)
A linear mixed model for predicting a binary event from longitudinal data under random effects misspecification Paul S. Albert Stat. Med., doi: 10.1002/sim.4405 (2011)
Antimicrobial Properties of Amyloid Peptides Bruce Kagan , Hyunbum Jang , Ricardo Capone , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , and Ruth Nussinov Molecular Pharmaceutics, doi: 10.1021/mp200419b (2011)
Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis Rasmus Siersbæk, Ronni Nielsen, Sam John, Myong-Hee Sung, Songjoon Baek, Anne Loft, Gordon L Hager and Susanne Mandrup Embo J. , doi:10.1038/emboj.2011.65 (2011)

Material properties of matrix lipids determine the conformation and intermolecular reactivity of diacetylenic phosphatidylcholine in the lipid bilayer Anu Puri , Hyunbum Jang , Amichai Yavlovich , Athar M Masood , Timothy D. Veenstra , Carlos Luna , Helim Aranda-Espinoza , Ruth Nussinov , and Robert Blumenthal Langmuir, doi: 10.1021/la203453x (2011)
Expressão e caracterização de fragmentos de anticorpos recominanes Anti-CD3 humano em Pichia pastoris Sousa, Victor Edgard Tavares Master's thesis, University of Brasilia (2011)
Genome-Wide Association Analysis of Ischemic Stroke in Young Adults Yu-Ching Cheng, Jeffrey R. O'Connel et al Genes | Genomes | Genetics, doi: 10.1534/g3.111.001164 (2011)
Three-Dimensional Structures of Soluble CD4-Bound States of Trimeric Simian Immunodeficiency Virus Envelope Glycoproteins Determined by Using Cryo-Electron Tomography Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, M. Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne and Sriram Subramaniam J. Virol., doi: 10.1128/?JVI.05297-11 (2011)
Dehydratase Mediated 1-Propanol Production in Metabolically Engineered Escherichia coli. Rachit Jain, Yajun Yan Microbial Cell Factories, doi:10.1186/1475-2859-10-97 (2011)
The Histone Database: an integrated resource for histones and histone fold-containing proteins Leonardo Mariño-Ramírez, Kevin M. Levine, Mario Morales, Suiyuan Zhang, R. Travis Moreland, Andreas D. Baxevanis and David Landsman J. Biol. Databases and Curation, doi: 10.1093/database/bar048 (2011)

Water-Exclusion Effects and Liquid-Structure Forces in Implicit Solvation Sergio A Hassan and Peter J Steinbach J. Phys. Chem. B, doi: 10.1021/jp208184e (2011)
Impact of surface roughness on diffusion of confined fluids William P. Krekelberg, Vincent K. Shen, Jeffrey R. Errington, and Thomas M. Truskett J. Chem. Phys. , doi:10.1063/1.3651478 (2011)
An electrostatic switch controls palmitoylation of the large conductance voltage-and calcium-activated potassium (BK) channel Owen Jeffries, Lijun Tian, Heather McClafferty & Michael J. Shipston. J. Biol. Chem. , doi: 10.1074/jbc.M111.224840 (2011)
Energetics of direct and water-mediated proton-coupled electron transfer. Ville R. I. Kaila and Gerhard Hummer JACS, doi: 10.1021/ja2082262 (2011)
Resting and Active States of the ERK2: HePTP Complex Dana M. Francis, Bartosz Rózycki, Antoni Tortajada, Gerhard Hummer, Wolfgang Peti, and Rebecca Page JACS, doi: 10.1021/ja2075136 (2011)
Dynamic water networks in cytochrome cbb3 oxidase Vivek Sharma, Mårten Wikströma, Ville R.I. Kaila Biochim. et Biophys. Acta, doi:10.1016/j.bbabio.2011.09.010 (2011)

Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry N'Diaye A, Chen GK et al. PLoS Genetics, doi:10.1371/journal.pgen.1002298 (2011)
Synthesis and bio-evaluation of human macrophage migration inhibitory factor inhibitor to develop anti-inflammatory agent Athar Alama, Chinmay Pala, Manish Goyala, Milan Kumar Kundub, Rahul Kumara, Mohd Shameel Iqbala, Sumanta Deya, Samik Bindua, Souvik Sarkara, Uttam Palc, Nakul C. Maitic, Susanta Adhikarid, Uday Bandyopadhyay Bioorganic and Medicinal Chemistry, doi:10.1016/j.bmc.2011.10.056 (2011)
Investigation of Anatomical Thalamo-Cortical Connectivity and fMRI Activation in Schizophrenia Stefano Marenco, Jason L Stein, Antonina A Savostyanova, Fabio Sambataro, Hao-Yang Tan, Aaron L Goldman, Beth A Verchinski, Alan S Barnett, Dwight Dickinson, José A Apud, Joseph H Callicott, Andreas Meyer-Lindenberg and Daniel R Weinberger Neuropsychopharmacology, doi: 10.1038/npp.2011.215 (2011)
NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies Trairak Pisitkun, Jason D. Hoffert, Fahad Saeed, and Mark A. Knepper Am. J. Cell. Physiol. , doi: 10.1152/ajpcell.00325.201 (2011)
A coarse-grained model for PEGylated lipids: the effect of PEGylation on size and shape of self-assembled structures Hwankyu Lee, Richard W. Pastor J. Phys. Chem. B, doi: 10.1021/jp2020148 (2011)
Oncogenically active MYD88 mutations in human lymphoma V.N. Ngo, R.M. Young, R. Schmitz et al Nature, doi:10.1038/nature09671 (2011)
Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel Ying Wang, Huimin Yu, Wensi Song, Ming An, Jing Zhang, Hui Luo, Zhongyao Shen J. Biosci. Bioeng., doi:10.1016/j.jbiosc.2011.08.027 (2011)
Capsomer Vaccines Protect Mice from Vaginal Challenge with Human Papillomavirus Wai-Hong Wu, Elizabeth Gersch, Kihyuck Kwak, Subhashini Jagu, Balasubramanyam Karanam, Warner K. Huh, Robert L. Garcea, Richard B. S. Roden PLoS One, doi:10.1371/journal.pone.0027141 (2011)
N-Protonated Isomers as Gateways to Peptide Ion Fragmentation Fredrik Haeffner, John K. Merle and Karl K. Irikura J. Am. Soc. Mass Spec., doi: 10.1007/s13361-011-0241-6 (2011)
PubChem3D: Biologically relevant 3-D similarity Sunghwan Kim , Evan E Bolton and Stephen H Bryant J. Cheminform., doi:10.1186/1758-2946-3-26 (2011)
Genomic Risk Profiling of Ischemic Stroke: Results of an International Genome-Wide Association Meta-Analysis James F. Meschia, Andrew Singleton, Michael A. Nalls, Stephen S. Rich, Pankaj Sharma, Luigi Ferrucci, Mar Matarin, Dena G. Hernandez, Kerra Pearce, Thomas G. Brott, Robert D. Brown Jr., John Hardy, Bradford B. Worrall PLoS One, doi:10.1371/journal.pone.0023161 (2011)
Large-Scale Phosphotyrosine Proteomic Profiling of Rat Renal Collecting Duct Epithelium Reveals Predominance of Proteins Involved in Cell Polarity Determination Boyang Zhao, Mark A. Knepper, Chung-Lin Chou, and Trairak Pisitkun Cell Physiol. , doi: 10.?1152/ajpcell.00300.2011 (2011)
Logistic regression analysis of biomarker data subject to pooling and dichotomization Z. Zhang, A. Liu, R.H., Lyles, B. Mukherjee Statistics in Medicine, doi: 10.1002/sim.4367 (2011)
Generalized degrees of freedom and adaptive model selection in linear mixed-effects models Bo Zhang, Xiaotong Shen, Sunni L. Mumford Comp. Stats & Data Anal., doi:10.1016/j.csda.2011.09.001 (2011)
Flexible cullins in cullin-ring E3 ligases allosterically regulate ubiquitination Jin Liu and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.277236 (2011)
Application of a yeast two-hybrid based screening system in the identification of amyloid-beta aggregation inhibitors in pharmaceutical plants Li-Wei Wang, Yan-Fang Yang, Ying-Tao Zhang J. Chinese Pharm. Sciences 20(5):510-517 (2011)
Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo Shehab A Ismail, Yong-Xiang Chen, Alexandra Rusinova, Anchal Chandra, Martin Bierbaum, Lothar Gremer, Gemma Triola, Herbert Waldmann, Philippe I H Bastiaens & Alfred Wittinghofer Nature Chem. Bio. , doi:10.1038/nchembio.686 (2011)
In silico implementation of synthetic gene networks. Mario Andrea Marchisio Methods in Mol. Bio. , doi: 10.1007/978-1-61779-412-4_1 (2011)
Selective cell-surface labeling of the molecular motor protein prestin Ryan M. McGuire, Jonathan J. Silberg, Fred A. Pereira, c, Robert M. Raphael Biochem. Biophys. Res. Comm., doi://10.1016/j.bbrc.2011.05.121 (2011)
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR Dmitry S. Kryndushkin, Reed B. Wickner, Robert Tycko J. Mol. Biol. , doi://10.1016/j.jmb.2011.03.067 (2011)
Latent class models for joint analysis of disease prevalence and high-dimensional semicontinuous biomarker data Bo Zhang, Zhen Chen and Paul S. Albert Biostatistics, doi: 10.1093/biostatistics/kxr024 (2011)
White Matter Microstructural Correlates of Superior Long-term Skill Gained Implicitly under Randomized Practice Sunbin Song, Nikhil Sharma, Ethan R. Buch and Leonardo G. Cohen Cerebral Cortex, doi: 10.1093/cercor/bhr247 (2011)
Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function C-T Liu, MK Garnaas et al. PLoS Genetics, doi:10.1371/journal.pgen.1002264 (2011)
A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies N. Akula, A. Baranova, D Seto, J Solka, MA Nalls, A Singleton, L Ferrucci, T Tanaka, S Bandinelli, YS Cho, YJ Kim, J-Y Lee, B-G Han, Bipolar Disorder Genome Study (BiGS) Consortium, The Wellcome Trust Case-Control Consortium, FJ McMahon PLoS One, doi:10.1371/journal.pone.0024220 (2011)
Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles Jason D. Hoffert, Trairak Pisitkun, R. Lance Miller. Transgenic Research, doi: 10.1007/s11248-011-9545-3 (2011)
Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water Jeetain MIttal and Robert B. Best Biophys. J. , doi: 10.1016/j.bpj.2010.05.005 (2011)
Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation Jin Liu and Ruth Nussinov Biophys. J. , doi: 10.1016/j.bpj.2010.05.021 (2011)
Polymorphic Triple β-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid β42 Peptide Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.241141 (2011)
Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials Holmes MV, Newcombe, P, Hubacek JA et a. The Lancet, doi:10.1016/S0140-6736 (2011)
Genome-wide Association Study for Serum Urate Concentrations and Gout among African Americans Identifies Genomic Risk Loci and a Novel URAT1 Loss-of-Function Allele Tin, A, Woordward OM et al. Hum. Mol. Genet., doi: 10.1093/hmg/ddr307 (2011)
Structural variants of IFNα preferentially promote antiviral functions Nancy Vázquez, Hana Schmeisser, Michael A. Dolan, Joseph Bekisz, Kathryn C. Zoon and Sharon M. Wahl Blood, doi:10.1182/blood-2010-12-325027 (2011)
Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs Kotb Abdelmohsen, Kumiko Tominaga, Eun Kyung Lee, Subramanya Srikantan, Min-Ju Kang, Mihee M. Kim, Roza Selimyan, Jennifer L. Martindale, Xiaoling Yang, France Carrier, Ming Zhan, Kevin G. Becker and Myriam Gorospe Nucleic Acids Research, doi: 10.1093/nar/gkr488 (2011)
A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease. International Parkinson's Disease Genomics Consortium (IPDGC) and Wellcome Trust Case Control Consortium 2 (WTCCC2) PLoS Genetics, doi: 10.1371/journal.pgen.1002142 (2011)
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers Kan-Nian Hu, Wei Qiang and Robert Tycko J. Biomol. NMR, doi: 10.1007/s10858-011-9517-1 (2011)
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures Audray Harris, Mario J. Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun (Kenneth) Kang, Rafael Depetris, Andre J. Marozsan, Rogier W. Sanders, Per Johan Klasse, Jacqueline L. S. Milne, Ian A. Wilson, William C. Olson, John P. Moore, and Sriram Subramaniam PNAS, doi: 10.1073/pnas.1101414108 (2011)
Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT) Reiner AP, Lettre G, Nalls MA, Ganesh SK, Mathias R, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002108 (2011)

Multiple Loci Are Associated with White Blood Cell Phenotypes Nalls MA, Couper DJ, Tanaka T, van Rooij FJA, Chen M-H, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002113 (2011)
Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): Identification of selective inhibitors of collagenase-1 (MMP-1) Harinath Bahudhanapati, Yingnan Zhang, Sachdev S. Sidhu and Keith Brew J. Biol. Chem. , doi: 10.1074/jbc.M111.253328 (2011)
Energetics and dynamics of proton transfer reactions along short water wires Ville R. I. Kaila and Gerhard Hummer Phys. Chem. Chem. Phys. , doi:10.1039/C1CP21112A (2011)
A survival analysis approach to modeling human fecundity Rajeshwari Sundaram, Alexander C. Mclain and Germaine M. Buck Louis Biostatistics, doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr01 (2011)
Simulated Self-Assembly of the HIV-1 Capsid: Protein Shape and Native Contacts Are Sufficient for Two-Dimensional Lattice Formation Bo Chen and Robert Tycko Biophys. J. , doi: 10.1016/j.bpj.2011.05.025 (2011)
PubChem3D: Similar conformers Evan Bolton, Sunghwan Kim and Stephen H Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-13. (2011)

Microscopic events in β-hairpin folding from alternative unfolded ensembles Robert Best & Jeetain Mittal PNAS, doi: 10.1073/pnas.1016685108 (2011)
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example Yongping Pan, Ruth Nussinov PLoS Computational Biology, doi:10.1371/journal.pcbi.1002077 (2011)
Thermodynamics of Boroxine Formation from the Aliphatic Boronic Acid Monomers R-B (OH) 2 (R= H, H3C, H2N, HO, and F): A Computational Investigation Krishna L. Bhat, George D. Markham, Joseph D. Larkin, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp202409m (2011)
Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis Juliet R. C. Pulliam, Jonathan H. Epstein, Jonathan Dushoff, Sohayati A. Rahman, Michel Bunning, Aziz A. Jamaluddin, Alex D. Hyatt, Hume E. Field, Andrew P. Dobson and Peter Daszak, the Henipavirus Ecology Research Group (HERG) Journal of the Royal Society Interface, doi: 10.1098/?rsif.2011.0223 (2011)
Tools for Vaccine Design: Prediction and Validation of Highly Immunogenic and Conserved Class II Epitopes and Development of Epitope-Driven Vaccines Manmohan Singh, Indresh K. Srivastava Anne S. De Groot, Matthew Ardito, Ryan Tassone, Paul Knopf, Leonard Moise, William Martin Development of Vaccines: From Discovery to Clinical Testing, John Wiley & Sons, doi: 10.1002/9781118023648.ch3 (2011)
Improved genetic association tests for an ordinal outcome representing the disease progression process Hong Zhang, Sholom Wacholder, Jing Qin, Allan Hildesheim, Kai Yu Genetic Epidemiology, doi: 10.1002/gepi.20599 (2011)
Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication Jeong-Yun Choi, Robert L. Eoff, Matthew G. Pence, Jian Wang, Martha V. Martin, Eun-Jin Kim, Lindsay M. Folkmann and F. Peter Guengerich J. Biol. Chem. , doi: 10.1074/jbc.M111.258038 (2011)
RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP Genes Dev., doi: 10.1101/gad.16651211 (2011)
Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation Fernando Terán Arce, Hyunbum Jang, Srinivasan Ramachandran, Preston B. Landon, Ruth Nussinov and Ratnesh Lal Soft Matter, doi: 10.1039/C1SM05162H (2011)
Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations Edina Rosta , Marcin Nowotny , Wei Yang , and Gerhard Hummer JACS, doi: 10.1021/ja200173a (2011)
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements Ofir Hakim, Myong-Hee Sung, Ty C. Voss, Erik Splinter, Sam John, Peter J. Sabo, Robert E. Thurman, John A. Stamatoyannopoulos, Wouter de Laat, and Gordon L. Hager Genome Research, doi:10.1101/gr.111153.110 (2011)
The association between inflammation-related genes and serum androgen levels in men: The prostate, lung, colorectal, and ovarian study Tamra E. Meyer, Lisa W. Chu, Qizhai Li, Kai Yu, Philip S. Rosenberg, Idan Menashe, Anand P. Chokkalingam, Sabah M. Quraishi, Wen-Yi Huang, Jocelyn M. Weiss, Rudolf Kaaks, Richard B. Hayes, Stephen J. Chanock, Ann W. Hsing The Prostate, doi: 10.1002/pros.21407 (2011)
Cystine knot peptides binding to Alpha IIb Beta 3 integrins and methods of use Cochran, J, Silverman, AP, Kariolis, Mihalis S. US Patent application 20110136740 (2011)
Protein Tertiary Structure Prediction based on main chain angle using a hybrid Bees Colony Optimization Algorithm ZN Mahmood, M. Mahmuddin, M.N. Mahmood International Journal of Modern Physics: Conference Series, DOI: 10.1142/S201019451200520X (2011)
Cloning and overexpression of influenza a H1N1 NS1 protein in escherichia coli Ong, Lih Lih Masters thesis, Universiti Teknologi Malaysia (2011)
Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states Yifat Miller, Buyong Ma, and Ruth Nussinov Biochemistry, doi: 10.1021/bi200400u (2011)
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli Claire R. Shen, Ethan I. Lan, Yasumasa Dekishima, Antonino Baez, Kwang Myung Cho, and James C. Liao App. Env. Microbiology, doi:10.1128/AEM.03034-10 (2011)
A joint modeling approach to data with informative cluster size: Robustness to the cluster size model Zhen Chen, Bo Zhang, Paul S. Albert Statistics in Medicine, doi: 10.1002/sim.4239 (2011)

On the stability and ranking of predictors from random forest variable importance measures Kristin K Nicodemus Brief. Bioinfo., doi: 10.1093/bib/bbr016 (2011)
Human Insulin production in E.Coli: Gene optimization, Assembly, Cloning and Protein Expression Gamal Abd El-Aziz, Metwali M.Reda, S.H.Abdel-Aziz, EL-Rashdy M. Redwan J. Biotech. Res. 11:37 (2011)
Thermochemistry of imidazolium-based ionic liquids: experiment and first-principles calculations Sergey P. Verevkin, Vladimir N. Emel'yanenko, Dzmitry H. Zaitsau, Andreas Heintz, Chris D. Muzny and Michael Frenkel Phys. Chem. Chem. Phys., doi:10.1039/C0CP00747A (2011)
Intermittent Hypoxia-Induced Sensitization of Central Chemoreceptors Contributes to Sympathetic Nerve Activity during Late Expiration in Rats Yaroslav I. Molkov, Daniel B Zoccal, Davi J.A. Moraes, Julian F.R. Paton, Benedito H. Machado, and Ilya A Rybak J. Neurophysiol., doi: 10.?1152/jn.00070.2011 (2011)
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide Guillem Revilla-López, Juan Torras, Ruth Nussinov, Carlos Alemán and David Zanuy Physical Chemistry Chemical Physics, doi: 10.1039/C0CP02572K (2011)
PubChem3D: Diversity of shape Evan Bolton, Sunghwan Kim, and Stephen Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-9 (2011)
Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1, 4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase Takuya Yoshizawa, Toshiyuki Shimizu, Mayuki Yamabe, Misako Taichi, Yuji Nishiuchi, Naoki Shichijo, Satoru Unzai, Hisashi Hirano, Mamoru Sato, Hiroshi Hashimoto FEBS Journal, doi: 10.1111/j.1742-4658.2011.08111.x (2011)
Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins Ana Damjanovic, Bernard R. Brooks, and Bertrand García-Moreno E J. Phys. Chem. , published online 23 Mar (2011)
Efficient Adaptively Weighted Analysis of Secondary Phenotypes in Case-Control Genome-Wide Association Studies Huilin Li and Mitchell Gail Human Heredity, DOI: 10.1159/000338943 (2011)
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase Dana M Francis, Bartosz Rózycki, Dorothy Koveal, Gerhard Hummer, Rebecca Page & Wolfgang Peti Nature Chem. Bio. , doi:10.1038/nchembio.707 (2011)
Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence Sergio A. Hassan J. Chem. Phys. 134:114508 (2011)
PubChem3D: a new resource for scientists Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen and Jiyao Wang, et al. J. Cheminform. 3:32 (2011)
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water Matthew Melillo, Fangqiang Zhu, Mark A. Snyder, and Jeetain Mittal J. Phys. Chem. Letters (2011)
Large-scale Exploration of Gene-Gene Interactions in Prostate Cancer Using a Multistage Genome-wide Association Study Julia Ciampa, Meredith Yeager, Laufey Amundadottir, Kevin Jacobs, Peter Kraft, Charles Chung, Sholom Wacholder, Kai Yu, William Wheeler, Michael J Thun, W Ryan Divers, Susan Gapstur, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Edward Giovannucci, Walter C Willet, Geraldine Cancel-Tassin, Olivier Cussenot, Antoine Valeri, David Hunter, Robert Hoover, Gilles Thomas, Stephen Chanock, and Nilanjan Chatterjee Cancer Res., doi: 10.1158/0008-5472.CAN-10-2646 (2011)
PubChem3D: Conformer generation. Evan E Bolton, Sunghwan Kim, and Stephen H Bryant J. Cheminform., doi: 10.1186/1758-2946-3-4 (2011)
Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's β by Solid-State NMR Spectroscopy Sudhakar Parthasarathy, Fei Long, Yifat Miller, Yiling Xiao, Dan McElheny, Kent Thurber, Buyong Ma, Ruth Nussinov, and Yoshitaka Ishii JACS, published online 22 Feb (2011)
Symmetry-Based Self-Assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers Buch, Idit; Tsai, Chung-Jung; J. Wolfson, Haim; Nussinov, Ruth Protein & Peptide Letters 18(4):362-372 (2011)
Genome-Wide Association Studies of the PR Interval in African Americans JG Smith, JW. Magnani, C Palmer, YA Meng, EZ Soliman, SK Musani, KF Kerr, RB Schnabel, SA Lubitz, N Sotoodehnia, S Redline, A Pfeufer, M Müller, DS Evans, MA Nalls, Y Liu, AB Newman, AB Zonderman, MK Evans, R Deo, PT Ellinor, DN Paltoo, C Newton-Cheh, E J Benjamin, R Mehra, A Alonso, SR Heckbert, ER Fox, Candidate-gene Association Resource (CARe) Consortium PLoS Genetics, doi:10.1371/journal.pgen.1001304 (2011)

Modelling batched Gaussian longitudinal weight data in mice subject to informative dropout Paul S. Albert, Joanna H Shih Stat. Meth. in Med. Res., doi: 10.1177/0962280210397886 (2011)
The Unique Alzheimer's β-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions Yifat Miller, Buyong Ma, and Ruth Nussinov J. Am. Chem. Soc., doi: 10.1021/ja1100273 (2011)
Novel HIV-1 protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran, that are potent against multi-PI-resistant HIV-1 variants Kazuhiko Ide, Manabu Aoki, Masayuki Amano, Yasuhiro Koh, Ravikiran S. Yedidi, Debananda Das, Sofiya Leschenko, Bruno Chapsal, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob Agents Chemother., doi:10.1128/AAC.01540-10 (2011)
Binding of a C-end rule peptide to neuropilin-1 receptor: A molecular modeling approach Nurit Haspel , David Zanuy , Ruth Nussinov , Tambet Teesalu , Erkki Ruoslahti , and Carlos Aleman Biochemistry, doi: 10.1021/bi101662j (2011)
SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions Bartosz Rózycki, Young C. Kim and Gerhard Hummer Structure, doi:10.1016/j.str.2010.10.006 (2011)
Distinct DNA methylation changes highly correlated with chronological age in the human brain Dena G Hernandez, Michael A Nalls, J Raphael Gibbs, Sampath Arepalli, Marcel van der Brug, Sean Chong, Matthew Moore, Dan L Longo, Mark Cookson, Bryan J Traynor and Andrew Singleton Human Molecular Genetics, published online 7 Jan (2011)
An Audit Strategy for Progression-Free Survival Lori E. Dodd, Edward L. Korn, Boris Freidlin, Robert Gray, Suman Bhattacharya Biometrics, doi: 10.1111/j.1541-0420.2010.01539.x (2011)
Atomistic modeling of peptides bound to a chemically active surface: conformational implications David Curcó, Guillem Revilla-López, Carlos Alemán, David Zanuy J. Peptide Science, doi: 10.1002/psc.1321 (2011)
Genome-wide association study implicates PARD3B-based AIDS restriction Troyer, J.L., Nelson, G.W., Lautenberger, J.A., Chinn, L., McIntosh, C., Johnson, R.C., Sezgin, E., Kessing, B., Malasky, M., Hendrickson, S.L., Li, G., Pontius, J., Tang, M., An, P., Winkler, C.A., Limou, S., Le Clerc, S., Delaneau, O., Zagury, J.-F., Schuitemaker, H., van Manen, D., Bream, J.H., Gomperts, E.D., Buchbinder, S., Goedert, J.J., Kirk, G.D., O'Brien, S.J. J. Infect. Dis 203(10):1491-502 (2011)
De novo Synthesis and Expression of a Thermostable Xylanase from Geobacillus stearothermophilus in Escherichia coli Zhang Zhigang, Pei Xiaoqiong & Wu Zhongliu Chin. J. Appl. Environ. Biol., doi: 10.3724/SP.J.1145.2009.00271 (2011)

2010 (94 papers)

Polymorphic C-terminal β-sheet interactions determine the formation of fibril or ADDL-like globulomer for the Alzheimer Aβ42 dodecamer Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M110.133488 (2010)
Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders Jeetain Mittal and Robert B Best BIophys. J. 98(2):315-320 (2010)

Predicting In Vitro Drug Sensitivity using Random Forests Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, and Howard A. Fine Bioinformatics, published online 5 Dec (2010)
Large-Scale Phosphoproteomic Analysis of Membrane Proteins in Renal Proximal and Distal Tubule Marina Feric, Boyang Zhao, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper Am. J. Physiol. - Cell Physiol. , doi: 10.1152/ajpcell.00360.2010 (2010)
Microarray Meta-Miner (MMM): An integrated method and a web tool to identify genes with similar expression profile Nagarajan, V.; Varma, S.; Hurt, D.; Yongjian Guo; Huyen, Y Computer Technology and Development, doi:10.1109/ICCTD.2010.5646068 (2010)
Atomic-Scale Simulations Confirm that Soluble β-Sheet-Rich Peptide Self-Assemblies Provide Amyloid Mimics Presenting Similar Conformational Properties Xiang Yu, Jingdai Wang, Jui-Chen Yang, Qiuming Wang, Stephen Z.D. Cheng, Ruth Nussinov, and Jie Zheng Biophys. J. 98(1):27-36 (2010)
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks Margaret E. Johnson and Gerhard Hummer PNAS, doi: 10.1073/pnas.1010954108 (2010)
Molecular Architectures of Trimeric SIV and HIV-1 Envelope Glycoproteins on Intact Viruses: Strain-Dependent Variation in Quaternary Structure Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, Joel R. Meyerson, M. Jason V. de la Cruz, Julian W. Bess, Rachna Nandwani, James A. Hoxie, Jeffrey D. Lifson, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1001249 (2010)

Nanoscale architecture of integrin-based cell adhesions Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, Hess HF, Waterman CM. Nature 468(7323):580-4 (2010)
Accounting for multiple comparisons in a genome-wide association study (GWAS) Randall C Johnson, George W Nelson, Jennifer L Troyer, James A Lautenberger, Bailey D Kessing, Cheryl A Winkler, Stephen J O'Brien BMC Genomics 11:724 (2010)
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations Sijung Yun and Robert H Guy J. Mol. Graph. and Modeling, doi:10.1016/j.jmgm.2010.12.002 (2010)
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences Robert B Best, Jeetain Mittal Proteins: Structure, Function and Bioinf, doi: 10.1002/prot.22972 (2010)
The Human Glucocorticoid Receptor as an RNA-Binding Protein: Global Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif Ishmael FT, Fang X, Houser KR, Pearce K, Abdelmohsen K, Zhan M, Gorospe M, Stellato C. J. Immunol. , doi:10.4049/jimmunol.1001794 (2010)
Comprehensive engineering of Escherichia coli for enhanced expression of IgG antibodies Tomohiro Makinoa, Georgios Skretas, Tae Hyun Kang and George Georgiou Metabolic Engg. , doi:10.1016/j.ymben.2010.11.002 (2010)

Analysis of progression-free survival data using a discrete time survival model that incorporates measurements with and without diagnostic error Sally Hunsberger, Paul S Albert, Lori Dodd Clinical Trials, doi: 10.1177/1740774510384887 (2010)
Microscopic properties of nanopore water from its time-dependent dielectric response Jürgen Köfinger and Christoph Dellago Phy. Rev. B 82:205416 (2010)
Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero and Teresa M Przytycka Genome Biology 11:R103, doi:10.1186/gb-2010-11-10-r103 (2010)
Expression of Recombinant Cytochromes c in E. coli. Yuri Londer Methods in Molecular Biology 705:123-150 (2010)
Analysis of the stabilities of hexameric amyloid-β (1-42) models using discrete molecular dynamics simulations Sijung Yun, Sajung Yun and H. Robert Guy J. Mol. Graphics and Modelling, doi:10.1016/j.jmgm.2010.11.008 (2010)
Crystal Structures Exploring the Origins of the Broader Specificity of Escherichia coli Heat-Labile Enterotoxin Compared to Cholera Toxin Holmner A, Mackenzie A, Okvist M, Jansson L, Lebens M, Teneberg S, Krengel U. J. Mol. Biol. , doi:10.1016/j.jmb.2010.11.060 (2010)

RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics Gelio Alves, Aleksey Y. Ogurtsov, and Yi-Kuo Yu PLoS One 5(11):e15438 (2010)
Origin of Twist-Bend Coupling in Actin Filaments Enrique M. De La Cruz, Jeremy Roland, Brannon R. McCullough, Laurent Blanchoin, Jean-Louis Martiel Biophys. J. , doi:10.1016/j.bpj.2010.07.009 (2010)
Approximating probabilities of correlated events Li QiZhai, Zheng Gang, Liu AiYi, Li ZhaoHai & Yu Kai Science China Mathematics 53(11):2937-2948 (2010)
Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1β Hao Yin, Guogang Feng, G. Marius Clore, Gerhard Hummer, and Jayendran C. Rasaiah J. Phy. Chem. B, doi: 10.1021/jp108731r (2010)
Assigning statistical significance to proteotypic peptides via database searches Gelio Alves, Aleksey Ogurtsov, Yi-Kuo Yu J. Proteomics, doi:10.1016/j.jprot.2010.10.005 (2010)
A Computational Investigation of the Nitrogen-Boron Interaction in o-(N, N-Dialkylaminomethyl) arylboronate Systems Joseph D. Larkin, John S. Fossey, Tony D. James, Bernard R. Brooks, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp1087674 (2010)

Multiple imputation for estimating the risk of developing dementia and its impact on survival Binbing Yu, Jane S. Saczynski, Lenore Launer Biometrical Journal 52(5) :616-627 (2010)
Pore opening and closing of a pentameric ligand-gated ion channel Fangqiang Zhu and Gerhard Hummer PNAS, doi: 10.1073/pnas.1009313107 (2010)
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse Robert B Best and Jeetain Mittal J. Phys. Chem. B, doi: 10.1021/jp108618d (2010)
Nematic Order in Small Systems: Measuring the Elastic and Wall-Anchoring Constants in Vibrofluidized Granular Rods Jennifer Galanis, Ralph Nossal, Wolfgang Losert, and Daniel Harries Phys. Rev. Let. 105:168001 (2010)
β-Barrel Topology of Alzheimer's β-Amyloid Ion Channels Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal, and Ruth Nussinov J. Mol. Biol. , doi:10.1016/j.jmb.2010.10.025 (2010)
Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells Sookkasem Khositseth, Trairak Pisitkun, Dane H. Slentz, Guanghui Wang, Jason D. Hoffert, Mark A. Knepper* and Ming-Jiun Yu Molecular & Cellular Proteomics, doi: 10.1074/mcp.M110.004036 (2010)
An approach for jointly modeling multivariate longitudinal measurements and discrete time-to-event data Paul S. Albert and Joanna H. Shih Ann. Appl. Stat. 4(3):1517-1532 (2010)
Electrostatic Interactions and Binding Orientation of HIV-1 Matrix Studied by Neutron Reflectivity Hirsh Nanda, Siddhartha A.K. Datta, Frank Heinrich, Mathias L�sche, Alan Rein, Susan Krueger, Joseph E. Curtis Biophys. J. , doi: 10.1016/j.bpj.2010.07.062 (2010)
Biological Validation of Increased Schizophrenia Risk With NRG1, ERBB4, and AKT1 Epistasis via Functional Neuroimaging in Healthy Controls Kristin K. Nicodemus, Amanda J. Law, Eugenia Radulescu, Augustin Luna, Bhaskar Kolachana, Radhakrishna Vakkalanka, Dan Rujescu, Ina Giegling, Richard E. Straub, Kate McGee, Bert Gold, Michael Dean, Pierandrea Muglia, Joseph H. Callicott, Hao-Yang Tan, Daniel R. Weinberger Arch. Gen. Psych. 67(10):991-1001 (2010)
Conformational Profile of a Proline-Arginine Hybrid Guillermo Revilla-López, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán, and David Zanuy J. Chem. Inf. and Modeling, doi: 10.1021/ci100135f (2010)
Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis Satish K Madala, Michael A. Dolan, Deepak Sharma, Thirumalai R. Ramalingam, Mark S. Wilson, Margaret M. Mentink-Kane, Daniel C. Masison, Thomas A. Wynn Proteins: Structure, Function and Bioinf, doi: 10.1002/prot.22881 (2010)
Robust and accurate data enrichment statistics via distribution function of sum of weights. Stojmirovic A, Yu YK Bioinformatics, doi: 10.1093/bioinformatics/btq511 (2010)

Using Principal Components of Genetic Variation for Robust and Powerful Detection of Gene-Gene Interactions in Case-Control and Case-Only Studies Samsiddhi Bhattacharjee, Zhaoming Wang, Julia Ciampa, Peter Kraft, Stephen Chanock, Kai Yu and Nilanjan Chatterjee Am. J. Hum. Genet. 86(3):331-342 (2010)
Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber Sun-Shin Cha1, Young Jun An, Chang Ro Lee, Hyun Sook Lee, Yeon-Gil Kim, Sang Jin Kim, Kae Kyoung Kwon, Gian Marco De Donatis, Jung-Hyun Lee, Michael R Maurizi and Sung Gyun Kang Embo J. , doi:10.1038/emboj.2010.226 (2010)
Models of membrane-bound Alzheimer's abeta peptide assemblies Yinon Shafrir, Stewart Durell, Nelson Arispe, H. Robert Guy Proteins, doi: 10.1002/prot.22853 (2010)
In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors Yasuhiro Koh, Masayuki Amano, Tomomi Towata, Matthew Danish, Sofiya Leshchenko-Yashchuk, Debananda Das, Maki Nakayama, Yasushi Tojo, Arun K. Ghosh, and Hiroaki Mitsuya J. Virol. , doi:10.1128/JVI.00967-10 (2010)
Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP A. Cardone, S.A. Hassan, R.W. Albers, R.D. Sriram and H.C. Pant J. Mol. Biol., doi:10.1016/j.jmb.2010.06.040 (2010)
Hollow core of Alzheimer's Aβ42 amyloid observed by cryoEM is relevant at physiological pH Yifat Miller, Buyong Ma, Chung-Jung Tsai, Ruth Nussinov PNAS, 10.1073/pnas.1004704107 (2010)

Population dynamics of a pathogen: the conundrum of vivax malaria Philip G. McQueen Biophys. Revs. 2(3):111-120 (2010)
Scaling Factors and Uncertainties for ab Initio Anharmonic Vibrational Frequencies Russell D. Johnson, III, Karl K. Irikura, Raghu N. Kacker and Rdiger Kessel J. Chem. Theory. Comp., doi: 10.1021/ct100244d (2010)
Molecular Basis for the Structural Stability of an Enclosed β Barrel Loop Pu Tian and Harris D. Bernstein J. Mol. Biol. , doi:10.1016/j.jmb.2010.07.035 (2010)
Predictive Correlations Based on Large Experimental Datasets: Critical Constants for Pure Compounds Andrei Kazakov, Chris D. Muzny, Vladimir Diky, Robert D. Chirico and Michael Frenkel Fluid Phase Equilibria 298(1):131-142 (2010)
Using Cases to Strengthen Inference on the Association between Single Nucleotide Polymorphisms and a Secondary Phenotype in Genome-Wide Association Studies Huilin Li, Mitchell H. Gail, Sonja Berndt, and Nilanjan Chatterjee Genet. Epidemiol. 34(5):427-433 (2010)
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization Yongping Pan and Ruth Nussinov PLoS Computational Biology, doi: 10.1371/journal.pcbi.1000878. (2010)
Release of genotype 1 hepatitis E virus from cultured hepatoma and polarized intestinal cells depends on ORF3 protein and requires an intact PXXP motif Suzanne U. Emerson, Hanh T. Nguyen, Udana Torian, Danielle Burke, Ronald Engle and Robert H. Purcell J. Virol. , doi:10.1128/JVI.00593-10 (2010)
Structural Convergence Among Diverse, Toxic β-Sheet Ion Channels Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp104073k (2010)
The Influence of GABRA2, Childhood Trauma and their Interaction on Alcohol, Heroin and Cocaine Dependence Mary-Anne Enoch, Colin A Hodgkinson, Qiaoping Yuan, Pei-Hong Shen, David Goldman, Alec Roy Biol Psychiatry., doi: 10.1016/j.biopsych.2009.08.019 (2010)
Genome-wide association identifies candidate genes that influence the human electroencephalogram Colin A. Hodgkinson, Mary-Anne Enoch, Vibhuti Srivastava et al. PNAS, doi: 10.1073/pnas.0908134107 (2010)
Multiple chronic pain states are associated with a common amino acid�changing allele in KCNS1 Michael Costigan, Inna Belfer, Robert S. Griffin et al. Brain, doi: 10.1093/brain/awq195 (2010)
Haplotype-Based Study of the Association of Alcohol Metabolizing Genes with Alcohol Dependence in Four Independent Populations Jixia Liu, Zhifeng Zhou, Colin A. Hodgkinson, Qiaoping Yuan, Pei-Hong Shen, Connie J. Mulligan, Alex Wang, Rebecca R. Gray, Alec Roy, Matti Virkkunen, David Goldman, Mary-Anne Enoch Alcohol Clin Exp Res., doi: 10.1111/j.1530-0277.2010.01346.x (2010)
Mutations from a family-shuffling-library reveal amino acid residues responsible for the thermostability of endoglucanase CelA from Clostridium thermocellum Zhuo-Lin Yi and Zhong-Liu Wu Biotech. Letters, 10.1007/s10529-010-0363-0 (2010)
Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA Randall A. Hughes and Andrew D. Ellington Nucleic Acids Research, doi:10.1093/nar/gkq521 (2010)
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA. J. Am. Soc. Nephrol. 21(2):303-15 (2010)
De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. Protein Science 19(2):349-56 (2010)
Balance between α and β Structures in Ab Initio Protein Folding Robert B. Best and Jeetain Mittal J. Phys. Chem. B , doi: 10.1021/jp102575b (2010)
Tautomerism and Magnesium Chelation of HIV-1 Integrase Inhibitors: A Theoretical Study Chenzhong Liao and Marc C. Nicklaus Chem Med Chem, published online 8 Jun (2010)

FastMEDUSA: A parallelized tool to infer gene regulatory networks Serdar Bozdag, Aiguo Li, Stefan Wuchty, Howard A. Fine Bioinformatics, doi:10.1093/bioinformatics/btq275 (2010)
Structural basis of G protein-coupled receptor-G protein interactions Jianxin Hu, Yan Wang, Xiaohong Zhang, John R Lloyd, Jian Hua Li, Joel Karpiak, Stefano Costanzi, J¨rgen Wess Nature Chem. Biol., doi:10.1038/nchembio.385 (2010)
Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies Ricardo Capone, Mirela Mustata, Hyunbum Jang, Fernando Teran Arce, Ruth Nussinov, and Ratnesh Lal Biophys. J., doi: 10.1016/j.bpj.2010.02.024 (2010)
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor J. Phys. Chem. B, published online 24 May (2010)
Comparison of multivariate classifiers and response normalizations for pattern-information fMRI Masaya Misaki, Youn Kima, Peter A. Bandettini and Nikolaus Kriegeskorte Neuroimage, doi:10.1016/j.neuroimage.2010.05.051 (2010)
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain J. Raphael Gibbs, Marcel P. van der Brug, Dena G. Hernandez, Bryan J. Traynor, Michael A. Nalls, Shiao-Lin Lai, Sampath Arepalli, Allissa Dillman, Ian P. Rafferty, Juan Troncoso, Robert Johnson, H. Ronald Zielke, Luigi Ferrucci, Dan L. Longo, Mark R. Cookson, Andrew B. Singleton PLoS Genetics 6(5):e1000952, doi:10.1371/journal.pgen.1000952 (2010)

Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states Yifat Miller, Buyong Ma, and Ruth Nussinov PNAS, published online 6 May (2010)
Efficient expression and purification of human aglycosylated Fcγ receptors in Escherichia coli Sang Taek Jung, Tae Hyun Kang, George Georgiou Biotech. and Bioengg., published online 7 May (2010)
Emotional Automaticity Is a Matter of Timing Qian Luo, Tom Holroyd, Catherine Majestic, Xi Cheng, Julia Schechter, and R. James Blair J. Neuroscience 30(17):5825-5829 (2010)
How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel? Dan Fishelovitch, Sason Shaik, Haim J. Wolfson and Ruth Nussinov J. Phys. Chem. B 114(17):5964-5970 (2010)
Improving polyp detection algorithms for CT colonography: Pareto front approach Adam Huang, Jiang Li, Ronald M. Summers, Nicholas Petrick, Amy K. Hara Pattern Recognition Letters, doi:10.1016/j.patrec.2010.03.013 (2010)
Solution conformation and dynamics of the HIV-1 integrase core domain Nicholas C. Fitzkee, James E. Masse, Yang Shen, David R. Davies, and Ad Bax J. Biol. Chem. , doi/10.1074/jbc.M110.113407 (2010)
Use of Multiple Assays Subject to Detection Limits With Regression Modeling in Assessing the Relationship Between Exposure and Outcome Albert, Paul S, Harel, Ofer, Perkins, Neil, Browne, Richard Epidemiology, doi: 10.1097/EDE.0b013e3181ce9eed (2010)
Low-Temperature Dynamic Nuclear Polarization at 9.4 Tesla With a 30 Milliwatt microwave source Kent R. Thurber, Wai-Ming Yau and Robert Tycko J. Magnetic Resonance :doi:10.1016/j.jmr.20 (2010)
Neural substrates of graphomotor sequence learning: A combined fMRI and kinematic study Bruce A. Swett, Jose L. Contreras-Vidal, Rasmus Birn and Allen R. Braun J. Neurophysiol., doi:10.1152/jn.00449.2009 (2010)
Extensive and Modular Intrinsically Disordered Segments in C. elegans TTN-1 and Implications in Filament Binding, Elasticity and Oblique Striation Jeffrey G. Forbes, Denise B. Flaherty, Kan Ma, Hiroshi Qadota, Guy M. Benian, and Kuan Wang J. Mol. Biol. , doi:10.1016 (2010)
A Novel Point Mutation in Helix 10 of the Human Glucocorticoid Receptor Causes Generalized Glucocorticoid Resistance by Disrupting the Structure of the Ligand-Binding Domain Nancy Nader, Bert E. Bachrach, Darrell E. Hurt, Sonia Gajula, Amy Pittman, Rachel Lescher, and Tomoshige Kino J. Clin. Endocrin. & Metab., published online 24 March (2010)
Engineering anti-VEGF disulfide-stabilized single chain antibody variable fragments (sc-dsFv) with phage displayed sc-dsFv libraries Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Ching-Ching Tung, Hung-Ju Chang and An-Suei Yang J. Biol. Chem. , published online 12 Jan (2010)
Engineering Anti-vascular Endothelial Growth Factor Single Chain Disulfide-stabilized Antibody Variable Fragments (sc-dsFv) with Phage-displayed sc-dsFv Libraries Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Tung Ching Ching, Hung-Ju Chang, An-Suei Yang J. Biol. Chem. 285:7880-7891 (2010)
Depletion forces drive polymer-like self-assembly in vibrofluidized granular materials Jennifer Galanis, Ralph Nossal, and Daniel Harries Soft Matter 6:1026-1034 (2010)
The behaviour of random forest permutation-based variable importance measures under predictor correlation Kristin Nicodemus, James Malley, Carolin Srobl, Andreas Ziegler BMC Bioinformatics 11:110 (2010)
Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases Jin Liu and Ruth Nussinov J. Mol. Biol. 396(5):1508-1523 (2010)
Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells Markus M. Rinschen, Ming-Jiun Yu, Guanghui Wang, Emily S. Boja, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper PNAS, doi/10.1073/pnas.0910646107 (2010)
Noncoding RNA Gas5 Is a Growth Arrest-and Starvation-Associated Repressor of the Glucocorticoid Receptor Tomoshige Kino, Darrell E. Hurt, Takamasa Ichijo, Nancy Nader, and George P. Chrousos Sci. Signal. 3(107):ra8 (2010)

Functional Significance for an Heterogenous Ribonucleoprotein A18 (hnRNP A18) Signature RNA Motif in the 3'UTR of Ataxia Telengiectasia Mutated and RAD3 Related (ATR) Transcript Ruiqing Yang, Ming Zhan, Narasimha Rao Nalabothula, Qingyuan Yang, Fred E. Indig and France Carrier J. Biol. Chem., published online 26 Jan (2010)
Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging Kristin K. Nicodemus, Joseph H. Callicott, Rachel G. Higier, Augustin Luna, Devon C. Nixon, Barbara K. Lipska, Radhakrishna Vakkalanka, Ina Giegling, Dan Rujescu, David St. Clair, Pierandrea Muglia, Yin Yao Shugart and Daniel R. Weinberger Human Genetics 10.1007:s00439-009-0782-y (2010)
Meta-analysis of genome-wide association data detects a risk locus for major mood disorders on chromosome 3p21. 1 Francis J McMahon, Nirmala Akula, Thomas G Schulze, Pierandrea Muglia, Federica Tozzi, Sevilla D Detera-Wadleigh, C J M Steele, René Breuer, Jana Strohmaier, Jens R Wendland, Manuel Mattheisen, Thomas W Mühleisen, Wolfgang Maier, Markus M Nöthen, Sven Cichon, Anne Farmer, John B Vincent, Florian Holsboer, Martin Preisig & Marcella Rietschel for the Bipolar Disorder Genome Study (BiGS) Consortium Nature Genetics 42:128-131 (2010)
Interfacial thermodynamics of confined water near molecularly rough surfaces Jeetain Mittal and Gerhard Hummer Faraday Discussions: Wetting Dynamics of Hydrophobic and Str (2010)
Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map Pavel P. Khil and R. Daniel Camerini-Otero PLoS Genetics 6(1):e1000831 (2010)
Genome Wide Association for Addiction: Replicated Results and Comparisons of Two Analytic Approaches Tomas Drgon, Ping-Wu Zhang, Catherine Johnson, Donna Walther, Judith Hess, Michelle Nino, and George R. Uhl PLoS One 5(1):e8832 (2010)
Construction of synthetic open reading frame encoding human interferon alpha 2b for high expression in Escherichia coli and characterization of its gene product Debbie S. Retnoningrum, Ratih A. Ningruma, Yohanes N. Kurniawana, Ana Indrayatia and Heni Rachmawati J. Biotechnol. 145(2):193-198 (2010)
JAGS Version 2.2.0 user manual Martyn Plummer Testing of JAGS was carried out on Helix. (2010)

2009 (84 papers)

Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios Yongpin Pan and Ruth Nussinov J. Mol. Recognit. 23(2):232-40 (2009)
Computational Investigation of the Oxidative Deboronation of Boroglycine, H2N-CH2-B (OH) 2, Using H2O and H2O2 Larkin JD, Markham GD, Milkevitch M, Brooks BR, Bock CW. J. Phys. Chem. A 113(41):11028-34 (2009)
Modeling Familial Association of Ages at Onset of Disease in the Presence of Competing Risk Joanna Shih and Paul S Albert Biometrics, published online 9 Dec (2009)
JAGS v2.0 Martyn Plummer (2009)
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts Yang Shen and Ad Bax J. Biomolec. NMR 10.1007:s10858-009-9395-y (2009)
Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA Juan A. Castelán-Vega, Alicia Jiménez-Alberto and Rosa M. Ribas-Aparicio J. Molecular Modeling 10.1007:s00894-009-0632-9 (2009)
An experimentally based computer search identifies unstructured membrane-binding sites in proteins: Application to class-I myosins, PAKs and CARMIL Hanna Brzeska, Jake Guag, Kirsten Remmert, Susan Chacko and Edward D. Korn J. Biol. Chem. 285:5738-5747 (2009)
Using Compressibility Factor as a Predictor of Confined Hard-Sphere Fluid Dynamics Jeetain Mittal J. Phys. Chem. B 113(42):13800-13804 (2009)
Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh and Hiroaki Mitsuya J. Chem. Inf. Mod. 49(12):2851-2862 (2009)
Misfolded Amyloid Ion Channels Present Mobile β-Sheet Subunits in Contrast to Conventional Ion Channels Hyunbum Jang, Fernando Teran Arce, Ricardo Capone, Srinivasan Ramachandran, Ratnesh Lal, and Ruth Nussinov Biophys. J. 97(11):3029-3037 (2009)

Effectiveness of Hair Bundle Motility as the Cochlear Amplifier Bora Sul and Kuni H. Iwasa Biophys. J. 97(10):2653-2663 (2009)
Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis Paul Jamesen Steiner Master's Thesis, MIT (2009)
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels. Anishkin A, Milac AL, Guy HR. Proteins 78(4):932-949 (2009)
Electrophysiological investigation of prestin function: Impact of cysteine replacement and characterization of self-association during voltage stimulation Ryan M. McGuire PhD Thesis, Rice University (2009)
NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif Yuki Kuwano, Rudolf Pullmann, Jr., Bernard S. Marasa, Kotb Abdelmohsen, Eun Kyung Lee, Xiaoling Yang, Jennifer L. Martindale, Ming Zhan and Myriam Gorospe Nucleic Acids Research 38(1):225-38 (2009)
Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils ? Edward P. O'Brien, Yuko Okamoto, John E. Straub, Bernard R. Brooks and D. Thirumalai J. Phys. Chem. B 113(43):14421-14430 (2009)

MicroRNA Expression in Squamous Cell Carcinoma and Adenocarcinoma of the Esophagus: Associations with Survival Ewy A. Mathé, Giang Huong Nguyen, Elise D. Bowman, Yiqiang Zhao, Anuradha Budhu, Aaron J. Schetter, Rosemary Braun, Mark Reimers, Kensuke Kumamoto, Duncan Hughes, Nasser K. Altorki, Alan G. Casson, Chang-Gong Liu, Xin Wei Wang, Nozomu Yanaihara, Nobutoshi Hagiwara, Andrew J. Dannenberg, Masao Miyashita, Carlo M. Croce and Curtis C. Harris Clin. Cancer. Res. 15:6192 (2009)
K3 Fragment of Amyloidogenic β2-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis Mirela Mustata, Ricardo Capone, Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ratnesh Lal and Ruth Nussinov J. Am. Chem. Soc. 131(41):14938-14945 (2009)
Modeling Aqueous Solvent Effects through Local Properties of Water S.A. Hassan and E.L. Mehler , in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (2009)
Evidence for a Partially Structured State of the Amylin Monomer Sara M. Vaiana, Robert B. Best, Wai-Ming Yau, William A. Eaton, and James Hofrichter Biophys. J. 97(11):2948-2957 (2009)
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation Jin Lui and Ruth Nussinov PLoS Computational Biology 5(10):e1000527 (2009)
Generalized Rosenfeld scalings for tracer diffusivities in not-so-simple fluids: Mixtures and soft particles William P. Krekelberg, Mark J. Pond, Gaurav Goel, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett Phys. Rev. E 80:061205 (2009)
Enhanced bacterial expression of several mammalian cytochrome P450s by codon optimization and chaperone coexpression Zhong-Liu Wu, Jing Qiao, Zhi-Gang Zhang, F. Peter Guengerich, Yan Liu and Xiao-Qiong Pei Biotechnology Letters 31(10):1589-1593 (2009)
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism Dan Fishelovitch, Sason Shaik, Haim J. Wolfson, and Ruth Nussinov J. Phys. Chem B 113(39):13018-13025 (2009)
A simple and efficient algorithm for genome-wide homozygosity analysis in disease Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton Molecular Systems Biology 5:304 (2009)
A fast mean-field method for large-scale high-dimensional data and its application in colonic polyp detection at CT colonography Shijun Wang, Ronald M Summers, Changshui Zhang IEEE International Joint Conference on Neural Networks ijcnn:32511-3258 (2009)
Polymorphism of Alzheimer's A β 17-42(p3) Oligomers: The Importance of the Turn Location and Its Conformation Yifat Miller, Buyong Ma, and Ruth Nussinov Biophys. J. 97(4):1168-1177 (2009)
Quantitative Mitochondrial Phosphoproteomics Using iTRAQ on an LTQ-Orbitrap with High Energy Collision Dissociation Emily Boja, Darci Phillips, Stephanie A French, Robert A. Harris, and Robert Stephen Balaban J. Proteome Research 8(10):4665-4675 (2009)
Molecular Dynamics Simulations of PIP 2 and PIP 3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Zheng Li, Richard M. Venable, Laura A. Rogers, Diana Murray, and Richard W. Pastor Biophys. J. 97(1):155-163 (2009)
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View Yongpin Pan and Ruth Nussinov PLoS Computational Biology :e1000448. (2009)
Functional but not structural changes associated with learning: An exploration of longitudinal Voxel-Based Morphometry (VBM) Thomas AG, Marrett S, Saad ZS, Ruff DA, Martin A, Bandettini PA. Neuroimage 48(1):117-25 (2009)
Phosphine Polymerization by Nitric Oxide: Experimental Characterization and Theoretical Predictions of Mechanism Yi-Lei Zhao, Jason W. Flora, William David Thweatt, Stephen L. Garrison, Carlos Gonzalez, K. N. Houk and Manuel Marquez Inorg. Chem. 48(3):1223-1231 (2009)
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale David Zanuy, Gema Ballano, Ana I. Jimnez, Jordi Casanovas, Nurit Haspel, Carlos Cativiela, David Curc, Ruth Nussinov and Carlos Alemán J. Chem. Info. and Modeling 49(7):1623=9 (2009)
Amygdala function and 5-HTT gene variants in adolescent anxiety and major depressive disorder Lau JY, Goldman D, Buzas B, Fromm SJ, Guyer AE, Hodgkinson C, Monk CS, Nelson EE, Shen PH, Pine DS, Ernst M. Biol. Psychiatry , doi: 10.1016/j.biopsych.2008.08.037 (2009)

HTR3B is associated with alcoholism with antisocial behavior and alpha EEG power�an intermediate phenotype for alcoholism and co-morbid behaviors Ducci F, Enoch MA, Yuan Q, Shen PH, White KV, Hodgkinson C, Albaugh B, Virkkunen M, Goldman D. Alcohol, doi: 10.1016/j.alcohol.2008.09.005 (2009)
Association of Substance Use Disorders With Childhood Trauma but not African Genetic Heritage in an African American Cohort Ducci F, Roy A, Shen PH, Yuan Q, Yuan NP, Hodgkinson CA, Goldman LR, Goldman D. Am. J. Psychiatry, doi: 10.1176/appi.ajp.2009.08071068 (2009)
Kinetic Barriers of H-Atom Transfer Reactions in Alkyl, Allylic, and Oxoallylic Radicals as Calculated by Composite Ab Initio Methods Carrigan J. Hayes and Donald R. Burgess, Jr. J. Phys. Chem. A 113(11):2473-2482 (2009)
On the Mechanism of Nitrosoarene-Alkyne Cycloaddition Andrea Penoni, Giovanni Palmisano, Yi-Lei Zhao, Kendall N. Houk, Jerome Volkman and Kenneth M. Nicholas J. Am. Chem. Soc. 131(2):653-661 (2009)
Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H Edina Rosta, H. Lee Woodcock, Bernard R. Brooks, Gerhard Hummer J. Comput. Chem. 30(11):1634-41 (2009)
Building and assessing atomic models of proteins from structural templates: Learning and benchmarks Brinda Kizhakke Vallat, Jaroslaw Pillardy, Peter M�jek, Jaroslaw Meller, Thomas Blom, BaoQiang Cao, Ron Elber Proteins 76(4):930-945 (2009)

Imaging incorporation of circulating docosahexaenoic acid into the human brain using positron emission tomography John C. Umhau, Weiyin Zhou, Richard E. Carson, Stanley I. Rapoport, Alla Polozova, James Demar, Nahed Hussein, Abesh K. Bhattacharjee, Kaizong Ma, Giuseppe Esposito, Sharon Majchrzak, Peter Herscovitch, William C. Eckelman, Karen A. Kurdziel, and Norman Salem . Jr J. Lipid Res. 50(7):1259-68 (2009)
Error and efficiency of replica exchange molecular dynamics simulations Edina Rosta and Gerhard Hummer J. Chem. Phys. 131:165102 (2009)
Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model VK Shen, J Cheung, JR Errington, TM Truskett J. Biomech. Engg. 131(7):0710002 (2009)
The bis-Electrophile Diepoxybutane Cross-Links DNA to Human Histones but Does Not Result in Enhanced Mutagenesis in Recombinant Systems Elisabeth M. Loecken, Surendra Dasari, Salisha Hill, David L. Tabb and F. Peter Guengerich Chem. Res. Toxicol. 22(6):1069-1076 (2009)
Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease Louis JM, Ishima R, Aniana A, Sayer JM. Protein Science 18(12):2442-53 (2009)
Molecular dynamics study of the structure and interparticle interactions of polyethylene glycol-conjugated PAMAM dendrimers Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 113(40):13202-13207 (2009)
Computer Assisted Analysis of Genes MV Fachal, M Furlan Reproductive Endocrinology Part 2:113-117 (2009)
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides Robert B Best, Gerhard Hummer J. Phys. Chem B 113(26):9004-9015 (2009)
Predictor Correlation Impacts Machine Learning Algorithms: Implications for Genomic Studies Kristin K. Nicodemus and James D. Malley Bioinformatics 25:1884-1889 (2009)
A Partially Linear Tree-based Regression Model for Multivariate Outcomes Kai Yu, William Wheeler, Qizhai Li, Andrew W. Bergen, Neil Caporaso, Nilanjan Chatterjee, and Jinbo Chen Biometrics, published online 10 May (2009)
A finite mixture survival model to characterize risk groups of neuroblastoma Sally Hunsberger, Paul S. Albert and Wendy B. London Stat. Med. 28:1301-1314 (2009)
Post-rituximab Burkitt transformation of PTLD: loss of CD20 expression accompanied by a switch in light-chain expression Yu-Yan Hwang, Kai Y. Wong, Rock Y. Y. Leung, Simon H. M. Wong, See-Ching Chan, Gopesh Srivastava and Wing Y. Au Annals of Hematology 89(1):1432-0584 (2009)

De novo protein structure generation from incomplete chemical shift assignments Yang Shen, Robert Vernon, David Baker, and Ad Bax J. Biomol. 43(2):63-78 (2009)
In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide. Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C. J. Phys. Chem. B 113(22):7879-89 (2009)
Widespread Reductions of Cortical Thickness in Schizophrenia and Spectrum Disorders and Evidence of Heritability Aaron L. Goldman, Lukas Pezawas, Venkata S. Mattay, Bruce Fischl, Beth A. Verchinski, Qiang Chen, Daniel R. Weinberger, Andreas Meyer-Lindenberg. Archives of General Psychiatry 66(5):467-477 (2009)
Gene Composer: database software for protein construct design, codon engineering, and gene synthesis Don Lorimer, Amy Raymond, John Walchli. Mark Mixon, Adrienne Barrow, Ellen Wallace, Rena Grice, Alex Burgin, Lance Stewart BMC Biotechnology 9:36 (2009)
Available states and available space: static properties that predict self-diffusivity of confined fluids Gaurav Goel, William P Krekelberg, Mark J Pond, Jeetain Mittal, Vincent K Shen, Jeffrey R Errington and Thomas M Truskett J. Stat. Mech., doi:10.1088/1742-5468/2009/04/P04006 (2009)
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM. Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D. Methods Mol. Biol. 541:1-22 (2009)

Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations Edina Rosta, Nicolae-Viorel Buchete and Gerhard Hummer J. Chem. Theory and Computation 5(5):1393-1399 (2009)
Pathway analysis by adaptive combination of P-values Kai Yu, Qizhai Li, Andrew W. Bergen, Ruth M. Pfeiffer, Philip S. Rosenberg, Neil Caporaso, Peter Kraft, Nilanjan Chatterjee Genetic Epidemiology 33(8):700-9 (2009)
Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers Richard M. Venable, Linda E. Chen and Richard W. Pastor J. Phys. Chem B 113(17):5855-5862 (2009)
Genetic background comparison using distance-based regression, with applications in population stratification evaluation and adjustment Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, Gilles Thomas, Kai Yu Genetic Epidemiology 33(5):432-441 (2009)
Self-guided langevin dynamics study of regulatory interactions in NtrC Ana Damjanovic, Betrand Garcia-Moreno E., Bernard R. Brooks Proteins: Structure, Function and Bioinformatics 76(4):1007-19 (2009)
Engineered Integrin Binding Peptides Cochran, Jennifer R., Kimura, Richard, Levin, Aron M., Silverman, Adam, Gambhir, Sanjiv S., Cheng, Zhen, Lahti, Jennifer Patent # 12/418376 (2009)
Different Patterns of Regulation for the Copper and Cadmium Metallothioneins of the Ectomycorrhizal Fungus Hebeloma cylindrosporum G. Ramesh, G. K. Podila, G. Gay, R. Marmeisse, and M. S. Reddy App. Env. Microbiology 75(8):2266-2274 (2009)
Hybrid Structural Model of the Complete Human ESCRT-0 Complex Xuefeng Ren, Daniel P. Kloer, Young C. Kim, Rodolfo Ghirlando, Layla F. Saidi, Gerhard Hummer and James H. Hurley Structure 17(3):406-416 (2009)
Combining heterogeneous features for colonic polyp detection in CTC based on semi-definite programming Shijun Wang ; Jianhua Yao ; Nicholas A. Petrick ; Ronald M. Summers SPIE Proceedings, doi:10.1117/12.811219 (2009)
Identification of active sites of biomolecules II: Saccharide and transition metal ion in aqueous solution Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. J. Phys. Chem. A 113(11):2491-9 (2009)
Intramolecular Disulfide Bonds of the Prolactin Receptor Short Form are Required for its Inhibitory Action on the Function of the Long form of the Receptor Y-L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau Mol. Cell. Biol. 29(10):2546-55 (2009)
Adjacency Method for Finding Connected Subsets of a Graph: An Application of Graph Theory to Spatial Statistics Jun Luo, Lan Huang, Mark Hachey, Ram Tiwari Comm. in Stat.: Simulation and Computation 38(5):1136-1151 (2009)
Genetic Studies on Stuttering Families Muhammed Hashim Raza PhD Thesis, University of the Punjab, Lahore, Pakistan (2009)
Large-scale production and characterization of an engineered human olfactory receptor Brian Lee Cook PhD thesis in Biological Engineering at MIT (2009)
Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water Yi-Lei Zhao, Michael Meot-Ner (Mautner) and Carlos Gonzalez J. Phys. Chem. A 113(12):2967-74 (2009)
High-Level Production, Solubilization and Purification of Synthetic Human GPCR Chemokine Receptors CCR5, CCR3, CXCR4 and CX3CR1 Hui Ren, Daoyong Yu, Baosheng Ge, Brian Cook, Zhinan Xu, and Shuguang Zhang PLoS ONE 4(2):e4509 (2009)
A Model for Fine Mapping in Family Based Association Studies Stefan Boehringer and Ruth M. Pfeiffer Hum. Heredit. 67(4):226-236 (2009)
The Factor VIIIa C2 Domain (Residues 2228-2240) Interacts with the Factor IXa Gla Domain in the Factor Xase Complex Tetsuhiro Soeda, Keiji Nogami, Katsumi Nishiya, Masahiro Takeyama, Kenichi Ogiwara, Yoichi Sakata, Akira Yoshioka, and Midori Shima J. Biol. Chem. 284(6):3379-3388 (2009)
Proteomic Analysis of Human Urinary Exosomes Patricia Amalia Gonzales Mancilla PhD thesis, U. Maryland (2009)
Available states and available space: Static properties that predict dynamics of confined fluids Gaurav Goel, William P. Krekelberg, Mark J. Pond, Jeetain Mittal, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett J. Stat. Mech. :P04006 (2009)
Optimizing computer-aided colonic polyp detection for CT colonography by evolving the Pareto front Jiang Li, Adam Huang, Jack Yao, Jiamin Liu, Robert L. Van Uitert, Nicholas Petrick, Ronald M. Summers Medical Physics 36:201-212 (2009)
Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization O. I. Obolensky, T. P. Doerr, R. Ray, and Yi-Kuo Yu Bulletin of the American Physical Society 54:P40.00008 (2009)
A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics. Lee H, de Vries AH, Marrink SJ, Pastor RW. J. Phys. Chem. B 113(40):13186-94 (2009)
Visual Awareness, Emotion, and Gamma Band Synchronization Qian Luo, Derek Mitchell, Xi Cheng, Krystal Mondillo, Daniel McCaffrey, Tom Holroyd, Frederick Carver, Richard Coppola and James Blair Cerebral Cortex 19(8):1896-1904 (2009)

Bayesian Inference for Smoking Cessation with a Latent Cure State Luo S, Crainiceanu, CM, Louis TA, Chatterjee, N Biometrics 65(3):970-8 (2009)
Bio-Sensing Nanodevice Zhang, Shuguang, Mershin, Andreas, Kaiser, Liselotte, Cook, Brian, Graveland-bikker, Johanna F., Prakash, Manu, Kong, David, Maguire, Yael Patent # 12/183916 (2009)

2008 (102 papers)

Dislocation nucleation during nanoindentation of aluminum R. J. Wagner, L. Ma, F. Tavazza, and L. E. Levine J. Applied Physics 104:114311 (2008)
Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl) tetrahydropyran. Woodcock HL, Brooks BR, Pastor RW. JACS 130(20):6345-7 (2008)
Biological Entity Recognition with Conditional Random Fields Ying He and Mehmet Kayaalp AMIA Annu Symp Proc. 2008:293-297 (2008)
Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: the effect of molecular shape Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(39):12279-12285 (2008)

The point mutation A34F causes dimerization of GB1. JunGoo Jee, In-Ja L. Byeon, John M. Louis, Angela M. Gronenborn Proteins 71(3):1420-31 (2008)
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration Alves G, Ogurtsov AY, Yu YK. BMC Genomics 9:505 (2008)
Enhancing peptide identification confidence by combining search methods. Alves G, Wu WW, Wang G, Shen RF, Yu YK J. Proteome Res. 7(8):3102-13 (2008)
Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth-and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(26):7778-7784 (2008)
RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways Marcel P. van der Brug, Jeff Blackinton, Jayanth Chandran, Ling-Yang Hao, Ashish Lal, Krystyna Mazan-Mamczarz, Jennifer Martindale, Chengsong Xie, Rili Ahmad, Kelly J. Thomas, Alexandra Beilina, J. Raphael Gibbs, Jinhui Ding, Amanda J. Myers, Ming Zhan, Huaibin Cai, Nancy M. Bonini, Myriam Gorospe and Mark R. Cookson PNAS 105(29):10244-10249 (2008)
Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide. Zanuy D, Curcó D, Nussinov R, Alemán C Biopolymers 92(2):83-93 (2008)

Analysis of Smoking Cessation Patterns Using a Stochastic Mixed-Effects Model With a Latent Cured State Sheng Luo, Ciprian M Crainiceanu, Thomas A Louis, Nilanjan Chatterjee J. Am. Stat. Assoc. 103(483):1002-1013 (2008)
Inference of non-centrality parameter of a truncated non-central chi-squared distribution Qizhai Li and Kai Yu J. Stat. Planning and Inference 139(7):2431-2444 (2008)
Static and dynamic correlations in water at hydrophobic interfaces Jeetain Mittal and Gerhard Hummer PNAS 105:20130-20135 (2008)
Thermodynamics and kinetics of protein folding under confinement Jeetain Mittal and Robert Best PNAS 105(51):20233-8 (2008)
Characterization of a protective Escherichia coli-expressed Plasmodium falciparum merozoite surface protein 3 indicates a non-linear, multi-domain structure Tsai CW, Duggan PF, Jin AJ, Macdonald NJ, Kotova S, Lebowitz J, Hurt DE, Shimp RL Jr, Lambert L, Miller LH, Long CA, Saul A, Narum DL. Mol. Biochem. Parasitol. 164(1):45-56 (2008)
Self-assembly of fused homo-oligomers to create nanotubes Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Methods Mol. Biol. 474:117-31 (2008)

Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein Yongsu Jeong, Federico Coluccio Leskow, Kenia El-Jaick, Erich Roessler, Maximilian Muenke, Anastasia Yocum, Christele Dubourg, Xue Li, Xin Geng, Guillermo Oliver & Douglas J Epstein Nature Genetics 40:1348-1353 (2008)
Identification of a signature motif in target mRNAs of RNA-binding protein AUF1 Krystyna Mazan-Mamczarz, Yuki Kuwano, Ming Zhan, Elizabeth J. White, Jennifer L. Martindale, Ashish Lal and Myriam Gorospe Nucleic Acids Research 37(1):204-14 (2008)
GRL-02031, a Novel Nonpeptidic Protease Inhibitor (PI) Containing a Stereochemically Defined Fused Cyclopentanyltetrahydrofuran Potent against Multi-PI-Resistant HIV-1 In Vitro Yasuhiro Koh, Debananda Das, Sofiya Leschenko, Hirotomo Nakata, Hiromi Ogata-Aoki, Masayuki Amano, Maki Nakayama, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob Agents Chemother. 53(3):997-1006 (2008)
A class comparison method with filtering-enhanced variable selection for high-dimensional data sets Lara Lusa, Edward L. Korn, Lisa M. McShane Stat. Med 28:5834-5849 (2008)
Models of voltage-dependent conformational changes in NaChBac channels Shafrir Y, Durell SR, Guy HR. Biophys. J. 95(8):3663-76 (2008)
Prediction of evolutionarily conserved interologs in Mus musculus. Yellaboina S, Dudekula DB, Ko MS. BMC Genomics 9:465 (2008)
Comparing the Use of Gibbs Ensemble and Grand-Canonical Transition-Matrix Monte Carlo Methods to Determine Phase Equilibria Andrew S. Paluch, Vincent K. Shen and Jeffrey R. Errington Ind. Eng. Chem. Res. 47(13):4533-4541 (2008)
Molecular Dynamics Simulations of Perylene and Tetracene Librations: Comparison With Femtosecond Upconversion Data Tilman Rosales, Jianhua Xu, Xiongwu Wu, Milan Hodoscek, Patrik Callis, Bernard R. Brooks and Jay R. Knutson J. Phys. Chem. A 112(25):5593-5597 (2008)
Efficient cell-free production of olfactory receptors: Detergent optimization, structure, and ligand binding analyses Liselotte Kaiser, Johanna Graveland-Bikker, Dirk Steuerwald, Mélanie Vanberghem, Kara Herlihy, and Shuguang Zhang PNAS 105(41):15726-15731 (2008)
Models of Toxic β-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer β-Amyloid Ion Channels. Jang H, Ma B, Lal R, Nussinov R. Biophys. J. 95(10):4631-42 (2008)
Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions Sergio A. Hassan J. Phys. Chem. B 112:10573-10584 (2008)
Study on allotopic expression of recoded human mitochondrial ND4L genes in mammalian cells Mou-Chieh Kao Master's thesis, National Tsing Hua University, Taiwan (2008)

Considerations for Lipid Force Field Development Jeffery B. Klauda, Richard M. Venable, Alexander D. MacKerell Jr., Richard W. Pastor in Computational Modeling of Membrane Bilayers, in Current Topics in Membranes Vol 60. (2008)
Developmental and epigenetic regulation of the human TLR3 gene Analia Porrás, Sarah Kozar, Valya Russanova, Paraskevi Salpea, Tazuko Hirai, Nicholas Sammons, Pooja Mittal, Ji Young Kim, Keiko Ozato, Roberto Romero and Bruce H. Howard Mol. Immunol. 46(1):27-36 (2008)
Glycosidic linkage conformation of methyl-α-mannopyranoside Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Chem. Phys. 129:045102 (2008)
Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Campo E, Jaffe ES, Delabie J, Smeland EB, Rimsza LM, Fisher RI, Weisenburger DD, Chan WC, Staudt LM. PNAS 105(36):13520-5 (2008)
Ligand Exchange Reactions in the Formation of Diphosphine-Protected Gold Clusters Denis E. Bergeron, Orkid Coskuner, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Phys. Chem. C 112(33):12808-12814 (2008)
Evidence That Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase (EC 2.3. 1.87) Jiri Pavlicek, Steven L. Coon, Surajit Ganguly, Joan L. Weller, Sergio A. Hassan, Dan L. Sackett, and David C. Klein J. Biol. Chem. 283(21):14552-14558 (2008)

NEIBank: Genomics and bioinformatics resources for vision research Graeme Wistow, Katherine Peterson, James Gao, Patee Buchoff, Cynthia Jaworski, Catherine Bowes-Rickman, Jessica N. Ebright, Michael A. Hauser, and David Hoover Molecular Vision 14:1327-1337 (2008)
mRNA Distribution and Heterologous Expression of Orphan Cytochrome P450 20A1 Katarina Stark, Zhong-Liu Wu, Cheryl J. Bartleson and F. Peter Guengerich Drug Metabolism and Disposition 36(9):1930-1937 (2008)
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy Hwankyu Lee, Richard M. Venable, Alexander D. MacKerell, Jr. and Richard W. Pastor Biophysical Journal 95(4):1590-9 (2008)
Positron Emission Tomography Imaging Using an Inverse Agonist Radioligand to Assess Cannabinoid CB1 Receptors in Rodents Terry G, Liow J-S, Chernet E; Zoghbi SS, Phebus L, Felder CC, Tauscher J, Schaus JM, Pike VW, Halldin C, Innis RB. Neuroimage 41(3):690-8 (2008)
p53-Induced DNA Bending: The Interplay between p53-DNA and p53-p53 Interactions Yongpin Pan, Ruth Nussinov J. Phys. Chem. B 112(21):6716-24 (2008)
11C-Loperamide and its N-desmethyl radiometabolite are avid substrates for brain P-glycoprotein efflux Zoghbi SS, Liow J-S,Yasuno F, Hong J, Tuan E; Lazarova N, Gladding RL; Pike VW, Innis RB J. Nucl. Med. 49(4):649-56 (2008)
CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes Klauda JB, Brooks BR J. Chem. Theory and Computation 4(1):107-115 (2008)
Binding-induced folding of a natively unstructured transcription factor Turjanski, A. G., Gutkind, J.S., Best, R. and Hummer. G. PLoS Computational Biology, e1000060 doi:10.1371 (2008)
Study of a Synthetic Human Olfactory Receptor 17-4: Expression and Purification from an Inducible Mammalian Cell Line Brian L. Cook, Karin E. Ernberg, Hyeyoun Chung, and Shuguang Zhang PLoS One 3(8):e2920 (2008)
Privileged scaffolds targeting reverse-turn and helix recognition Che, Ye & Marshall, Garland. Expert Opinion on Therapeutic Targets 12(1):101-114 (2008)
Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Nature 451(7181):998-1003 (2008)
Cluster Without Fluster: The Effect of Correlated Outcomes on Inference in Randomized Clinical Trials Proschan MA, Follmann, DA. Statistics in Medicine 27(6):795-809 (2008)

Sigma Stellation: A Design Strategy for Electron Boxes Irikura, Karl K J. Phys. Chem A 112:983-988 (2008)
Coordination Studies of Al-EDTA in Aqueous Solution Orkid Coskuner, Emily A. A. Jarvis J. Phys. Chem. 112(12):2628-2633 (2008)
Layering and Position-Dependent Diffusive Dynamics of Confined Fluids Jeetain Mittal, Thomas M. Truskett, Jeffrey R. Errington, and Gerhard Hummer Phys. Rev. Let. 100:145901 (2008)
Genetic variation in human NPY expression affects stress response and emotion Zhou Z, Zhu G, Hariri AR, Enoch MA et al. Nature, doi: 10.1038/nature06858 (2008)
Addictions biology: haplotype-based analysis for 130 candidate genes on a single array Hodgkinson CA, Yuan Q, Xu K, Shen PH, Heinz E, Lobos EA, Binder EB, Cubells J, Ehlers CL, Gelernter J, Mann J, Riley B, Roy A, Tabakoff B, Todd RD, Zhou Z, Goldman D. Alcohol and Alcoholism, doi: 10.1093/alcalc/agn032 (2008)
Common Genetic Origins for EEG, Alcoholism and Anxiety: The Role of CRH-BP Enoch MA, Shen PH, Ducci F, Yuan Q, Liu J, White KV, Albaugh B, Hodgkinson CA, Goldman D. PLoS One, doi: 10.1371/journal.pone.0003620 (2008)
Comprehensive Structural Studies of 2', 3'-Difluorinated Nucleosides: Comparison of Theory, Solution, and Solid State Joseph J. Barchi, Jr., Rajeshri G. Karki, Marc C. Nicklaus, Maqbool A. Siddiqui, Clifford George, Igor A. Mikhailopulo and Victor E. Marquez J. Am. Chem. Soc. 130(28):9048-9057 (2008)
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins Vallat BK, Pillardy J, Elber R. Proteins 72(3):910-28 (2008)
MAX-rank: a simple and robust genome-wide scan for case-control association studies. Li Q, Yu K, Li Z, Zheng G. Hum. Genet. 123(6):617-23 (2008)
Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study Ana Damjanovic, Xiongwu Wu, Bertrand Garcia-Moreno and Bernard R Brooks Biophys. J. 95(9):4091-101 (2008)
The Cytoplasmic Terminus of Kaposi's Sarcoma-Associated Herpesvirus Glycoprotein B Is Not Essential for Virion Egress and Infectivity{triangledown} R. Subramanian, O. D'Auvergne, Haixia Kong, and K. G. Kousoulas J. Virol. 82(14):7144-7154 (2008)
Expression and purification of orphan cytochrome P450 4X1 and oxidation of anandamide Stark K, Dostalek M, Guengerich FP. FEBS J. 275(14):3706-17 (2008)

Towards an automatic classification of protein structural domains based on structural similarity Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics 9(1):74 (2008)
Endogenous retrotransposon sequences of the Schistosoma mansoni intermediate snail host, Biomphalaria glabrata Knight M, Bridger J, Ittiprasert W, Odoemelam E, Masabanda J, Miller A, Raghavan, N. Mobile Genetic Elements in Metazoan Para, Brindley PJ (ed). Landes Bioscience, in press. (2008)
The Imaging Probe Development Center and the Production of Molecular Imaging Probes Gary L Griffiths Curr. Chem. Genomics 1:65-69 (2008)
On estimating diagnostic accuracy from studies with multiple raters and partial gold standard evaluation Paul S. Albert and Lori E Dodd J. Am. Stat. Assoc 103(481):61-73 (2008)
In Situ Gas Phase Diagnostics for Hafnium Oxide Atomic Layer Deposition J.E. Maslar, W.S. Hurst, D.R. Burgess, W.A. Kimes, N.V. Nguyen, E.F. Moore, J.T. Hodges ECS Transactions 13(2):139-149 (2008)
Differences in Cysteine Protease Activity in Schistosoma mansoni-Resistant and-Susceptible Biomphalaria glabrata and Characterization of the Hepatopancreas Cathepsin B Full-length cDNA Jocelyn Myers, Wannaporn Ittiprasert, Nithya Raghavan, André Miller, and Matty Knight J. Parasitol. 94:3:659-668 (2008)

Molecular architecture of native HIV-1 gp 120 trimers Jun Liu, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro & Sriram Subramaniam Nature 455:109-113 (2008)
Dissecting contact potentials for proteins: relative contributions of individual amino acids Buchete NV, Straub JE, Thirumalai D. Proteins 70(1):119-30 (2008)
Synthesis and evaluation of N-Methyl and S-Methyl 11C-Labeled 6-Methylthio-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridines as radioligands for imaging beta-amyloid plaques in Alzheimer's disease Cai L, Liow JS, Zoghbi SS, Cuevas J, Baetas C, Hong J, Shetty HU, Seneca NM, Brown AK, Gladding R, Temme SS, Herman MM, Innis RB, Pike VW. J. Med. Chem. 51(1):148-58 (2008)
Residual multiparticle entropy does not generally change sign near freezing Krekelberg WP, Shen VK, Errington JR, Truskett TM. J. Chem. Phys. 128(16):161101 (2008)
Synthesis and pharmacological effects of the enantiomers of the N-phenethyl analogues of the ortho and para e-and f-oxide-bridged phenylmorphans Josef Zezula, Lisa Singer, Anna K. Przyby, Akihiro Hashimoto, Christina M. Dersch, Richard B. Rothman, Jeffrey Deschamps, Yong Sok Lee, Arthur E. Jacobson and Kenner C. Rice Org. and Biomol. Chem. 6:2868-2883 (2008)
A pseudopotential for improving the packing of ellipsoidal protein structures determined by NMR C.D. Schwieters and G.M. Clore. J. Phys. Chem 112(19):6070-6073 (2008)
PCR-based gene synthesis to produce recombinant proteins for crystallization Damien Marsic, Ronny C Hughes, Miranda L Byrne-Steele and Joseph D Ng BMC Biotechnology 8:44 (2008)
Dynamics of Cholesterol Exchange in the OSBP-Related Protein Family Canagarajah, B., Hummer, G., Prinz, W. and Hurley, J. H. J. Mol. Biol. 378(3):737-48 (2008)
Population Substructure and Control Selection in Genome-Wide Association Studies Kai Yu, Zhaoming Wang, Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, and Gilles Thomas PLoS One 3(7):2551 (2008)
Testing logistic regression coefficients with clustered data and few positive outcomes Sally Hunsberger, Ed Korn, and Barry Graubard. Statistics in Medicine 27(8):1305-24 (2008)
Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics McQueen PG, McKenzie FE PLoS Computational Biology 4(8):e1000149 (2008)
Identification of the transition states in the inversion of 1, 4-benzodiazepines with the Ab Initio Replica Path Method Yong-Sok Lee, Victor W. Pike, and Milan Hodoscek. J. Phys. Chem A 112:1604-1611 (2008)

A frailty mixture cure model with application to hospital readmission cata Yu, B. Biometrical J. 50(3):386-94 (2008)
Efficient Approximation of P-value of the Maximum of Correlated Tests, with Applications to Genome-Wide Association Studies. Li Q.Z., Zheng G., Li Z.H. and Yu K. Annals of Human Genetics 72(3):397-406 (2008)
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements Ma B, Levine AJ. Nucleic Acids Research 35(22):7733-7747 (2008)
Improved Classifier for Computer-aided Polyp Detection in CT Colonography by Nonlinear Dimensionality Reduction Shijun Wang, Jianhua Yao and Ronald M. Summers Med. Phys. 35(4):1377-86 (2008)
β2-microglobulin amyloid fragment organization and morphology and its comparison to Aβ suggests that amyloid aggregation pathways are sequence specific Zheng J, Jang H, Nussinov R. Biochemistry. Feb 26;47(8):2497-2509 (2008)
Morphology of Ion Clusters in Aqueous Electrolytes SA Hassan. Phys. Rev. E 77:03151 (2008)

Involvement of the second extracellular loop and transmembrane residues of CCR5 in inhibitor binding and HIV-1 fusion: insights into the mechanism of allosteric inhibition Maeda K, Das D, Yin PD, Tsuchiya K, Ogata-Aoki H, Nakata H, Norman RB, Hackney LA, Takaoka Y, Mitsuya H. J. Mol. Biol. 381:956-974 (2008)
Are Current Molecular Dynamics Force Fields too Helical? Robert B Best, Nicolae-Viorel Buchete and Gerhard Hummer Biophysical Letters 95(1):L07-9 (2008)
Concentration and crowding effects on protein stability from a coarse-grained model J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. in Statistical Mechanics of Cellular System, MH Zaman ed, Cambridge University Press. (2008)
Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Zoltick B, Weinberger DR, Meyer-Lindenberg A. Biol. Psychiatry 63(5):475-83 (2008)
Models of the Structure and Gating Mechanisms of the Pore Domain of the NaChBac Ion Channel Yinon Shafrir, Stewart R Durell and H. Robert Guy Biophys. J. 95(8):3650-62 (2008)
NIST Computational Chemistry Comparison and Benchmark Database Some of the calculations in the CCBD were performed by Russell Johnson on the Biowulf cluster. (2008)

Modeling Longitudinal Biomarker Data from Multiple Assays that Have Different Known Detection Limits Paul S. Albert Biometrics 64:527-537 (2008)
Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. Rodriguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Aleman C. J Chem Inf Model. 48(2):333-43 (2008)
Calcium-dependent inactivation terminates calcium release in skeletal muscle of amphibians Eduardo Rios, Jingsong Zhou, Gustavo Brum, Bradley S. Launikonis, and Michael D. Stern. J. Gen. Physiol. 131(4):335-48 (2008)
Classification and 3D averaging with missing wedge correction in biological electron tomography A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro and S. Subramaniam J. Struct. Biol. 162(3):436-450 (2008)
Detection of co-eluted peptides using database search methods Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, and Yi-Kuo Yu Biol. Direct. 3:27 (2008)
Coarse Master Equations for Peptide Folding Dynamics N.V. Buchete and G. Hummer. J. Phys. Chem. B 112(19):6057-69 (2008)

Interfacial polar interactions affect gramicidin channel kinetics Rostovtseva, TK; Petrache, HI; Kazemi, N; Hassanzadeh, E; Bezrukov, SM; Biophys. J., DOI://10.1529/biophysj.107.120261 (2008)
Effective approaches for the production of heterologous proteins using the Thermococcus kodakaraensis-based translation system Takashi Endoha, Tamotsu Kanaia and Tadayuki Imanaka J. Biotech. 133(2):177-182 (2008)
Metabolic engineering of Escherichia coli for biosynthesis of hyaluronic acid Huimin Yua and Gregory Stephanopoulos Metabolic Engg. 10(1):24-32 (2008)
Identification of the Active Sites of Biomolecules I: Methyl-alpha-mannopyranoside and Fe(III) Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez J. Phys. Chem. A 112(3):2940-2947 (2008)
New structures help the modeling of toxic amyloidβ ion channels Jang H, Zheng J, Lal R, Nussinov R. Trends Biochem Sci. Feb;33(2):91-100 (2008)
Peptide folding kinetics from replica exchange molecular dynamics Nicolae-Viorel Buchete and Gerhard Hummer Phys. Rev. E 77:030902 (2008)

Structure and dynamics of Helix-0 of the N-BAR domain in Lipid Micelles and Bilayers Christian Löw, Ulrich Weininger, Hwankyu Lee, Kristian Schweimer, Ines Neundorf, Annette G. Beck-Sickinger, Richard W. Pastor and Jochen Balbach Biophys. J. 95(9):4315-23 (2008)
Reactions of Glyceraldehyde 3-Phosphate Dehydrogenase Sulfhydryl Groups with Bis-Electrophiles Produce DNA-Protein Cross-Links but Not Mutations Elisabeth M. Loecken and F. Peter Guengerich Chem. Res. Toxicol. 21(2):453-358 (2008)

2007 (82 papers)

Validating Pareto optimal operation parameters of polyp detection algorithms for CT colonography Jiang Li ; Adam Huang ; Nicholas Petrick ; Jianhua Yao ; Ronald M. Summers Proc. SPIE 6514, Medical Imaging 2007, doi:10.1117/12.707965 (2007)
Multiple comparisons distortions of parameter estimates Jeffries, NO. Biostatistics 8(2):500-4 (2007)
Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn Scaffolds. Y Che, Bernard Brooks, Dennis P Riley, Andrea JH Reaka, Garland R Marshall. Chemical Biology & Drug Design 69 (2) : 99-110 (2007)
RAId_DbS: Peptide identification using database searches with realistic statistics Alves G, Ogurtsov AY, Yu YK. Biol. Direct. 2:25 (2007)

Cysteine-cysteine contact preference leads to target-focusing in protein folding Sardiu ME, Cheung MS, Yu YK. Biophys. J. 93(3):938-51 (2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project The ENCODE Project Consortium Nature 447:799-816 (2007)
The structure of receptor-associated protein (RAP) Donghan Lee, Joseph D. Walsh, Molly Migliorini, Ping Yu Tao Cai, Charles D. Schwieters, Susan Krueger, Dudley K. Strickland, and Yun-Xing Wang. Protein Science 16:1628-1640 (2007)
Accounting for Variability in Sample Size Estimation with Applications to Nonadherence and Estimation of Variance and Effect Size Fay, MP, Halloran, ME, Follmann, DA. Biometrics 63(2): 465-474 (2007)
Modeling the Alzheimer A β 17-42 Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R. Biophys. J. 93(9):3046-57 (2007)
Molecular and functional analyses of a novel class I secretory nuclease from the human pathogen, Leishmania donovani Joshi MB, Dwyer DM. J. Biol. Chem. 282(13):10079-95 (2007)
Induction of Epitope-Specific Neutralizing Antibodies against West Nile Virus Theodore Oliphant, Grant E. Nybakken, S. Kyle Austin, Qing Xu, Jonathan Bramson, Mark Loeb, Mark Throsby, Daved H. Fremont, Theodore C. Pierson, and Michael S. Diamond J. Virol. 81(21):11828-11839 (2007)
Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2-Ethoxy Tetrahydropyran H. Lee Woodcock, Damian Moran, Richard W. Pastor, Alexander D. MacKerell, Jr. and Bernard R. Brooks Biophys. J. 93:1-10 (2007)
Analysis of failure time data with multilevel clustering, with application to the child vitamin a intervention trial in Nepal Shih JH, Lu SE. Biometrics 63(3):673-80 (2007)
Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution SA Hassan. J. Phys. Chem B 111(1):227-41 (2007)
Natural resonance structures and aromaticity of the nucleobases Guangyu Sun & Marc Nicklaus. Theoretical Chemistry Accounts: Theory, 117(2): 323-332 (2007)
Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2 Francesca Deflorian, Stanislav Engel, Anny-Odile Colson, Bruce M. Raaka, Marvin C. Gershengorn, Stefano Costanzi Proteins: Structure, Function and Bioinf 71(2):783 - 794 (2007)
Stability of Tubular Structures Based on β-Helical Proteins: Self-Assembled versus Polymerized Nanoconstructs and Wild-Type versus Mutated Sequences David Zanuy, Francisco Rodríguez-Ropero, Nurit Haspel, Jie Zheng, Ruth Nussinov, and Carlos Alem´n BIomacromolecules 8(10):3135-3146 (2007)
N-Nitrosation of amines by NO2 and NO: A theoretical study Yi-Lei Zhao, Stephen L. Garrison, Carlos Gonzalez, William David Thweatt, and Manuel Marquez J. Phys. Chem. A 111(11):2200-2205 (2007)
Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms H. Lee Woodcock, Milan Hodošček, and Bernard R. Brooks J. Phys. Chem A 111(26):5720-5728 (2007)
Comparative Study of the Effect of Tail Corrections on Surface Tension Determined by Molecular Simulation V. K. Shen, R. D. Mountain, and J. R. Errington. J. Phys. Chem B 111:6198 (2007)
A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release. Matarin M, Brown WM, Scholz S, Simon-Sanchez J, Fung HC, Hernandez D, Gibbs JR, De Vrieze FW, Crews C, Britton A, Langefeld CD, Brott TG, Brown RD Jr, Worrall BB, Frankel M, Silliman S, Case LD, Singleton A, Hardy JA, Rich SS, Meschia JF. Lancet Neurol. 6(5):414-20 (2007)
A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data. Schwieters CD, Clore GM. Biochemistry 46(5):1152-66 (2007)

Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. Klauda JB, Brooks BR. J Mol Biol. 367(5):1523-34 (2007)
Using Pareto fronts to evaluate polyp detection algorithms for CT colonography Adam Huang ; Jiang Li ; Ronald M. Summers ; Nicholas Petrick ; Amy K. Hara Medical Imaging: Computer-Aided Diagnosis, doi:10.1117/12.709426 (2007)
Spiral structure of Escherichia coli HUαβ provides foundation for DNA supercoiling Fusheng Guo and Sankar Adhya PNAS 104:4309-4314 (2007)
Two-sample Comparison Based on Prediction Error, with Applications to Candidate Gene Association Studies K. Yu, R. Martin, N. Rothman, T. Zheng, Q. Lan. Annals of Human Genetics 71 (1) :107- 118 (2007)
Preferred conformation of the glycosidic linkage of methyl-beta-mannose Coskuner O. J. Chem. Phys 127(1):015101 (2007)
Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer's A β Fibrils Buchete NV, Hummer G. Biophys. J. 92(9):3032-9 (2007)

Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety Ivanov, A. A.; Fricks, I; Harden, T. K.; Jacobson, K. A. Bioorg. Med. Chem. Lett. 17:761-766 (2007)
Calculation of the Free Energy and Cooperativity of Protein Folding Kentsis A, Gindin T, Mezei M, Osman R. PLoS One 2:e446 (2007)
Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. Biophys. J. 92:4316 (2007)
Context-specific amino acid substitution matrices and their use in the detection of protein homologs Goonesekere NC, Lee B. Proteins 71(2):910-919 (2007)
The Origin of Quantal Size Variation: Vesicular Glutamate Concentration Plays a Significant Role Xin-Sheng Wu, Lei Xue, Raja Mohan, Kenneth Paradiso, Kevin D. Gillis, and Ling-Gang Wu. J. Neurosc. 27(11):3046-3056 (2007)
In Situ Monitoring of Hafnium Oxide Atomic Layer Deposition J.E. Maslar, W.S. Hurst, D.R. Burgess, Jr., W.A. Kimes, N.V. Nguyen, and E.F. Moore Frontiers of Char. and Metr. for Nanoelectrics (2007)
Challenges in Projecting Clustering Results Across Gene Expression-Profiling Datasets Lara Lusa, Lisa M. McShane, James F. Reid, Loris De Cecco, Federico Ambrogi, Elia Biganzoli, Manuela Gariboldi, Marco A. Pierotti. J. National Cancer Institute 99(22): 1715-1723 (2007)
The bootstrap variance of the square of a sample mean Dodd, LE and Korn, EL. The American Statistician. 1(2):127-131 (2007)
qPrimerDepot: a primer database for quantitative real time PCR Wenwu Cui, Dennis D. Taub and Kevin Gardner Nucleic Acids Research 35:D805-D809 (2007)
Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent μ-Agonist δ-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series Anne-C�cile Hiebel, Yong Sok Lee, Edward Bilsky, Denise Giuvelis, Jeffrey R. Deschamps, Damon A. Parrish, Mario D. Aceto, Everette L. May, Louis S. Harris, Andrew Coop, Christina M. Dersch, John S. Partilla, Richard B. Rothman, Kejun Cheng, Arthur E. Jacobson, and Kenner C. Rice J. Med. Chem. 50(16):3765-3776 (2007)
Effects of Chain Length on the Rates of CC Bond Dissociation in Linear Alkanes and Polyethylene Knyazev V J. Phys. Chem. A 111(19):3875-83 (2007)
Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate. Ivanov AA, Ko H, Cosyn L, Maddileti S, Besada P, Fricks I, Costanzi S, Harden TK, Calenbergh SV, Jacobson KA. J. Med. Chem 50(6):1166-76 (2007)

Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study D. Zanuy, F. Rodriguez-Ropero, R. Nussinov, C. Aleman. J. Struct. Biol. 160(2): 177-189 (2007)
Nanostructure Design Using Protein Building Blocks Enhanced by Conformationally Constrained Synthetic Residues Zheng J, Zanuy D, Haspel N, Tsai CJ, Alem C and Nussinov R. Biochemistry 46(5):1205 -1218 (2007)
Substrate-induced Conformational Changes and Dynamics of UDP-N-Acetylgalactosamine: Polypeptide N-Acetylgalactosaminyltransferase-2 Adina L Milac, Nicolae-Viorel Buchete, Timothy A Fritz, Gerhard Hummer, Lawrence A Tabak J. Mol. Biol. Oct 19;373(2):439-51 (2007)
A 2-Year Prospective Study of Human Papillomavirus Persistence among Women with a Cytological Diagnosis of Atypical Squamous Cells of Undetermined Significance or Low-Grade Squamous Intraepithelial Lesion Plummer M, Schiffman M, Castle PE, Maucort-Boulch D, Wheeler CM; ALTS Group. J Infect Dis. 195(11):1582-9 (2007)
Nimbus( BgI): An active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata Raghavan N, Tettelin H, Miller A, Hostetler J, Tallon L, Knight M. Int. J. Parasitol. 37(12):1307-18 (2007)
Competition between Hydrogen Abstraction and Halogen Displacement in the Reaction of Br with CH3I, CH3Br, and CH3Cl Irikura, Karl K.; Francisco, J. S. J. Phys. Chem 111:6852-6859 (2007)

Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, Wilce JA. Mol. Cell. Biol. 27(19):6806-17 (2007)
Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4 Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. J Am Chem Soc. 14;129(6):1602-11 (2007)
Limits on variations in protein backbone dynamics from precise measurements of scalar couplings Vogeli B, Ying J, Grishaev A, Bax A. J. Am. Chem. Soc 129(30):9377-85 (2007)
Effects of chain length on the rates of C-C bond dissociation in linear alkanes and polyethylene Knyazev, VD J Phys Chem A, DOI://10.1021/jp066419e (2007)
Identification and regional distribution in rat brain of radiometabolites of the dopamine transporter PET radioligand [11C]PE2I Shetty HU, Zoghbi SS, Liow JS, Ichise M, Hong J, Musachio JL, Halldin C, Seidel J, Innis RB, Pike VW. Eur. J. Nucl. Med. Mol. Imaging 34(5):667-78 (2007)
Effect of a P-glycoprotein inhibitor, Cyclosporin A, on the disposition in rodent brain and blood of the 5-HT1A receptor radioligand, [11C](R)-(-)-RWAY Liow JS, Lu S, McCarron JA, Hong J, Musachio JL, Pike VW, Innis RB, Zoghbi SS. Synapse 61(2):96-105 (2007)
Electron Transport Pathway for a Streptomyces Cytochrome P450: Cytochrome P450 105D5-catalyzed fatty acid hydroxylation in Streptomyces Coelicolor A3 (2) Young-Jin Chun, Tsutomu Shimada, Raymundo Sanchez-Ponce, Martha V. Martin, Li Lei, Bin Zhao, Steven L. Kelly, Michael R. Waterman, David C. Lamb and F. Peter Guengerich J. Biol. Chem. 282:17486-17500 (2007)
A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences Joseph C Lee, David Stiles, Jun Lu, and Margaret C Cam. BMC Genomics 8: 284 (2007)
Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chio A, Singleton A, Hardy J, Traynor BJ. Lancet Neurol. 6(4):322-8 (2007)
The LeFE algorithm, embracing the complexity of gene expression in the interpretation of microarray data Eichler, GS, Reimers, M, Kane, D, Weinstein, JN. Genome Biology 8(9):R185 (2007)
Imputation Approaches for Estimating Diagnostic Accuracy for Multiple Tests from Partially Verified Designs Paul S. Albert. Biometrics 63:947-957 (2007)
An investigation of two multivariate permutation methods for controlling the false discovery proportion Edward L. Korn , Ming-Chung Li , Lisa M. McShane and Richard Simon. Statistics in Medicine 26:4428-4440 (2007)

A survey of genetic human cortical gene expression Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nature Genetics 39(12):1494-9 (2007)
Changing the Charge Distribution of β-Helical-Based Nanostructures Can Provide the Conditions for charge transfer. Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Biophys. J. 93(1):245-53 (2007)
Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways Keskin O and Nussinov R. Structure 15:341-354 (2007)
Random Effects Modeling Approaches for Estimating ROC Curves from Repeated Ordinal Tests without a Gold Standard Paul Albert. Biometrics 63:593-602 (2007)
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. Jang H, Ma B, Nussinov R. BMC Struct Biol. 2;7:21 (2007)
Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites Miranda S. M. Oakley, Sanjai Kumar, Vivek Anantharaman, Hong Zheng, Babita Mahajan, J. David Haynes, J. Kathleen Moch Rick Fairhurst Thomas F. McCutchan and L. Aravind. Infection and Immunity 75: 2012-2025 (2007)
Expression and Purification of Recombinant Wheat Translation Initiation Factors eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(iso)4F, and eIF5 Laura K. Mayberry, Michael D. Dennis, M. Leah Allen, Kelley Ruud Nitka, Patricia A. Murphy, Lara Campbell and Karen S. Browning Methods in Enzymology 430:397-408 (2007)
N-MYC Regulates Focal Adhesion Kinase Expression in Human Neuroblastoma Elizabeth A. Beierle, Angelica Trujillo, Abhilasha Nagaram, Elena V. Kurenova, Richard Finch, Xiaojie Ma, Jennifer Vella, William G. Cance and Vita M. Golubovskaya J. Biol. Chem. 282:12503-12516 (2007)
Calibrating E-values for MS2 database search methods Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Biol. Direct. 2:26 (2007)
Structural basis for p53 binding-induced DNA bending. Pan Y, Nussinov R. J Biol Chem. 5;282(1):691-9 (2007)
Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures. Mittal J, Shen VK, Errington JR, Truskett TM. J Chem Phys. Oct 21;127(15):154513 (2007)
An Evaluation of Power and Type I Error of Single-Nucleotide Polymorphism Transmission/Disequilibrium-Based Statistical Methods under Different Family Structures, Missing Parental Data, and Population Stratification Kristin K. Nicodemus Augustin Luna and Yin Yao Shugart. Am. J. Hum. Genet. 80:178-185 (2007)
Density functional theory study of the clean and hydrated hematite (1[overline 1]02) surfaces Cynthia S. Lo, Kunaljeet S. Tanwar, Anne M. Chaka, and Thomas P. Trainor Phys. Rev. B 75(7):209901 (2007)
Density-functional study of magnetism in bare Au nanoclusters: Evidence of permanent size-dependent spin polarization without geometry relaxation Magyar, R. J.; Mujica, V.; Marquez, M.; Gonzalez, C. Phys. Rev. B 75(14):14421 (2007)
Optimized clonotypic analysis of T-cell receptor repertoire in immune reconstitution Packer AN, Muraro PA. Exp. Hematol. 35(3):516-21 (2007)
Neural dynamics for facial threat processing as revealed by gamma band synchronization using MEG Qian Luo, Tom Holroyd, Matthew Jones, Talma Hendler and James Blair Neuroimage 34:839-847 (2007)
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. Woodcock HL 3rd, Hodoscek M, Gilbert AT, Gill PM, Schaefer HF 3rd, Brooks BR. J. Comput. Chem 28(9):1485-502 (2007)
Intrinsic Conformational Characteristics of α, α-Diphenylglycine Casanovas J, Zanuy D, Nussinov R, Aleman C. J. Org. Chem. 16;72(6):2174-81 (2007)
Identification and Biochemical Characterization of Unique Secretory Nucleases of the Human Enteric Pathogen, Entamoeba histolytica Glen C. McGugan, Jr., Manju B. Joshi, and Dennis M. Dwyer J. Biol. Chem. 282(43):31789-31802 (2007)
Use of constrained synthetic amino acids in β-helix proteins for conformational control. Zanuy D, Jimenez AI, Cativiela C, Nussinov R, Aleman C. J Phys Chem B. 111(12):3236-42 (2007)
Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a Dynamic Process. Jang H, Zheng J, Nussinov R. Biophys. J. 93(6):1938-49 (2007)
Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4 Chih-chin Huang, Son N. Lam, Priyamvada Acharya, Min Tang, Shi-Hua Xiang, Syed Shahzad-ul Hussan, Robyn L. Stanfield, James Robinson, Joseph Sodroski, Ian A. Wilson, Richard Wyatt, Carole A. Bewley, Peter D. Kwong Science 317:1930-1934 (2007)
Protein recognition motifs: Design of peptidomimetics of helix surfaces Ye Che, Bernard Brooks, Garland R Marshall. Biopolymers 86(4):288 - 297 (2007)
Water dissociation in the presence of metal ions Coskuner O, Jarvis EA, Allison TC. Angew. Chem. Int. Ed 46(41): 7853 (2007)

2006 (57 papers)

Functionalized Self-Assembled Monolayers on Ultraflat Gold as Platforms for Single Molecule Force Spectroscopy and Imaging Yadavalli VK, Forbes JG, Wang K. Langmuir 22(16):6969-76 (2006)
Kinetic Study of the Gas-Phase Reaction of OH with Br2 Mikhail G. Bryukov, Barry Dellinger, and Vadim D. Knyazev J. Phys. Chem. A 110(29):9169-9174 (2006)
Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc₁ complex Lothar Esser, Xing Gong, Shaoqing Yang, Linda Yu, Chang-An Yu and Di Xia PNAS 103(35):13045-13050 (2006)
System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics Mountain RD. J Chem Phys. 124(10):104109 (2006)
Membrane biophysics Joshua Zimmerberg. Current Biology 16:R272-R276 (2006)
De Novo Tubular Nanostructure Design Based on Self-Assembly of β-Helical Protein Motifs Nurit Haspel, David Zanuy, Carlos Alemán, Haim Wolfson and Ruth Nussinov Structure 14(7):1137-1148 (2006)

Structure by design: from single proteins and their building blocks to nanostructures Tsai C-J, Zheng J, Aleman C, Nussinov R. Trends in Biotechnoloy 24:449-454 (2006)
Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose R. M. Venable, A. Skibinsky and R. W. Pastor. Molecular Simulation 32:849-855 (2006)
Effects of electric fields on proton transport through water chains S A Hassan, G Hummer and Y S Lee J. Chem. Phys 124:204510 (2006)
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements MAQC Consortium. Nature Biotechnology 24: 1151 - 1161 (2006)
Global similarity and local divergence in human and mouse gene co-expression networks. Tsaparas, P., Marino-Ramirez, L., Bodenreider, O., Koonin, E. V. and Jordan, I. K. BMC Evol Biol. 6:70 (2006)
Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins Clore GM, Schwieters CD. J. Mol. Biol. 355(5):879-86 (2006)

Determination of surface tension in binary mixtures using transition-matrix Monte Carlo V. K. Shen and J. R. Errington. J. Chem. Phys 124:24721 (2006)
Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma. Dodd LE, Sengupta S, Chen IH, den Boon JA, Cheng YJ, Westra W, Newton MA, Mittl BF, McShane L, Chen CJ, Ahlquist P, Hildesheim A. Cancer Epidemiol Biomarkers Prev. 15(11):2216-25 (2006)
Predicting domain-domain interactions using a parsimony approach Katia S Guimaraes, Raja Jothi, Elena Zotenko and Teresa M Przytycka. Genome Biol. 7(11): R104 (2006)
De novo peptide sequencing using exhaustive enumeration of peptide composition. Olson MT, Epstein JA, Yergey AL. J. Am. Soc. Mass. Spectrum 17(8):1041-9 (2006)
PET imaging of brain 5-HT1A receptors in rat in vivo with 18F-FCWAY and improvement by successful inhibition of radioligand defluorination with miconazole Tipre DN, Zoghbi SS, Liow JS, Green MV, Seidel J, Ichise M, Innis RB, Pike VW. J. Nucl. Med 47(2):345-53 (2006)
Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements. Ying J, Grishaev A, Bryce DL, Bax A. J. Am. Chem. Soc 128(35):11443-54 (2006)

Using RNA sample titrations to assess microarray platform performance and normalization techniques Shippy R et al. Nature Biotechnology 24: 1123-1131 (2006)
Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect Jang H, Ma B, Woolf TB., Nussinov R Biophysical J. 91:2848-2859 (2006)
The snail (Biomphalaria glabrata) genome project Raghavan N. and Knight M. Trends Parasitol. 22(4):148-51 (2006)
CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome Sharov A, Dudekula D, Ko MSH. DNA Research 13(3):123-34 (2006)
Using ancestry-informative markers to define populations and detect population stratification Enoch MA, Shen PH, Xu K, Hodgkinson C, Goldman D. J Psychopharmacol 20:19-26 (2006)
Augmented designs to assess immune response in vaccine trials Follmann, DA. Biometrics 62(4):1161-9 (2006)

“Similarity Trap” in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains Liu J, Pan Y, Ma B, and Nussinov R. Structure 14(12):1811-21 (2006)
Engineering Cyclic Tetrapeptides Containing Chimeric Amino Acids as Preferred Reverse-Turn Scaffolds Ye Che and Garland Marshall. J. Med. Chem. 49 (1):111 -124, (2006)
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways Ma K, Forbes JG, Gutierrez-Cruz G, and Wang K. J. Biol Chem. 281(37):27539-56 (2006)
Development of small molecules designed to modulate protein-protein interactions Ye Che, Bernard Brooks, Garland Marshall. J. Computer-Aided Molecular Design 20(2): 109-130 (2006)
Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35 Zheng J, Ma B, Tsai C-J, Nussinov R. Biophysical Journal 91: 824-833 (2006)
Development of a substrate-based cyclic phosphopeptide inhibitor of protein phosphatase 2Cδ, Wip1 Yamaguchi H, Durell SR, Feng H, Bai Y, Anderson CW, Appella E. Biochemistry 45(44):13193-202 (2006)

Computational Study of the Fibril Organization of Polyglutamine Repeats Reveals a Common Motif Identified in β-Helices David Zanuy, Kannan Gunasekaran, Arthur M. Lesk and Ruth Nussinov J. Mol. Biol. 358(1):330-345 (2006)
Dynamical motions of lipids and a finite size effect in simulations of bilayers Klauda JB, Brooks BR, Pastor RW. J Chem Phys. 125(14):144710 (2006)
The Stability of Monomeric Intermediates Controls Amyloid Formation: A{beta}25-35 and its N27Q Mutant Ma B, Nussinov R. Biophys. J. 90(10):3365-74 (2006)
Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services Ying He, and Mehmet Kayaalp. AMIA Annu Symp Proc. : 946 (2006)
Rat toxicogenomic study reveals analytical consistency across microarray platforms Guo, L, Edward K Lobenhofer, Charles Wang, Richard Shippy, Stephen C Harris, Lu Zhang, Nan Mei, Tao Chen, Damir Herman, Federico M Goodsaid, Patrick Hurban, Kenneth L Phillips, Jun Xu, Xutao Deng, Yongming Andrew Sun, Weida Tong, Yvonne P Dragan & Leming Shi Nature Biotechnology. 24: 1162 - 1169 (2006)
Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene Expression Relations Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Michael L. Bittner, Yidong Chen, Daniel E. Russ and Robert L. Martino Computational and Statistical Approaches to Genomics (2006)
SCIMS: A new algorithm for associating anticancer drug mechanisms with gene ontology categories Gabriel S. Eichler, Mark Reimers and John N. Weinstein Proc. Amer. Assoc. Cancer Res. 47:1565 (2006)
Getting practical with molecular chaperones VM Longshaw, WS Nicoll, M Botha, MH Ludewig, A Shonhai, LL Stephens and GL Blatch Protein Folding (2006)
Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems L. G. MacDowell, V. K. Shen, and J. R. Errington. J. Chem. Phys 125(3): 34705 (2006)
Altered HIV-1 Gag protein interactions with cyclophilin A (CypA) on the acquisition of H219Q and H219P substitutions in the CypA binding loop Gatanaga H, Das D, Suzuki Y, Yeh DD, Hussain KA, Ghosh AK, Mitsuya H. J Biol Chem. 281(2):1241-50 (2006)
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure Jie Zheng, Buyong Ma and Ruth Nussinov. Phys. Biol. 3: 1478-3975 (2006)
Impact of Cis-proline analogs on peptide conformation Ye Che, Garland R. Marshall. Biopolymers 81(5): 392 - 406 (2006)

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior. V. K. Shen, J. K. Cheung, J. R. Errington, and T. M. Truskett. Biophys. J. 90:1949 (2006)
The influence of tumor oxygenation on 18 F-FDG (Fluorine-18 Deoxyglucose) uptake: A mouse study using positron emission tomography (PET) Linda W Chan, Sebastien Hapdey, Sean English, Jurgen Seidel, Joann Carson, Anastasia L Sowers, Murali C Krishna, Michael V Green, James B Mitchell and Stephen L Bacharach. Radiation Oncology 1:3 (2006)
A Missense Mutation in the Seven-transmembrane Domain of the Human Ca2+ Receptor Converts a Negative Allosteric Modulator into a Positive Allosteric Modulator Jianxin Hu, Jiankang Jiang, Stefano Costanzi, Craig Thomas, Wu Yang, Jean H. M. Feyen, Kenneth A. Jacobson, and Allen M. Spiegel. J. Biol. Chem Vol. 281(3): 21558-21565 (2006)
The histone database: A comprehensive resource for histones and histone fold-containing proteins Marino-Ramirez, L., Hsu, B., Baxevanis, A. D. and Landsman, D Proteins 62:838-842 (2006)
Structural and Molecular Interactions of CCR5 Inhibitors with CCR5 Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF, Arnold E, Mitsuya H. J Biol Chem. 281(18):12688-98 (2006)
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics 7:206 (2006)
Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Lancet Neurol. 5:911-916 (2006)
Multiple independent evolutionary solutions to core histone gene regulation Marino-Ramirez L, Jordan IK, Landsman D. Genome Biol. 7(12):R122 (2006)
Comparison of the Human and Worm p53 Structures Suggests a Way for Enhancing Stability Pan Y, Ma B, Levine AJ, Nussinov R. Biochemistry 45 (12):3925 -3933 (2006)
PET imaging of the dopamine transporter with 18F-FECNT: a polar radiometabolite confounds brain radioligand measurements Zoghbi SS, Shetty HU, Ichise M, Fujita M, Imaizumi M, Liow JS, Shah J, Musachio JL, Pike VW, Innis RB. J. Nucl. Med 47(3):520-7 (2006)
Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data Lusa L, McShane LM, Radmacher MD, Shih JH, Wright GW, Simon R. Stat Med. 26(5):1102-13 (2006)
Co-evolutionary Rates of Functionally Related Yeast Genes Leonardo Marino-Ramirez, Olivier Bodenreider, Natalie Kantz and I. King Jordan Evolutionary Bioinformatics, Donald Forsdyke (ed), Springer (2006)

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L. J. Mol. Biol. 360(1):213-27 (2006)
Automatic colonic polyp detection using multiobjective evolutionary techniques Jiang Li, Adam Huang, Jianhua Yao, and Ingmar Bitter, Nicholas Petrick, Ronald M. Summers, Perry J. Pickhardt, J. Richard Choi. In Medical Imaging 2006: Image Processing, Joseph M. Reinhardt, Josien P. W. Pluim (eds) (2006)
Backbone Conformational Preferences and Pseudorotational Ring Puckering of 1-Aminocyclopentane-1-carboxylic Acid Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. J Phys Chem B 110 (42): 21264 -21271 (2006)

2005 (42 papers)

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem Sardiu ME, Alves G, Yu Y-K. Phys. Rev. E 72: 061917 (2005)
Agonist-Induced Conformational Changes in Thyrotropin-Releasing Hormone Receptor Type I: Disulfide Cross-Linking and Molecular Modeling Approaches. Huang W, Osman R, Gershengorn MC. Biochemistry. 44(7):2419-2431 (2005)
CD4 binding partially locks the bridging sheet in gp120 but leaves the β2/3 strands flexible Pan Y, Ma B, Nussinov R. J Mol Biol. 350(3):514-27 (2005)

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics Alves G, Yu Y-K. Bioinformatics 21(19):3726-3732 (2005)
Molecular Dynamics Simulations of Alzheimer's beta-Amyloid Protofilaments Buchete NV, Tycko R, and Hummer G. Mol. Biol. 353 (4): 804-821 (2005)
PET imaging of brain with the beta-amyloid probe, [11C]6-OH-BTA-1, in a transgenic mouse model of Alzheimer's disease Toyama H, Ye D, Ichise M, Liow JS, Cai L, Jacobowitz D, Musachio JL, Hong J, Crescenzo M, Tipre D, Lu JQ, Zoghbi S, Vines DC, Seidel J, Katada K, Green MV, Pike VW, Cohen RM, Innis RB. Eur. J. Nucl. Med. Mol. Imaging 32(5):593-600 (2005)
Mutations in PIP5K3 are associated with François-Neetens mouchetée fleck corneal dystrophy Li S, Tiab L, Jiao X, Munier FL, Zografos L, Frueh BE, Sergeev Y, Smith J, Rubin B, Meallet MA, Forster RK, Hejtmancik JF, Schorderet DF. Am. J. Hum. Genet. 77(1):54-63 (2005)
Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference Costanzi S, Joshi BV, Maddileti S, Mamedova L, Gonzalez-Moa MJ, Marquez VE, Harden TK, Jacobson KA. J Med Chem. 48(26):8108-11 (2005)
In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1. Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R. Biochemistry 44(5):1423-32 (2005)
Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis Jeffery B. Klauda, Richard W. Pastor, and Bernard R. Brooks J. Phys. Chem. 109(33):15684-15686 (2005)
An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer Klauda J, Brooks BR, MacKerell AD, Venable RM, Pastor RW. J. Phys. Chem. B 109 (11): 5300 -5311 (2005)
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. PNAS 102(23):8174-9 (2005)
Molecular architecture of a eukaryotic DNA transposase. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F. Nat Struct Mol Biol. 12: 715 - 721 (2005)
A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose Skibinsky A, Venable RM, Pastor RW. Biophys. J. 89: 4111-4121 (2005)
Sequential testing for efficacy in clinical trials with non-transient effects James F. Troendle, Aiyi Liu, Chengqing Wu, Kai F. Yu. Statistics in Medicine 24(21):3239 - 3250 (2005)

Amino Acid Side Chain Interactions in the Presence of Salts Sergio A. Hassan J. Phys. Chem. 109(46):21989-21996 (2005)
Variable tick protein in two genomic groups of the relapsing fever spirochete Borrelia hermsii in western North America Porcella SF, Raffel SJ, Anderson DE Jr, Gilk SD, Bono JL, Schrumpf ME, Schwan TG. Infect. Immun. 73(10):6647-58 (2005)
Distinguishing Modes of Eukaryotic Gradient Sensing R. Skupsky, W. Losert, and R. J. Nossal Biophys. J. 89(4):2806-2823 (2005)
Bacterial 16S ribosomal DNA in house dust mite cultures Valerio CR, Murray P, Arlian LG, Slater JE. J. Allergy Clin. Immunol. 116(6):1296-300 (2005)
Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15 N/13 C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings: Application to the 34-kDa Enzyme IIAChitobiose Chun Tang, Junji Iwahara and G. Marius Clore J. Biomol. NMR 33(2):1573-5001 (2005)
Multiple comparisons between two groups on multiple Bernoulli outcomes while accounting for covariates. JF Troendle Stat. Med. 24(23):3581-91 (2005)

Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence ? Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. PNAS 102(8):2754-9 (2005)
Measurement of Ribose Carbon Chemical Shift Tensors for A-form RNA by Liquid Crystal NMR Spectroscopy David L. Bryce, Alexander Grishaev, and Ad Bax. J. Am. Chem. Soc 127 (20):7387 -7396 (2005)
Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids Lague P, Roux B, Pastor RW. J. Mol. Biol 354: 1129-1141 (2005)
From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations SA Hassan, EL Mehler. Int.Quantum Chem. 102(5): 986 - 1001 (2005)
A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core. Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. J Mol Biol. 345(5):1213-27 (2005)
SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli Hansen AM, Qiu Y, Yeh N, Blattner FR, Durfee T, Jin DJ. Mol. Microbiol. 56(3):719-34 (2005)

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. PNAS 102(11):3988-93 (2005)
Comprehensive analysis of heterochromatin-and RNAi-mediated epigenetic control of the fission yeast genome Cam H, Sugiyama T, Chen ES, Chen X, Fitzgerald P, Grewal SI. Nat Genet. 37: 809 - 819 (2005)
Modelling longitudinal semicontinuous emesis volume data with serial correlation in an acupuncture clinical trial Paul S. Albert and Joannie Shen Appl. Statist. 54(4):707-720 (2005)
Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations Christine Peter and Gerhard Hummer. Biophys. J. 89:2222-2234 (2005)
Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1 Lopez de Silanes I, Galban S, Martindale JL, Yang X, Mazan-Mamczarz K, Indig FE, Falco G, Zhan M, Gorospe M. Mol. Cell. Biol. 25(21):9520-31 (2005)
The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli Scholl D, Merril C. J. Bacteriol. 187(24):8499-503 (2005)
Utilization of a Common Pathway for the Synthesis of High Affinity Macrocyclic Grb 2 SH 2 Domain-Binding Peptide Mimetics That Differ in the Configuration at One Ring Junction Zhen-Dan Shi, Rajeshri G. Karki, Karen M. Worthy, Lakshman K. Bindu, Marc C. Nicklaus, Robert J. Fisher, and Terrence R. Burke Jr. Chem. & Biodiversity 2:447-456 (2005)
Solution Structure of Enzyme IIAChitobiose from the N, N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System ? Chun Tang, David C. Williams, Jr., Rodolfo Ghirlando, and G. Marius Clore. J. Biol. Chem 280, Issue 12:11770-11780 (2005)
Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties Li X, Hassan SA, Mehler EL. Proteins. 60(3):464 - 484 (2005)
Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR. Chem. & Biodivers 2:447-456 (2005)
Genome-wide assembly and analysis of alternative transcripts in mouse. Sharov AA, Dudekula DB, Ko MSH. Genome Res. 15:748-754 (2005)
Computed tomographic virtual colonoscopy computer-aided polyp detection in a screening population. Summers RM, Yao J, Pickhardt PJ, Franaszek M, Bitter I, Brickman D, Krishna V, Choi JR. Gastroenterology 129(6):1832-44 (2005)
Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte Forbes JG, Jin AJ, Ma K, Gutierrez-Cruz G, Tsai WL, Wang K. J Muscle Res Cell Motil. 26(6-8):291-301 (2005)
Expression of estrogen receptor alpha exon-deleted mRNA variants in the human and non-human primate frontal cortex W.R. Perlman, M. Matsumoto, S. Beltaifa, T.M. Hyde, R.C. Saunders, M.J. Webster, D.R. Rubinow, J.E. Kleinman and C.S. Weickert Neuroscience 134(1):81-95 (2005)
Quantification of brain phosphodiesterase 4 in rat with (R)-[11C]Rolipram-PET Fujita M, Zoghbi SS, Crescenzo MS, Hong J, Musachio JL, Lu JQ, Liow JS, Seneca N, Tipre DN, Cropley VL, Imaizumi M, Gee AD, Seidel J, Green MV, Pike VW, Innis RB. Neuroimage 26(4):1201-10 (2005)

2004 (57 papers)

Nucleic acid transport through carbon nanotube membranes In-Chul Yeh and Gerhard Hummer. PNAS 101(33): 12177-12182 (2004)
Performance of a genetic algorithm for mass spectrometry proteomics Jeffries, NO. BMC Bioinformatics 5:180 (2004)
A Spontaneous Translational Fusion of Bacillus cereus PlcR and PapR Activates Transcription of PlcR-Dependent Genes in Bacillus anthracis via Binding with a Specific Palindromic Sequence Andrei P. Pomerantsev, Olga M. Pomerantseva, and Stephen H. Leppla Infection & Immunity 72(10):5814-5823 (2004)

Combinatorial modeling of protein folding kinetics: free energy profiles and rates Eric R. Henry and William A. Eaton Chemical Physics 307:163-185 (2004)
Dynamics of proton transfer in bacteriorhodopsin Lee YS, Krauss M. J Am Chem Soc. 126(7):2225-30 (2004)
Exploring peptide energy landscapes: A test of force fields and implicit solvent models. Steinbach PJ. Proteins 57(4):665-677 (2004)
Correcting log ratios for signal saturation in cDNA microarrays Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Bioinformatics 20(16):2685-93 (2004)
An efficient algorithm for generating two-way contingency tables with fixed marginal totals and arbitrary mean proportions, with applications to permutation tests Craig Borkowf. Comp. Stat. and Data Analysis 44(3): 431-449 (2004)
Modulating Functional Loop Movements: The Role of Highly Conserved Residues in the Correlated Loop Motions Kannan Gunasekaran, Ruth Nussinov Chem.Bio.Chem. 5(2):224-230 (2004)
IL-15 and IL-2 reciprocally regulate expression of the chemokine receptor CX3CR1 through selective NFAT1- and NFAT2-dependent mechanisms Jana Barlic, David H. McDermott, Maya N. Merrell, Jacqueline Gonzales, Laura E. Via, and Philip M. Murphy J. Biol. Chem. 279(47):48520-48534 (2004)
Side chain interactions determine the amyloid organization: a single layer β-sheet molecular structure of the calcitonin peptide segment 15-19 David Zanuy, Nurit Haspel, Hui-Hsu (Gavin) Tsai, Buyong Ma, Kannan Gunasekaran, Haim J Wolfson and Ruth Nussinov Physical Biology 1(2):89-99 (2004)
How Much Backbone Motion in Ubiquitin Is Required To Account for Dipolar Coupling Data Measured in Multiple Alignment Media as Assessed by Independent Cross-Validation? G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 126(9):2923-2938 (2004)
Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase Yong-Sok Lee and Morris Krauss J. Phys. Chem. B 108(14):4508-4515 (2004)
Large-scale validation of a computer-aided polyp detection algorithm for CT colonography using cluster computing I Bitter, JE Brown, D Brickman, RM Summers Medical Imaging 2004 (2004)
Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans- Cis Isomerization of Geldanamycin Lee YS, Marcu MG, Neckers L. Chem Biol. 11(7):991-8 (2004)

DBParser: web-based software for shotgun proteomic data analyses. Yang X, Dondeti V, Dezube R, Maynard DM, Geer LY, Epstein J, Chen X, Markey SP, Kowalak JA. J. Proteome Res. 3(5):1002-8 (2004)
Clustering of DNA sequences in human promoters. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Genome Research 14(8):1562-74 (2004)
Amplitudes of Protein Backbone Dynamics and Correlated Motions in a Small α/β Protein: Correspondence of Dipolar Coupling and Heteronuclear Relaxation Measurements G. Marius Clore and Charles D. Schwieters Biochemistry 43(33):10678-10691 (2004)
Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling Valya R. Russanova, Tazuko H. Hirai and Bruce H. Howard J. Gerontology 59:1221-1233 (2004)
Three Roads to Islet Bursting: Emergent Oscillations in Coupled Phantom Bursters Charles L. Zimliki, David Mears and Arthur Sherman. Biophys. J 87:193-206 (2004)
A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin D. R. Clifton, K. A. Fields, S. S. Grieshaber, C. A. Dooley, E. R. Fischer, D. J. Mead, R. A. Carabeo, and T. Hackstadt PNAS 101(27):10166-10171 (2004)

β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water. Wu X and Bernard R. Brooks. Biophys. J. 86(4):1946-58 (2004)
Visualization of α-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase Borgnia MJ, Shi D, Zhang P, Milne JL J. Struct. Biol. 147(2):136-45 (2004)
A Model of Inverse Agonist Action at Thyrotropin-Releasing Hormone Receptor Type 1: Role of a Conserved Tryptophan in Helix 6. Lu X, Huang W, Worthington S, Drabik P, Osman R, Gershengorn MC. Mol Pharmacol. 66(5):1192-200 (2004)
Simian cytomegalovirus encodes five rapidly evolving chemokine receptor homologues Sahagun-Ruiz A, Sierra-Honigmann AM, Krause P, Murphy PM. Virus Genes 28(1):71-83 (2004)
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function Goonesekere NC, Lee B. Nucleic Acids Research 32(9):2838-43 (2004)
Absolute quantification of regional cerebral glucose utilization in mice by 18F-FDG small animal PET scanning and 2-14C-DG autoradiography Toyama H, Ichise M, Liow JS, Modell KJ, Vines DC, Esaki T, Cook M, Seidel J, Sokoloff L, Green MV, Innis RB. J. Nucl. Med 45(8):1398-405 (2004)
Identification and functional characterization of novel scorpion venom peptides with no disulfide bridge from Buthus martensii Karsch Zeng XC, Wang SX, Zhu Y, Zhu SY, Li WX. Peptides 25(2):143-50 (2004)
Rydberg-London potential for diatomic molecules and unbonded atom pairs Kevin Cahill, V. Adrian Parsegian J. Chem. Phys. 121:10839 (2004)
Statistical analysis of over-represented words in human promoter sequences. Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Nucleic Acids Research 32(3):949-58 (2004)
Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Templeton TJ, Iyer LM, Anantharaman V, Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L. Genome Res. 14(9):1686-95 (2004)
Evolutionary and functional relationships within the DJ1 superfamily. Bandyopadhyay S, Cookson MR. BMC Evol Biol. 4(1):6 (2004)
Functionalization of tumor necrosis factor-alpha using phage display technique and PEGylation improves its antitumor therapeutic window Shibata H, Yoshioka Y, Ikemizu S, Kobayashi K, Yamamoto Y, Mukai Y, Okamoto T, Taniai M, Kawamura M, Abe Y, Nakagawa S, Hayakawa T, Nagata S, Yamagata Y, Mayumi T, Kamada H, Tsutsumi Y. Clin. Cancer Res. 10(24):8293-300 (2004)

Peptide sequence and amyloid formation: molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs Zanuy D, Porat Y, Gazit E, Nussinov R. Structure 12(3):439-55 (2004)
Synthesis and evaluation of two 18F-labeled 6-iodo-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridine derivatives as prospective radioligands for beta-amyloid in Alzheimer's disease Cai L, Chin FT, Pike VW, Toyama H, Liow JS, Zoghbi SS, Modell K, Briard E, Shetty HU, Sinclair K, Donohue S, Tipre D, Kung MP, Dagostin C, Widdowson DA, Green M, Gao W, Herman MM, Ichise M, Innis RB. J. Med. Chem 47(9):2208-18 (2004)
Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3 Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H. J Biol Chem 279(23):24624-30 (2004)
In silico protein design by combinatorial assembly of protein building blocks Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Buyong Ma and Ruth Nussinov. Protein Science 13:2753-2765 (2004)
The stability and dynamics of the human calcitonin amyloid peptide DFNKF Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. Biophys. J. 87(1):146-58 (2004)
Mapping Development-Related and Age-Related Chromatin Remodeling by a High Throughput ChIP-HPLC Approach Valya R. Russanova, Tazuko H. Hirai, Andrei V. Tchernov and Bruce H. Howard J. Gerontology 59:1234-1243 (2004)
An Example of Slow Convergence of the Bootstrap in High Dimensions. Troendle J.F.; Korn E.L.; McShane L.M. The American Statistician 58(1): 25-29 (2004)
Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation Daron I. Freedberg, Richard M. Venable, Angelo Rossi, Thomas E. Bull, and Richard W. Pastor. J. Am. Chem. Soc 126:10478-10484 (2004)
Impact of Azaproline on Peptide Conformation Ye Che and Garland Marshall. J. Org. Chem 69 (26): 9030 -9042 (2004)
Reversible proton transfer dynamics in bacteriorhodopsin Lee YS and Krauss M. J. Mol. Stru. 700(3):243-246 (2004)
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design Karki RG, Tang Y, Burke TR Jr, Nicklaus MC. J Comput Aided Mol Des. 18(12):739-60 (2004)
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms Robert J Clifford, Michael N Edmonson, Cu Nguyen, Kenneth J Buetow. Bioinformatics 20(7):1006-1014 (2004)
Controlling the number of false discoveries: application to high-dimensional genomic data Korn EL, Troendle JF, McShane LM, and Simon R. Journal of Statistical Planning and Infe 124(2):379-398 (2004)
Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces Patrick Lague, Richard W. Pastor, Bernard R Brooks. J. Phys. Chem. B 108:363-368 (2004)
Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain Pan Y, Ma B, Keskin O, Nussinov R. J Biol Chem 16;279(29):30523-30 (2004)
Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations In-Chul Yeh and Gerhard Hummer. Biophys. J. 86:681-689 (2004)
LdARF1 in Trafficking and Structural Maintenance of the trans-Golgi Cisternal Network in the Protozoan Pathogen Leishmania donovani Johanna M. Porter-Kelley, Noel J. Gerald, Juan C. Engel, Elodie Ghedin and Dennis M. Dwyer Traffic 5(11):868-883 (2004)
Insights into amyloid structural formation and assembly through computational approaches. Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R. Amyloid. 11(3):143-61 (2004)
Identifying multiple changepoints in heterogeneous binary data with an application to molecular genetics Albert PS, Hunsberger SA, Hu N, Taylor PR. Biostatistics 5(4):515-529 (2004)
A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard Albert PS, Dodd LE. Biometrics 60(2):427-35 (2004)
Evaluation of anesthesia effects on [18F]FDG uptake in mouse brain and heart using small animal PET Toyama H, Ichise M, Liow JS, Vines DC, Seneca NM, Modell KJ, Seidel J, Green MV, Innis RB. Nucl. Med. Biol. 31(2):251-6 (2004)
Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. Ma B, Nussinov R. J Biol Chem. 279(51):53875-85 (2004)
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli Chen S, Zhang A, Blyn LB, Storz G. J. Bacteriol. 186(20):6689-97 (2004)
Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium Hassan SA J. Phys. Chem. B. 108 (50):19501-19509 (2004)

2003 (27 papers)

Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup D. Scholl, J. Kieleczawa, P. Kemp, J. Rush, C. C. Richardson, C. Merril. Adhya5 and I. J. Molineux J. Mol. Biol. 335(5):1151-1171 (2003)
Synthesis and Conformational Analysis of a Locked Analogue of Carbovir Built on a Bicyclo [3.1. 0]-hex-2-enyl template. Choi Y, Sun G, George C, Nicklaus MC, Kelley JA, Marquez VE. Nucleotides Nucleic Acids. 22(12):2077-91 (2003)
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL Zanuy D, Ma B, Nussinov R. Biophys. J. 84(3):1884-94 (2003)
A peptide with three hyaluronan binding motifs inhibits tumor growth and induces apoptosis Xu XM, Chen Y, Chen J, Yang S, Gao F, Underhill CB, Creswell K, Zhang L. Cancer Res. 63(18):5685-90 (2003)
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase H. Lee Woodcock, Milan Hodoŝĉek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III and Bernard R. Brooks Theoretical Chemistry Accounts 109(3):140-148 (2003)
Interdependence of Backbone Flexibility, Residue Conservation, and Enzyme Function: A Case Study on β1, 4-Galactosyltransferase-I Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R. Biochemistry. 42(13):3674-87 (2003)
A Random Effects Transition Model For Longitudinal Binary Data With Informative Missingness Paul S Albert & Dean Follmann. Statistica Neerlandica 57 Issue 1:100-111, (2003)
Binding and Hydrolysis of Ampicillin in the Active Site of a Zinc Lactamase M. Krauss, N. Gresh, and J. Antony J. Phys. Chem B 107(5):1215-1229 (2003)
A super-linear minimization scheme for the nudged elastic band method Jhih-Wei Chu, Bernhardt L. Trout, Bernard R Brooks J. Chem. Phys. 119:12708-12717 (2003)
Changes in mumps virus gene sequence associated with variability in neurovirulent phenotype Rubin SA, Amexis G, Pletnikov M, Li Z, Vanderzanden J, Mauldin J, Sauder C, Malik T, Chumakov K, Carbone KM. J. Virol. 77(21):11616-24 (2003)
On the kinematics of protein folding Sean Cahill, Michael Cahill, Kevin Cahill. J. Comp. Chem Volume 24, Issue 11: Pages 1364-1370 (2003)
Triggering loops and enzyme function: identification of loops that trigger and modulate movements Gunasekaran K, Ma B, Nussinov R. J Mol Biol. 332(1):143-59 (2003)

Characterization of a New γ TuRC Subunit with WD Repeats Ruwanthi N. Gunawardane, Ona C. Martin, and Yixian Zheng Mol. Biol. Cell 14(3):1017-1026 (2003)
The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. Zanuy D, Nussinov R. J Mol Biol. 329(3):565-84 (2003)
Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N/1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 125(10):2902-2912 (2003)
Modeling tumor growth with random onset Albert PS, Shih JH. Biometrics 59(4):897-906 (2003)
Molecular dynamics simulations of the unfolding of β2-microglobulin and its variants Ma B, Nussinov R. Protein Eng. 16(8):561-75 (2003)
Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW. Biopolymers 69(4):448-60 (2003)

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. J Struct Biol. 141(1):63-76 (2003)
Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency Krakowiak PA, Wassif CA, Kratz L, Cozma D, Kovárová M, Harris G, Grinberg A, Yang Y, Hunter AG, Tsokos M, Kelley RI, Porter FD. Hum. Mol. Genet. 12(13):1631-41 (2003)
Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS. PLoS Biol. 1(3):E74 (2003)
Parallel computation for coefficients of determination in the context of multivariate gene-expression analysis Edward B Suh, Daniel E Russ, Edward R Dougherty, Seungchan Kim, Michael L Bittner, Yidong Chen, Robert L. Martino in Biocomputing, editor Phillip A Laplante (2003)
The influenza A virus PB1-F2 protein targets the inner mitochondrial membrane via a predicted basic amphipathic helix that disrupts mitochondrial function Gibbs JS, Malide D, Hornung F, Bennink JR, Yewdell JW. J. Virol. 77(13):7214-24 (2003)
Direct Observation of the Folding and Unfolding of a Hairpin in Explicit Water through Computer Simulation Xiongwu Wu, Shaomeng Wang, and Bernard R. Brooks. J. Am. Chem. Soc. 124(19):5282-3 (2003)
Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5− diffuse large B-cell lymphomas Tohru Kobayashi, Motoko Yamaguchi, Seungchan Kim, Jun Morikawa, Shoko Ogawa, Satoshi Ueno, Edward Suh, Edward Dougherty, Ilya Shmulevich, Hiroshi Shiku, and Wei Zhang Cancer Res. 63:60 (2003)
Hydrogen bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay Lee YS, Hodoscek M, Kador PF, Sugiyama K. Chem. Biol. Interact 143-144:307-16 (2003)
Cyclin E expression during development in Caenorhabditis elegans Brodigan TM, Liu J, Park M, Kipreos ET, Krause M. Dev. Biol. 254(1):102-115 (2003)

2002 (18 papers)

Cyclin-dependent kinase 5 (cdk5) activation requires interaction with three domains of p35 Amin, ND; Albers, W; Pant, HC; J. Neurosci. Res., DOI://10.1002/jnr.10116 (2002)
A preliminary transcriptome map of non-small cell lung cancer Fujii T, Dracheva T, Player A, Chacko S, Clifford R, Strausberg RL, Buetow K, Azumi N, Travis WD, Jen J. Cancer Res. 62(12):3340-6 (2002)
The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. Mol. Cell 9(1):11-22 (2002)

Features of the NIH ATLAS Small Animal PET Scanner and Its Use with a Coaxial Small Animal Volume CT Scanner Seidel J, Vacquero JJ, Pascua J, Desco M, Johnson CA, Green M IEEE International Symposium on Biomedic, Washington, DC, 2002:TP-P1.9 (2002)
Hydrophobicity Maps of the N-Peptide Coiled Coil of HIV-1 gp41 Xavier Siebert and Gerhard Hummer Biochemistry 41(9):2956-2961 (2002)
A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness Albert, PS, Follmann, DA, Wang, SA, Suh, EB. Biometrics 58 Issue 3:631-642 (2002)
Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study Dixon AM, Venable RM, Pastor RW, Bull TE. Biopolymers 65(4):284-98 (2002)
Structure Activity of 3-Aryl-1, 3-diketo-Containing Compounds as HIV-1 Integrase Inhibitors1 Godwin C. G. Pais, Xuechun Zhang, Christophe Marchand, Nouri Neamati, Kiriana Cowansage, Evguenia S. Svarovskaia, Vinay K. Pathak, Yun Tang, Marc Nicklaus, Yves Pommier, and Terrence R. Burke, Jr. J. Med. Chem. 45(15):3184-3194 (2002)
Isolation and sequencing of a putative promoter region of the murine G protein beta 1 subunit (GNB1) gene Kitanaka J, Kitanaka N, Takemura M, Wang XB, Hembree CM, Goodman NL, Uhl GR. DNA Seq. 13(1):39-45 (2002)
Parametric and semiparametric approaches to testing for seasonal trend in serial count data Hunsberger S, Albert PS, Follmann DA, Suh E. Biostatistics. 3(2):289-98 (2002)
Fast-growth Thermodynamic Integration: Results for Sodium Ion Hydration G. Hummer Molecular Simulation 28:81-90 (2002)
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent Yeh IC, Hummer G. J Am Chem Soc. 124(23):6563-8 (2002)
Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H. PNAS 99(22):14320-5 (2002)
Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ_16-22, Aβ_16-35, and Aβ_10-35): Sequence effects Buyong Ma and Ruth Nussinov PNAS 99(22):14126-14131 (2002)
Ixolaris, a novel recombinant tissue factor pathway inhibitor (TFPI) from the salivary gland of the tick, Ixodes scapularis: identification of factor X and factor Xa as scaffolds for the inhibition of factor VIIa/tissue factor complex Francischetti IM, Valenzuela JG, Andersen JF, Mather TN, Ribeiro JM. Blood 99(10):3602-12 (2002)

Assembly, verification, and initial annotation of the NIA mouse 7.4 K cDNA clone set VanBuren V, Piao Y, Dudekula DB, Qian Y, Carter MG, Martin PR, Stagg CA, Bassey UC, Aiba K, Hamatani T, Kargul GJ, Luo AG, Kelso J, Hide W, Ko MS. Genome Res. 12(12):1999-2003 (2002)
Mutant deoxynucleotide carrier is associated with congenital microcephaly Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schaffer AA, Biesecker LG. Nat Genet. 32(1):175-9 (2002)
The neurogenetics of mucolipidosis type IV G. Altarescu, MD, M. Sun, MD, PhD, D. F. Moore, MD, PhD, DIC, J. A. Smith, MD, E. A. Wiggs, PhD, B. I. Solomon, MS, N. J. Patronas, MD, K. P. Frei, MD, S. Gupta, MD, C. R. Kaneski, MS, O. W. Quarrell, MD, S. A. Slaugenhaupt, PhD, E. Goldin, PhD and R. Schiffmann, MD Neurology 59:306-313 (2002)

2001 (14 papers)

Identification of fifteen novel mutations and genotype-phenotype relationship in Fabry disease Altarescu GM, Goldfarb LG, Park KY, Kaneski C, Jeffries N, Litvak S, Nagle JW, Schiffmann R. Clin. Genet. 60(1):46-51 (2001)
Circularly permuted proteins in the protein structure database Jongsun Jung and Byungkook Lee. Protein Science 10:1881-1886 (2001)
Limited heterogeneity of T cell receptor BV usage in aplastic anemia Zeng W, Maciejewski JP, Chen G, Young NS. J. Clin. Invest. 108(5):765-73 (2001)

Molecular Dynamics Simulations of Octyl Glucoside Micelles: Dynamic Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 105(35):8312-8321 (2001)
ERGL, a novel gene related to ERGIC-53 that is highly expressed in normal and neoplastic prostate and several other tissues Yerushalmi N, Keppler-Hafkemeyer A, Vasmatzis G, Liu XF, Olsson P, Bera TK, Duray P, Lee B, Pastan I. Gene 265(1-2):55-60 (2001)
Simultaneous Determination of Orientational and Order Parameter Distributions from NMR Spectra of Partially Oriented Model Membranes Edward Sternin, Hartmut Schafer, Ivan V. Polozov and Klaus Gawrisch. J. Mag. Res 149(1): 110-113 (2001)
Parallel Computing Methods for Analyzing Gene Expression Relationships Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Daniel E. Russ, and Robert L. Martino Proc. SPIE 4266:213-221 (2001)
Lowering the isoelectric point of the Fv portion of recombinant immunotoxins leads to decreased nonspecific animal toxicity without affecting antitumor activity Onda M, Nagata S, Tsutsumi Y, Vincent JJ, Wang Q, Kreitman RJ, Lee B, Pastan I. Cancer Res. 61(13):5070-7 (2001)
Cloning, mRNA distribution, and functional expression of an avian counterpart of the chemokine receptor/HIV coreceptor CXCR4 Liang TS, Hartt JK, Lu S, Martins-Green M, Gao JL, Murphy PM. J. Leukoc. Biol. 69(2):297-305 (2001)

Fast-growth thermodynamic integration: Error and efficiency analysis G. Hummer J. Chem. Phys. 114(17):7330 (2001)
Genomic organization of the murine G protein beta subunit genes and related processed pseudogenes J. Kitanaka, XB Wang, N Kitanaka, CM Hembree, GR Uhl DNA Sequence 12:345-354 (2001)
PET, CT, and MR Image Registration of the Rat Brain and Skull Juan José Vaquero, Manuel Desco, Javier Pascau, Andrés Santos, E, Injae Lee, Jürgen Seidel, and Michael V. Green IEEE Transactions on Nuclear Science 48(4):1440-1445 (2001)
Crystal structure of the 14-3-3ζ: serotonin N-acetyltransferase complex: a role for scaffolding in enzyme regulation Obsil T, Ghirlando R, Klein DC, Ganguly S, Dyda F. Cell 105(2):257-67 (2001)
A novel myeloid-restricted zebrafish CCAAT/enhancer-binding protein with a potent transcriptional activation domain Lyons SE, Shue BC, Oates AC, Zon LI, Liu PP. Blood 97(9):2611-7 (2001)

2000 (17 papers)

Prediction of IC50 values for ACAT inhibitors from molecular structure Patankar, SJ; Jurs, PC; , J Chem Inf Comput Sci, DOI://10.1021/ci990125r (2000)
Immunomorphometric Study of Rat Renal Inner Medulla Raymond Mejia and James B Wade Am. J. Physiol. - Renal Physiol. 10.1152:ajprenal.00340.2000 (2000)
Structure and Promoter Analysis of the Human unc-33-like Phosphoprotein Gene Tatsuya Matsuo, Jimmy K. Stauffer, Robert L. Walker , Paul Meltzer , and Carol J. Thiele J. Biol. Chem. 275(22):16560-16568 (2000)
Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. Antzutkin ON, Balbach JJ, Leapman RD, Rizzo NW, Reed J, Tycko R. PNAS 97(24):13045-50 (2000)
Characterization and Sequencing of Prototypic Human T-Lymphotropic Virus Type 1 (HTLV-1) from an HTLV-1/2 Seroindeterminate Patient Allen Waziri, Samantha S. Soldan, Michael D. Graf, Jim Nagle, and Steven Jacobson J. Virol. 74(5):2178-2185 (2000)
Amyloid fibril formation by Aβ16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Biochemistry 39(45):13748-59 (2000)
Oligodendrocytes in aging mice lacking myelin-associated glycoprotein are dystrophic but not apoptotic Weiss MD, Hammer J, Quarles RH. J. Neurosci. Res. 62(6):772-80 (2000)
Genomic imbalance in rat mammary gland carcinomas induced by 2-Amino-1-methyl-6-phenylimidazo(4,5-b)pyridine Minshu Yu, Doug-Young Ryu, Elizabeth G. Snyderwine Molecular Carcinogenesis 27(2):76-83 (2000)
Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 104(23):5462-5470 (2000)
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays Kim S, Dougherty ER, Bittner ML, Chen Y, Sivakumar K, Meltzer P, Trent JM. J. Biomed. Opt. 5(4):411-24 (2000)
Multivariate measurement of gene expression relationships. Kim S, Dougherty ER, Chen Y, Sivakumar K, Meltzer P, Trent JM, Bittner M. Genomics 67(2):201-9 (2000)
XAGE-1, a new gene that is frequently expressed in Ewing's sarcoma Liu XF, Helman LJ, Yeung C, Bera TK, Lee B, Pastan I. Cancer Res. 60(17):4752-5 (2000)
Bioactive motifs of agouti signal protein Virador VM, Santis C, Furumura M, Kalbacher H, Hearing VJ. Exp. Cell Res. 259(1):54-63 (2000)

Mutation analysis and description of sixteen RSH/Smith-Lemli-Opitz syndrome patients: Polymerase chain reaction-based assays to simplify genotyping Patrycja A. Krakowiak, Ngozi A. Nwokoro, Christopher A. Wassif, Kevin P. Battaile, Magorzata J.M. Nowaczyk, William E. Connor, Cheryl Maslen, Robert D. Steiner, Forbes D. Porter Am. J. Med. Genetics 94(3):214-227 (2000)
Rhesus and pig-tailed macaque parvoviruses: identification of two new members of the erythrovirus genus in monkeys Green SW, Malkovska I, O'Sullivan MG, Brown KE. Virology 269(1):105-12 (2000)
A stage-specific preparation to study the Ca2+-triggered fusion steps of exocytosis: Rationale and perspectives Joshua Zimmerberg, Paul S. Blank, Irina Kolosova, Myoung-Soon Cho, Masahiro Tahara, and Jens R. Coorssen Biochimie 82(4):303-314 (2000)
Theoretical formalism for kinesin motility I. Bead movement powered by single one-headed kinesins. Chen Y. Biophys. J. 78(1):313-21 (2000)

1999 (9 papers)

The zebrafish genome contains two distinct selenocysteine tRNA[Ser]sec genes Xu XM, Zhou X, Carlson BA, Kim LK, Huh TL, Lee BJ, Hatfield DL FEBS Lett. 454(1-2):16-20 (1999)
Characterization of a multicopy family of genes encoding a surface-expressed serine endoprotease in rat Pneumocystis carinii Russian DA, Andrawis-Sorial V, Goheen MP, Edman JC, Vogel P, Turner RE, Klivington DL, Angus CW, Kovacs JA. Proc. Assoc. Am. Physicians 111(4):347-56 (1999)

Asymmetry and direction reversal in fluctuation-induced biased Brownian motion Chen YD, Yan B, Miura R. Phys Rev E Stat Phys Plasmas Fluids Rela 60(4 Pt A):3771-5 (1999)
Novel Genes in the PAGE and GAGE Family of Tumor Antigens Found by Homology Walking in the dbEST Database Ulrich Brinkmann, George Vasmatzis, Byungkook Lee and Ira Pastan Cancer Res. 59:1445-1448 (1999)
Reduction of the nonspecific animal toxicity of anti-Tac(Fv)-PE38 by mutations in the framework regions of the Fv which lower the isoelectric point Onda M, Kreitman RJ, Vasmatzis G, Lee B, Pastan I. J. Immunol. 163(11):6072-7 (1999)
Expression profiling using cDNA microarrays Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Nat Genet. 21(1 Suppl):10-4 Review. (1999)
Genomic organization and mapping of the human and mouse neuronal β2-nicotinic acetylcholine receptor genes Lueders KK, Elliott RW, Marenholz I, Mischke D, DuPree M, Hamer D. Mamm. Genome 10(9):900-5 (1999)
GalR mutants defective in repressosome formation Geanacopoulos M, Vasmatzis G, Lewis DE, Roy S, Lee B, Adhya S. Genes Dev. 13(10):1251-62 (1999)

Analysis of selenocysteine (Sec) tRNA([Ser]Sec) genes in Chinese hamsters Xu XM, Carlson BA, Kim LK, Lee BJ, Hatfield DL, Diamond AM. Gene 239(1):49-53 (1999)

1998 (2 papers)

Information technology applications in biomedical research Martino, R.L. Kempner, K.M. Johnson, C.A. Information Technology Applications in B ITAB98:28-34 (1998)
Parallel computing strategies for determining viral capsidstructure by cryoelectron microscopy Lanczycki, C.J. Johnson, C.A. Trus, B.L. Conway, J.F. Steven, A.C. Martino, R.L. Computational Science & Engineering, IEE 5(2):76-91 (1998)