Papers that used NIH HPC (Biowulf) resources

If you have published research that has made significant use of these systems, please let us know by sending email to staff@hpc.nih.gov

2024 to date (461 papers)

Excess shed mesothelin disrupts pancreatic cancer cell clustering to impair peritoneal colonization Ewa, T; Panchwagh, N; Tai, CH et al. FASEB J, DOI://10.1096/fj.202400446R (2024)
SLC26A4-AP-2 mu2 interaction regulates SLC26A4 plasma membrane abundance in the endolymphatic sac Lee, HJ; Fenollar-Ferrer, C; Isgrig, K et al. Sci Adv, DOI://10.1126/sciadv.adm8663 (2024)
African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1 Álvarez Jerez, P; Wild Crea, P; Ramos, DM et al. Nat Struct Mol Biol, DOI://10.1038/s41594-024-01423-2 (2024)
A genome-first approach to characterize DICER1 pathogenic variant prevalence, penetrance and cancer, thyroid, and other phenotypes in 2 population-scale cohorts Kim, J; Haley, J; Hatton, JN et al. Genet Med Open, DOI://10.1016/j.gimo.2024.101846 (2024)
Increased frequency of CHEK2 germline pathogenic variants among individuals with dermatofibrosarcoma protuberans Sargen, MR; Kim, J; Haley, JS et al. Genet Med Open, DOI://10.1016/j.gimo.2024.101895 (2024)
Doxorubicin resistance involves modulation of interferon signaling, transcriptional bursting, and gene co-expression patterns of U-ISGF3-related genes Trzaskoma, P; Jung, S; Kanno, Y et al. Neoplasia, DOI://10.1016/j.neo.2024.101071 (2024)
HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state Lee, M; Lu, M; Zhang, B et al. Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2024.11.020 (2024)
Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues Sanghvi, N; Calvo-Alcañiz, C; Rajagopal, PS et al. Sci Adv, DOI://10.1126/sciadv.adn0220 (2024)
Blood-brain barrier disruption and increased free water are associated with worse cognitive performance in patients with chronic cerebrovascular disease Kern, KC; Zagzoug, MS; Gottesman, RF et al. Neuroimage Clin, DOI://10.1016/j.nicl.2024.103706 (2024)
Hierarchical individual variation and socioeconomic impact on personalized functional network topography in children Zhao, S; Su, H; Cong, J et al. BMC Med, DOI://10.1186/s12916-024-03784-3 (2024)
Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis Malhotra, N; Oh, S; Finin, P et al. PLoS Biol, DOI://10.1371/journal.pbio.3002852 (2024)
Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice Zamba-Campero, M; Soliman, D; Yu, H et al. Nat Commun, DOI://10.1038/s41467-024-54806-w (2024)
Mechanism-free repurposing of drugs for C9orf72-related ALS/FTD using large-scale genomic data Saez-Atienzar, S; Souza, CDS; Chia, R et al. Cell Genom, DOI://10.1016/j.xgen.2024.100679 (2024)
Novel polyomavirus in the endangered garden dormouse Eliomys quercinus Vasiliūnaitė, E; Repšytė, M; Kramer, EM et al. Virol J, DOI://10.1186/s12985-024-02581-x (2024)
Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide Reveiz, M; Xu, K; Lee, M et al. Front Immunol, DOI://10.3389/fimmu.2024.1484029 (2024)
Does Remdesivir Lower COVID-19 Mortality? A Subgroup Analysis of Hospitalized Adults Receiving Supplemental Oxygen Potter, GE; Proschan, MA; , Stat Med, DOI://10.1002/sim.10241 (2024)
The glucocorticoid receptor potentiates aldosterone-induced transcription by the mineralocorticoid receptor Johnson, TA; Fettweis, G; Wagh, K et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2413737121 (2024)
Processing, evaluating, and understanding FMRI data with afni_proc.py Reynolds, RC; Glen, DR; Chen, G et al. Imaging Neurosci (Camb), DOI://10.1162/imag_a_00347 (2024)
Balance between asymmetric allocation and repair of somatic damage in unicellular life forms as an ancient form of r/K selection Biba, DA; Wolf, YI; Koonin, EV; Rochman, ND; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2400008121 (2024)
Phosphorylation by JNK switches BRD4 functions Devaiah, BN; Singh, AK; Mu, J et al. Mol Cell, DOI://10.1016/j.molcel.2024.09.030 (2024)
The endometrial cancer A230V-ALK5 (TGFBR1) mutant attenuates TGF-β signaling and exhibits reduced in vitro sensitivity to ALK5 inhibitors Yu, EJ; Bell, DW; , PLoS One, DOI://10.1371/journal.pone.0312806 (2024)
On the role of native contact cooperativity in protein folding Wang, D; Frechette, LB; Best, RB; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2319249121 (2024)
Genomic analysis of the early COVID-19 pandemic in Haiti reveals Caribbean-specific variant dynamics Mushegian, A; Kreitman, A; Nelson, MI et al. PLOS Glob Public Health, DOI://10.1371/journal.pgph.0003536 (2024)
Glycocalyx Interactions Modulate the Cellular Uptake of Albumin-Coated Nanoparticles Olivieri, PH; Assis, IF; Lima, AF et al. ACS Appl Bio Mater, DOI://10.1021/acsabm.4c01012 (2024)
Epidemiological data of an influenza A/H5N1 outbreak in elephant seals in Argentina indicates mammal-to-mammal transmission Uhart, MM; Vanstreels, RET; Nelson, MI et al. Nat Commun, DOI://10.1038/s41467-024-53766-5 (2024)
Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic Chambers, MJ; Scobell, SB; Sadhu, MJ; , Elife, DOI://10.7554/eLife.99575 (2024)
Functional characteristics and computational model of abundant hyperactive loci in the human genome Hudaiberdiev, S; Ovcharenko, I; , Elife, DOI://10.7554/eLife.95170 (2024)
Cellular-resolution optogenetics reveals attenuation-by-suppression in visual cortical neurons LaFosse, PK; Zhou, Z; O'Rawe, JF et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2318837121 (2024)
Structural basis for α-tubulin-specific and modification state-dependent glutamylation Mahalingan, KK; Grotjahn, DA; Li, Y et al. Nat Chem Biol, DOI://10.1038/s41589-024-01599-0 (2024)
Exploring the longitudinal expression dynamics of midguts in adult female Amblyomma americanum ticks Lu, S; de Sousa-Paula, LC; Ribeiro, JMC; Tirloni, L; , BMC Genomics, DOI://10.1186/s12864-024-10905-y (2024)
RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility Choi, H; Zhou, L; Zhao, Y; Dean, J; , Nucleic Acids Res, DOI://10.1093/nar/gkae712 (2024)

Cryo-EM structure of a natural prion: chronic wasting disease fibrils from deer Alam, P; Hoyt, F; Artikis, E et al. Acta Neuropathol, DOI://10.1007/s00401-024-02813-y (2024)
The Bor1 elevator transport cycle is subject to autoinhibition and activation Jiang, Y; Jiang, J; , Nat Commun, DOI://10.1038/s41467-024-53411-1 (2024)
MYB/MYBL1-altered gliomas frequently harbor truncations and non-productive fusions in the MYB and MYBL1 genes Chung, HJ; Rajan, S; Wu, Z et al. Acta Neuropathol, DOI://10.1007/s00401-024-02803-0 (2024)
Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity Updegrove, TB; Delerue, T; Anantharaman, V et al. Sci Adv, DOI://10.1126/sciadv.adq0791 (2024)
The Myc-associated zinc finger protein epigenetically controls expression of interferon-γ-stimulated genes by recruiting STAT1 to chromatin Xiao, T; Li, X; Felsenfeld, G; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2320938121 (2024)
Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity Xu, M; Hong, JJ; Zhang, X et al. EMBO J, DOI://10.1038/s44318-024-00206-1 (2024)
A machine learning model reveals expansive downregulation of ligand-receptor interactions that enhance lymphocyte infiltration in melanoma with developed resistance to immune checkpoint blockade Sahni, S; Wang, B; Wu, D et al. Nat Commun, DOI://10.1038/s41467-024-52555-4 (2024)
SMARCD1 is an essential expression-restricted metastasis modifier Ross, C; Gong, LY; Jenkins, LM et al. Commun Biol, DOI://10.1038/s42003-024-07018-3 (2024)
Highly efficient generation of self-renewing trophoblast from human pluripotent stem cells Slamecka, J; Ryu, S; Tristan, CA et al. iScience, DOI://10.1016/j.isci.2024.110874 (2024)
Unsupervised Multi-parametric MRI Registration Using Neural Optimal Transport Kim, B; Mathai, TS; Summers, RM; , Proc SPIE Int Soc Opt Eng, DOI://10.1117/12.3006289 (2024)
Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics Sundby, RT; Szymanski, JJ; Pan, AC et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-24-0797 (2024)
Mutational signatures in 175 Chinese gastric cancer patients Liu, F; Hu, N; Jiang, K et al. BMC Cancer, DOI://10.1186/s12885-024-12968-2 (2024)
Automated Classification of Multi-parametric Body MRI Series Kim B, Mathai TS, Helm K, Summers RM IEEE International Symposium on Biomedical Imaging, https://doi.org/10.1109/ISBI56570.2024.10635686 (2024)
Normalization of Fronto-Parietal Activation by Cognitive-Behavioral Therapy in Unmedicated Pediatric Patients With Anxiety Disorders Haller, SP; Linke, JO; Grassie, HL et al. Am J Psychiatry, DOI://10.1176/appi.ajp.20220449 (2024)
PARP-1 selectively impairs KRAS-driven phenotypic and molecular features in intrahepatic cholangiocarcinoma Keggenhoff, FL; Castven, D; Becker, D et al. Gut, DOI://10.1136/gutjnl-2023-331237 (2024)
Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance Thurber, KR; Yau, WM; Tycko, R; , J Phys Chem B, DOI://10.1021/acs.jpcb.3c07867 (2024)
Disease flares with baricitinib dose reductions and development of flare criteria in patients with CANDLE/PRAAS Cetin Gedik, K; Ortega-Villa, AM; Materne, G et al. Ann Rheum Dis, DOI://10.1136/ard-2023-225463 (2024)
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics Hoang, DT; Dinstag, G; Shulman, ED et al. Nat Cancer, DOI://10.1038/s43018-024-00793-2 (2024)
A Multiomic Analysis to Identify Drivers of Subclinical Vascular Disease in Systemic Lupus Erythematosus Oliveira, C; Temesgen-Oyelakin, Y; Naqi, M et al. Arthritis Rheumatol, DOI://10.1002/art.42925 (2024)
Enrichment of Rare Variants of Hemophagocytic Lymphohistiocytosis Genes in Systemic Juvenile Idiopathic Arthritis Correia Marques, M; Rubin, D; Shuldiner, EG et al. Arthritis Rheumatol, DOI://10.1002/art.42938 (2024)
OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in the Drosophila female germline Benner, L; Muron, S; Gomez, JG; Oliver, B; , Elife, DOI://10.7554/eLife.94631 (2024)
Impact of HLA class I functional divergence on HIV control Viard, M; O'hUigin, C; Yuki, Y et al. Science, DOI://10.1126/science.adk0777 (2024)
Segmentation of mediastinal lymph nodes in CT with anatomical priors Mathai, TS; Liu, B; Summers, RM; , Int J Comput Assist Radiol Surg, DOI://10.1007/s11548-024-03165-4 (2024)
Enhanced muscle and fat segmentation for CT-based body composition analysis: a comparative study Hou, B; Mathai, TS; Liu, J et al. Int J Comput Assist Radiol Surg, DOI://10.1007/s11548-024-03167-2 (2024)

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections Nooruzzaman, M; Johnson, KEE; Rani, R et al. Nat Commun, DOI://10.1038/s41467-024-51924-3 (2024)
LIM-domain-only 4 (LMO4) enhances CD8+ T-cell stemness and tumor rejection by boosting IL-21-STAT3 signaling Schelker, RC; Fioravanti, J; Mastrogiovanni, F et al. Signal Transduct Target Ther, DOI://10.1038/s41392-024-01915-z (2024)
Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results Parkhurst, M; Goff, SL; Lowery, FJ et al. Nat Med, DOI://10.1038/s41591-024-03109-0 (2024)
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models Afshar, M; Gao, Y; Gupta, D et al. J Biomed Inform, DOI://10.1016/j.jbi.2024.104707 (2024)
Cell type- and transcription-independent spatial proximity between enhancers and promoters Mian, Y; Wang, L; Keikhosravi, A et al. Mol Biol Cell, DOI://10.1091/mbc.E24-02-0082 (2024)
In vivo mapping of the mouse Galnt3-specific O-glycoproteome Dalal, K; Yang, W; Tian, E et al. J Biol Chem, DOI://10.1016/j.jbc.2024.107628 (2024)

HOXD12 defines an age-related aggressive subtype of oligodendroglioma Nuechterlein, N; Cimino, S; Shelbourn, A et al. Acta Neuropathol, DOI://10.1007/s00401-024-02802-1 (2024)
Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes Long, E; Yin, J; Shin, JH et al. Nat Commun, DOI://10.1038/s41467-024-52356-9 (2024)
Sexually dimorphic renal expression of mouse Klotho is directed by a kidney-specific distal enhancer responsive to HNF1b Jankowski, J; Lee, HK; Liu, C et al. Commun Biol, DOI://10.1038/s42003-024-06855-6 (2024)
A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth, and interactive QC with afni_proc.py and more Taylor, PA; Glen, DR; Chen, G et al. Imaging Neurosci (Camb), DOI://10.1162/imag_a_00246 (2024)
A sex-stratified analysis of the genetic architecture of human brain anatomy Shafee, R; Moraczewski, D; Liu, S et al. Nat Commun, DOI://10.1038/s41467-024-52244-2 (2024)
Thermodynamics-inspired explanations of artificial intelligence Mehdi, S; Tiwary, P; , Nat Commun, DOI://10.1038/s41467-024-51970-x (2024)
Bromodomain protein BRD4 directs mitotic cell division of mouse fibroblasts by inhibiting DNA damage Wu, T; Hou, H; Dey, A et al. iScience, DOI://10.1016/j.isci.2024.109797 (2024)
PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy Yoshida, T; Latt, KZ; Rosenberg, AZ et al. Elife, DOI://10.7554/eLife.91260 (2024)
Genomic approach to determine sources of neonatal Staphylococcus aureus infection from carriage in the Gambia Bojang, A; Chung, M; Camara, B et al. BMC Infect Dis, DOI://10.1186/s12879-024-09837-5 (2024)
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states Guan, Y; Levy, D; , Bioinformatics, DOI://10.1093/bioinformatics/btae082 (2024)
Generation of antitumor chimeric antigen receptors incorporating T cell signaling motifs Balagopalan, L; Moreno, T; Qin, H et al. Sci Signal, DOI://10.1126/scisignal.adp8569 (2024)
De Novo Genome Assemblies From Two Indigenous Americans from Arizona Identify New Polymorphisms in Non-Reference Sequences Köroğlu, Ç; Chen, P; Traurig, M et al. Genome Biol Evol, DOI://10.1093/gbe/evae188 (2024)
Innate protection against intrarectal SIV acquisition by a live SHIV vaccine Sui, Y; Meyer, TJ; Fennessey, CM et al. JCI Insight, DOI://10.1172/jci.insight.175800 (2024)
Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq Morgan, IL; McKie, SJ; Kim, R et al. Nucleic Acids Res, DOI://10.1093/nar/gkae638 (2024)
Genome-Wide and Transcriptome-Wide Association Studies on Northern New England and Ohio Amyotrophic Lateral Sclerosis Cohorts Li, S; Gui, J; Passarelli, MN et al. Neurol Genet, DOI://10.1212/NXG.0000000000200188 (2024)
Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival Kim, J; Vaksman, Z; Egolf, LE et al. J Natl Cancer Inst, DOI://10.1093/jnci/djad183 (2024)
The association of GNB5 with Alzheimer disease revealed by genomic analysis restricted to variants impacting gene function Zhang, J; Pandey, M; Awe, A et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2024.01.005 (2024)
Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing Rodriguez, I; Rossi, NM; Keskus, AG et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2024.01.002 (2024)

Inferring Characteristics of the Tumor Immune Microenvironment of Patients with HNSCC from Single-Cell Transcriptomics of Peripheral Blood Cao, Y; Chang, T; Schischlik, F et al. Cancer Res Commun, DOI://10.1158/2767-9764.CRC-24-0092 (2024)
Softening in Two-Component Lipid Mixtures by Spontaneous Curvature Variance Hossein, A; Beaven, AH; Sapp, K; Sodt, AJ; , J Phys Chem B, DOI://10.1021/acs.jpcb.3c08117 (2024)
Salivary Gland Tissue Recombination Can Modify Cell Fate Sekiguchi, R; Martin, D; Doyle, AD et al. J Dent Res, DOI://10.1177/00220345241247484 (2024)
Gα13 restricts nutrient driven proliferation in mucosal germinal centers Nguyen, HT; Li, M; Vadakath, R et al. Nat Immunol, DOI://10.1038/s41590-024-01910-0 (2024)
An enhancer RNA recruits KMT2A to regulate transcription of Myb Kim, J; Diaz, LF; Miller, MJ et al. Cell Rep, DOI://10.1016/j.celrep.2024.114378 (2024)
Crystal structure and mechanistic studies of the PPM1D serine/threonine phosphatase catalytic domain Kumar, JP; Kosek, D; Durell, SR et al. J Biol Chem, DOI://10.1016/j.jbc.2024.107561 (2024)
Weakly supervised detection of pheochromocytomas and paragangliomas in CT using noisy data Oluigbo, D; Mathai, TS; Santra, B et al. Comput Med Imaging Graph, DOI://10.1016/j.compmedimag.2024.102419 (2024)
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics Martinek, V; Martin, J; Belair, C et al. NAR Genom Bioinform, DOI://10.1093/nargab/lqae116 (2024)
Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation Patel, VN; Aure, MH; Choi, SH et al. Nat Commun, DOI://10.1038/s41467-024-51862-0 (2024)
CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder Folimonova, V; Chen, X; Negi, H et al. Commun Biol, DOI://10.1038/s42003-024-06770-w (2024)
Paralogue-Selective Degradation of the Lysine Acetyltransferase EP300 Chen, X; Crawford, MC; Xiong, Y et al. JACS Au, DOI://10.1021/jacsau.4c00442 (2024)
Evidence of association between higher cardiorespiratory fitness and higher cerebral myelination in aging Faulkner, ME; Gong, Z; Bilgel, M et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2402813121 (2024)
Identification and functional validation of rare coding variants in genes linked to monogenic obesity Köroğlu, Ç; Traurig, M; Muller, YL et al. Obesity (Silver Spring), DOI://10.1002/oby.24101 (2024)
The immune factors involved in the rapid clearance of bacteria from the midgut of the tick Ixodes ricinus Guizzo, MG; Frantová, H; Lu, S et al. Front Cell Infect Microbiol, DOI://10.3389/fcimb.2024.1450353 (2024)
Tyrosine phosphorylation of both STAT5A and STAT5B is necessary for maximal IL-2 signaling and T cell proliferation Lin, JX; Ge, M; Liu, CY et al. Nat Commun, DOI://10.1038/s41467-024-50925-6 (2024)
Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark Wang, L; Pattnaik, A; Sahoo, SS et al. Nat Commun, DOI://10.1038/s41467-024-51859-9 (2024)
An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome Snyder, A; Ryan, VH; Hawrot, J et al. Alzheimers Dement, DOI://10.1002/alz.13915 (2024)
Time- and cell-specific activation of BMP signaling restrains chondrocyte hypertrophy Gadomski, SJ; Mui, BWH; Gorodetsky, R et al. iScience, DOI://10.1016/j.isci.2024.110537 (2024)
Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription Sundara Rajan, S; Ebegboni, VJ; Pichling, P et al. Mol Cell Biol, DOI://10.1080/10985549.2024.2315425 (2024)
POU4F3 Is Necessary for Normal Merkel Cell Formation, whereas POU4F1 Is Dispensable Jarvis, JE; Miao, L; Hallaert, P et al. J Invest Dermatol, DOI://10.1016/j.jid.2024.06.1284 (2024)
Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells Pasterczyk, KR; Li, XL; Singh, R et al. Mol Cell Biol, DOI://10.1080/10985549.2024.2307574 (2024)
AlphaFold predictions of fold-switched conformations are driven by structure memorization Chakravarty, D; Schafer, JW; Chen, EA et al. Nat Commun, DOI://10.1038/s41467-024-51801-z (2024)
Detection of ac4C in human mRNA is preserved upon data reassessment Beiki, H; Sturgill, D; Arango, D et al. Mol Cell, DOI://10.1016/j.molcel.2024.03.018 (2024)
DNA polymerase swapping in Caudoviricetes bacteriophages Yutin, N; Tolstoy, I; Mutz, P et al. Virol J, DOI://10.1186/s12985-024-02482-z (2024)

Taurine-conjugated bile acids and their link to hepatic S1PR2 play a significant role in hepatitis C-related liver disease Ali, RO; Haddad, JA; Quinn, GM et al. Hepatol Commun, DOI://10.1097/HC9.0000000000000478 (2024)
The Time-Dependent Association Between Irritable Bowel Syndrome and All-Cause and Cause-Specific Mortality: A Prospective Cohort Study Within the UK Biobank Li, F; Yano, Y; Étiévant, L et al. Am J Gastroenterol, DOI://10.14309/ajg.0000000000002675 (2024)
Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia Tan, Y; Aravind, L; Zhang, D; , Genome Biol Evol, DOI://10.1093/gbe/evae171 (2024)
Childhood obesity's effect on cognition and brain connectivity worsens with low family income Tomasi, D; Volkow, ND; , JCI Insight, DOI://10.1172/jci.insight.181690 (2024)
Immunosuppressive CD29+ Treg accumulation in the liver in mice on checkpoint inhibitor therapy Green, BL; Myojin, Y; Ma, C et al. Gut, DOI://10.1136/gutjnl-2023-330024 (2024)
Tumor-derived RHOA mutants interact with effectors in the GDP-bound state Lin, Y; Ramelot, TA; Senyuz, S et al. Nat Commun, DOI://10.1038/s41467-024-51445-z (2024)
PLCG2-associated immune dysregulation (PLAID) comprises broad and distinct clinical presentations related to functional classes of genetic variants Baysac, K; Sun, G; Nakano, H et al. J Allergy Clin Immunol, DOI://10.1016/j.jaci.2023.08.036 (2024)
Pharmacologic ascorbate induces transient hypoxia sensitizing pancreatic ductal adenocarcinoma to a hypoxia activated prodrug Kishimoto, S; Crooks, DR; Yasunori, O et al. Free Radic Biol Med, DOI://10.1016/j.freeradbiomed.2024.07.008 (2024)
Mutant mice with rod-specific VPS35 deletion exhibit retinal α-synuclein pathology-associated degeneration Fu, C; Yang, N; Chuang, JZ et al. Nat Commun, DOI://10.1038/s41467-024-50189-0 (2024)
CAR T-cells targeting FGFR4 and CD276 simultaneously show potent antitumor effect against childhood rhabdomyosarcoma Tian, M; Wei, JS; Cheuk, AT et al. Nat Commun, DOI://10.1038/s41467-024-50251-x (2024)
Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease Lemire, G; Sanchis-Juan, A; Russell, K et al. Am J Hum Genet, DOI://10.1016/j.ajhg.2024.03.008 (2024)
Deep Learning Segmentation of Ascites on Abdominal CT Scans for Automatic Volume Quantification Hou, B; Lee, S; Lee, JM et al. Radiol Artif Intell, DOI://10.1148/ryai.230601 (2024)
Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii Cissé, OH; Ma, L; Kovacs, JA; , Microbiol Mol Biol Rev, DOI://10.1128/mmbr.00202-22 (2024)
Structure and repair of replication-coupled DNA breaks Pavani, R; Tripathi, V; Vrtis, KB et al. Science, DOI://10.1126/science.ado3867 (2024)
The recovery of parabolic avalanches in spatially subsampled neuronal networks at criticality Srinivasan, K; Ribeiro, TL; Kells, P; Plenz, D; , Sci Rep, DOI://10.1038/s41598-024-70014-4 (2024)
Comprehensive Proteomics Analysis of the Hemolymph Composition of Sugar-Fed Aedes aegypti Female and Male Mosquitoes Alvarenga, PH; Alves E Silva, TL; Suzuki, M et al. J Proteome Res, DOI://10.1021/acs.jproteome.3c00918 (2024)
Novel signals and polygenic score for height are associated with pubertal growth traits in Southwestern American Indians Ramírez-Luzuriaga, MJ; Kobes, S; Hsueh, WC et al. Hum Mol Genet, DOI://10.1093/hmg/ddae030 (2024)
The landscape of etiological patterns of hepatocellular carcinoma and intrahepatic cholangiocarcinoma in Thailand Pupacdi, B; Loffredo, CA; Budhu, A et al. Int J Cancer, DOI://10.1002/ijc.35034 (2024)
Emergency Myelopoiesis Distinguishes Multisystem Inflammatory Syndrome in Children From Pediatric Severe Coronavirus Disease 2019 Roznik, K; Andargie, TE; Johnston, TS et al. J Infect Dis, DOI://10.1093/infdis/jiae032 (2024)
Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD Seddighi, S; Qi, YA; Brown, AL et al. Sci Transl Med, DOI://10.1126/scitranslmed.adg7162 (2024)
ETS1, a Target Gene of the EWSR1::FLI1 Fusion Oncoprotein, Regulates the Expression of the Focal Adhesion Protein TENSIN3 Ebegboni, VJ; Jones, TL; Brownmiller, T et al. Mol Cancer Res, DOI://10.1158/1541-7786.MCR-23-1090 (2024)
Maternal age is related to offspring DNA methylation: A meta-analysis of results from the PACE consortium Yeung, E; Biedrzycki, RJ; Gómez Herrera, LC et al. Aging Cell, DOI://10.1111/acel.14194 (2024)
ModDotPlot-rapid and interactive visualization of tandem repeats Sweeten, AP; Schatz, MC; Phillippy, AM; , Bioinformatics, DOI://10.1093/bioinformatics/btae493 (2024)
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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)
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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)
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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 (637 papers)

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)
Genome-Wide Meta-Analysis of Cerebrospinal Fluid Biomarkers in Alzheimer's Disease and Parkinson's Disease Cohorts Ta, M; Blauwendraat, C; Antar, T et al. Mov Disord, DOI://10.1002/mds.29511 (2023)
Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev Eren, E; Watts, NR; Randazzo, D et al. Structure, DOI://10.1016/j.str.2023.07.009 (2023)
Artificial Intelligence-Based PTEN Loss Assessment as an Early Predictor of Prostate Cancer Metastasis After Surgery: A Multicenter Retrospective Study Patel, P; Harmon, S; Iseman, R et al. Mod Pathol, DOI://10.1016/j.modpat.2023.100241 (2023)
Feasibility of Using the Privacy-preserving Large Language Model Vicuna for Labeling Radiology Reports Mukherjee, P; Hou, B; Lanfredi, RB; Summers, RM; , Radiology, DOI://10.1148/radiol.231147 (2023)
σ28-dependent small RNA regulation of flagella biosynthesis Melamed, S; Zhang, A; Jarnik, M et al. Elife, DOI://10.7554/eLife.87151 (2023)
Elementary intracellular Ca signals approximated as a transition of release channel system from a metastable state Veron, G; Maltsev, VA; Stern, MD; Maltsev, AV; , J Appl Phys, DOI://10.1063/5.0151255 (2023)
Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble Suddala, KC; Yoo, J; Fan, L et al. Nat Commun, DOI://10.1038/s41467-023-41155-3 (2023)
Serum biomarkers are altered in UK Biobank participants with mosaic chromosomal alterations Hubbard, AK; Brown, DW; Zhou, W et al. Hum Mol Genet, DOI://10.1093/hmg/ddad133 (2023)
Selection and Interpretation of Molecular Diagnostics in Heart Transplantation Goldberg, JF; Truby, LK; Agbor-Enoh, S et al. Circulation, DOI://10.1161/CIRCULATIONAHA.123.062847 (2023)
Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer Crooks, DR; Cawthon, GM; Fitzsimmons, CM et al. Hum Mol Genet, DOI://10.1093/hmg/ddad131 (2023)
VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities Gerson, TM; Ott, AM; Karney, MMA et al. mBio, DOI://10.1128/mbio.01519-23 (2023)
Experimental bacterial dysbiosis with consequent immune alterations increase intrarectal SIV acquisition susceptibility Ortiz, AM; Baker, PJ; Langner, CA et al. Cell Rep, DOI://10.1016/j.celrep.2023.112020 (2023)
Innate attraction and aversion to odors in locusts Ray, S; Sun, K; Stopfer, M; , PLoS One, DOI://10.1371/journal.pone.0284641 (2023)
Dietary and supplemental intake of vitamins C and E is associated with altered DNA methylation in an epigenome-wide association study meta-analysis Keshawarz, A; Joehanes, R; Ma, J et al. Epigenetics, DOI://10.1080/15592294.2023.2211361 (2023)
Quantitative flow cytometry enables end-to-end optimization of cross-platform extracellular vesicle studies Cook, S; Tang, VA; Lannigan, J et al. Cell Rep Methods, DOI://10.1016/j.crmeth.2023.100664 (2023)
A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline Reilly, L; Lara, E; Ramos, D et al. Cell Rep Methods, DOI://10.1016/j.crmeth.2023.100593 (2023)
The substrate and inhibitor binding mechanism of polyspecific transporter OAT1 revealed by high-resolution cryo-EM Dou, T; Lian, T; Shu, S et al. Nat Struct Mol Biol, DOI://10.1038/s41594-023-01123-3 (2023)
Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor Tröster, A; DiPrima, M; Jores, N et al. Chemistry, DOI://10.1002/chem.202203967 (2023)
Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization Willems, SM; Ng, NHJ; Fernandez, J et al. Wellcome Open Res, DOI://10.12688/wellcomeopenres.18754.1 (2023)
Recent Advances in Molecular Dynamics Simulations of Tau Fibrils and Oligomers Barredo, PA; Balanay, MP; , Membranes (Basel), DOI://10.3390/membranes13030277 (2023)
TScan-II: A genome-scale platform for the de novo identification of CD4+ T cell epitopes Dezfulian, MH; Kula, T; Pranzatelli, T et al. Cell, DOI://10.1016/j.cell.2023.10.024 (2023)
Transcriptome-wide association study of circulating IgE levels identifies novel targets for asthma and allergic diseases Recto, KA; Huan, T; Lee, DH et al. Front Immunol, DOI://10.3389/fimmu.2023.1080071 (2023)
Numbers and odds: TCR repertoire size and its age changes impacting on T cell functions Weng, NP Semin Immunol, DOI://10.1016/j.smim.2023.101810 (2023)
TCF3 haploinsufficiency defined by immune, clinical, gene-dosage, and murine studies Boast, B; Goel, S; González-Granado, LI et al. J Allergy Clin Immunol, DOI://10.1016/j.jaci.2023.05.017 (2023)
Nix interacts with WIPI2 to induce mitophagy Bunker, EN; Le Guerroué, F; Wang, C et al. EMBO J, DOI://10.15252/embj.2023113491 (2023)
First Potent Macrocyclic A3 Adenosine Receptor Agonists Reveal G-Protein and β-Arrestin2 Signaling Preferences Tosh, DK; Fisher, CL; Salmaso, V et al. ACS Pharmacol Transl Sci, DOI://10.1021/acsptsci.3c00126 (2023)
Neutrophil extracellular trap-associated carbamylation and histones trigger osteoclast formation in rheumatoid arthritis O'Neil, LJ; Oliveira, CB; Wang, X et al. Ann Rheum Dis, DOI://10.1136/ard-2022-223568 (2023)
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HAND2 Assists MYCN Enhancer Invasion to Regulate a Noradrenergic Neuroblastoma Phenotype Xu, M; Sun, M; Zhang, X et al. Cancer Res, DOI://10.1158/0008-5472.CAN-22-2042 (2023)
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Identification of SARS-CoV-2 Mpro inhibitors containing P1’ 4-fluorobenzothiazole moiety highly active against SARS-CoV-2 Higashi-Kuwata, N; Tsuji, K; Hayashi, H et al. Nat Commun, DOI://10.1038/s41467-023-36729-0 (2023)
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Rickettsia parkeri hijacks tick hemocytes to manipulate cellular and humoral transcriptional responses Adegoke, A; Ribeiro, JMC; Brown, S et al. Front Immunol, DOI://10.3389/fimmu.2023.1094326 (2023)
A highly replicable decline in mood during rest and simple tasks Jangraw, DC; Keren, H; Sun, H et al. Nat Hum Behav, DOI://10.1038/s41562-023-01519-7 (2023)
Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs Lee, BD; Neri, U; Roux, S et al. Cell, DOI://10.1016/j.cell.2022.12.039 (2023)
Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD Chen, Y; Prévost, J; Ullah, I et al. iScience, DOI://10.1016/j.isci.2022.105783 (2023)
Discovery of clinical and demographic determinants of symptom burden in primary brain tumor patients using network analysis and unsupervised clustering Bergsneider, BH; Vera, E; Gal, O et al. Neurooncol Adv, DOI://10.1093/noajnl/vdac188 (2023)
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The NLM indexer assignment dataset: a new large-scale dataset for reviewer assignment research Rae, AR; Mork, JG; Demner-Fushman, D; , J Assoc Inf Sci Technol, DOI://10.1002/asi.24722 (2023)
Fear-potentiated startle reveals diminished threat extinction in pathological anxiety Newsome, P; Ruiz, SG; Gold, AL et al. Int J Psychophysiol, DOI://10.1016/j.ijpsycho.2022.11.011 (2023)
Measures of Brain Connectivity and Cognition by Sex in US Children Tomasi, D; Volkow, ND; , JAMA Netw Open, DOI://10.1001/jamanetworkopen.2023.0157 (2023)
Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis Ali, RO; Quinn, GM; Umarova, R et al. Nat Microbiol, DOI://10.1038/s41564-022-01273-y (2023)

Identification and characterization of the long non-coding RNA NFIA-AS2 as a novel locus for body mass index in American Indians Bandesh, K; Traurig, M; Chen, P et al. Int J Obes (Lond), DOI://10.1038/s41366-023-01278-5 (2023)
Bispecific antibody CAP256.J3LS targets V2-apex and CD4-binding sites with high breadth and potency Zhang, B; Gorman, J; Kwon, YD et al. MAbs, DOI://10.1080/19420862.2023.2165390 (2023)
A de novo hexokinase 1 (HK1) variant presenting as Boucher-Neuhäuser syndrome Peretz, RH; Zein, WM; Hufnagel, RB et al. Am J Med Genet A, DOI://10.1002/ajmg.a.63045 (2023)
Autophagy Requirements for Eye Lens Differentiation and Transparency Brennan, L; Costello, MJ; Hejtmancik, JF et al. Cells, DOI://10.3390/cells12030475 (2023)
De novo human brain enhancers created by single-nucleotide mutations Li, S; Hannenhalli, S; Ovcharenko, I; , Sci Adv, DOI://10.1126/sciadv.add2911 (2023)
Role of ultra-high b-value DWI in the imaging of hereditary leiomyomatosis and renal cell carcinoma (HLRCC) Chaurasia, A; Gopal, N; Dehghani Firouzabadi, F et al. Abdom Radiol (NY), DOI://10.1007/s00261-022-03689-w (2023)

A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation Su, S; Xue, Y; Lee, SK et al. Nucleic Acids Res, DOI://10.1093/nar/gkad086 (2023)
Telomere-to-telomere assembly of diploid chromosomes with Verkko Rautiainen, M; Nurk, S; Walenz, BP et al. Nat Biotechnol, DOI://10.1038/s41587-023-01662-6 (2023)
A 64-year-old woman with frontal lobe lesion and drug-resistant epilepsy Jin, X; Abdullaev, Z; Butman, JA et al. Brain Pathol, DOI://10.1111/bpa.13133 (2023)
Intrinsically dysregulated cellular stress signaling genes and gene networks in postpartum depression Rudzinskas, SA; Goff, AC; Mazzu, MA et al. Mol Psychiatry, DOI://10.1038/s41380-023-01985-5 (2023)
Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment Morimoto, M; Bhambhani, V; Gazzaz, N et al. NPJ Genom Med, DOI://10.1038/s41525-022-00343-8 (2023)
MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain Becht, DC; Klein, BJ; Kanai, A et al. Nat Commun, DOI://10.1038/s41467-023-36368-5 (2023)

Pleural fluid microbiota as a biomarker for malignancy and prognosis Kwok, B; Wu, BG; Kocak, IF et al. Sci Rep, DOI://10.1038/s41598-023-29001-4 (2023)
CD47-Dependent Regulation of Immune Checkpoint Gene Expression and MYCN mRNA Splicing in Murine CD8 and Jurkat T Cells Kaur, S; Awad, D; Finney, RP et al. Int J Mol Sci, DOI://10.3390/ijms24032612 (2023)
Deep Domain Adversarial Learning for Species-Agnostic Classification of Histologic Subtypes of Osteosarcoma Patkar, S; Beck, J; Harmon, S et al. Am J Pathol, DOI://10.1016/j.ajpath.2022.09.009 (2023)
Analysis of immune responses in CLL patients after heterologous COVID-19 vaccination Lee, HK; Hoechstetter, MA; Buchner, M et al. Blood Adv, DOI://10.1182/bloodadvances.2022008445 (2023)
Organ-specific effects on target binding due to knockout of thyroid hormone receptor α during Xenopus metamorphosis Tanizaki, Y; Zhang, H; Shibata, Y; Shi, YB; , Dev Growth Differ, DOI://10.1111/dgd.12825 (2023)
Racial/Ethnic Differences in Associations Between Traumatic Childhood Experiences and Both Metabolic Syndrome Prevalence and Type 2 Diabetes Risk Among a Cohort of U.S. Women Gaston, SA; Riley, NM; Parks, CG et al. Diabetes Care, DOI://10.2337/dc22-1486 (2023)

Transcription factors underlying photoreceptor diversity Angueyra, JM; Kunze, VP; Patak, LK et al. Elife, DOI://10.7554/eLife.81579 (2023)
Heterogeneous clinicopathological findings and patient-reported outcomes in adults with MN1-altered CNS tumors: A case report and systematic literature review Frederico, SC; Vera, E; Abdullaev, Z et al. Front Oncol, DOI://10.3389/fonc.2023.1099618 (2023)
Oral microbiome and risk of incident head and neck cancer: A nested case-control study Wu, Z; Han, Y; Wan, Y et al. Oral Oncol, DOI://10.1016/j.oraloncology.2022.106305 (2023)
Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein Kuhn, CC; Basnet, N; Bodakuntla, S et al. Nat Commun, DOI://10.1038/s41467-023-36279-5 (2023)
Estimation of cell lineages in tumors from spatial transcriptomics data Ru, B; Huang, J; Zhang, Y et al. Nat Commun, DOI://10.1038/s41467-023-36062-6 (2023)
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Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1 Campbell, K; Cawley, NX; Luke, R et al. Biomark Res, DOI://10.1186/s40364-023-00448-x (2023)
Expanded NK cells used for adoptive cell therapy maintain diverse clonality and contain long-lived memory-like NK cell populations Allan, DSJ; Wu, C; Mortlock, RD et al. Mol Ther Oncolytics, DOI://10.1016/j.omto.2022.12.006 (2023)
Spleen tyrosine kinase inhibition restores myeloid homeostasis in COVID-19 Wigerblad, G; Warner, SA; Ramos-Benitez, MJ et al. Sci Adv, DOI://10.1126/sciadv.ade8272 (2023)
Genetic Influences on Fetal Alcohol Spectrum Disorder Sambo, D; Goldman, D; , Genes (Basel), DOI://10.3390/genes14010195 (2023)
Chromatin landscape governing murine epidermal differentiation Nayak, S; Jiang, K; Hope, E et al. J Invest Dermatol, DOI://10.1016/j.jid.2022.12.020 (2023)

Inflated expectations: Rare-variant association analysis using public controls Kim, J; Karyadi, DM; Hartley, SW et al. PLoS One, DOI://10.1371/journal.pone.0280951 (2023)
Middle-age high normal serum sodium as a risk factor for accelerated biological aging, chronic diseases, and premature mortality Dmitrieva, NI; Gagarin, A; Liu, D et al. EBioMedicine, DOI://10.1016/j.ebiom.2022.104404 (2023)
Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy Nagel-Wolfrum, K; Fadl, BR; Becker, MM et al. Hum Mol Genet, DOI://10.1093/hmg/ddac211 (2023)
Revisiting the sialome of the cat flea Ctenocephalides felis Lu, S; Danchenko, M; Macaluso, KR; Ribeiro, JMC; , PLoS One, DOI://10.1371/journal.pone.0279070 (2023)
Upper age-limits for US male HPV-vaccination for oropharyngeal cancer prevention: A microsimulation-based modeling study Landy, R; Haber, G; Graubard, BI et al. J Natl Cancer Inst, DOI://10.1093/jnci/djad009 (2023)
GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas Machiela, MJ; Huang, WY; Wong, W et al. Sci Data, DOI://10.1038/s41597-022-01921-2 (2023)

Transcriptomic Analysis of Human Podocytes In Vitro: Effects of Differentiation and APOL1 Genotype Yoshida, T; Latt, KZ; Rosenberg, AZ et al. Kidney Int Rep, DOI://10.1016/j.ekir.2022.10.011 (2023)
The repertoire of CSF antiviral antibodies in patients with neuroinflammatory diseases Enose-Akahata, Y; Wang, L; Almsned, F et al. Sci Adv, DOI://10.1126/sciadv.abq6978 (2023)
Preclinical optimization of a GPC2-targeting CAR T-cell therapy for neuroblastoma Sun, M; Cao, Y; Okada, R et al. J Immunother Cancer, DOI://10.1136/jitc-2022-005881 (2023)
Characterization of diverse populations of sinoatrial node cells and their proliferation potential at single nucleus resolution Qu, JH; Telljohann, R; Byshkov, R; Lakatta, EG; , Heliyon, DOI://10.1016/j.heliyon.2022.e12708 (2023)
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Novel polyomaviruses identified in fecal samples from four carnivore species Kraberger, S; Serieys, LEK; Riley, SPD et al. Arch Virol, DOI://10.1007/s00705-022-05675-5 (2023)

Comparison of busulfan and total body irradiation conditioning on hematopoietic clonal dynamics following lentiviral gene transfer in rhesus macaques Abraham, DM; Lozano, RJ; Guitart, X et al. Mol Ther Methods Clin Dev, DOI://10.1016/j.omtm.2022.12.001 (2023)
Prenatal social support in low-risk pregnancy shapes placental epigenome Tesfaye, M; Wu, J; Biedrzycki, RJ et al. BMC Med, DOI://10.1186/s12916-022-02701-w (2023)
Epigenetic gestational age and the relationship with developmental milestones in early childhood Polinski, KJ; Robinson, SL; Putnick, DL et al. Hum Mol Genet, DOI://10.1093/hmg/ddac302 (2023)
A dataset for plain language adaptation of biomedical abstracts Attal, K; Ondov, B; Demner-Fushman, D; , Sci Data, DOI://10.1038/s41597-022-01920-3 (2023)
A stem cell epigenome is associated with primary nonresponse to CD19 CAR T-cells in pediatric acute lymphoblastic leukemia Masih, KE; Gardner, RA; Chou, HC et al. Blood Adv, DOI://10.1182/bloodadvances.2022008977 (2023)
Variable selection for discrete survival model with frailty in presence of left truncation and right censoring: Studying association of environmental toxicants on time-to-pregnancy Saha, A; Sundaram, R; , Stat Med, DOI://10.1002/sim.9609 (2023)

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 (620 papers)

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)
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Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation Formenti, G; Rhie, A; Walenz, BP et al. Nat Methods, DOI://10.1038/s41592-022-01445-y (2022)
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)
Segmental duplications and their variation in a complete human genome Vollger, MR; Guitart, X; Dishuck, PC et al. Science, DOI://10.1126/science.abj6965 (2022)
Complete genomic and epigenetic maps of human centromeres Altemose, N; Logsdon, GA; Bzikadze, AV et al. Science, DOI://10.1126/science.abl4178 (2022)
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)

Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain Lee, DR; Rhodes, C; Mitra, A et al. Elife, DOI://10.7554/eLife.71864 (2022)
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 (605 papers)

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)
The NIH Lipo-COVID Study: A Pilot NMR Investigation of Lipoprotein Subfractions and Other Metabolites in Patients with Severe COVID-19 Ballout, RA; Kong, H; Sampson, M et al. Biomedicines, DOI://10.3390/biomedicines9091090 (2021)
The SIRPα-CD47 immune checkpoint in NK cells Deuse, T; Hu, X; Agbor-Enoh, S et al. J Exp Med, DOI://10.1084/jem.20200839 (2021)
Trial and error: A hierarchical modeling approach to test-retest reliability Chen, G; Pine, DS; Brotman, MA et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.118647 (2021)
Response by Shah et al to Letter Regarding Article, "Cell-Free DNA to Detect Heart Allograft Acute Rejection" Shah, P; Agbor-Enoh, S; Tunc, I et al. Circulation, DOI://10.1161/CIRCULATIONAHA.121.055697 (2021)
Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes Chiba, Y; Yoshizaki, K; Tian, T et al. J Dent Res, DOI://10.1177/00220345211049785 (2021)
Donor-Derived Cell-Free DNA for Acute Rejection Monitoring in Heart and Lung Transplantation Keller, M; Agbor-Enoh, S; , Curr Transplant Rep, DOI://10.1007/s40472-021-00349-8 (2021)
Incorporating survival data into case-control studies with incident and prevalent cases Mandal, S; Qin, J; Pfeiffer, RM; , Stat Med, DOI://10.1002/sim.9183 (2021)
Cancer incidence, patterns, and genotype-phenotype associations in individuals with pathogenic or likely pathogenic germline TP53 variants: an observational cohort study de Andrade, KC; Khincha, PP; Hatton, JN et al. Lancet Oncol, DOI://10.1016/S1470-2045(21)00580-5 (2021)
Donor derived cell free DNA% is elevated with pathogens that are risk factors for acute and chronic lung allograft injury Bazemore, K; Rohly, M; Permpalung, N et al. J Heart Lung Transplant, DOI://10.1016/j.healun.2021.05.012 (2021)

Building the mega single-cell transcriptome ocular meta-atlas Swamy, VS; Fufa, TD; Hufnagel, RB; McGaughey, DM; , Gigascience, DOI://10.1093/gigascience/giab061 (2021)
Mechanistic Insights into Photodynamic Regulation of Adenosine 5'-Triphosphate-Binding Cassette Drug Transporters Liang, BJ; Lusvarghi, S; Ambudkar, SV; Huang, HC; , ACS Pharmacol Transl Sci, DOI://10.1021/acsptsci.1c00138 (2021)
Role of 53BP1 in end protection and DNA synthesis at DNA breaks Paiano, J; Zolnerowich, N; Wu, W et al. Genes Dev, DOI://10.1101/gad.348667.121 (2021)
Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices Malikić, S; Mehrabadi, FR; Azer, ES et al. J Comput Biol, DOI://10.1089/cmb.2020.0595 (2021)
Long-Term Report of a Comprehensive Molecular and Genomic Analysis in NRG Oncology/RTOG 0424: A Phase II Study of Radiation and Temozolomide in High-Risk Grade II Glioma Fleming, JL; Pugh, SL; Fisher, BJ et al. JCO Precis Oncol, DOI://10.1200/PO.21.00112 (2021)
Report of Canonical BCR-ABL1 Fusion in Glioblastoma Pang, Y; Yu, G; Butler, M et al. JCO Precis Oncol, DOI://10.1200/PO.20.00519 (2021)

Comparison of approaches to transcriptomic analysis in multi-sampled tumors Ku, AT; Wilkinson, S; Sowalsky, AG; , Brief Bioinform, DOI://10.1093/bib/bbab337 (2021)
Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity Hild, B; Dreier, MS; Oh, JH et al. Nat Metab, DOI://10.1038/s42255-021-00439-y (2021)
Privacy-Preserving Genotype Imputation in a Trusted Execution Environment Dokmai, N; Kockan, C; Zhu, K et al. Res Comput Mol Biol (2021)
The power of genetic diversity in genome-wide association studies of lipids Graham, SE; Clarke, SL; Wu, KH et al. Nature, DOI://10.1038/s41586-021-04064-3 (2021)
Clinical and Histopathologic Correlates of Asymmetric Retinitis Pigmentosa Lal, T; Yu, ZX; Guan, B et al. JAMA Ophthalmol, DOI://10.1001/jamaophthalmol.2021.2688 (2021)
Blood DNA Methylation and Incident Coronary Heart Disease: Evidence From the Strong Heart Study Navas-Acien, A; Domingo-Relloso, A; Subedi, P et al. JAMA Cardiol, DOI://10.1001/jamacardio.2021.2704 (2021)
A Longitudinal Study of Resting-State Connectivity and Response to Psychostimulant Treatment in ADHD Norman, LJ; Sudre, G; Bouyssi-Kobar, M et al. Am J Psychiatry, DOI://10.1176/appi.ajp.2021.20091342 (2021)
Cortical and subcortical brain structure in generalized anxiety disorder: findings from 28 research sites in the ENIGMA-Anxiety Working Group Harrewijn, A; Cardinale, EM; Groenewold, NA et al. Transl Psychiatry, DOI://10.1038/s41398-021-01622-1 (2021)
α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics Chen, J; Kholina, E; Szyk, A et al. Dev Cell, DOI://10.1016/j.devcel.2021.05.005 (2021)
Transcriptome of HPβCD-treated Niemann-Pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics Rodriguez-Gil, JL; Baxter, LL; Watkins-Chow, DE et al. Hum Mol Genet, DOI://10.1093/hmg/ddab194 (2021)
Exploring and Targeting the Tumor Immune Microenvironment of Neuroblastoma Masih, KE; Wei, JS; Milewski, D; Khan, J; , J Cell Immunol, DOI://10.33696/immunology.3.111 (2021)
BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma Laubscher, D; Gryder, BE; Sunkel, BD et al. Nat Commun, DOI://10.1038/s41467-021-27176-w (2021)
Androgen receptor and MYC equilibration centralizes on developmental super-enhancer Guo, H; Wu, Y; Nouri, M et al. Nat Commun, DOI://10.1038/s41467-021-27077-y (2021)
Use of donor-derived-cell-free DNA as a marker of early allograft injury in primary graft dysfunction (PGD) to predict the risk of chronic lung allograft dysfunction (CLAD) Keller, M; Bush, E; Diamond, JM et al. J Heart Lung Transplant, DOI://10.1016/j.healun.2021.02.008 (2021)
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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)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish Kon, T; Omori, Y; Fukuta, K et al. Curr Biol, DOI://10.1016/j.cub.2020.04.034 (2020)
Safety and feasibility of anti-CD19 CAR T cells with fully human binding domains in patients with B-cell lymphoma Brudno, JN; Lam, N; Vanasse, D et al. Nat Med, DOI://10.1038/s41591-019-0737-3 (2020)
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs Scott, MJ; Benoit, JB; Davis, RJ et al. Commun Biol, DOI://10.1038/s42003-020-01152-4 (2020)
Transcriptome analysis of desmoplastic small round cell tumors identifies actionable therapeutic targets: a report from the Children's Oncology Group Hingorani, P; Dinu, V; Zhang, X et al. Sci Rep, DOI://10.1038/s41598-020-69015-w (2020)
LSH mediates gene repression through macroH2A deposition Ni, K; Ren, J; Xu, X et al. Nat Commun, DOI://10.1038/s41467-020-19159-0 (2020)
Improved reference genome of the arboviral vector Aedes albopictus Palatini, U; Masri, RA; Cosme, LV et al. Genome Biol, DOI://10.1186/s13059-020-02141-w (2020)
Whole-Exome Profiling of NSCLC Among African Americans Arauz, RF; Byun, JS; Tandon, M et al. J Thorac Oncol, DOI://10.1016/j.jtho.2020.08.029 (2020)
HLA tapasin independence: broader peptide repertoire and HIV control Bashirova, AA; Viard, M; Naranbhai, V et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2013554117 (2020)
Disappearance of the polyelectrolyte peak in salt-free solutions Chremos, A; Horkay, F; , Phys Rev E, DOI://10.1103/PhysRevE.102.012611 (2020)
Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease Beck, DB; Ferrada, MA; Sikora, KA et al. N Engl J Med, DOI://10.1056/NEJMoa2026834 (2020)
Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome Johnstone, T; Wang, J; Ross, D et al. Mol Genet Metab, DOI://10.1016/j.ymgme.2020.09.008 (2020)
Multilayer MEG functional connectivity as a potential marker for suicidal thoughts in major depressive disorder Nugent, AC; Ballard, ED; Gilbert, JR et al. Neuroimage Clin, DOI://10.1016/j.nicl.2020.102378 (2020)
Development and validation of prognostic gene signature for basal-like breast cancer and high-grade serous ovarian cancer Zhang, Y; Liu, J; Raj-Kumar, PK et al. Breast Cancer Res Treat, DOI://10.1007/s10549-020-05884-z (2020)
A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles Claesen, J; Spagnolo, JB; Ramos, SF et al. Sci Transl Med, DOI://10.1126/scitranslmed.aay5445 (2020)
Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair Myles, IA; Castillo, CR; Barbian, KD et al. Sci Transl Med, DOI://10.1126/scitranslmed.aaz8631 (2020)
Comparative Transcriptomics Analyses in Livers of Mice, Humans, and Humanized Mice Define Human-Specific Gene Networks Jiang, C; Li, P; Ruan, X et al. Cells, DOI://10.3390/cells9122566 (2020)
IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues Radtke, AJ; Kandov, E; Lowekamp, B et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2018488117 (2020)
The Central Role of Salivary Metalloproteases in Host Acquired Resistance to Tick Feeding Perner, J; Helm, D; Haberkant, P et al. Front Cell Infect Microbiol, DOI://10.3389/fcimb.2020.563349 (2020)
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development Ates, KM; Wang, T; Moreland, T et al. Dis Model Mech, DOI://10.1242/dmm.041913 (2020)
The outcome of TGFβ antagonism in metastatic breast cancer models in vivo reflects a complex balance between tumor-suppressive and pro-progression activities of TGFβ Yang, Y; Yang, HH; Tang, B et al. Clin Cancer Res, DOI://10.1158/1078-0432.CCR-19-2370 (2020)
APOBEC3A catalyzes mutation and drives carcinogenesis in vivo Law, EK; Levin-Klein, R; Jarvis, MC et al. J Exp Med, DOI://10.1084/jem.20200261 (2020)
Polygenic analysis of the effect of common and low-frequency genetic variants on serum uric acid levels in Korean individuals Cho, SK; Kim, B; Myung, W et al. Sci Rep, DOI://10.1038/s41598-020-66064-z (2020)
Dynamics of genomic and immune responses during primary immunotherapy resistance in mismatch repair-deficient tumors Takahashi, N; Rajapakse, VN; Pongor, L et al. Cold Spring Harb Mol Case Stud, DOI://10.1101/mcs.a005678 (2020)
Systematic investigation of synthetic polyelectrolyte bottlebrush solutions by neutron and dynamic light scattering, osmometry, and molecular dynamics simulation Horkay, F; Chremos, A; Douglas, JF et al. J Chem Phys, DOI://10.1063/5.0007271 (2020)
Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758) Wen, M; Feron, R; Pan, Q et al. BMC Genomics, DOI://10.1186/s12864-020-06959-3 (2020)

Structural insight into toxin secretion by contact-dependent growth inhibition transporters Guerin, J; Botos, I; Zhang, Z et al. Elife, DOI://10.7554/eLife.58100 (2020)
An RNA Repair Operon Regulated by Damaged tRNAs Hughes, KJ; Chen, X; Burroughs, AM et al. Cell Rep, DOI://10.1016/j.celrep.2020.108527 (2020)
Effect of sequence depth and length in long-read assembly of the maize inbred NC358 Ou, S; Liu, J; Chougule, KM et al. Nat Commun, DOI://10.1038/s41467-020-16037-7 (2020)
Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci de Las Fuentes, L; Sung, YJ; Noordam, R et al. Mol Psychiatry, DOI://10.1038/s41380-020-0719-3 (2020)
Rapid image deconvolution and multiview fusion for optical microscopy Guo, M; Li, Y; Su, Y et al. Nat Biotechnol, DOI://10.1038/s41587-020-0560-x (2020)
Language lateralization from task-based and resting state functional MRI in patients with epilepsy Rolinski, R; You, X; Gonzalez-Castillo, J et al. Hum Brain Mapp, DOI://10.1002/hbm.25003 (2020)

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Moser, KA; Drábek, EF; Dwivedi, A et al. Genome Med, DOI://10.1186/s13073-019-0708-9 (2020)
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AGO2 Mediates MYC mRNA Stability in Hepatocellular Carcinoma Zhang, K; Pomyen, Y; Barry, AE et al. Mol. Cancer Res., DOI://10.1158/1541-7786.MCR-19-0805 (2020)
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells Hardison, RC; Zhang, Y; Keller, CA et al. IUBMB Life, DOI://10.1002/iub.2195 (2020)
Confidence intervals for the difference between two relative risks Sampson, JN; Gail, MH; Stat Methods Med Res, DOI://10.1177/0962280220915737 (2020)
High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase Cerritelli, SM; Iranzo, J; Sharma, S et al. Nucleic Acids Res., DOI://10.1093/nar/gkaa103 (2020)
Ketamine metabolites, clinical response, and gamma power in a randomized, placebo-controlled, crossover trial for treatment-resistant major depression Farmer, CA; Gilbert, JR; Moaddel, R et al. Neuropsychopharmacology, DOI://10.1038/s41386-020-0663-6 (2020)
Erasure machine: Inverse Ising inference from reweighting of observation frequencies Jo, J; Hoang, DT; Periwal, V; , Phys Rev E, DOI://10.1103/PhysRevE.101.032107 (2020)
Skin Microbiota Perturbations Are Distinct and Disease Severity-Dependent in Hidradenitis Suppurativa Naik, HB; Jo, JH; Paul, M; Kong, HH; , J. Invest. Dermatol., DOI://10.1016/j.jid.2019.08.445 (2020)
Investigation of the Influence of Thyroid Location on Iodine-131 S Values Yeom, YS; Villoing, D; Greenstein, N et al. Radiat Prot Dosimetry, DOI://10.1093/rpd/ncaa027 (2020)
A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications Wright, GW; Huang, DW; Phelan, JD et al. Cancer Cell, DOI://10.1016/j.ccell.2020.03.015 (2020)
In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits Ruan, X; Li, P; Chen, Y et al. Nat Commun, DOI://10.1038/s41467-019-13688-z (2020)
A hidden Markov modeling approach for identifying tumor subclones in next-generation sequencing studies Choo-Wosoba, H; Albert, PS; Zhu, B; Biostatistics, DOI://10.1093/biostatistics/kxaa013 (2020)

Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge Jones, MR; Brooks, BR; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-020-00286-1 (2020)
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge Krämer, A; Hudson, PS; Jones, MR; Brooks, BR; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-020-00285-2 (2020)
Feedback inhibition and its control in an insect olfactory circuit Ray, S; Aldworth, ZN; Stopfer, MA; Elife, DOI://10.7554/eLife.53281 (2020)
Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles Bradshaw, RT; Marinelli, F; Faraldo-Gómez, JD; Forrest, LR; Biophys. J., DOI://10.1016/j.bpj.2020.02.005 (2020)
A Shared Regulatory Element Controls the Initiation of Tcf7 Expression During Early T Cell and Innate Lymphoid Cell Developments Harly, C; Kenney, D; Wang, Y et al. Front Immunol, DOI://10.3389/fimmu.2020.00470 (2020)
Idiosynchrony: From shared responses to individual differences during naturalistic neuroimaging Finn, ES; Glerean, E; Khojandi, AY et al. Neuroimage, DOI://10.1016/j.neuroimage.2020.116828 (2020)

The quaternary assembly of KRas4B with Raf-1 at the membrane Jang, H; Zhang, M; Nussinov, R; Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2020.03.018 (2020)
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle Rice, ES; Koren, S; Rhie, A et al. Gigascience, DOI://10.1093/gigascience/giaa029 (2020)
Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein Tang, WK; Borgnia, MJ; Hsu, AL et al. Nat. Struct. Mol. Biol., DOI://10.1038/s41594-020-0373-0 (2020)
Predisposition to hematologic malignancies in patients with xeroderma pigmentosum Oetjen, KA; Levoska, MA; Tamura, D et al. Haematologica, DOI://10.3324/haematol.2019.223370 (2020)
Levels of early-childhood behavioral inhibition predict distinct neurodevelopmental pathways to pediatric anxiety Abend, R; Swetlitz, C; White, LK et al. Psychol Med, DOI://10.1017/S0033291718003999 (2020)
Structure elucidation and absolute configuration of metabolites from the soil-derived fungus Dictyosporium digitatum using spectroscopic and computational methods Tran, TD; Wilson, BAP; Henrich, CJ et al. Phytochemistry, DOI://10.1016/j.phytochem.2020.112278 (2020)

Differential DNA Methylation in Placenta Associated With Maternal Blood Pressure During Pregnancy Workalemahu, T; Ouidir, M; Shrestha, D; Wu, J; Grantz, KL; Tekola-Ayele, F; Hypertension, DOI://10.1161/HYPERTENSIONAHA.119.14509 (2020)
Family-based exome sequencing identifies rare coding variants in age-related macular degeneration Ratnapriya, R; Acar, İE; Geerlings, MJ et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddaa057 (2020)
Next-generation sequencing of the intrahepatic antibody repertoire delineates a unique B-cell response in HBV-associated acute liver failure Chen, Z; Shen, CH; Engle, RE et al. J. Viral Hepat., DOI://10.1111/jvh.13290 (2020)
CRISPR-Cas9/phosphoproteomics identifies multiple noncanonical targets of myosin light chain kinase Isobe, K; Raghuram, V; Krishnan, L; Chou, CL; Yang, CR; Knepper, MA; Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00431.2019 (2020)
Genotype-phenotype association and variant characterization in Diamond-Blackfan anemia caused by pathogenic variants in RPL35A Gianferante, DM; Wlodarski, MW; Atsidaftos, E et al. Haematologica, DOI://10.3324/haematol.2020.246629 (2020)
Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption Nakajima, K; Tanizaki, Y; Luu, N; Zhang, H; Shi, YB; Gen. Comp. Endocrinol., DOI://10.1016/j.ygcen.2019.113349 (2020)

Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1 Lukovic, D; Artero Castro, A; Kaya, KD et al. Sci Rep, DOI://10.1038/s41598-020-62047-2 (2020)
mTORC2/Rac1 Pathway Predisposes Cancer Aggressiveness in IDH1-Mutated Glioma Liu, Y; Lu, Y; Li, A et al. Cancers (Basel), DOI://10.3390/cancers12040787 (2020)
Gene co-expression networks are associated with obesity-related traits in kidney transplant recipients Jaime-Lara, RB; Roy, A; Wang, Y; Stanfill, A; Cashion, AK; Joseph, PV; BMC Med Genomics, DOI://10.1186/s12920-020-0702-5 (2020)
RNAseq expression patterns of canine invasive urothelial carcinoma reveal two distinct tumor clusters and shared regions of dysregulation with human bladder tumors Parker, HG; Dhawan, D; Harris, AC et al. BMC Cancer, DOI://10.1186/s12885-020-06737-0 (2020)
Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress Murai, J; Zhang, H; Pongor, L et al. Cell Rep, DOI://10.1016/j.celrep.2020.02.117 (2020)
Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity Sciascia, N; Wu, W; Zong, D et al. Elife, DOI://10.7554/eLife.53447 (2020)

Understanding the Cause and Consequence of Tumor Heterogeneity Khatib, S; Pomyen, Y; Dang, H; Wang, XW; , Trends Cancer, DOI://10.1016/j.trecan.2020.01.010 (2020)
YAP1/TAZ-TEAD transcriptional networks maintain skin homeostasis by regulating cell proliferation and limiting KLF4 activity Yuan, Y; Park, J; Feng, A et al. Nat Commun, DOI://10.1038/s41467-020-15301-0 (2020)
De novo assembly of the cattle reference genome with single-molecule sequencing Rosen, BD; Bickhart, DM; Schnabel, RD et al. Gigascience, DOI://10.1093/gigascience/giaa021 (2020)
Association of polygenic score for major depression with response to lithium in patients with bipolar disorder Amare, AT; Schubert, KO; Hou, L et al. Mol. Psychiatry, DOI://10.1038/s41380-020-0689-5 (2020)
Stylized versus voxel phantoms: a juxtaposition of organ depth distributions Griffin, KT; Cuthbert, TA; Dewji, SA; Lee, C; Phys Med Biol, DOI://10.1088/1361-6560/ab7686 (2020)
Tautomer Database: A Comprehensive Resource for Tautomerism Analyses Dhaked, DK; Guasch, L; Nicklaus, MC; J Chem Inf Model, DOI://10.1021/acs.jcim.9b01156 (2020)

Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2 Dhaked, DK; Ihlenfeldt, WD; Patel, H; Delannée, V; Nicklaus, MC; J Chem Inf Model, DOI://10.1021/acs.jcim.9b01080 (2020)
Multiple testing correction overcontrasts for brain imaging Alberton, BAV; Nichols, TE; Gamba, HR; Winkler, AM; Neuroimage, DOI://10.1016/j.neuroimage.2020.116760 (2020)
Prediction of stress and drug craving ninety minutes in the future with passively collected GPS data Epstein, DH; Tyburski, M; Kowalczyk, WJ et al. NPJ Digit Med, DOI://10.1038/s41746-020-0234-6 (2020)
Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma Mitra, S; Lauss, M; Cabrita, R et al. Mol Oncol, DOI://10.1002/1878-0261.12663 (2020)
Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism Lane, JR; Abramyan, AM; Adhikari, P et al. Elife, DOI://10.7554/eLife.52189 (2020)
Modulating the Stiffness of the Myosin VI Single α-Helical Domain Barnes, CA; Shen, Y; Ying, J; Bax, A; Biophys. J., DOI://10.1016/j.bpj.2020.01.003 (2020)

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability Auslander, N; Wolf, YI; Koonin, EV; Nat Commun, DOI://10.1038/s41467-020-15094-2 (2020)
Outcome-related signatures identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated After Starting Hu14.18-IL2 Yang, RK; Kuznetsov, IB; Ranheim, EA et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-19-3294 (2020)
Longitudinal Positron Emission Tomography of Dopamine Synthesis in Subjects with GBA1 Mutations Lopez, G; Eisenberg, DP; Gregory, MD et al. Ann. Neurol., DOI://10.1002/ana.25692 (2020)
Combining fMRI during resting state and an attention bias task in children Harrewijn, A; Abend, R; Linke, J et al. Neuroimage, DOI://10.1016/j.neuroimage.2019.116301 (2020)
Sex-biased trajectories of amygdalo-hippocampal morphology change over human development Fish, AM; Nadig, A; Seidlitz, J et al. Neuroimage, DOI://10.1016/j.neuroimage.2019.116122 (2020)
Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells Chu, PH; Chen, G; Kuo, D et al. Chem. Res. Toxicol., DOI://10.1021/acs.chemrestox.9b00363 (2020)

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes Yamamoto, E; Domanski, J; Naughton, FB et al. Sci Adv, DOI://10.1126/sciadv.aay5736 (2020)
Tick-Borne Encephalitis Virus Infection Alters the Sialome of Ixodes ricinus Ticks During the Earliest Stages of Feeding Hart, CE; Ribeiro, JM; Kazimirova, M; Thangamani, S; Front Cell Infect Microbiol, DOI://10.3389/fcimb.2020.00041 (2020)
Low-frequency parietal repetitive transcranial magnetic stimulation reduces fear and anxiety Balderston, NL; Beydler, EM; Goodwin, M et al. Transl Psychiatry, DOI://10.1038/s41398-020-0751-8 (2020)
Molecular and cellular determinants of motor asymmetry in zebrafish Horstick, EJ; Bayleyen, Y; Burgess, HA; Nat Commun, DOI://10.1038/s41467-020-14965-y (2020)
C. elegans pronuclei fuse after fertilization through a novel membrane structure Rahman, M; Chang, IY; Harned, A et al. J. Cell Biol., DOI://10.1083/jcb.201909137 (2020)
Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP) Gryder, BE; Khan, J; Stanton, BZ; Nat Protoc, DOI://10.1038/s41596-019-0285-9 (2020)

Characterizing Adult Cochlear Supporting Cell Transcriptional Diversity Using Single-Cell RNA-Seq: Validation in the Adult Mouse and Translational Implications for the Adult Human Cochlea Hoa, M; Olszewski, R; Li, X et al. Front Mol Neurosci, DOI://10.3389/fnmol.2020.00013 (2020)
Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling Muratcioglu, S; Aydin, C; Odabasi, E et al. J. Mol. Biol., DOI://10.1016/j.jmb.2020.01.002 (2020)
Modeling repeated labor curves in consecutive pregnancies: Individualized prediction of labor progression from previous pregnancy data Buhule, OD; Choo-Wosoba, H; Albert, PS; Stat Med, DOI://10.1002/sim.8462 (2020)
Serial evaluation of CD19 surface expression in pediatric B-cell malignancies following CD19-targeted therapy Libert, D; Yuan, CM; Masih, KE et al. Leukemia, DOI://10.1038/s41375-020-0760-x (2020)
Integrative analysis suggests cell type-specific decoding of NF-κB dynamics Martin, EW; Pacholewska, A; Patel, H; Dashora, H; Sung, MH; Sci Signal, DOI://10.1126/scisignal.aax7195 (2020)
Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation Lee, SY; Hung, S; Esnault, C et al. Cell Rep, DOI://10.1016/j.celrep.2020.01.094 (2020)

Low Serum Insulinlike Growth Factor II Levels Correlate with High BMI in American Indian Adults Muller, YL; Hanson, RL; Mahkee, D et al. Obesity (Silver Spring), DOI://10.1002/oby.22741 (2020)
CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG Liu, Z; Zhang, X; Lei, H et al. Nat Commun, DOI://10.1038/s41467-020-14684-4 (2020)
A case report of multiple primary prostate tumors with differential drug sensitivity Wilkinson, S; Harmon, SA; Terrigino, NT et al. Nat Commun, DOI://10.1038/s41467-020-14657-7 (2020)
A resource for the detailed 3D mapping of white matter pathways in the marmoset brain Liu, C; Ye, FQ; Newman, JD et al. Nat. Neurosci., DOI://10.1038/s41593-019-0575-0 (2020)
The Pharmacopea within Triatomine Salivary Glands Santiago, PB; de Araújo, CN; Charneau, S et al. Trends Parasitol., DOI://10.1016/j.pt.2019.12.014 (2020)
MY-5445, a phosphodiesterase type 5 inhibitor, resensitizes ABCG2-overexpressing multidrug-resistant cancer cells to cytotoxic anticancer drugs Wu, CP; Lusvarghi, S; Tseng, PJ et al. Am J Cancer Res, 2156-6976 (2020)

The Glu102 mutation disrupts higher-order oligomerization of the sigma 1 receptor Abramyan, AM; Yano, H; Xu, M et al. Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2019.12.012 (2020)
High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1 Liao, TJ; Jang, H; Nussinov, R; Fushman, D; J. Am. Chem. Soc., DOI://10.1021/jacs.9b10710 (2020)
Placental DNA methylation changes associated with maternal prepregnancy BMI and gestational weight gain Shrestha, D; Ouidir, M; Workalemahu, T; Zeng, X; Tekola-Ayele, F; Int J Obes (Lond), DOI://10.1038/s41366-020-0546-2 (2020)
Refining genome-wide associated loci for serum uric acid in individuals with African ancestry Chen, G; Shriner, D; Doumatey, AP et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddz272 (2020)
A customizable deep learning model for nosocomial risk prediction from critical care notes with indirect supervision Goodwin, TR; Demner-Fushman, D; J Am Med Inform Assoc, DOI://10.1093/jamia/ocaa004 (2020)
Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes Pascini, TV; Ramalho-Ortigão, M; Ribeiro, JM; Jacobs-Lorena, M; Martins, GF; BMC Genomics, DOI://10.1186/s12864-020-6543-y (2020)
Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans Mitchell, KA; Nichols, N; Tang, W et al. Nat Commun, DOI://10.1038/s41467-020-14448-0 (2020)
Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study Smith, JL; Ries, RE; Hylkema, T et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-19-1800 (2020)
TCR Repertoires of Thymic Conventional and Regulatory T Cells: Identification and Characterization of Both Unique and Shared TCR Sequences Ko, A; Watanabe, M; Nguyen, T et al. J. Immunol., DOI://10.4049/jimmunol.1901006 (2020)
Whole Exome Sequencing of Highly Aggregated Lung Cancer Families Reveals Linked Loci for Increased Cancer Risk on Chromosomes 12q, 7p, and 4q Musolf, AM; Moiz, BA; Sun, H et al. Cancer Epidemiol. Biomarkers Prev., DOI://10.1158/1055-9965.EPI-19-0887 (2020)
Evaluating global brain connectivity as an imaging marker for depression: influence of preprocessing strategies and placebo-controlled ketamine treatment Kraus, C; Mkrtchian, A; Kadriu, B; Nugent, AC; Zarate, CA; Evans, JW; Neuropsychopharmacology, DOI://10.1038/s41386-020-0624-0 (2020)
CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention Pugacheva, EM; Kubo, N; Loukinov, D et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1911708117 (2020)

Discovery of several thousand highly diverse circular DNA viruses Tisza, MJ; Pastrana, DV; Welch, NL et al. Elife, DOI://10.7554/eLife.51971 (2020)
Sub-millimeter fMRI reveals multiple topographical digit representations that form action maps in human motor cortex Huber, L; Finn, ES; Handwerker, DA et al. Neuroimage, DOI://10.1016/j.neuroimage.2019.116463 (2020)
Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates Zakrevsky, P; Kasprzak, WK; Heinz, WF et al. Nanoscale, DOI://10.1039/c9nr08197f (2020)
SAMPL6 logP challenge: machine learning and quantum mechanical approaches Patel, P; Kuntz, DM; Jones, MR; Brooks, BR; Wilson, AK; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-020-00287-0 (2020)
A deep learning approach for the blind logP prediction in SAMPL6 challenge Prasad, S; Brooks, BR; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-020-00292-3 (2020)
Whole Genome Sequence-Based Haplotypes Reveal a Single Origin of the 1393 Bp HBB Deletion Wang, X; Xu, JZ; Conrey, A et al. J. Med. Genet., DOI://10.1136/jmedgenet-2019-106698 (2020)

Complete Genome Sequence of Myophage Ec_Makalu_002, Which Infects Uropathogenic Escherichia coli Dhungana, G; Malla, R; Rajaure, M; Adhya, S; Microbiol Resour Announc, DOI://10.1128/MRA.01530-19 (2020)
A dual apolipoprotein C-II mimetic-apolipoprotein C-III antagonist peptide lowers plasma triglycerides Wolska, A; Lo, L; Sviridov, DO et al. Sci Transl Med, DOI://10.1126/scitranslmed.aaw7905 (2020)
Characterization of Specific Ion Effects on PI(4,5)P 2 Clustering: Molecular Dynamics Simulations and Graph-Theoretic Analysis Han, K; Gericke, A; Pastor, RW; J Phys Chem B, DOI://10.1021/acs.jpcb.9b10951 (2020)
In search of genetic factors predisposing to familial hairy cell leukemia (HCL): exome-sequencing of four multiplex HCL pedigrees Pemov, A; Pathak, A; Jones, SJ et al. Leukemia, DOI://10.1038/s41375-019-0702-7 (2020)
ABC-transporter upregulation mediates resistance to the CDK7 inhibitors THZ1 and ICEC0942 Sava, GP; Fan, H; Fisher, RA et al. Oncogene, DOI://10.1038/s41388-019-1008-y (2020)
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)
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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)
Complement receptor CD46 co-stimulates optimal human CD8+ T cell effector function via fatty acid metabolism Arbore, G; West, EE; Rahman, J et al. Nat Commun, DOI://10.1038/s41467-018-06706-z (2018)
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.1007806 (2018)
Intraclass correlation: Improved modeling approaches and applications for neuroimaging Chen, G; Taylor, PA; Haller, SP et al. Hum Brain Mapp, DOI://10.1002/hbm.23909 (2018)
Exome sequencing of a large family identifies potential candidate genes contributing risk to bipolar disorder Zhang, T; Hou, L; Chen, DT; McMahon, FJ; Wang, JC; Rice, JP; Gene, DOI://10.1016/j.gene.2017.12.025 (2018)
Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis Abusleme, L; Diaz, PI; Freeman, AF et al. JCI Insight, DOI://10.1172/jci.insight.122061 (2018)
Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma Sanford, T; Meng, MV; Railkar, R; Agarwal, PK; Porten, SP; Clin Epigenetics, DOI://10.1186/s13148-018-0451-x (2018)
Pain control through selective chemo-axotomy of centrally projecting TRPV1+ sensory neurons Sapio, MR; Neubert, JK; LaPaglia, DM et al. J. Clin. Invest., DOI://10.1172/JCI94331 (2018)
Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity Turcot, V; Lu, Y; Highland, HM et al. Nat. Genet., DOI://10.1038/s41588-017-0011-x (2018)
Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation Grobler, Y; Yun, CY; Kahler, DJ et al. PLoS Pathog., DOI://10.1371/journal.ppat.1007445 (2018)
Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila Lee, SK; Xue, Y; Shen, W et al. Nat Commun, DOI://10.1038/s41467-018-07101-4 (2018)

Frequency-dependent tACS modulation of BOLD signal during rhythmic visual stimulation Chai, Y; Sheng, J; Bandettini, PA; Gao, JH; Hum Brain Mapp, DOI://10.1002/hbm.23990 (2018)
Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes Mahajan, A; Wessel, J; Willems, SM et al. Nat. Genet., DOI://10.1038/s41588-018-0084-1 (2018)
Neurological soft signs and cognitive performance in early childhood Alamiri, B; Nelson, C; Fitzmaurice, GM; Murphy, JM; Gilman, SE; Dev Psychol, DOI://10.1037/dev0000566 (2018)
Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen Inwood, S; Buehler, E; Betenbaugh, M; Lal, M; Shiloach, J; Biotechnol J, DOI://10.1002/biot.201700342 (2018)
Learning recurrent dynamics in spiking networks Kim, CM; Chow, CC; Elife, DOI://10.7554/eLife.37124 (2018)
Decrypting the Heat Activation Mechanism of TRPV1 Channel by Molecular Dynamics Simulation Wen, H; Zheng, W; Biophys. J., DOI://10.1016/j.bpj.2017.10.034 (2018)
Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development Uehara, R; Cerritelli, SM; Hasin, N et al. Cell Rep, DOI://10.1016/j.celrep.2018.10.019 (2018)
Patterns of Physical Activity and Sedentary Behavior for Older Adults with Alzheimer's Disease, Mild Cognitive Impairment, and Cognitively Normal in Hong Kong Lu, Z; Harris, TB; Shiroma, EJ; Leung, J; Kwok, T; J. Alzheimers Dis., DOI://10.3233/JAD-180805 (2018)
Re-annotation of eight Drosophila genomes Yang, H; Jaime, M; Polihronakis, M et al. Life Sci Alliance, DOI://10.26508/lsa.201800156 (2018)
Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design Ciancetta, A; Jacobson, KA; Methods Mol. Biol., DOI://10.1007/978-1-4939-7465-8_3 (2018)
A small single-domain protein folds through the same pathway on and off the ribosome Guinn, EJ; Tian, P; Shin, M; Best, RB; Marqusee, S; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1810517115 (2018)
Development and differentiation of early innate lymphoid progenitors Harly, C; Cam, M; Kaye, J; Bhandoola, A; J. Exp. Med., DOI://10.1084/jem.20170832 (2018)

Metabolic remodelling of glucose, fatty acid and redox pathways in the heart of type 2 diabetic mice Cortassa, S; Caceres, V; Tocchetti, CG et al. J. Physiol. (Lond.), DOI://10.1113/JP276824 (2018)
The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding Kudva, R; Tian, P; Pardo-Avila, F et al. Elife, DOI://10.7554/eLife.36326 (2018)
Dose coefficients of mesh-type ICRP reference computational phantoms for idealized external exposures of photons and electrons Yeom YS; Choi C; et al Nuclear Engineering and Technology, doi://10.1016/j.net.2018.12.006 (2018)
A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression Kycia, I; Wolford, BN; Huyghe, JR et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.02.020 (2018)
On the convergence of multi-scale free energy simulations König, G; Brooks, BR; Thiel, W; York, DM; Mol Simul, DOI://10.1080/08927022.2018.1475741 (2018)
Accelerated and Improved Differentiation of Retinal Organoids from Pluripotent Stem Cells in Rotating-Wall Vessel Bioreactors DiStefano, T; Chen, HY; Panebianco, C et al. Stem Cell Reports, DOI://10.1016/j.stemcr.2017.11.001 (2018)

Investigation of a Cluster of Sphingomonas koreensis Infections Johnson, RC; Deming, C; Conlan, S et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1803238 (2018)
Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity Rodriguez, J; Ren, G; Day, CR; Zhao, K; Chow, CC; Larson, DR; Cell, DOI://10.1016/j.cell.2018.11.026 (2018)
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A dysbiotic microbiome triggers TH17 cells to mediate oral mucosal immunopathology in mice and humans Nicolas Dutzan, Tetsuhiro Kajikawa, Loreto Abusleme et al. Mucosal Immunity, 10.1126/scitranslmed.aat0797 (2018)
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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)

Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience Gall, T; Valkanas, E; Bello, C et al. Front Med (Lausanne), DOI://10.3389/fmed.2017.00062 (2017)
Discovery and fine-mapping of loci associated with MUFAs through trans-ethnic meta-analysis in Chinese and European populations Hu, Y; Tanaka, T; Zhu, J et al. J. Lipid Res., DOI://10.1194/jlr.P071860 (2017)
Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning Dong, X; Sun, Y; Wei, G; Nussinov, R; Ma, B; Phys Chem Chem Phys, DOI://10.1039/c7cp05959k (2017)
Temporal similarity perfusion mapping: A standardized and model-free method for detecting perfusion deficits in stroke Song, S; Bokkers, RPH; Luby, M et al. PLoS ONE, DOI://10.1371/journal.pone.0185552 (2017)
Genome Wide Association Study (GWAS) between Attention Deficit Hyperactivity Disorder (ADHD) and Obsessive Compulsive Disorder (OCD) Ritter, ML; Guo, W; Samuels, JF et al. Front Mol Neurosci, DOI://10.3389/fnmol.2017.00083 (2017)
Extending electrostatics of dielectric spheres to arbitrary charge distributions with applications to biosystems T. P. Doerr, O. I. Obolensky, and Yi-Kuo Yu Phys. Rev. E , doi://10.1103/PhysRevE.96.062414 (2017)

The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues Xue, XY; Majerciak, V; Uberoi, A et al. PLoS Pathog., DOI://10.1371/journal.ppat.1006715 (2017)
Reduced Local and Increased Long-Range Functional Connectivity of the Thalamus in Autism Spectrum Disorder Tomasi, D; Volkow, ND; Cereb. Cortex, DOI://10.1093/cercor/bhx340 (2017)
Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection Watkins-Chow, DE; Varshney, GK; Garrett, LJ et al. G3 (Bethesda), DOI://10.1534/g3.116.038091 (2017)
CDC14A Phosphatase is Essential for Hearing and Male Fertility in Mouse and Human Imtiaz, A; Belyantseva, IA; Beirl, AJ et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddx440 (2017)
Identifying subgroups of enhanced predictive accuracy from longitudinal biomarker data using tree-based approaches: applications to fetal growth Foster, JC; Liu, D; Albert, PS; Liu, A; J R Stat Soc Ser A Stat Soc, DOI://10.1111/rssa.12182 (2017)
Generation and characterization of Kctd15 mutations in zebrafish Heffer, A; Marquart, GD; Aquilina-Beck, A; Saleem, N; Burgess, HA; Dawid, IB; PLoS ONE, DOI://10.1371/journal.pone.0189162 (2017)

Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins Shen, Y; Roche, J; Grishaev, A; Bax, A; Protein Sci., DOI://10.1002/pro.3292 (2017)
Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep Harbison, ST; Serrano Negron, YL; Hansen, NF; Lobell, AS; PLoS Genet., DOI://10.1371/journal.pgen.1007098 (2017)
Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N Chittori, S; Hong, J; Saunders, H et al. Science, DOI://10.1126/science.aar2781 (2017)
Identity-by-Descent Mapping Identifies Major Locus for Serum Triglycerides in Amerindians Largely Explained by an APOC3 Founder Mutation Hsueh, WC; Nair, AK; Kobes, S et al. Circ Cardiovasc Genet, DOI://10.1161/CIRCGENETICS.117.001809 (2017)
Detecting treatment differences in group sequential longitudinal studies with covariate adjustment Jeffries, NO; Troendle, JF; Geller, NL; Biometrics, DOI://10.1111/biom.12837 (2017)
Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations Leonard, AN; Simmonett, AC; Pickard, FC et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.7b00948 (2017)

Structural basis for nucleotide-modulated p97 association with the ER membrane Tang, WK; Zhang, T; Ye, Y; Xia, D; Cell Discov, DOI://10.1038/celldisc.2017.45 (2017)
Structural host-microbiota interaction networks Guven-Maiorov, E; Tsai, CJ; Nussinov, R; PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1005579 (2017)
Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq Chen, L; Lee, JW; Chou, CL et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1710964114 (2017)
Exploring Effects of Sex and Diet on Drosophila melanogaster Head Gene Expression Jaime, MDLA; Hurtado, J; Loustalot-Laclette, MR; Oliver, B; Markow, T; J Genomics, DOI://10.7150/jgen.22393 (2017)
The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States Nelson, MI; Culhane, MR; Trovão, NS et al. J. Gen. Virol., DOI://10.1099/jgv.0.000924 (2017)
New Multiple Sclerosis Disease Severity Scale Predicts Future Accumulation of Disability Weideman, AM; Barbour, C; Tapia-Maltos, MA et al. Front Neurol, DOI://10.3389/fneur.2017.00598 (2017)

CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level Yuen, G; Khan, FJ; Gao, S et al. Nucleic Acids Res., DOI://10.1093/nar/gkx843 (2017)
Graph theory reveals amygdala modules consistent with its anatomical subdivisions Caparelli, EC; Ross, TJ; Gu, H; Liang, X; Stein, EA; Yang, Y; Sci Rep, DOI://10.1038/s41598-017-14613-4 (2017)
Molecular Anatomy of the Developing Human Retina Hoshino, A; Ratnapriya, R; Brooks, MJ et al. Dev. Cell, DOI://10.1016/j.devcel.2017.10.029 (2017)
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Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions Kim, J; Sturgill, D; Sebastian, R et al. Mol. Cell, DOI://10.1016/j.molcel.2017.11.021 (2017)
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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)
A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next-generation sequencing Chiu, CY; Jung, J; Wang, Y et al. Genet. Epidemiol., DOI://10.1002/gepi.22014 (2016)
Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data Ying, J; Delaglio, F; Torchia, DA; Bax, A; J. Biomol. NMR, DOI://10.1007/s10858-016-0072-7 (2016)
Robust skull stripping using multiple MR image contrasts insensitive to pathology Roy, S; Butman, JA; Pham, DL; Neuroimage, DOI://10.1016/j.neuroimage.2016.11.017 (2016)
Association of Irritability and Anxiety With the Neural Mechanisms of Implicit Face Emotion Processing in Youths With Psychopathology Stoddard, J; Tseng, WL; Kim, P et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2016.3282 (2016)
Early generated B1 B cells with restricted BCRs become chronic lymphocytic leukemia with continued c-Myc and low Bmf expression Hayakawa, K; Formica, AM; Brill-Dashoff, J et al. J. Exp. Med., DOI://10.1084/jem.20160712 (2016)

Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains Zhao, J; Nussinov, R; Ma, B; Protein Eng. Des. Sel., DOI://10.1093/protein/gzw065 (2016)
Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing Roberts, L; Ratnapriya, R; du Plessis, M; Chaitankar, V; Ramesar, RS; Swaroop, A; Invest. Ophthalmol. Vis. Sci., DOI://10.1167/iovs.16-19785 (2016)
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont Bennuru, S; Cotton, JA; Ribeiro, JM et al. MBio, DOI://10.1128/mBio.02028-16 (2016)
NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors Kim, JW; Yang, HJ; Brooks, MJ et al. Cell Rep, DOI://10.1016/j.celrep.2016.10.074 (2016)
Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping Dreger, DL; Rimbault, M; Davis, BW; Bhatnagar, A; Parker, HG; Ostrander, EA; Dis Model Mech, DOI://10.1242/dmm.027037 (2016)
Integrative network analysis reveals molecular mechanisms of blood pressure regulation Tianxiao Huan, Qingying Meng et al. Mol Syst Biol., doi: 10.15252/msb.20145399 (2016)

C. elegans DAF-2 as a Model for Human Insulin Receptoropathies David A. Bulger, Tetsunari Fukushige, Sijung Yun, Robert K. Semple, John A. Hanover, and Michael W. Krause Genes|Genomes|Genetics, doi:10.1534/g3.116.03718 (2016)
Generation and differentiation of induced pluripotent stem cells reveal ankylosing spondylitis risk gene expression in bone progenitors Gerlinde Layh-Schmitt, Shajia Lum Fatemehm Navid, Stephen R. Brooks, Emily Lazowick, Kathryn M. Davis, Cristina Montagna, Massimo Gadina, Robert A. Colbert Clinical Rheumatology, doi:10.1007/s10067-016-3469-5 (2016)
The genome of Onchocerca volvulus, agent of river blindness Cotton, JA; Bennuru, S; Grote, A et al. Nat Microbiol, DOI://10.1038/nmicrobiol.2016.216 (2016)
Two Na+ Sites Control Conformational Change in a Neurotransmitter Transporter Homolog Sotiria Tavoulari, Eleonora Margheritis, Anu Nagarajan, David C. DeWitt, Yuan -Wei Zhang, Edwin Rosado, Silvia Ravera, Elizabeth Rhoades, Lucy R. Forrest and Gary Rudnick J Biol Chem. , doi: 10.1074/jbc.M115.692012. (2016)
Techniques for blood volume fMRI with VASO: From low-resolution mapping towards sub-millimeter layer-dependent applications Huber, L; Ivanov, D; Handwerker, DA et al. Neuroimage, DOI://10.1016/j.neuroimage.2016.11.039 (2016)
Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity Esser, L; Zhou, F; Pluchino, KM et al. J. Biol. Chem., DOI://10.1074/jbc.M116.755884 (2016)
Physiological basis of vascular autocalibration (VasA): Comparison to hypercapnia calibration methods Kazan, SM; Huber, L; Flandin, G; Ivanov, D; Bandettini, P; Weiskopf, N; Magn Reson Med, DOI://10.1002/mrm.26494 (2016)
Serine/Threonine Phosphatases and Aquaporin-2 Regulation in Renal Collecting Duct Sophia LeMaire, Viswanathan Raghuram, Cameron R. Grady, Christina M. Pickering, Chung-Lin Chou, Ezigbobiara N Umejiego, Mark A. Knepper Am. J. Physiol. - Renal Physiol. , DOI: 10.1152/ajprenal.00455.2016 (2016)
Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains Scott M. Gordon, Mohsen Pourmousa, Maureen Sampson, Denis Sviridov, Rafique Islam, B. Scott Perrin Jr., Georgina Kemeh, Richard W. Pastor, Alan T. Remaley Biochimica et Biophysica Acta - Membranes, doi://10.1016/j.bbamem.2016.10.019 (2016)
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association Jan Domanski, George Hedger, Robert B. Best, Phillip James Stansfeld, and Mark S. P. Sansom J. Phys. Chem. B, doi://10.1021/acs.jpcb.6b08445 (2016)
Transcriptome Profiling of NIH3T3 Cell Lines Expressing Opsin and the P23H Opsin Mutant Identifies Candidate Drugs for the Treatment of Retinitis Pigmentosa Yuanyuan Chen, Matthew J. Brooks, Linn Gieser, Anand Swaroop, Krzysztof Palczewski Pharmacological Research, doi://10.1016/j.phrs.2016.10.031 (2016)
RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks Perner, J; Provazník, J; Schrenková, J; Urbanová, V; Ribeiro, JM; Kopáček, P; Sci Rep, DOI://10.1038/srep36695 (2016)
Transgenic mouse model of IgM(+) lymphoproliferative disease mimicking Waldenström macroglobulinemia Tompkins, VS; Sompallae, R; Rosean, TR et al. Blood Cancer J, DOI://10.1038/bcj.2016.95 (2016)
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Structure and function of the AAA+ ATPase p97/Cdc48p Xia D, Tang WK, Ye Y Gene, DOI://10.1016/j.gene.2016.02.042 (2016)
Colitis susceptibility in p47(phox-/-) mice is mediated by the microbiome Falcone, EL; Abusleme, L; Swamydas, M et al. Microbiome, DOI://10.1186/s40168-016-0159-0 (2016)

MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research Wendy Chang, Andrew Brohl, Rajesh Patidar, Sivasish Sindiri, Jack F. Shern, Jun S. Wei, Young K. Song, Marielle E Yohe, Berkley E. Gryder, Shile Zhang, Kathleen A Calzone, Nityashree Shivaprasad, Xinyu Wen, Thomas Badgett, Markku Miettinen, Kip R Hartman, James C League-Pascual, Toby Trahair, Brigitte C. Widemann, Melinda S. Merchant, Rosandra N Kaplan, Jimmy C Lin, and Javed Khan Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-15-2717 (2016)
Aberrant intrinsic functional connectivity within and between corticostriatal and temporal-parietal networks in adults and youth with bipolar disorder Stoddard, J; Gotts, SJ; Brotman, MA et al. Psychol Med, DOI://10.1017/S0033291716000143 (2016)
Cajal bodies are linked to genome conformation Qiuyan Wang, Iain A. Sawyer, Myong-Hee Sung, David Sturgill, Sergey P. Shevtsov, Gianluca Pegoraro, Ofir Hakim, Songjoon Baek, Gordon L. Hager & Miroslav Dundr Nature Communications, doi:10.1038/ncomms10966 (2016)
Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Influenza Vaccine Candidate Erin E. H. Tran, Kira A. Podolsky, Alberto Bartesaghi, Oleg Kuybeda, Giovanna Grandinetti, Teddy John Wohlbold, Gene S. Tan, Raffael Nachbagauer, Peter Palese, Florian Krammer, Sriram Subramaniam mBio, doi: 10.1128/mBio.00257-16 (2016)
Subtle in-scanner motion biases automated measurement of brain anatomy from in vivo MRI Aaron Alexander-Bloch, Liv Clasen, Michael Stockman, Lisa Ronan, Francois Lalonde, Jay Giedd and Armin Raznahan Human Brain Mapping, DOI: 10.1002/hbm.23180 (2016)
Detection of benign prostatic hyperplasia nodules in T2W MR images using fuzzy decision forest Nathan Lay ; Sabrina Freeman ; Baris Turkbey ; Ronald Summers SPIE Proceedings, doi:10.1117/12.2217906 (2016)

2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition Soojay Banerjee, Alberto Bartesaghi, Alan Merk, Prashant Rao, Stacie L. Bulfer, Yongzhao Yan, Neal Green, Barbara Mroczkowski, R. Jeffrey Neitz, Peter Wipf, Veronica Falconieri, Raymond J. Deshaies, Jacqueline L. S. Milne, Donna Huryn, Michelle Arkin, Sriram Subramaniam Science, DOI: 10.1126/science.aad7974 (2016)
Design and synthesis of small molecule-sulfotyrosine mimetics that inhibit HIV-1 entry Dogo-Isonagie, C; Lee, SL; Lohith, K et al. Bioorg. Med. Chem., DOI://10.1016/j.bmc.2016.02.044 (2016)
Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture Hughes, HY; Conlan, SP; Lau, AF et al. J. Clin. Microbiol., DOI://10.1128/JCM.03229-15 (2016)
Whole-Exome Sequencing Analyses of Inflammatory Bowel Disease-Associated Colorectal Cancers Robles, AI; Traverso, G; Zhang, M et al. Gastroenterology, DOI://10.1053/j.gastro.2015.12.036 (2016)
Emerging Functions of Natural IgM and Its Fc Receptor FCMR in Immune Homeostasis Wang, H; Coligan, JE; Morse, HC; Front Immunol, DOI://10.3389/fimmu.2016.00099 (2016)
A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet Xin, A; Masson, F; Liao, Y et al. Nat. Immunol., DOI://10.1038/ni.3410 (2016)

caOmicsV: an R package for visualizing multidimensional cancer genomic data Zhang H, Meltzer PS, Davis SR BMC Bioinformatics, DOI://10.1186/s12859-016-0989-6 (2016)
Brain-Derived Neurotrophic Factor Val66Met Polymorphism Affects the Relationship Between an Anxiety-Related Personality Trait and Resting Regional Cerebral Blood Flow Wei, SM; Eisenberg, DP; Nabel, KG et al. Cereb. Cortex, DOI://10.1093/cercor/bhw072 (2016)
Redox-induced activation of the proton pump in the respiratory complex I Vivek Sharma, Galina Belevich, Ana P. Gamiz-Hernandez, Tomasz Ròg, Ilpo Vattulainen, Marina L. Verkhovskaya Mårten Wikström, Gerhard Hummer, and Ville R. I. Kaila PNAS, doi://10.1073/pnas.1503761112 (2016)
NMDA Receptors Multiplicatively Scale Visual Signals and Enhance Directional Motion Discrimination in Retinal Ganglion Cells Poleg-Polsky A, Diamond JS Neuron, DOI://10.1016/j.neuron.2016.02.013 (2016)
MEGSA: A Powerful and Flexible Framework for Analyzing Mutual Exclusivity of Tumor Mutations Xing Hua, Paula L. Hyland, Jing Huang, Lei Song, Bin Zhu, Neil E. Caporaso, Maria Teresa Landi, Nilanjan Chatterjee, and Jianxin Shi Am J. Hum. Genet. , doi://10.1016/j.ajhg.2015.12.021 (2016)
Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300 Shrimp JH, Sorum AW, Garlick JM, Guasch L, Nicklaus MC, Meier JL ACS Med Chem Lett, DOI://10.1021/acsmedchemlett.5b00385 (2016)
Plasticity of Sensorimotor Networks: Multiple Overlapping Mechanisms Buch, ER; Liew, SL; Cohen, LG; Neuroscientist, DOI://10.1177/1073858416638641 (2016)
Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q ACS Chem Neurosci, DOI://10.1021/acschemneuro.5b00242 (2016)
Seeking Optimal Region-Of-Interest (ROI) Single-Value Summary Measures for fMRI Studies in Imaging Genetics Tong, Y; Chen, Q; Nichols, TE et al. PLoS ONE, DOI://10.1371/journal.pone.0151391 (2016)
Microscopic interpretation of folding φ-values using the transition path ensemble Robert B. Best and Gerhard Hummer PNAS, doi: 10.1073/pnas.1520864113 (2016)
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold Takako Takeda, Yanli Wang , Stephen H. Bryant J. Computer-Aided Molecular Design, doi://10.1007/s10822-016-9905-4 (2016)
Modulation of Folding Internal Friction by Local and Global Barrier Heights Wenwei Zheng, David de Sancho, and Robert B. Best J. Phys. Chem. Letters, DOI: 10.1021/acs.jpclett.6b00329 (2016)

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo Josefina Ocampo, Razvan V. Chereji, Peter R. Eriksson and David J. Clark Nucleic Acids Research, doi://10.1093/nar/gkw068 (2016)
Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations Alioscka A. Sousa, Sergio A. Hassan, Luiza L. Knittel, Andrea Balbo, Maria A. Aronova, Patrick H. Brown, Peter Schuck and Richard D. Leapman Nanoscale, DOI: 10.1039/C5NR07642K (2016)
The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes Rinschen, MM; Bharill, P; Wu, X et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddw016 (2016)
Mucolipidosis types II and III and non-syndromic stuttering are associated with different variants in the same genes Raza, MH; Domingues, CE; Webster, R et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2015.154 (2016)
The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities Afonin, KA; Viard, M; Tedbury, P et al. Nano Lett., DOI://10.1021/acs.nanolett.5b04676 (2016)
Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning Hoo-Chang Shin Holger R. Roth ; Mingchen Gao ; Le Lu ; Ziyue Xu ; Isabella Nogues ; Jianhua Yao ; Daniel Mollura ; Ronald M. Summers IEEE Transactions on Medical Imaging, DOI://10.1109/TMI.2016.2528162 (2016)

Preterm birth and air pollution: Critical windows of exposure for women with asthma Pauline Mendola, Maeve Wallace, Beom Seuk Hwang, Danping Liu, Candace Robledo, Tuija Mӓnnistö, Rajeshwari Sundaram, Seth Sherman, Qi Ying, Katherine L. Grantz J. Allergy Clin. Immunology, doi:10.1016/j.jaci.2015.12.1309 (2016)
Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc Minnkyong Lee, Sarah M. Beggs, Derek Gildea, Sujata Bupp, Jens Lichtenberg, Niraj S. Trivedi, NISC Comparative Sequencing Program, Ying Hu, David M. Bodine, and Nigel P.S. Crawford1 Oncotarget, doi: 10.18632/oncotarget.5230 (2016)
Genome-wide footprinting: ready for prime time? Myong-Hee Sung, Songjoon Baek & Gordon L Hager Nature Methods, doi:10.1038/nmeth.3766 (2016)
A Comparison of Methods to Reweight from Classical Molecular Simulations to QM/MM Potentials Eric Christopher Dybeck, Gerhard König, Bernard R. Brooks, and Michael R. Shirts J. Chem. Theory. Comput, DOI: 10.1021/acs.jctc.5b01188 (2016)
Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches Eckart Bindewald, Kirill A. Afonin, Mathias Viard, Paul Zakrevsky, Taejin Kim, and Bruce A. Shapiro Nano Letters, DOI: 10.1021/acs.nanolett.5b04651 (2016)
Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation Reynier Suardiaz, Pablo Garcia Jambrina, Laura Masgrau, Ángels Gonzàlez-Lafont, Edina Rosta, and Josè M. Lluch J. Chem. Theory. Comput, DOI: 10.1021/acs.jctc.5b01236 (2016)

Impact of time-of-day on brain morphometric measures derived from T₁-weighted magnetic resonance imaging Aaron Trefler, Neda Sadeghi, Adam G. Thomas, Carlo Pierpaoli, Chris I. Baker, Cibu Thomas Neuroimage, doi:10.1016/j.neuroimage.2016.02.034 (2016)
Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly Sugiyama, T; Thillainadesan, G; Chalamcharla, VR et al. Mol. Cell, DOI://10.1016/j.molcel.2016.01.029 (2016)
Deubiquitylation of protein cargo is not an essential step in exosome formation Alyssa R. Huebner, Lei Cheng, Poorichaya Somparn, Mark A. Knepper, Robert A. Fenton and Trairak Pisitkun Molecular and Cellular Proteomics, doi: 10.1074/mcp.M115.054965 (2016)
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes Grabundzija, I; Messing, SA; Thomas, J et al. Nat Commun, DOI://10.1038/ncomms10716 (2016)
A genome landscape of SRSF3-regulated splicing events and gene expression in human osteosarcoma U2OS cells Ajiro M, Jia R, Yang Y, Zhu J, Zheng ZM Nucleic Acids Res., DOI://10.1093/nar/gkv1500 (2016)
Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients Alena Gros, Maria R Parkhurst, Eric Tran, Anna Pasetto, Paul F Robbins, Sadia Ilyas, Todd D Prickett, Jared J Gartner, Jessica S Crystal, Ilana M Roberts, Kasia Trebska-McGowan, John R Wunderlich, James C Yang & Steven A Rosenberg Nature Medicine, doi:10.1038/nm.4051 (2016)

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts Liang Ma, Zehua Chen, Da Wei Huang et. al. Nature Communications, doi:10.1038/ncomms10740 (2016)
Gene-Based Association Analysis for Censored Traits Via Fixed Effect Functional Regressions. Fan R, Wang Y, Yan Q, Ding Y, Weeks DE, Lu Z, Ren H, Cook RJ, Xiong M, Swaroop A, Chew EY, Chen W Genet Epidemiol. , doi: 10.1002/gepi.21947 (2016)
Finite sample pointwise confidence intervals for a survival distribution with right-censored data Michael P. Fay and Erica H. Brittain Statistics in Medicine, DOI: 10.1002/sim.6905 (2016)
Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept Franke, B; Stein, JL; Ripke, S et al. Nat. Neurosci., DOI://10.1038/nn.4228 (2016)
High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics Day CR, Chen H, Coulon A, Meier JL, Larson DR, Methods, DOI://10.1016/j.ymeth.2015.11.025 (2016)
Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing Yu-Chih Tsai, Sean Conlan, Clayton Deming, NISC Comparative Sequencing Program, Julia A. Segre, Heidi H. Kong Jonas Korlach, and Julia Oh mBio, doi: 10.1128/mBio.01948-15 (2016)

Recessive mutations of TMC1 associated with moderate to severe hearing loss Ayesha Imtiaz , Azra Maqsood , Atteeq U. Rehman, Robert J. Morell, Jeffrey R. Holt, Thomas B. Friedman, Sadaf Naz Neurogenetics, DOI 10.1007/s10048-016-0477-1 (2016)
Light-regulated Molecular Trafficking in a Synthetic Water-soluble Host Jesús del Barrio, Sean T. J. Ryan, Pablo G. Jambrina, Edina Rosta, and Oren A Scherman JACS, DOI: 10.1021/jacs.5b11642 (2016)
Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating Doreen Matthies, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, Shahidul Islam, Alberto Bartesaghi, Eduardo Perozo, Sriram Subramaniam Cell, doi:10.1016/j.cell.2015.12.055 (2016)
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin Chanhyung Bae, Claudio Anselmi, Jeet Kalia, Andres Jara-Oseguera, Charles D Schwieters, Dmitriy Krepkiy ,Chul Won Lee, Eun-Hee Kim, Jae Il Kim, Josè D Faraldo-Gòmez and Kenton J Swartz eLife, DOI: http://dx.doi.org/10.7554/eLife.11273 (2016)
Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant Jiangtao Lei , Ruxi Qi , Guanghong Wei , Ruth Nussinov and Buyong Ma Phys. Chem. Chem. Phys., DOI: 10.1039/C5CP06538K (2016)
Cutting Edge: Expression of IRF8 in Gastric Epithelial Cells Confers Protective Innate Immunity against Helicobacter pylori Infection Yan, M; Wang, H; Sun, J et al. J. Immunol., DOI://10.4049/jimmunol.1500766 (2016)

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation Thompson B, Varticovski L, Baek S, Hager GL PLoS ONE, DOI://10.1371/journal.pone.0148619 (2016)
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology Zhao Z, Martin C, Fan R, Bourne PE, Xie L BMC Bioinformatics, DOI://10.1186/s12859-016-0941-9 (2016)
Vibratory Urticaria Associated with a Missense Variant in ADGRE2 Boyden, SE; Desai, A; Cruse, G et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1500611 (2016)
Identifying subgroups of enhanced predictive accuracy from longitudinal biomarker data by using tree-based approaches: applications to fetal growth Jared C. Foster, Danping Liu, Paul S. Albert and Aiyi Liu Journal of the Royal Statistical Society: Series A (Statisti, 10.1111/rssa.12182 (2016)
How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability? Liang Xu, Jie Zheng, Martin Margittai, Ruth Nussinov, and Buyong Ma ACS Chemical Neuroscience, 10.1021/acschemneuro.5b00294 (2016)
In vivo tissue has non-linear rheological behavior distinct from 3D biomimetic hydrogels, as determined by AMOTIV microscopy Blehm BH, Devine A, Staunton JR, Tanner K Biomaterials, DOI://10.1016/j.biomaterials.2015.12.019 (2016)

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium van den Berg, SM; de Moor, MH; Verweij, KJ et al. Behav. Genet., DOI://10.1007/s10519-015-9735-5 (2016)
Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain Dotson GA, , Dekker JP, Palmore TN, Segre JA, Conlan S Genome Announc, DOI://10.1128/genomeA.01663-15 (2016)
The Histone Variant MacroH2A1.2 Is Necessary for the Activation of Muscle Enhancers and Recruitment of the Transcription Factor Pbx1 Dell'Orso, S; Wang, AH; Shih, HY et al. Cell Rep, 2211-1247 (2016)
Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice Davies, B; Hatton, E; Altemose, N et al. Nature, DOI://10.1038/nature16931 (2016)
r2VIM: A new variable selection method for random forests in genome-wide association studies Silke Szymczak, Emily Holzinger, Abhijit Dasgupta, James D. Malley, Anne M. Molloy, James L. Mills, Lawrence C. Brody, Dwight Stambolian and Joan E. Bailey-Wilson BioData Mining, 10.1186/s13040-016-0087-3 (2016)
Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance Gelio Alves, Guanghui Wang, Aleksey Y. Ogurtsov, Steven K. Drake, Marjan Gucek, Anthony F. Suffredini, David B. Sacks, Yi-Kuo Yu J Am Soc Mass Spectrom 27:194-210, 10.1007/s13361-015-1271-2 (2016)
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs Dudekula, DB; Panda, AC; Grammatikakis, I; De, S; Abdelmohsen, K; Gorospe, M; RNA Biol, DOI://10.1080/15476286.2015.1128065 (2016)
Somatic mutational landscape of AML with inv(16) or t(8;21) identifies patterns of clonal evolution in relapse leukemia Sood, R; Hansen, NF; Donovan, FX et al. Leukemia, DOI://10.1038/leu.2015.141 (2016)
Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function Pattaro, C; Teumer, A; Gorski, M et al. Nat Commun, DOI://10.1038/ncomms10023 (2016)
Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium Ma, Y; Follis, JL; Smith, CE et al. Am. J. Clin. Nutr., DOI://10.3945/ajcn.115.112987 (2016)
New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk Lu, Y; Day, FR; Gustafsson, S et al. Nat Commun, DOI://10.1038/ncomms10495 (2016)
Is the MC1R variant p. R160W associated with Parkinson's? Lubbe, SJ; Escott-Price, V; Brice, A et al. Ann. Neurol., DOI://10.1002/ana.24527 (2016)

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels Kilpeläinen, TO; Carli, JF; Skowronski, AA et al. Nat Commun, DOI://10.1038/ncomms10494 (2016)
Comparison of the Conformations of KRAS Isoforms, K-Ras4A and K-Ras4B, Points to Similarities and Significant Differences Mayukh Chakrabarti, Hyunbum Jang, and Ruth Nussinov J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.5b11110 (2016)
Risk of End-stage Renal Disease in Patients with Lupus Nephritis, 1970 to 2015 A systematic review and Bayesian meta-analysis Maria G. Tektonidou, Abhijit Dasgupta and Michael M. Ward Arthritis and Rheumatology, DOI: 10.1002/art.39594 (2016)
Coupling of the Non-Amyloid-Component (NAC) Domain and the KTK(E/Q)GV Repeats Stabilize the α-Synuclein Fibrils Liang Xu, Ruth Nussinov, Buyong Ma Eur. J. Med. Chem. , doi:10.1016/j.ejmech.2016.01.044 (2016)
Novel nucleosomal particles containing core histones and linker DNA but no histone H1 Cole, HA; Cui, F; Ocampo, J et al. Nucleic Acids Res., DOI://10.1093/nar/gkv943 (2016)
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)
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Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile Martha Nelson, Marie R. Culhane, Albert Rovira, Montserrat Torremorell, Pedro Guerrero, and Julio Norambuena PLoS Currents, doi: 10.1371/currents.outbreaks.c8b3207c9bad98474eca3013fa933ca6 (2015)
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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)
Challenges and solutions for gene identification in the presence of familial locus heterogeneity Atteeq U Rehman, Regie Lyn P Santos-Cortez et al. Eur. J. Human Genetics, doi: 10.1038/ejhg.2014.266 (2014)
Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer Ana-Patricia Gàmiz-Hernàndez , Artiom Magomedov , Gerhard Hummer , and Ville R. I. Kaila J. Phys. Chem. B, DOI: 10.1021/jp508790n (2014)
B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity Jason Qian, Qiao Wang, Marei Dose et al. Cell, doi:10.1016/j.cell.2014.11.013 (2014)
Free energies from dynamic weighted histogram analysis using unbiased Markov state model Edina Rosta and Gerhard Hummer J. Chem. Theory Comput., DOI: 10.1021/ct500719p (2014)

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes Raghunath Chatterjee, Ximiao He, Di Huang, Peter Fitzgerald, Andrew Smith and Charles Vinson Epigenetics and Chromatin, doi:10.1186/1756-8935-7-35 (2014)
Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes Ximiao He, Raghunath Chatterjee, Desiree Tillo, Andrew Smith, Peter FitzGerald and Charles Vinson Epigenetics and Chromatin, doi:10.1186/1756-8935-7-34 (2014)
Genetic diversity is a predictor of mortality in humans Bihlmeyer NA, Brody JA, et al. BMC Genetics, doi:10.1186/s12863-014-0159-7 (2014)
TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells Steinke FC, Yu S, Zhou X, He B, Yang W, Zhou B, Kawamoto H, Zhu J, Tan K8, Xue HH Naturesteinc Immunol. , doi: 10.1038/ni.2897. (2014)
Brain Structural Substrates of Reward Dependence during Behavioral Performance Dayan E, Hamann JM, Averbeck BB, Cohen LG J. Neurosci. , doi: 10.1523/JNEUROSCI.3141-14.2014 (2014)
Early-Onset Stroke and Vasculopathy Associated with Mutations in ADA2 Zhou Q, Yang D, Ombrello AK, et al. N. Engl. J. Med. , doi: 10.1056/NEJMoa1307361 (2014)

Modern perspectives on numerical modeling of cardiac pacemaker cell Maltsev VA, Yaniv Y, Maltsev AV, Stern MD, Lakatta EG J. Pharmacological Sci. , doi://10.1254/jphs.13R04CR (2014)
Risk estimation using probability machines. Dasgupta A1, Szymczak S, Moore JH, Bailey-Wilson JE, Malley JD BioData Min. , doi: 10.1186/1756-0381-7-2. (2014)
Rbfox3 controls the biogenesis of a subset of microRNAs Kim KK, Yang Y, Zhu J, Adelstein RS, Kawamoto S. Nat Struct Mol Biol., doi: 10.1038/nsmb.2892 (2014)
Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies Pilar Cossio and Gerhard Hummer J Struct Biol. , doi: 10.1016/j.jsb.2013.10.006 (2014)
Valence-specific effects of BDNF Val66Met polymorphism on dopaminergic stress and reward processing in humans Peciña M, Martìnez-Jauand M, Love T, Heffernan J, Montoya P, Hodgkinson C, Stohler CS, Goldman D, Zubieta JK. J. Neurosci., doi: 10.1523/JNEUROSCI.2152-13 (2014)
Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture Markus M. Rinschen, Caroline Pahmeyer, Trairak Pisitkun, Nicole Schnell, Xiongwu Wu, Martina Maa, Malte P. Bartram, Tobias Lamkemeyer, Bernhard Schermer, Thomas Benzing andPaul T. Brinkkoetter Proteomics, DOI: 10.1002/pmic.201400235 (2014)

A Systems Genetics Approach Identifies CXCL14, ITGAX, and LPCAT2 as Novel Aggressive Prostate Cancer Susceptibility Genes Kendra A. Williams, Minnkyong Lee, Ying Hu et al. PLoS Genetics, doi: 10.1371/journal.pgen.1004809 (2014)
Charge Neutralization of the Central Lysine Cluster in Prion Protein (PrP) Promotes PrPSc-Like Folding of Recombinant PrP Amyloids Bradley R. Groveman, Allison Kraus, Lynne D. Raymond, Michael A. Dolan, Kelsie J. Anson, David W. Dorward and Byron Caughey J. Biol. Chem. , doi: 10.1074/jbc.M114.619627 (2014)
Pathogenic Ischemic Stroke Phenotypes in the NINDS-Stroke Genetics Network Hakan Ay, Ethem Murat Arsava et al. Stroke, doi: 10.1161/STROKEAHA.114.007362 (2014)
Variant GADL1 and response to lithium in bipolar I disorder Consortium on Lithium Genetics, Hou L, Heilbronner U, Rietschel M, Kato T, Kuo PH, McMahon FJ, Schulze TG. N. Engl. J. Med. , doi: 10.1056/NEJMc1401817#SA4 (2014)
Investigation of the interactions between the EphB2 receptor and SNEW peptide variants Buyong Ma, Stephanie Kolb, Michael Diprima, Molleshree Karna, Giovanna Tosato, Qiqi Yang, Qiang Huang, and Ruth Nussinov Growth Factors, DOI: 10.3109/08977194.2014.985786 (2014)
Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports Joel R. Meyerson, Prashant Rao, Janesh Kumar, Sagar Chittori, Soojay Banerjee, Jason Pierson, Mark L. Mayer & Sriram Subramaniam Nature, doi:10.1038/srep07084 (2014)

Diversity and dynamics of the Drosophila transcriptome. Brown JB, Boley N, Eisman R, May GE et al Nature, doi:10.1038/nature12962 (2014)
Database of osmoregulated proteins in mammalian cells Cameron R. Grady , Mark A. Knepper , Maurice B. Burg , Joan D. Ferraris Physiological Reports, DOI: 10.14814/phy2.12180 (2014)
Simple subgroup approximations to optimal treatment regimes from randomized clinical trial data Jared C. Foster, Jeremy M.G. Taylor, Niko Kaciroti and Bin Nan Biostatistics, doi: 10.1093/biostatistics/kxu049 (2014)
Mitochondrial DNA Sequence Variation Associated With Peripheral Nerve Function in the Elderly Shana M. Katzman, Elsa S. Strotmeyer, Michael A. Nalls et al. J. Gerontology A, doi: 10.1093/gerona/glu175 (2014)
Role of solvation in pressure-induced helix stabilization Robert B. Best, Cayla Miller and Jeetain Mittal J. Chem. Physics, doi:///10.1063/1.4901112 (2014)
Mass spectrometry based protein identification with accurate statistical significance assignment Gelio Alves and Yi-Kuo Yu Bioinformatics, doi: 10.1093/bioinformatics/btu717 (2014)
Modeling vocalization with ECoG cortical activity recorded during vocal production in the macaque monkey Makoto Fukushima, Richard C Saunders, Naotaka Fujii, Bruno B Averbeck, Mortimer Mishkin Engineering in Medicine and Biology, DOI://10.1109/EMBC.2014.6945188 (2014)
DNA recombination. Recombination initiation maps of individual human genomes Pratto, F; Brick, K; Khil, P; Smagulova, F; Petukhova, GV; Camerini-Otero, RD; Science, DOI://10.1126/science.1256442 (2014)
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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)

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants Parker, SC; Stitzel, ML; Taylor, DL et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1317023110 (2013)
Using exome sequencing to reveal mutations in TREM2 presenting as a frontotemporal dementia-like syndrome without bone involvement Guerreiro, RJ; Lohmann, E; Brás, JM et al. JAMA Neurol, DOI://10.1001/jamaneurol.2013.579 (2013)
Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion Huyghe, JR; Jackson, AU; Fogarty, MP et al. Nat. Genet., DOI://10.1038/ng.2507 (2013)
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data Fahad Saeed, Trairak Pisitkun, Jason D Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek and Mark A Knepper Proteome Sci. , doi: 10.1186/1477-5956-11-S1-S14 (2013)
Molecular insights into the reversible formation of tau protein fibrils Yin Luo, Paul Dinkel, Xiang Yu, Martin Margittai, Jie Zheng, Ruth Nussinov, Guanghong Wei and Buyong Ma Chem. Commun., DOI: 10.1039/C3CC00241A (2013)
Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation Kyong-Rim Kieffer-Kwon, Zhonghui Tang, Ewy Mathe et al. Cell, doi://10.1016/j.cell.2013.11.039 (2013)

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki) David Sturgill, John H Malone, Xia Sun, Harold E Smith, Leonard Rabinow, Marie-Laure Samson and Brian Oliver BMC Bioinformatics, doi:10.1186/1471-2105-14-320 (2013)
Theta band activity in response to emotional expressions and its relationship with gamma band activity as revealed by MEG and advanced beamformer source imaging Qian Luo, Xi Cheng, Tom Holroyd, Duo Xu, Frederick W. Carver and James Blair Frontiers in Human Neuroscience, doi: 10.3389/fnhum.2013.00940 (2013)
Overfitting, generalization, and MSE in class probability estimation with high-dimensional data Kyung In Kim, Richard Simon Biometric Journal, DOI: 10.1002/bimj.201300083 (2013)
Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain Young Jun Seo, Lisa Muench, Alicia Reid, Jinzhu Chen, Yeona Kang, Jacob M. Hooker, Nora D. Volkow, Joanna S. Fowler, Sung Won Kim Bioorganic and Medicinal Chemistry Letters 23:6700-6705 (2013)
An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease Farhoud Faraji, Ying Hu, Gang Wu, Natalie E. Goldberger, Renard C. Walker, Jinghui Zhang and Kent W. Hunter Genome Research, doi: 10.1101/gr.166223.113 (2013)
Efficacy of Cyclin Dependent Kinase 4 Inhibitors as Potent Neuroprotective Agents against Insults Relevant to Alzheimer's Disease Priyankar Sanphui, Sumit Kumar Pramanik, Nandini Chatterjee, Ponnusamy Moorthi, Biswadip Banerji, Subhas Chandra Biswas PLoS One, doi: 10.1371/journal.pone.0078842 (2013)

Multiple Transport-Active Binding Sites Are Available for a Single Substrate on Human P-Glycoprotein (ABCB1) Eduardo E. Chufan, Khyati Kapoor, Hong-May Sim, Satyakam Singh, Tanaji T. Talele, Stewart R. Durell, Suresh V. Ambudkar PLoS One, DOI: 10.1371/journal.pone.0082463 (2013)
Prediction of the location and size of the stomach using patient characteristics for retrospective radiation dose estimation following radiotherapy Stephanie Lamart, Rebecca Imran, Steven L Simon, Kazutaka Doi, Lindsay M Morton, Rochelle E Curtis, Choonik Lee, Vladimir Drozdovitch, Roberto Maass-Moreno, Clara C Chen, Millie Whatley, Donald L Miller, Karel Pacak and Choonsik Lee Physics in Medicine and Biology, doi:10.1088/0031-9155/58/24/8739 (2013)
Optimization of virus detection in cells using massively parallel sequencing Shasta D. McClenahan, Christine Uhlenhaut, Philip R. Krause Biologicals, DOI://10.1016/j.biologicals.2013.11.002 (2013)
Whole exome sequencing identifies variation in CYB5A and RNF10 associated with adiposity and type 2 diabetes. Huang K, Nair AK, Muller YL, Piaggi P, Bian L, Del Rosario M, Knowler WC, Kobes S, Hanson RL, Bogardus C, Baier LJ. Obesity, doi: 10.1002/oby.20647 (2013)
Antimicrobial activity of eugenol and cinnamaldehyde against extended spectrum beta lactamase producing enterobacteriaceae by in vitro and molecular docking analysis Lena Dhara, Anusri Tripathi Eur.J.Integrative Med., 10.1016/j.eujim.2013.08.005 (2013)
Efficient logistic regression designs under an imperfect population identifier Paul S. Albert, Aiyi Liu, Tonja Nansel Biometrics, DOI: 10.1111/biom.12106 (2013)

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu J. Am. Soc. for Mass Spectrometry, doi://10.1007/s13361-013-0733-7 (2013)
Vitamin D-Binding Protein and Vitamin D Status of Black Americans and White Americans Camille E. Powe, , Michele K. Evans, Julia Wenger, Alan B. Zonderman, Anders H. Berg, Michael Nalls, Hector Tamez, Dongsheng Zhang, Ishir Bhan, S. Ananth Karumanchi, Neil R. Powe, and Ravi Thadhani New England J. Medicine, DOI: 10.1056/NEJMoa1306357 (2013)
PW02-001 - Exome sequencing for autoinflammatory disorders SE Boyden, Q Zhou, I Aksentijevich and DL Kastner Pediatric Rheumatology, doi:10.1186/1546-0096-11-S1-A141 (2013)
Endogenous Carbamylation of Renal Medullary Proteins J'Neka S. Claxton, Pablo C. Sandoval, Gary Liu, Chung-Lin Chou, Jason D. Hoffert, and Mark A. Knepper PLoS One, doi: 10.1371/journal.pone.0082655 (2013)
Interpreting the effects of altered brain anatomical connectivity on fMRI functional connectivity: a role for computational neural modeling Barry Horwitz, Chuhern Hwang, and Jeff Alstott Frontiers in Human Neuroscience, doi: 10.3389/fnhum.2013.00649 (2013)
Shared Genetic Susceptibility to Ischemic Stroke and Coronary Artery Disease Dichgans, Malik et al. Stroke, doi: 10.1161/STROKEAHA.113.002707 (2013)

Mtr4-like Protein Coordinates Nuclear RNA Processing for Heterochromatin Assembly and for Telomere Maintenance Nathan N. Lee, Venkata R. Chalamcharla, Francisca Reyes-Turcu, Sameet Mehta, Martin Zofall, Vanivilasini Balachandran, Jothy Dhakshnamoorthy, Nitika Taneja, Soichiro Yamanaka, 5, Ming Zhou, Shiv I.S. Grewal Cell, doi://10.1016/j.cell.2013.10.027 (2013)
Testing multiple biological mediators simultaneously Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore and Joshua N. Sampson Bioinformatics, doi: 10.1093/bioinformatics/btt633 (2013)
Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data Sandro Bottaro, Kresten Lindorff-Larsen, and Robert B. Best J. Chem. Theory and Computation, DOI: 10.1021/ct400730n (2013)
Mechanism of Membrane Permeation Induced by Synthetic β-Hairpin Peptides Kshitij Gupta, Hyunbum Jang, Kevin Harlen, Anu Puri, Ruth Nussinov, Joel P. Schneider, Robert Blumenthal Biophys. J. , doi: 10.1016/j.bpj.2013.09.040 (2013)
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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)