Papers that used NIH HPC Systems resources

Papers that used Biowulf or Helix 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

2020 to date (28 papers)

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 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)
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)

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)
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)
Mammalian Surface Display Screening of Diverse Cystine-Dense Peptide Libraries for Difficult-to-Drug Targets Crook, ZR; Sevilla, GP; Mhyre, AJ; Olson, JM; Methods Mol. Biol., DOI://10.1007/978-1-4939-9853-1_21 (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)

2019 (399 papers)

A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests Chen, G; Cox, RW; Glen, DR; Rajendra, JK; Reynolds, RC; Taylor, PA; Hum Brain Mapp, DOI://10.1002/hbm.24399 (2019)

Modeling ligand docking to RNA in the design of RNA-based nanostructures Kasprzak, WK; Ahmed, NA; Shapiro, BA; Curr. Opin. Biotechnol., DOI://10.1016/j.copbio.2019.10.010 (2019)
Integrating Hi-C links with assembly graphs for chromosome-scale assembly Ghurye, J; Rhie, A; Walenz, BP et al. PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1007273 (2019)
Magnetoencephalographic Correlates of Suicidal Ideation in Major Depression Gilbert, JR; Ballard, ED; Galiano, CS; Nugent, AC; Zarate, CA; Biol Psychiatry Cogn Neurosci Neuroimaging, DOI://10.1016/j.bpsc.2019.11.011 (2019)
Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis Korrapati, S; Taukulis, I; Olszewski, R et al. Front Mol Neurosci, DOI://10.3389/fnmol.2019.00316 (2019)
Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods Hu, X; Compton, JR; Legler, PM; J Vis Exp, DOI://10.3791/60421 (2019)
Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells Magen, A; Nie, J; Ciucci, T et al. Cell Rep, DOI://10.1016/j.celrep.2019.10.131 (2019)

Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal Kaya KD, Chen HY, Brooks MJ et al Mol Vis (2019)
Novel Protease Inhibitors Containing C-5-Modified bis-Tetrahydrofuranylurethane and Aminobenzothiazole as P2 and P2' Ligands That Exert Potent Antiviral Activity against Highly Multidrug-Resistant HIV-1 with a High Genetic Barrier against the Emergence of Drug Resistance Takamatsu, Y; Aoki, M; Bulut, H et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.00372-19 (2019)
Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores Shao, Y; Mei, Y; Sundholm, D; Kaila, VRI; J Chem Theory Comput, DOI://10.1021/acs.jctc.9b00823 (2019)
Novel Central Nervous System (CNS)-Targeting Protease Inhibitors for Drug-Resistant HIV Infection and HIV-Associated CNS Complications Amano, M; Salcedo-Gómez, PM; Yedidi, RS et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.00466-19 (2019)
HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry Gourh, P; Safran, SA; Alexander, T et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1906593116 (2019)
Maternal fatty acid concentrations and newborn DNA methylation Robinson, SL; Mumford, SL; Guan, W et al. Am. J. Clin. Nutr., DOI://10.1093/ajcn/nqz311 (2019)

DHHC20 Palmitoyl-Transferase Reshapes the Membrane to Foster Catalysis Stix, R; Song, J; Banerjee, A; Faraldo-Gómez, JD; Biophys. J., DOI://10.1016/j.bpj.2019.11.003 (2019)
Analysis of ordered composite endpoints Follmann, D; Fay, MP; Hamasaki, T; Evans, S; Stat Med, DOI://10.1002/sim.8431 (2019)
Large-scale state-dependent membrane remodeling by a transporter protein Zhou, W; Fiorin, G; Anselmi, C et al. Elife, DOI://10.7554/eLife.50576 (2019)
CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes Dalgleish, JL; Wang, Y; Zhu, J; Meltzer, PS; Cancer Inform, DOI://10.1177/1176935119890290 (2019)
Identification of 102 Correlations between Serum Metabolites and Habitual Diet in a Metabolomics Study of the Prostate, Lung, Colorectal, and Ovarian Cancer Trial Mazzilli, KM; McClain, KM; Lipworth, L et al. J. Nutr., DOI://10.1093/jn/nxz300 (2019)
Permeability of membranes in the liquid ordered and liquid disordered phases Ghysels, A; Krämer, A; Venable, RM et al. Nat Commun, DOI://10.1038/s41467-019-13432-7 (2019)

A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation Vacchio, MS; Ciucci, T; Gao, Y et al. Immunity, DOI://10.1016/j.immuni.2019.06.023 (2019)
SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics Song, L; Liu, A; Shi, J; , ; Bioinformatics, DOI://10.1093/bioinformatics/btz176 (2019)
Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates Rawi, R; Mall, R; Shen, CH et al. Sci Rep, DOI://10.1038/s41598-019-50635-w (2019)
Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence Iranzo, J; Wolf, YI; Koonin, EV; Sela, I; Nat Commun, DOI://10.1038/s41467-019-13429-2 (2019)
Mash Screen: high-throughput sequence containment estimation for genome discovery Ondov, BD; Starrett, GJ; Sappington, A et al. Genome Biol., DOI://10.1186/s13059-019-1841-x (2019)
The scale-invariant, temporal profile of neuronal avalanches in relation to cortical γ-oscillations Miller, SR; Yu, S; Plenz, D; Sci Rep, DOI://10.1038/s41598-019-52326-y (2019)

Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth Cowan, JE; Malin, J; Zhao, Y et al. Nat Commun, DOI://10.1038/s41467-019-13465-y (2019)
Ca2+-Dependent Switch of Calmodulin Interaction Mode with Tandem IQ Motifs in the Scaffolding Protein IQGAP1 Zhang, M; Li, Z; Jang, H; Hedman, AC; Sacks, DB; Nussinov, R; Biochemistry, DOI://10.1021/acs.biochem.9b00854 (2019)
Contribution of Common Genetic Variants to Familial Aggregation of Disease and Implications for Sequencing Studies Schlafly, A; Pfeiffer, RM; Nagore, E et al. PLoS Genet., DOI://10.1371/journal.pgen.1008490 (2019)
Mechanistic link between right prefrontal cortical activity and anxious arousal revealed using transcranial magnetic stimulation in healthy subjects Balderston, NL; Beydler, EM; Roberts, C et al. Neuropsychopharmacology, DOI://10.1038/s41386-019-0583-5 (2019)
Race-specific alterations in DNA methylation among middle-aged African Americans and Whites with metabolic syndrome Chitrala, KN; Hernandez, DG; Nalls, MA et al. Epigenetics, DOI://10.1080/15592294.2019.1695340 (2019)
A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states Ciancetta, A; Rubio, P; Lieberman, DI; Jacobson, KA; J. Comput. Aided Mol. Des., DOI://10.1007/s10822-019-00246-4 (2019)

Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls Flannick, J; Mercader, JM; Fuchsberger, C et al. Nature, DOI://10.1038/s41586-019-1231-2 (2019)
Knowing What You Know in Brain Segmentation Using Bayesian Deep Neural Networks McClure, P; Rho, N; Lee, JA et al. Front Neuroinform, DOI://10.3389/fninf.2019.00067 (2019)
Commensal microbiota drive the functional diversification of colon macrophages Kang, B; Alvarado, LJ; Kim, T et al. Mucosal Immunol, DOI://10.1038/s41385-019-0228-3 (2019)
Rotamer Jumps, Proton Exchange, and Amine Inversion Dynamics of Dimethylated Lysine Residues in Proteins Resolved by pH-Dependent 1H and 13C NMR Relaxation Dispersion Weininger, U; Modig, K; Ishida, H; Vogel, HJ; Akke, M; J Phys Chem B, DOI://10.1021/acs.jpcb.9b06408 (2019)
Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions Dell'Orso, S; Juan, AH; Ko, KD et al. Development, DOI://10.1242/dev.174177 (2019)
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle Taylor, DL; Jackson, AU; Narisu, N et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1814263116 (2019)

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function Lawlor, N; Márquez, EJ; Orchard, P et al. Cell Rep, DOI://10.1016/j.celrep.2018.12.083 (2019)
Oligonucleotide Preparation Approach for Assembly of DNA Synthons Yantsevich, AV; Shchur, VV; Usanov, SA; SLAS Technol, DOI://10.1177/2472630319850534 (2019)
Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC Oda, H; Beck, DB; Kuehn, HS et al. Front Immunol, DOI://10.3389/fimmu.2019.00479 (2019)
Katanin Grips the β-Tubulin Tail through an Electropositive Double Spiral to Sever Microtubules Zehr, EA; Szyk, A; Szczesna, E; Roll-Mecak, A; Dev. Cell, DOI://10.1016/j.devcel.2019.10.010 (2019)
Bilateral ureteral obstruction is rapidly accompanied by ER stress and activation of autophagic degradation of IMCD proteins including AQP2 Somparn, P; Boonkrai, C; Charngkaew, K et al. Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00113.2019 (2019)
Data augmentation using generative adversarial networks (CycleGAN) to improve generalizability in CT segmentation tasks Sandfort, V; Yan, K; Pickhardt, PJ; Summers, RM; Sci Rep, DOI://10.1038/s41598-019-52737-x (2019)

Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis Singer, JR; Blosser, EG; Zindl, CL et al. Nat. Med., DOI://10.1038/s41591-019-0640-y (2019)
Splicing factor DHX15 affects tp53 and mdm2 expression via alternate splicing and promoter usage McElderry, J; Carrington, B; Bishop, K et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddz261 (2019)
Tango1 coordinates the formation of ER/Golgi docking sites to mediate secretory granule formation Reynolds, HM; Zhang, L; Tran, DT; Ten Hagen, KG; J. Biol. Chem., DOI://10.1074/jbc.RA119.011063 (2019)
Williams syndrome hemideletion and LIMK1 variation both affect dorsal stream functional connectivity Gregory, MD; Mervis, CB; Elliott, ML et al. Brain, DOI://10.1093/brain/awz323 (2019)
Reducing motion sensitivity in 3D high-resolution T2*-weighted MRI by navigator-based motion and nonlinear magnetic field correction Liu, J; van Gelderen, P; de Zwart, JA; Duyn, JH; Neuroimage, DOI://10.1016/j.neuroimage.2019.116332 (2019)
Dose coefficients of percentile-specific computational phantoms for photon external exposures Yeom, YS; Han, H; Choi, C; Shin, B; Kim, CH; Lee, C; Radiat Environ Biophys, DOI://10.1007/s00411-019-00818-w (2019)

Characteristics of respiratory measures in young adults scanned at rest, including systematic changes and "missed" deep breaths Power, JD; Lynch, CJ; Dubin, MJ; Silver, BM; Martin, A; Jones, RM; Neuroimage, DOI://10.1016/j.neuroimage.2019.116234 (2019)
Impact of CMV Infection on Natural Killer Cell Clonal Repertoire in CMV-Naïve Rhesus Macaques Truitt, LL; Yang, D; Espinoza, DA et al. Front Immunol, DOI://10.3389/fimmu.2019.02381 (2019)
Prepontine non-giant neurons drive flexible escape behavior in zebrafish Marquart, GD; Tabor, KM; Bergeron, SA; Briggman, KL; Burgess, HA; PLoS Biol., DOI://10.1371/journal.pbio.3000480 (2019)
Approximation of Bias and Mean Squared Error in Two-sample Mendelian Randomization Analyses Deng, L; Zhang, H; Song, L; Yu, K; Biometrics, DOI://10.1111/biom.13169 (2019)
AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing Bhattacharya, T; Brettin, T; Doroshow, JH et al. Front Oncol, DOI://10.3389/fonc.2019.00984 (2019)
Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy Conlan, S; Lau, AF; Deming, C et al. MBio, DOI://10.1128/mBio.00652-19 (2019)

Stereotyped transcriptomic transformation of somatosensory neurons in response to injury Nguyen, MQ; Le Pichon, CE; Ryba, N; Elife, DOI://10.7554/eLife.49679 (2019)
Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides information on structure and stoichiometry Celia, H; Botos, I; Ni, X et al. Commun Biol, DOI://10.1038/s42003-019-0604-2 (2019)
Single-Cell RNA-seq Identifies Cell Diversity in Embryonic Salivary Glands Sekiguchi, R; Martin, D; , ; Yamada, KM; J. Dent. Res., DOI://10.1177/0022034519883888 (2019)
Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms Yoon, Y; Klomp, J; Martin-Martin, I et al. Elife, DOI://10.7554/eLife.46711 (2019)
Differential Nucleosome Spacing in Neurons and Glia Clark, SC; Chereji, RV; Lee, PR; Fields, RD; Clark, DJ; Neurosci. Lett., DOI://10.1016/j.neulet.2019.134559 (2019)
Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo Brooks, MJ; Chen, HY; Kelley, RA et al. Stem Cell Reports, DOI://10.1016/j.stemcr.2019.09.009 (2019)

Gata2 deficiency delays leukemogenesis while contributing to aggressive leukemia phenotype in Cbfb-MYH11 knockin mice Saida, S; Zhen, T; Kim, E et al. Leukemia, DOI://10.1038/s41375-019-0605-7 (2019)
Cell Type- and Sex-Dependent Transcriptome Profiles of Rat Anterior Pituitary Cells Fletcher, PA; Smiljanic, K; Maso Prévide, R et al. Front Endocrinol (Lausanne), DOI://10.3389/fendo.2019.00623 (2019)
Differences in Genome-wide DNA Methylation Profiles in Breast Milk by Race and Lactation Duration Davis Lynn, BC; Bodelon, C; Pfeiffer, RM et al. Cancer Prev Res (Phila), DOI://10.1158/1940-6207.CAPR-19-0169 (2019)
Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size Gerganova, V; Floderer, C; Archetti, A et al. Elife, DOI://10.7554/eLife.45983 (2019)
Strong dependence of the nano-bio interactions on core morphology and layer composition of ultrasmall nanostructures Hassan, SA J Chem Phys, DOI://10.1063/1.5115192 (2019)
Discovery and Development of Anti-HIV Therapeutic Agents: Progress Towards Improved HIV Medication Maeda, K; Das, D; Kobayakawa, T; Tamamura, H; Takeuchi, H; Curr Top Med Chem, DOI://10.2174/1568026619666190712204603 (2019)

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics Fiorin, G; Marinelli, F; Faraldo-Gómez, JD; J Comput Chem, DOI://10.1002/jcc.26075 (2019)
Clonal tracking of erythropoiesis in rhesus macaques Fan, X; Wu, C; Truitt, LL et al. Haematologica, DOI://10.3324/haematol.2019.231811 (2019)
Molecular Classification of Epithelial Ovarian Cancer Based on Methylation Profiling: Evidence for Survival Heterogeneity Bodelon, C; Killian, JK; Sampson, JN et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-18-3720 (2019)
Layer-dependent activity in human prefrontal cortex during working memory Finn, ES; Huber, L; Jangraw, DC; Molfese, PJ; Bandettini, PA; Nat. Neurosci., DOI://10.1038/s41593-019-0487-z (2019)
Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution Justice, AE; Karaderi, T; Highland, HM et al. Nat. Genet., DOI://10.1038/s41588-018-0334-2 (2019)
Dynamic Emergence of Mismatch Repair Deficiency Facilitates Rapid Evolution of Ceftazidime-Avibactam Resistance in Pseudomonas aeruginosa Acute Infection Khil, PP; Dulanto Chiang, A; Ho, J et al. MBio, DOI://10.1128/mBio.01822-19 (2019)

Drosophila Heterochromatin Stabilization Requires the Zinc-Finger Protein Small Ovary Benner, L; Castro, EA; Whitworth, C et al. Genetics, DOI://10.1534/genetics.119.302590 (2019)
Dual antagonist of cIAP/XIAP ASTX660 sensitizes HPV-and HPV+ head and neck cancers to TNFα, TRAIL, and radiation Therapy Xiao, R; An, Y; Ye, W et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-18-3802 (2019)
Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers Henderson, CA; Rail, CA; Butt, LE; Vincent, HA; Callaghan, AJ; Methods, DOI://10.1016/j.ymeth.2019.04.021 (2019)
Gene-based association analysis of survival traits via functional regression-based mixed effect cox models for related samples Chiu, CY; Zhang, B; Wang, S et al. Genet. Epidemiol., DOI://10.1002/gepi.22254 (2019)
Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan Trovão, NS; Khuri-Bulos, N; Tan, Y et al. Microb Genom, DOI://10.1099/mgen.0.000292 (2019)
A Novel Bromine-Containing Paroxetine Analogue Provides Mechanistic Clues for Binding Ambiguity at the Central Primary Binding Site of the Serotonin Transporter Slack, RD; Abramyan, AM; Tang, H et al. ACS Chem Neurosci, DOI://10.1021/acschemneuro.9b00375 (2019)

Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer Hennigan, ST; Trostel, SY; Terrigino, NT et al. JCO Precis Oncol, DOI://10.1200/PO.19.00176 (2019)
Automated Liver Fat Quantification at Nonenhanced Abdominal CT for Population-based Steatosis Assessment Graffy, PM; Sandfort, V; Summers, RM; Pickhardt, PJ; Radiology, DOI://10.1148/radiol.2019190512 (2019)
lncRNA expression predicts mRNA abundance Pacholewska, A; Sung, MH; Epigenomics, DOI://10.2217/epi-2019-0003 (2019)
Quantitative MNase-seq accurately maps nucleosome occupancy levels Chereji, RV; Bryson, TD; Henikoff, S; Genome Biol., DOI://10.1186/s13059-019-1815-z (2019)
Synthesis and Characterization of Bodipy-FL-Cyclosporine A as a Substrate for Multidrug Resistance-Linked P-Glycoprotein (ABCB1) Sajid, A; Raju, N; Lusvarghi, S; Vahedi, S; Swenson, RE; Ambudkar, SV; Drug Metab. Dispos., DOI://10.1124/dmd.119.087734 (2019)
Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation Chereji, RV; Eriksson, PR; Ocampo, J; Prajapati, HK; Clark, DJ; Genome Res., DOI://10.1101/gr.249326.119 (2019)

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Chittori, S; Hong, J; Bai, Y; Subramaniam, S; Nucleic Acids Res., DOI://10.1093/nar/gkz670 (2019)
De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia Kanca, O; Andrews, JC; Lee, PT et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2019.06.014 (2019)
A Monte Carlo model for organ dose reconstruction of patients in Pencil Beam Scanning (PBS) proton therapy for epidemiologic studies of late effects Yeom, YS; Kuzmin, G; Griffin, KT et al. J Radiol Prot, DOI://10.1088/1361-6498/ab437d (2019)
NMR characterization of rearranged staurosporine aglycone analogues from the marine sponge Damiria sp Tran, TD; Cartner, LK; Bokesch, HR et al. Magn Reson Chem, DOI://10.1002/mrc.4932 (2019)
The Spodoptera frugiperda Sf9 cell line is a heterogeneous population of rhabdovirus-infected and virus-negative cells: Isolation and characterization of cell clones containing rhabdovirus X-gene variants and virus-negative cell clones Ma, H; Nandakumar, S; Bae, EH; Chin, PJ; Khan, AS; Virology, DOI://10.1016/j.virol.2019.08.001 (2019)
Genome-wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between cytosine-phosphate-guanine methylation and histological subtypes Fiedler, D; Hirsch, D; El Hajj, N et al. Genes Chromosomes Cancer, DOI://10.1002/gcc.22787 (2019)

The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin Jang, H; Banerjee, A; Marcus, K et al. Structure, DOI://10.1016/j.str.2019.08.009 (2019)
Imaging the spontaneous flow of thought: Distinct periods of cognition contribute to dynamic functional connectivity during rest Gonzalez-Castillo, J; Caballero-Gaudes, C; Topolski, N; Handwerker, DA; Pereira, F; Bandettini, PA; Neuroimage, DOI://10.1016/j.neuroimage.2019.116129 (2019)
Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models Cladel, NM; Jiang, P; Li, JJ et al. Emerg Microbes Infect, DOI://10.1080/22221751.2019.1637072 (2019)
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Synaptic potentiation and rapid antidepressant response to ketamine in treatment-resistant major depression: A replication study Nugent, AC; Wills, KE; Gilbert, JR; Zarate, CA; Psychiatry Res Neuroimaging, DOI://10.1016/j.pscychresns.2018.09.001 (2019)
Biophysical mechanisms in the mammalian respiratory oscillator re-examined with a new data-driven computational model Phillips, RS; John, TT; Koizumi, H; Molkov, YI; Smith, JC; Elife, DOI://10.7554/eLife.41555 (2019)
A Bayesian hierarchical logistic regression model of multiple informant family health histories Lin, J; Myers, MF; Koehly, LM; Marcum, CS; BMC Med Res Methodol, DOI://10.1186/s12874-019-0700-5 (2019)
Automated Computational Detection, Quantitation, and Mapping of Mitosis in Whole-Slide Images for Clinically Actionable Surgical Pathology Decision Support Puri, M; Hoover, SB; Hewitt, SM et al. J Pathol Inform, DOI://10.4103/jpi.jpi_59_18 (2019)
Control and Regulation of Substrate Selection in Cytoplasmic and Mitochondrial Catabolic Networks. A Systems Biology Analysis Cortassa, S; Aon, MA; Sollott, SJ; Front Physiol, DOI://10.3389/fphys.2019.00201 (2019)
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination Ocampo, J; Chereji, RV; Eriksson, PR; Clark, DJ; Genome Res., DOI://10.1101/gr.242032.118 (2019)

The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila Bag, I; Dale, RK; Palmer, C; Lei, EP; J. Cell. Sci., DOI://10.1242/jcs.226092 (2019)
Brain Mechanisms of Attention Orienting Following Frustration: Associations With Irritability and Age in Youths Tseng, WL; Deveney, CM; Stoddard, J et al. Am J Psychiatry, DOI://10.1176/appi.ajp.2018.18040491 (2019)
Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification Ku, WL; Nakamura, K; Gao, W et al. Nat. Methods, DOI://10.1038/s41592-019-0361-7 (2019)
Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells Yost, KE; Clatterbuck Soper, SF; Walker, RL et al. Sci Rep, DOI://10.1038/s41598-019-41058-8 (2019)
Subset testing and analysis of multiple phenotypes Derkach, A; Pfeiffer, RM; Genet. Epidemiol., DOI://10.1002/gepi.22199 (2019)
CMCdG, a Novel Nucleoside Analog with Favorable Safety Features, Exerts Potent Activity against Wild-Type and Entecavir-Resistant Hepatitis B Virus Higashi-Kuwata, N; Hayashi, S; Das, D et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.02143-18 (2019)

Semi-Automated 3D Segmentation of Human Skeletal Muscle Using Focused Ion Beam-Scanning Electron Microscopic Images Caffrey, B; Maltsev, AV; Gonzalez-Freire, M; Hartnell, LM; Ferrucci, L; Subramaniam, S; J. Struct. Biol., DOI://10.1016/j.jsb.2019.03.008 (2019)
Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data Clark, JZ; Chen, L; Chou, CL; Jung, HJ; Lee, JW; Knepper, MA; Kidney Int., DOI://10.1016/j.kint.2018.11.028 (2019)
Activity and structural analysis of GRL-117C: a novel small molecule CCR5 inhibitor active against R5-tropic HIV-1s Nakata, H; Maeda, K; Das, D et al. Sci Rep, DOI://10.1038/s41598-019-41080-w (2019)
Cloning and characterization of a novel aspartate/glutamate racemase from the acorn worm Saccoglossus kowalevskii Uda, K; Ishizuka, N; Edashige, Y; Kikuchi, A; Radkov, AD; Moe, LA; Comp. Biochem. Physiol. B, Biochem. Mol. Biol., DOI://10.1016/j.cbpb.2019.03.006 (2019)
Inactivating Mutation in IRF8 Promotes Osteoclast Transcriptional Programs and Increases Susceptibility to Tooth Root Resorption Thumbigere-Math, V; Foster, BL; Bachu, M et al. J. Bone Miner. Res., DOI://10.1002/jbmr.3690 (2019)
S Values for neuroimaging procedures on Korean pediatric and adult head computational phantoms Villoing, D; Lee, AK; Choi, HD; Lee, C; Radiat Prot Dosimetry, DOI://10.1093/rpd/ncy287 (2019)

Population-based opportunistic osteoporosis screening: Validation of a fully automated CT tool for assessing longitudinal BMD changes Pickhardt, PJ; Lee, SJ; Liu, J et al. Br J Radiol, DOI://10.1259/bjr.20180726 (2019)
Genetic overlap between birthweight and adult cardiometabolic diseases has implications for genomic medicine Tekola-Ayele, F; Lee, A; Workalemahu, T et al. Sci Rep, DOI://10.1038/s41598-019-40834-w (2019)
Accounting for random observation time in risk prediction with longitudinal markers: An imputation approach Han, Y; Liu, D; Stat Methods Med Res, DOI://10.1177/0962280219833089 (2019)
Genomic deletions upstream of lamin B1 lead to atypical autosomal dominant leukodystrophy Nmezi, B; Giorgio, E; Raininko, R et al. Neurol Genet, DOI://10.1212/NXG.0000000000000305 (2019)
NELFE-Dependent MYC Signature Identifies a Unique Cancer Subtype in Hepatocellular Carcinoma Dang, H; Pomyen, Y; Martin, SP et al. Sci Rep, DOI://10.1038/s41598-019-39727-9 (2019)
Synthesis and evaluation of two new candidate high-affinity full agonist PET radioligands for imaging 5-HT1B receptors Lindberg, A; Lu, S; Nag, S et al. Nucl. Med. Biol., DOI://10.1016/j.nucmedbio.2019.01.005 (2019)

An insight into the sialotranscriptome and virome of Amazonian anophelines Scarpassa, VM; Debat, HJ; Alencar, RB et al. BMC Genomics, DOI://10.1186/s12864-019-5545-0 (2019)
Phosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells Limbutara, K; Kelleher, A; Yang, CR; Raghuram, V; Knepper, MA; Sci Rep, DOI://10.1038/s41598-019-39116-2 (2019)
Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase Anderson, CJ; Baird, MR; Hsu, A et al. Cell Rep, DOI://10.1016/j.celrep.2019.01.058 (2019)
DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers Das, S; Deng, X; Camphausen, K; Shankavaram, U; Bioinformatics, DOI://10.1093/bioinformatics/bty673 (2019)
Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting Chauhan, G; Adams, HHH; Satizabal, CL et al. Neurology, DOI://10.1212/WNL.0000000000006851 (2019)
Isothermal Titration Calorimetry of Be2+ with Phosphatidylserine Models Guides All-Atom Force-Field Development for LipidIon Interactions Leonard, AN; Klauda, JB; Sukharev, S; J Phys Chem B, DOI://10.1021/acs.jpcb.8b11884 (2019)

The transcription factor c-Myb regulates CD8+ T cell stemness and antitumor immunity Gautam, S; Fioravanti, J; Zhu, W et al. Nat. Immunol., DOI://10.1038/s41590-018-0311-z (2019)
Dosimetric Impact of a New Computational Voxel Phantom Series for the Japanese Atomic Bomb Survivors: Children and Adults Griffin, K; Paulbeck, C; Bolch, W et al. Radiat. Res., DOI://10.1667/RR15267.1 (2019)
Nanovesicles Versus Nanoparticle-Supported Lipid Bilayers: Massive Differences in Bilayer Structures and in Diffusivities of Lipid Molecules and Nanoconfined Water Jing, H; Wang, Y; Desai, PR; Ramamurthi, KS; Das, S; Langmuir, DOI://10.1021/acs.langmuir.8b03805 (2019)
ComPaSS-GWAS: A method to reduce type I error in genome-wide association studies when replication data are not available Sabourin, JA; Cropp, CD; Sung, H; Brody, LC; Bailey-Wilson, JE; Wilson, AF; Genet. Epidemiol., DOI://10.1002/gepi.22168 (2019)
Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses Kanekiyo, M; Joyce, MG; Gillespie, RA et al. Nat. Immunol., DOI://10.1038/s41590-018-0305-x (2019)
Spatial Attention Deficits Are Causally Linked to an Area in Macaque Temporal Cortex Bogadhi, AR; Bollimunta, A; Leopold, DA; Krauzlis, RJ; Curr. Biol., DOI://10.1016/j.cub.2019.01.028 (2019)
Memory T cells targeting oncogenic mutations detected in peripheral blood of epithelial cancer patients Cafri, G; Yossef, R; Pasetto, A et al. Nat Commun, DOI://10.1038/s41467-019-08304-z (2019)
Gustatory responses in macaque monkeys revealed with fMRI: Comments on taste, taste preference, and internal state Kaskan, PM; Dean, AM; Nicholas, MA; Mitz, AR; Murray, EA; Neuroimage, DOI://10.1016/j.neuroimage.2018.10.005 (2019)
Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires Bofill-De Ros, X; Kasprzak, WK; Bhandari, Y et al. Cell Rep, DOI://10.1016/j.celrep.2018.12.054 (2019)
Simultaneous targeting of linked loci in mouse embryos using base editing Lee, HK; Willi, M; Smith, HE et al. Sci Rep, DOI://10.1038/s41598-018-33533-5 (2019)
Molecular Dynamics Simulations of Membrane Permeability Venable, RM; Krämer, A; Pastor, RW; Chem. Rev., DOI://10.1021/acs.chemrev.8b00486 (2019)
Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration Ratnapriya, R; Sosina, OA; Starostik, MR et al. Nat. Genet., DOI://10.1038/s41588-019-0351-9 (2019)

Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families Simpson, CL; Musolf, AM; Li, Q et al. BMC Med. Genet., DOI://10.1186/s12881-019-0752-8 (2019)
Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping Tabor, KM; Marquart, GD; Hurt, C et al. Elife, DOI://10.7554/eLife.42687 (2019)
Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP Leone, V; Waclawska, I; Kossmann, K et al. J. Gen. Physiol., DOI://10.1085/jgp.201812111 (2019)
Shared polygenic risk and causal inferences in amyotrophic lateral sclerosis Bandres-Ciga, S; Noyce, AJ; Hemani, G et al. Ann. Neurol., DOI://10.1002/ana.25431 (2019)
Whole Transcriptome Analysis of Renal Intercalated Cells Predicts Lipopolysaccharide Mediated Inhibition of Retinoid X Receptor alpha Function Saxena, V; Fitch, J; Ketz, J et al. Sci Rep, DOI://10.1038/s41598-018-36921-z (2019)
High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue Fujiwara, S; Baek, S; Varticovski, L; Kim, S; Hager, GL; Sci Rep, DOI://10.1038/s41598-018-36927-7 (2019)

Pregnancy-Associated Plasma Protein-A (PAPP-A) in Ewing Sarcoma: Role in Tumor Growth and Immune Evasion Heitzeneder, S; Sotillo, E; Shern, JF et al. J. Natl. Cancer Inst., DOI://10.1093/jnci/djy209 (2019)
The FLT3 inhibitor midostaurin selectively resensitizes ABCB1-overexpressing multidrug-resistant cancer cells to conventional chemotherapeutic agents Hsiao, SH; Lusvarghi, S; Huang, YH; Ambudkar, SV; Hsu, SC; Wu, CP; Cancer Lett., DOI://10.1016/j.canlet.2019.01.001 (2019)
Antimicrobial Chrysophaentin Analogs Identified from Laboratory Cultures of the Marine Microalga Chrysophaeum taylorii Davison, JR; Bewley, CA; J. Nat. Prod., DOI://10.1021/acs.jnatprod.8b00858 (2019)
Distinct Clinical and Pathological Features of Melorheostosis Associated With Somatic MAP2K1 Mutations Jha, S; Fratzl-Zelman, N; Roschger, P et al. J. Bone Miner. Res., DOI://10.1002/jbmr.3577 (2019)
The prevalence of germline DICER1 pathogenic variation in cancer populations Kim, J; Schultz, KAP; Hill, DA; Stewart, DR; Mol Genet Genomic Med, DOI://10.1002/mgg3.555 (2019)
Sequence Variation Associated with SLC12A5 Gene Expression Is Linked to Brain Structure and Function in Healthy Adults Gregory, MD; Kippenhan, JS; Callicott, JH et al. Cereb. Cortex, DOI://10.1093/cercor/bhy344 (2019)
Interleukin-12 receptor β2 from grass carp: Molecular characterization and its involvement in Aeromonas hydrophila-induced intestinal inflammation Song, XH; Tang, J; Gao, TT et al. Fish Shellfish Immunol., DOI://10.1016/j.fsi.2019.01.016 (2019)
Structure and function of an ectopic Polycomb chromatin domain De, S; Cheng, Y; Sun, MA; Gehred, ND; Kassis, JA; Sci Adv, DOI://10.1126/sciadv.aau9739 (2019)
A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing Xie, G; Vo, TV; Thillainadesan, G et al. Nat Commun, DOI://10.1038/s41467-018-08273-9 (2019)
Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology Schwartz, DM; Farley, TK; Richoz, N et al. Immunity, DOI://10.1016/j.immuni.2018.12.014 (2019)
The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok Ciucci, T; Vacchio, MS; Gao, Y et al. Immunity, DOI://10.1016/j.immuni.2018.12.019 (2019)
Next-Generation Sequencing to Diagnose Suspected Genetic Disorders Adams, DR; Eng, CM; N. Engl. J. Med., DOI://10.1056/NEJMc1814955 (2019)
Effect of amino acids on transcription and translation of key genes in E. coli K and B grown at a steady state in minimal medium Baez, A; Kumar, A; Sharma, AK; Anderson, ED; Shiloach, J; N Biotechnol, DOI://10.1016/j.nbt.2018.10.004 (2019)
The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis Baechler, SA; Factor, VM; Dalla Rosa, I et al. Nat Commun, DOI://10.1038/s41467-018-07922-3 (2019)
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 (2019)
Secondary Metabolites from the Fungus Dictyosporium sp. and Their MALT1 Inhibitory Activities Tran, TD; Wilson, BAP; Henrich, CJ et al. J. Nat. Prod., DOI://10.1021/acs.jnatprod.8b00871 (2019)
The phenotypic landscape of a Tbc1d24 mutant mouse includes convulsive seizures resembling human early infantile epileptic encephalopathy Tona, R; Chen, W; Nakano, Y et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy445 (2019)
Early infantile-onset epileptic encephalopathy 28 due to a homozygous microdeletion involving the WWOX gene in a region of uniparental disomy Davids, M; Markello, T; Wolfe, LA et al. Hum. Mutat., DOI://10.1002/humu.23675 (2019)

Interface-Based Structural Prediction of Novel Host-Pathogen Interactions Guven-Maiorov, E; Tsai, CJ; Ma, B; Nussinov, R; Methods Mol. Biol., DOI://10.1007/978-1-4939-8736-8_18 (2019)
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)

2018 (519 papers)

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)
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)
Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics Abramyan, AM; Slack, RD; Meena, S et al. Neuropharmacology, DOI://10.1016/j.neuropharm.2018.10.040 (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)
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)
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SIRT1 is a transcriptional enhancer of the glucocorticoid receptor acting independently to its deacetylase activity Suzuki, S; Iben, JR; Coon, SL; Kino, T; Mol. Cell. Endocrinol., DOI://10.1016/j.mce.2017.09.012 (2018)
Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior Sathyamurthy, A; Johnson, KR; Matson, KJE et al. Cell Rep, DOI://10.1016/j.celrep.2018.02.003 (2018)
A mutational comparison of adult and adolescent and young adult (AYA) colon cancer Tricoli, JV; Boardman, LA; Patidar, R et al. Cancer, DOI://10.1002/cncr.31136 (2018)
Insufficient evidence for pathogenicity of SNCA His50Gln (H50Q) in Parkinson's disease Blauwendraat, C; Kia, DA; Pihlstrøm, L et al. Neurobiol. Aging, DOI://10.1016/j.neurobiolaging.2017.12.012 (2018)
Comprehensive Synthesis of Amino Acid-Derived Thiazole Peptidomimetic Analogues to Understand the Enigmatic Drug/Substrate-Binding Site of P-Glycoprotein Patel, BA; Abel, B; Barbuti, AM et al. J. Med. Chem., DOI://10.1021/acs.jmedchem.7b01340 (2018)

Homeobox transcription factor DLX4 is not necessary for skin development and homeostasis Bhattacharya, S; Duverger, O; Brooks, SR; Morasso, MI; Exp. Dermatol., DOI://10.1111/exd.13503 (2018)
Outcomes of Children and Adolescents with Advanced Hereditary Medullary Thyroid Carcinoma Treated with Vandetanib Kraft, IL; Akshintala, S; Zhu, Y et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-17-2101 (2018)
Feedforward Inhibition Allows Input Summation to Vary in Recurrent Cortical Networks Histed, MH eNeuro, DOI://10.1523/ENEURO.0356-17.2018 (2018)
Effects on gene expression and behavior of untagged short tandem repeats: the case of arginine vasopressin receptor 1a (AVPR1a) and externalizing behaviors Landefeld, CC; Hodgkinson, CA; Spagnolo, PA et al. Transl Psychiatry, DOI://10.1038/s41398-018-0120-z (2018)
Morphometric Similarity Networks Detect Microscale Cortical Organization and Predict Inter-Individual Cognitive Variation Seidlitz, J; Váša, F; Shinn, M et al. Neuron, DOI://10.1016/j.neuron.2017.11.039 (2018)
A multicohort, longitudinal study of cerebellar development in attention deficit hyperactivity disorder Shaw, P; Ishii-Takahashi, A; Park, MT et al. J Child Psychol Psychiatry, DOI://10.1111/jcpp.12920 (2018)

Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH Lee, JW; Alsady, M; Chou, CL et al. Kidney Int., DOI://10.1016/j.kint.2017.06.008 (2018)
Interrogating the Functions of PRDM9 Domains in Meiosis Thibault-Sennett, S; Yu, Q; Smagulova, F et al. Genetics, DOI://10.1534/genetics.118.300565 (2018)
Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation Maziarz, M; Pfeiffer, RM; Wan, Y; Gail, MH; Bioinformatics, DOI://10.1093/bioinformatics/bty297 (2018)
Electrophysiological heterogeneity of pacemaker cells in the rabbit intercaval region, including the SA node: insights from recording multiple ion currents in each cell Monfredi, O; Tsutsui, K; Ziman, B; Stern, MD; Lakatta, EG; Maltsev, VA; Am. J. Physiol. Heart Circ. Physiol., DOI://10.1152/ajpheart.00253.2016 (2018)
Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors Giannelou, A; Wang, H; Zhou, Q et al. Ann. Rheum. Dis., DOI://10.1136/annrheumdis-2017-212401 (2018)
ICE1 promotes the link between splicing and nonsense-mediated mRNA decay Baird, TD; Cheng, KC; Chen, YC et al. Elife, DOI://10.7554/eLife.33178 (2018)

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 (2018)
Somatic activating mutations in MAP2K1 cause melorheostosis Kang, H; Jha, S; Deng, Z et al. Nat Commun, DOI://10.1038/s41467-018-03720-z (2018)
Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient Kouprina, N; Liskovykh, M; Lee, NCO et al. Oncotarget, DOI://10.18632/oncotarget.24567 (2018)
Characterization of clinically used oral antiseptics as quadruplex-binding ligands Calabrese, DR; Zlotkowski, K; Alden, S et al. Nucleic Acids Res., DOI://10.1093/nar/gky084 (2018)
A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope Zhou, T; Zheng, A; Baxa, U et al. Immunity, DOI://10.1016/j.immuni.2018.02.013 (2018)
Statistical power comparisons at 3T and 7T with a GO / NOGO task Torrisi, S; Chen, G; Glen, D et al. Neuroimage, DOI://10.1016/j.neuroimage.2018.03.071 (2018)

Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast Rawal, Y; Chereji, RV; Valabhoju, V et al. Mol. Cell, DOI://10.1016/j.molcel.2018.03.007 (2018)
Deep sequencing of the mitochondrial genome reveals common heteroplasmic sites in NADH dehydrogenase genes Liu, C; Fetterman, JL; Liu, P et al. Hum. Genet., DOI://10.1007/s00439-018-1873-4 (2018)
A Latent Variable Approach to Differentiating Neural Mechanisms of Irritability and Anxiety in Youth Kircanski, K; White, LK; Tseng, WL et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2018.0468 (2018)
The impact of aging on primate hematopoiesis as interrogated by clonal tracking Yu, KR; Espinoza, DA; Wu, C et al. Blood, DOI://10.1182/blood-2017-08-802033 (2018)
Inferring properties of disordered chains from FRET transfer efficiencies Zheng, W; Zerze, GH; Borgia, A; Mittal, J; Schuler, B; Best, RB; J Chem Phys, DOI://10.1063/1.5006954 (2018)
A Novel Method to Extend a Partial-Body CT for the Reconstruction of Dose to Organs beyond the Scan Range Kuzmin, GA; Mille, MM; Jung, JW et al. Radiat. Res., DOI://10.1667/RR14999.1 (2018)

Association of Methylation Signals With Incident Coronary Heart Disease in an Epigenome-Wide Assessment of Circulating Tumor Necrosis Factor α Aslibekyan, S; Agha, G; Colicino, E et al. JAMA Cardiol, DOI://10.1001/jamacardio.2018.0510 (2018)
A method for determining haploid and triploid genotypes and their association with vascular phenotypes in Williams syndrome and 7q11.23 duplication syndrome Gregory, MD; Kolachana, B; Yao, Y et al. BMC Med. Genet., DOI://10.1186/s12881-018-0563-3 (2018)
IL1RN Variation Influences both Disease Susceptibility and Response to Human Recombinant IL-1RA Therapy in Systemic Juvenile Idiopathic Arthritis Arthur, VL; Shuldiner, E; Remmers, EF et al. , DOI://10.1002/art.40498 (2018)
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene Nicolas, A; Kenna, KP; Renton, AE et al. Neuron, DOI://10.1016/j.neuron.2018.02.027 (2018)
Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis Glatz, M; Jo, JH; Kennedy, EA et al. PLoS ONE, DOI://10.1371/journal.pone.0192443 (2018)
Quantification of Human Microbiome Stability Over Six Months: Implications for Epidemiologic Studies Sinha, R; Goedert, JJ; Vogtmann, E et al. Am. J. Epidemiol., DOI://10.1093/aje/kwy064 (2018)

A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity Debnath, S; Kosek, D; Tagad, HD et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001213 (2018)
Default Mode Connectivity in Major Depressive Disorder Measured Up to 10 Days After Ketamine Administration Evans, JW; Szczepanik, J; Brutsché, N; Park, LT; Nugent, AC; Zarate, CA; Biol. Psychiatry, DOI://10.1016/j.biopsych.2018.01.027 (2018)
An Extended Guinier Analysis for Intrinsically Disordered Proteins Zheng, W; Best, RB; J. Mol. Biol., DOI://10.1016/j.jmb.2018.03.007 (2018)
ZFR coordinates crosstalk between RNA decay and transcription in innate immunity Haque, N; Ouda, R; Chen, C; Ozato, K; Hogg, JR; Nat Commun, DOI://10.1038/s41467-018-03326-5 (2018)
Lifestyle, metabolite, and genetic determinants of formate concentrations in a cross-sectional study in young, healthy adults Brosnan, JT; Mills, JL; Ueland, PM et al. Am. J. Clin. Nutr., DOI://10.1093/ajcn/nqx065 (2018)
Shep regulates Drosophila neuronal remodeling by controlling transcription of its chromatin targets Chen, D; Dale, RK; Lei, EP; Development, DOI://10.1242/dev.154047 (2018)

Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association Domanski, J; Sansom, MSP; Stansfeld, PJ; Best, RB; J Chem Theory Comput, DOI://10.1021/acs.jctc.7b00983 (2018)
Metabolic profiles of triple-negative and luminal A breast cancer subtypes in African-American identify key metabolic differences Tayyari, F; Gowda, GAN; Olopade, OF et al. Oncotarget, DOI://10.18632/oncotarget.24433 (2018)
Targeting loss of the Hippo signaling pathway in NF2-deficient papillary kidney cancers Sourbier, C; Liao, PJ; Ricketts, CJ et al. Oncotarget, DOI://10.18632/oncotarget.24112 (2018)
Gestational cytokine concentrations and neurocognitive development at 7 years Ghassabian, A; Albert, PS; Hornig, M et al. Transl Psychiatry, DOI://10.1038/s41398-018-0112-z (2018)
LMTK3 confers chemo-resistance in breast cancer Stebbing, J; Shah, K; Lit, LC et al. Oncogene, DOI://10.1038/s41388-018-0197-0 (2018)
Argonaute2 and LaminB modulate gene expression by controlling chromatin topology Nazer, E; Dale, RK; Chinen, M; Radmanesh, B; Lei, EP; PLoS Genet., DOI://10.1371/journal.pgen.1007276 (2018)

A deep insight into the male and female sialotranscriptome of adult Culex tarsalis mosquitoes Ribeiro, JMC; Martin-Martin, I; Moreira, FR; Bernard, KA; Calvo, E; Insect Biochem. Mol. Biol., DOI://10.1016/j.ibmb.2018.03.001 (2018)
In Vitro Modeling of Human Germ Cell Development Using Pluripotent Stem Cells Zhao, Y; Ye, S; Liang, D et al. Stem Cell Reports, DOI://10.1016/j.stemcr.2018.01.001 (2018)
Evidence of subgroups in smokers as revealed in clinical measures and evaluated by neuroimaging data: a preliminary study Ding, X; Salmeron, BJ; Wang, J; Yang, Y; Stein, EA; Ross, TJ; Addict Biol, DOI://10.1111/adb.12620 (2018)
Co-evolutionary fitness landscapes for sequence design Tian, P; Louis, JM; Baber, JL; Aniana, A; Best, R; Angew. Chem. Int. Ed. Engl., DOI://10.1002/anie.201713220 (2018)
An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors Lu, YC; Zheng, Z; Robbins, PF et al. Mol. Ther., DOI://10.1016/j.ymthe.2017.10.018 (2018)
Mechanism of Darunavir (DRV)'s High Genetic Barrier to HIV-1 Resistance: A Key V32I Substitution in Protease Rarely Occurs, but Once It Occurs, It Predisposes HIV-1 To Develop DRV Resistance Aoki, M; Das, D; Hayashi, H et al. MBio, DOI://10.1128/mBio.02425-17 (2018)

Nanopore sequencing and assembly of a human genome with ultra-long reads Jain, M; Koren, S; Miga, KH et al. Nat. Biotechnol., DOI://10.1038/nbt.4060 (2018)
Impact of time-of-day on diffusivity measures of brain tissue derived from diffusion tensor imaging Thomas, C; Sadeghi, N; Nayak, A et al. Neuroimage, DOI://10.1016/j.neuroimage.2018.02.026 (2018)
Verdazyl-ribose: A new radical for solid-state dynamic nuclear polarization at high magnetic field Thurber, KR; Le, TN; Changcoco, V; Brook, DJR; J. Magn. Reson., DOI://10.1016/j.jmr.2018.02.016 (2018)
Minoxidil improves vascular compliance, restores cerebral blood flow and alters extracellular matrix gene expression in a model of chronic vascular stiffness Knutsen, R; Beeman, SC; Broekelmann, TJ et al. Am. J. Physiol. Heart Circ. Physiol., DOI://10.1152/ajpheart.00683.2017 (2018)
An insight into the salivary gland and fat body transcriptome of Panstrongylus lignarius (Hemiptera: Heteroptera), the main vector of Chagas disease in Peru Nevoa, JC; Mendes, MT; da Silva, MV; Soares, SC; Oliveira, CJF; Ribeiro, JMC; PLoS Negl Trop Dis, DOI://10.1371/journal.pntd.0006243 (2018)
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 (2018)

Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation Meng, F; Bellaiche, MMJ; Kim, JY; Zerze, GH; Best, RB; Chung, HS; Biophys. J., DOI://10.1016/j.bpj.2017.12.025 (2018)
Identification of Casz1 as a Regulatory Protein Controlling T Helper Cell Differentiation, Inflammation, and Immunity Bhaskaran, N; Liu, Z; Saravanamuthu, SS et al. Front Immunol, DOI://10.3389/fimmu.2018.00184 (2018)
GRL-079, a Novel HIV-1 Protease Inhibitor, Is Extremely Potent against Multidrug-Resistant HIV-1 Variants and Has a High Genetic Barrier against the Emergence of Resistant Variants Delino NS, Aoki M, Hayashi H, Hattori SI, Chang SB, Takamatsu Y, Martyr CD, Das D, Ghosh AK, Mitsuya H Antimicrob Agents Chemother. , doi: 10.1128/AAC.02060-17 (2018)
Design and statistical considerations for studies evaluating the efficacy of a single dose of the human papillomavirus (HPV) vaccine Sampson, JN; Hildesheim, A; Herrero, R; Gonzalez, P; Kreimer, A; Gail, MH; Contemp Clin Trials, DOI://10.1016/j.cct.2018.02.010 (2018)
Transcriptional regulation by NR5A2 links differentiation and inflammation in the pancreas Cobo, I; Martinelli, P; Flández, M et al. Nature, DOI://10.1038/nature25751 (2018)
Estimating recurrence and incidence of preterm birth subject to measurement error in gestational age: A hidden Markov modeling approach Albert, PS Stat Med, DOI://10.1002/sim.7624 (2018)

Extreme disorder in an ultrahigh-affinity protein complex Borgia, A; Borgia, MB; Bugge, K et al. Nature, DOI://10.1038/nature25762 (2018)
Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology Howard, BH; Hirai, TH; Russanova, VR; PLoS ONE, DOI://10.1371/journal.pone.0191033 (2018)
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells Hu, G; Cui, K; Fang, D et al. Immunity, DOI://10.1016/j.immuni.2018.01.013 (2018)
Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations Tofoleanu, F; Yuan, Y; Pickard, FC; Tywoniuk, B; Brooks, BR; Buchete, NV; J Phys Chem B, DOI://10.1021/acs.jpcb.7b12083 (2018)
Assessment of PCXMC for patients with different body size in chest and abdominal x ray examinations: a Monte Carlo simulation study Borrego, D; Lowe, EM; Kitahara, CM; Lee, C; Phys Med Biol, DOI://10.1088/1361-6560/aab13e (2018)
Dose coefficients for children and young adolescents exposed to external neutron fields Griffin, KT; Mille, M; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aab126 (2018)

CD63, MHC class 1, and CD47 identify subsets of extracellular vesicles containing distinct populations of noncoding RNAs Kaur, S; Elkahloun, AG; Arakelyan, A et al. Sci Rep, DOI://10.1038/s41598-018-20936-7 (2018)
Transient Receptor Potential Channels TRPM4 and TRPC3 Critically Contribute to Respiratory Motor Pattern Formation but not Rhythmogenesis in Rodent Brainstem Circuits Koizumi, H; John, TT; Chia, JX et al. eNeuro, DOI://10.1523/ENEURO.0332-17.2018 (2018)
Ridding fMRI data of motion-related influences: Removal of signals with distinct spatial and physical bases in multiecho data Power, JD; Plitt, M; Gotts, SJ et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1720985115 (2018)
The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance Yoshimura, T; McLean, MH; Dzutsev, AK et al. J. Immunol., DOI://10.4049/jimmunol.1602073 (2018)
Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance Weingarten, RA; Johnson, RC; Conlan, S et al. MBio, DOI://10.1128/mBio.02011-17 (2018)
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox Müller, F; Cunningham, T; Stookey, S et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1714512115 (2018)

Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling Li, S; Jang, H; Zhang, J; Nussinov, R; Structure, DOI://10.1016/j.str.2018.01.011 (2018)
Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho Brown, JL; Sun, MA; Kassis, JA; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1716299115 (2018)
Precise genome-wide mapping of single nucleosomes and linkers in vivo Chereji, RV; Ramachandran, S; Bryson, TD; Henikoff, S; Genome Biol., DOI://10.1186/s13059-018-1398-0 (2018)
Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer Klein, AP; Wolpin, BM; Risch, HA et al. Nat Commun, DOI://10.1038/s41467-018-02942-5 (2018)
The klotho-related protein KLPH (lctl) has preferred expression in lens and is essential for expression of clic5 and normal lens suture formation Fan, J; Lerner, J; Wyatt, MK et al. Exp. Eye Res., DOI://10.1016/j.exer.2018.02.001 (2018)
Self-reported executive function and hoarding in adults with obsessive-compulsive disorder Samuels, J; Bienvenu, OJ; Krasnow, J et al. Compr Psychiatry, DOI://10.1016/j.comppsych.2017.11.009 (2018)

Sequence determinants of protein phase behavior from a coarse-grained model Dignon, GL; Zheng, W; Kim, YC; Best, RB; Mittal, J; PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1005941 (2018)
Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy VanderWeele, DJ; Finney, R; Katayama, K et al. Eur Urol Focus, DOI://10.1016/j.euf.2018.01.006 (2018)
Extended amygdala connectivity changes during sustained shock anticipation Torrisi, S; Gorka, AX; Gonzalez-Castillo, J et al. Transl Psychiatry, DOI://10.1038/s41398-017-0074-6 (2018)
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2 Ozdemir, ES; Jang, H; Gursoy, A et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001596 (2018)
Binding kinetics of ultrasmall gold nanoparticles with proteins André Lira, Rodrigo Ferreira, Ricardo Torquato, Huaying Zhao, Maria Luiza Oliva, Sergio A. Hassan, Peter Schuck and Alioscka A Sousa Nanoscale, DOI: 10.1039/C7NR06810G (2018)
Cleavage of TL1A Differentially Regulates Its Effects on Innate and Adaptive Immune Cells Ferdinand, JR; Richard, AC; Meylan, F; Al-Shamkhani, A; Siegel, RM; J. Immunol., DOI://10.4049/jimmunol.1700891 (2018)

De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads Eccles, D; Chandler, J; Camberis, M et al. BMC Biol., DOI://10.1186/s12915-017-0473-4 (2018)
Accelerometer-Measured Physical Activity and Sedentary Behavior in Relation to All-Cause Mortality: The Women's Health Study Lee, IM; Shiroma, EJ; Evenson, KR; Kamada, M; LaCroix, AZ; Buring, JE; Circulation, DOI://10.1161/CIRCULATIONAHA.117.031300 (2018)
Altered avalanche dynamics in a developmental NMDAR hypofunction model of cognitive impairment Seshadri, S; Klaus, A; Winkowski, DE; Kanold, PO; Plenz, D; Transl Psychiatry, DOI://10.1038/s41398-017-0060-z (2018)
Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma Zheng, H; Pomyen, Y; Hernandez, MO et al. Hepatology, DOI://10.1002/hep.29778 (2018)
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 (2018)

2017 (396 papers)

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)

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)
Extracellular vesicles, exosomes and shedding vesicles in regenerative medicine - a new paradigm for tissue repair Bjørge, IM; Kim, SY; Mano, JF; Kalionis, B; Chrzanowski, W; Biomater Sci, DOI://10.1039/c7bm00479f (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)
The emerging importance and challenges of the human mycobiome Kong, HH; Morris, A; Virulence, DOI://10.1080/21505594.2017.1279780 (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)
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)
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)

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)
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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)
Immobilized MutS-Mediated Error Removal of Microchip-Synthesized DNA Wan, W; Wang, D; Gao, X; Hong, J; Methods Mol. Biol., DOI://10.1007/978-1-4939-6343-0_17 (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 (408 papers)

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; Taghdir, M; Naderi-Manesh, H; J. Photochem. Photobiol. B, Biol., 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)
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 (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)
High-level expression of improved thermo-stable alkaline xylanase variant in Pichia Pastoris through codon optimization, multiple gene insertion and high-density fermentation Lu, Y; Fang, C; Wang, Q; Zhou, Y; Zhang, G; Ma, Y; Sci Rep, DOI://10.1038/srep37869 (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)
Mechanism of O2 diffusion and reduction in FeFe hydrogenases Adam Kubas, Christophe Orain et al. Nature Chemistry, doi:10.1038/nchem.2592 (2016)
Variance Decomposition for Single-Subject task-based fMRI activity estimates across many sessions Javier Gonzalez-Castillo, Gang Chen, Thomas E. Nichols, Peter A. Bandettini NeuroImage, doi://10.1016/j.neuroimage.2016.10.024 (2016)
Explicit Incorporation of Hard and Soft Protein-Protein Interactions Into Models for Crowding Effects in Binary and Ternary Protein Mixtures I. Comparison of Approximate Analytical Solutions With Numerical Simulation Travis Hoppe, and Allen P. Minton J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.6b07736 (2016)

Resting State Connectivity of the Human Habenula at Ultra-High Field Salvatore Torrisi, Camilla L. Nord, Nicholas L. Balderston, Jonathan P. Roiser, Christian Grillon, Monique Ernst NeuroImage, 10.1016/j.neuroimage.2016.10.034 (2016)
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts Saini, N; Roberts, SA; Klimczak, LJ et al. PLoS Genet., DOI://10.1371/journal.pgen.1006385 (2016)
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells Juan, AH; Wang, S; Ko, KD et al. Cell Rep, DOI://10.1016/j.celrep.2016.09.087 (2016)
Deriving frequency-dependent spatial patterns in MEG-derived resting state sensorimotor network: A novel multiband ICA technique Nugent, A. C., Luber, B., Carver, F. W., Robinson, S. E., Coppola, R. and Zarate, C. A. Hum. Brain Mapp., doi:10.1002/hbm.23417 (2016)
Additional Rare Variant Analysis in Parkinson's Disease Cases with and Without Known Pathogenic Mutations: Evidence for Oligogenic Inheritance Steven J. Lubbe, Valentina Escott-Price et al. Human Molecular Genetics, doi://10.1093/hmg/ddw348 (2016)
Longitudinal imaging in C9orf72 mutation carriers: Relationship to phenotype Mary Kay Floeter, Devin Bageac, Laura E. Danielian, Laura E. Braun, Bryan J. Traynor, , Justin Kwan NeuroImage: Clinical, doi://10.1016/j.nicl.2016.10.014 (2016)
Racial differences in microRNA and gene expression in hypertensive women Dluzen, DF; Noren Hooten, N; Zhang, Y et al. Sci Rep, DOI://10.1038/srep35815 (2016)
Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases Gergely N Nagy, Reynier Suardiaz, Anna Lopata, Oliver Ozohanics, Karoly Vekey, Bernard R. Brooks, Ibolya Leveles, Judit Toth, Beata G Vertessy, and Edina Rost JACS, doi://10.1021/jacs.6b09012 (2016)
Molecular lock regulates binding of glycine to a primitive NMDA receptor Alvin Yu, Robert Alberstein, Alecia Thomas, Austin Zimmet, Richard Grey, Mark L. Mayer, and Albert Y. Lau PNAS, doi: 10.1073/pnas.1607010113 (2016)
Sources and implications of whole-brain fMRI signals in humans Jonathan D Power, Mark Plitt, Timothy O Laumann, Alex Martin Neuroimage, doi://10.1016/j.neuroimage.2016.09.038 (2016)
Diagnosis of Parkinson's disease on the basis of clinical-genetic classification: a population-based modelling study Mike A. Nalls, Cory Y. McLean et al. Lancet Neurol., doi: 10.1016/S1474-4422(15)00178-7 (2016)
Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster Lin, Y; Chen, ZX; Oliver, B; Harbison, ST; G3 (Bethesda), DOI://10.1534/g3.116.035444 (2016)

A RUNX2-Mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells Shin, MH; He, Y; Marrogi, E et al. PLoS Genet., DOI://10.1371/journal.pgen.1005884 (2016)
Sp5 and Sp8 recruit β-catenin and Tcf1-Lef1 to select enhancers to activate Wnt target gene transcription Kennedy, MW; Chalamalasetty, RB; Thomas, S; Garriock, RJ; Jailwala, P; Yamaguchi, TP; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1519994113 (2016)
Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number Lyons, JJ; Yu, X; Hughes, JD et al. Nat. Genet., DOI://10.1038/ng.3696 (2016)
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions Goar Sànchez-Sanz , Bartomiej Tywoniuk , David Matallanas, David Romano, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta , Walter Kolch , Nicolae-Viorel Buchete PLoS Computational Biology, doi://10.1371/journal.pcbi.1005051 (2016)
Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin Sandoval, PC; Claxton, JS; Lee, JW; Saeed, F; Hoffert, JD; Knepper, MA; Sci Rep, DOI://10.1038/srep34863 (2016)
Evaluation of KIR3DL1/KIR3DS1 polymorphism in Behçet's disease Erer, B; Takeuchi, M; Ustek, D et al. Genes Immun., DOI://10.1038/gene.2016.36 (2016)
Rapid development of a DNA vaccine for Zika virus Dowd, KA; Ko, SY; Morabito, KM et al. Science, DOI://10.1126/science.aai9137 (2016)
A Modified P1 Moiety Enhances in vitro Antiviral Activity against Various Multi-Drug-Resistant HIV-1 Variants and in vitro CNS Penetration Properties of a Novel Nonpeptidic Protease Inhibitor, GRL-10413 Masayuki Amano, Pedro Miguel Salcedo-Gomez, Rui Zhao, Ravikiran S. Yedidi, Debananda Das, Haydar Bulut, Nicole S. Delino, Sheri Venkata Reddy, Arun K. Ghosh and Hiroaki Mitsuya Antimicrobial Agents and Chemotherapy, doi: 10.1128/AAC.01428-16 (2016)
Peripheral Blood Transcriptomic Signatures of Fasting Glucose and Insulin Concentrations BH Chen, M-F Hivert et al. Diabetes, doi://10.2337/db16-0470 (2016)
On the Selective Packaging of Genomic RNA by HIV-1 Mauricio Comas-Garcia, Sean R. Davis and Alan Rein Viruses, doi://10.3390/v8090246 (2016)
Behavioral and Neural Sustained Attention Deficits in Bipolar Disorder and Familial Risk for Bipolar Disorder David Pagliaccio, Jillian Lee Wiggins, et al. Biological Psychiatry, doi://10.1016/j.biopsych.2016.09.006 (2016)
Mutations of SGO2 and CLDN14 collectively cause coincidental Perrault syndrome R Faridi, AR Rehman et al. Clinical Genetics, DOI: 10.1111/cge.12867 (2016)

CYP2A6 genetic variation alters striatal-cingulate circuits, network hubs, and executive processing in smokers Sufang Li, Yihong Yang, Ewa Hoffmann, Rachel F. Tyndale, Elliot A. Stein Biological Psychiatry, doi://10.1016/j.biopsych.2016.09.013 (2016)
Absolute binding free energies for octa-acids and guests in SAMPL5 Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard Kzönig, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks J. Computer-Aided Molecular Design, DOI: 10.1007/s10822-016-9965-5 (2016)
Introduction, evolution, and dissemination of influenza A viruses in exhibition swine, USA, 2009-2013 Martha I. Nelson, Karla M. Stucker, et al. J. Virology, doi: 10.1128/JVI.01457-16 (2016)
Novel genetic loci underlying human intracranial volume identified through genome-wide association Adams, HH; Hibar, DP; Chouraki, V et al. Nat. Neurosci., DOI://10.1038/nn.4398 (2016)
Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation Willi, M; Yoo, KH; Wang, C; Trajanoski, Z; Hennighausen, L; Nucleic Acids Res., DOI://10.1093/nar/gkw844 (2016)
DNA methylation-based measures of biological age: meta-analysis predicting time to death Chen, BH; Marioni, RE; Colicino, E et al. Aging (Albany NY), DOI://10.18632/aging.101020 (2016)
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology Pereira, EM; Labilloy, A; Eshbach, ML et al. Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00283.2016 (2016)
Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation Hartley, SW; Mullikin, JC; Klein, DC; Park, M; , ; Coon, SL; PLoS ONE, DOI://10.1371/journal.pone.0163590 (2016)
The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals Ehret, GB; Ferreira, T; Chasman, DI et al. Nat. Genet., DOI://10.1038/ng.3667 (2016)
Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators Yang, L; Li, P; Yang, W et al. Cell Metab., DOI://10.1016/j.cmet.2016.08.019 (2016)
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants Ioannidis, NM; Rothstein, JH; Pejaver, V et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2016.08.016 (2016)
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Association of Superoxide Dismutase 2 (SOD2) Genotype with Gray Matter Volume Shrinkage in Chronic Alcohol Users: Replication and Further Evaluation of an Addiction Gene Panel Gitik M, Srivastava V, Hodgkinson CA, Shen PH, Goldman D, Meyerhoff DJ Int. J. Neuropsychopharmacol., DOI://10.1093/ijnp/pyw033 (2016)
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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, OI 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)
Production of small cysteine-rich effector proteins in Escherichia coli for structural and functional studies Xiaoxiao Zhang, Neal Nguyen, Susan Breen, Megan A. Outram, Peter N. Dodds, Bostjan Kobe, Peter S. Solomon and Simon J. Williams Molecular Plant Pathology, DOI: 10.1111/mpp.12385 (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)
Mechanism of Protein Molecule Isolation by IR Laser Ablation of Droplet Beam Kensuke Komatsu, Takuya Nirasawa, Mariko Hoshino-Nagasaka, and Jun-ya Kohno J. Phys. Chem. A, DOI: 10.1021/acs.jpca.5b10873 (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 (340 papers)

miR-501-3p mediates the activity-dependent regulation of the expression of AMPA receptor subunit GluA1 Hu, Z; Zhao, J; Hu, T; Luo, Y; Zhu, J; Li, Z; J. Cell Biol., DOI://10.1083/jcb.201404092 (2015)

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

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

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

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

Intrinsic excitability measures track antiepileptic drug action and uncover increasing/decreasing excitability over the wake/sleep cycle Christian Meisel, Andreas Schulze-Bonhage, Dean Freestone, Mark James Cook, Peter Achermann, Dietmar Plenz PNAS, doi: 10.1073/pnas.1513716112 (2015)
Transcriptional and Chromatin Regulation during Fasting - The Genomic Era Goldstein I, Hager GL Trends Endocrinol. Metab., DOI://10.1016/j.tem.2015.09.005 (2015)
Evaluation of Genome Wide Association Study Associated Type 2 Diabetes Susceptibility Loci in Sub Saharan Africans Adeyemo, AA; Tekola-Ayele, F; Doumatey, AP et al. Front Genet, DOI://10.3389/fgene.2015.00335 (2015)
Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006 Rocío M. Gamez, Fernando Rodríguez, Johan F. Bernal, Richa Agarwala, David Landsman, Leonardo Mariño-Ramírez Genome Announc., doi: 10.1128/genomeA.01391-15 (2015)
HIV Therapeutics and Methods of Making and Using Same Paolo Lusso and Raffaelo Cimbro Patent, United States Patent Application 20150313990 (2015)
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A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies Gregory D. Marquart, Kathryn M. Tabor, Mary Brown, Jennifer L. Strykowski, Gaurav K. Varshney, Matthew C. LaFave, Thomas Mueller, Shawn M. Burgess, Shin-ichi Higashijima and Harold A. Burgess Frontiers in Neural Circuits, doi://10.3389/fncir.2015.00078 (2015)
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Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels Hyunbum Jang, Fernando Teran Arce, Joon Lee, Alan L. Gillman, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal, Ruth Nussinov Protein Amyloid Aggregation, doi://10.1007/978-1-4939-2978-8-16 (2015)
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GNL3 and SKA3 are novel prostate cancer metastasis susceptibility genes Minnkyong Lee, Kendra A. Williams, Ying Hu, Jonathan Andreas, Shashank J. Patel, Suiyuan Zhang, Nigel P. S. Crawford Clin Exp Metastasis, DOI 10.1007/s10585-015-9745-y (2015)
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Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach Julien Roche, John M. Louis, Ad Bax and Robert B. Best Proteins, DOI: 10.1002/prot.24931 (2015)
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Assessing FOXO1A as a potential susceptibility locus for type 2 diabetes and obesity in American Indians Yunhua L. Muller, Robert L. Hanson, Gregory Wiessner, Lori Nieboer, Sayuko Kobes, Paolo Piaggi, Mahdi Abdussamad, Chidinma Okani, William C. Knowler, Clifton Bogardus andLeslie J. Baier Obesity, DOI: 10.1002/oby.21236 (2015)
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Insights into the Mechanism of Inhibition of CXCR4: Identification of Piperidinylethanamine Analogs as Anti-HIV-1 Inhibitors Das D, Maeda K, Hayashi Y, Gavande N, Desai DV, Chang SB, Ghosh AK, Mitsuya H Antimicrob Agents Chemother., pii: AAC.04654-14. (2015)

Variable selection method for the identification of epistatic models Holzinger ER, Szymczak S, Dasgupta A, Malley J, Li Q, Bailey-Wilson JE Pac Symp Biocomput, 2335-6936 (2015)
CDD: NCBI's conserved domain database Marchler-Bauer, A; Derbyshire, MK; Gonzales, NR et al. Nucleic Acids Res., DOI://10.1093/nar/gku1221 (2015)
Analysis of soluble protein entry into primary cilia using semipermeabilized cells David K. Breslow, Maxence V. Nachury Methods in Cell Biology, doi:10.1016/bs.mcb.2014.12.006 (2015)
NRG1, ERBB4 and AKT1 Epistasis Increases Schizophrenia Risk and is Biologically Validated via Functional Neuroimaging in Healthy Controls Nicodemus KK, Law AJ, Radulescu E, Luna A, Kolachana B, Vakkalanka R, Rujescu D, Giegling I, Straub RE, McGee K, Gold B, Dean M, Muglia P, Callicott JH, Tan HY, Weinberger DR. Arch Gen Psychiatry, doi: 10.1001/archgenpsychiatry.2010.117 (2015)
Maturation of the HIV-1 core by a non-diffusional phase transition Frank GA, Narayan K, Bess JW Jr, Del Prete GQ, Wu X, Moran A, Hartnell LM, Earl LA, Lifson JD, Subramaniam S Nature Communications, doi: 10.1038/ncomms6854 (2015)
Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension Xiaofeng Zhu, Tao Feng, Bamidele O. Tayo et al. Am J Hum Genet., doi: 10.1016/j.ajhg.2014.11.011. (2015)

Protein structural information derived from NMR chemical shift with the neural network program TALOS-N Shen Y, Bax A Methods Mol. Biol., DOI://10.1007/978-1-4939-2239-0_2 (2015)
BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O'Shea JJ, Ozato K Nat Struct Mol Biol., doi: 10.1038/nsmb.2912 (2015)
Structures of oxalate oxidoreductase : C₂ activation by a microbial TPP-dependent ferredoxin oxidoreductase Gibson, Marcus Ian PhD Thesis, MIT Dept of Chemistry (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)
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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)
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Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy Alberto Bartesaghi, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam Nat Struct Mol Biol., doi: 10.1038/nsmb.2711 (2014)
Clinical correlates and genetic linkage of social and communication difficulties in families with obsessive-compulsive disorder: Results from the OCD Collaborative Genetics Study Samuels, J; Shugart, YY; Wang, Y et al. Am. J. Med. Genet. B Neuropsychiatr. Genet., DOI://10.1002/ajmg.b.32235 (2014)
The spatial structure of resting state connectivity stability on the scale of minutes Javier Gonzalez-Castillo, Daniel A Handwerker, Meghan E. Robinson, Colin Wier Hoy, Laura Cathleen Buchanan, Ziad S Saad and Peter A Bandettini Frontiers in Neuroscience, DOI://10.3389/fnins.2014.00138 (2014)
The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. King MR, Matzat LH, Dale RK, Lim SJ, Lei EP J. Cell. Sci., doi: 10.1242/jcs.151126 (2014)

Use of LC-MS/MS and Bayes' Theorem to Identify Protein Kinases That Phosphorylate Aquaporin-2 at Ser256 Davis Bradford, Viswanathan Raghuram, Justin L.L. Wilson, Chung-Lin Chou, Jason D. Hoffert, Mark A. Knepper, Trairak Pisitkun Am. J. Physiol. - Cell Physiol. , DOI: 10.1152/ajpcell.00377.2012 (2014)
Nill-Schiff base complex as an enzyme inhibitor of hen egg white lysozyme: a crystallographic and spectroscopic study Banabithi Koley Seth, Aurkie Ray, Sampa Biswas and Samita Basu Metallomics, DOI: 10.1039/C4MT00098F (2014)
Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing Yun Ji, Natalie Abrams, Wei Zhu, Eddie Salinas, Zhiya Yu, Douglas C. Palmer, Parthav Jailwala, Zulmarie Franco, Rahul Roychoudhuri, Eric Stahlberg, Luca Gattinoni, Nicholas P. Restifo PLoS One, DOI: 10.1371/journal.pone.0096650 (2014)
Combination of longitudinal biomarkers in predicting binary events Danping Liu and Paul S Albert Biostatistics, doi: 10.1093/biostatistics/kxu020 (2014)
Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma Shi J, Yang XR, Ballew B Nature Genetics, doi: 10.1038/ng.2941 (2014)
Pleiotropic genes for metabolic syndrome and inflammation Kraja AT, Chasman DI, North KE et al. Molecular Genetics & Metabolism, doi://10.1016/j.ymgme.2014.04.007 (2014)

Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves Kent R. Thurber and Robert Tycko J. Chem. Phys. , DOI: 10.1063/1.4874341 (2014)
Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome Yudkin, D; Hayward, BE; Aladjem, MI; Kumari, D; Usdin, K; Hum. Mol. Genet., DOI://10.1093/hmg/ddu006 (2014)
Rhythmic Bursting in the Pre-Bötzinger Complex: Mechanisms and Models Ilya A. Rybak, Yaroslav I. Molkov, Patrick E. Jasinski, Natalia A. Shevtsova, Jeffrey C. Smith Progress in Brain Research, doi://10.1016/B978-0-444-63274-6.00001-1 (2014)
Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2 Francesco Trepiccione, Trairak Pisitkun, Jason D Hoffert, Søren B Poulsen, Giovambattista Capasso, Søren Nielsen, Mark A Knepper, Robert A Fenton and Birgitte M Christensen Kidney International, doi: 10.1038/ki.2014.107 (2014)
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I Ville R. I. Kaila, Mârten Wikström and Gerhard Hummer PNAS, doi: 10.1073/pnas.1319156111 (2014)
Hierarchical clustering of ryanodine receptors enables emergence of a calcium clock in sinoatrial node cells Michael D. Stern, Larissa A. Maltseva, Magdalena Juhaszova, Steven J. Sollott, Edward G. Lakatta, and Victor A. Maltsev J. Gen. Physiol. , doi: 10.1085/jgp.201311123 (2014)

Conserved hydrogen-bonding network of P2 bis-tetrahydrofuran containing HIV-1 protease inhibitors (PI) with protease active site amino acid-backbone aid in their activity against PI-resistant HIV Ravikiran S. Yedidi, Harisha Garimella, Manabu Aoki, Hiromi Aoki, Darshan V. Desai, Simon B. Chang, David A. Davis, W. Sean Fyvie, Joshua D. Kaufman, David W. Smith, Debananda Das, Paul T. Wingfield, Kenji Maeda, Arun K. Ghosh and Hiroaki Mitsuya Antimicrob Agents Chemother., doi://10.1128/AAC.00107-14 (2014)
Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer Ewy A Mathe, Andrew D Patterson, Majda Haznadar, Soumen K Manna, Kristopher W. Krausz, Elise D Bowman, Peter G. Shields, Jeffrey R. Idle, Philip B Smith, Katsuhiro Anami, Dickran Kazandjian, Emmanuel Hatzakis, Frank J Gonzalez, and Curtis C. Harris Cancer Res., doi:10.1158/0008-5472.CAN-14-0109 (2014)
Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin J.-H. Kang, S.A. Hassan, 1, P. Zhao, C.H. Tsai-Morris, M.L. Dufau Biochim. et Biophys. Acta, doi://10.1016/j.bbagen.2014.04.006 (2014)
A Fast and Powerful Tree-Based Association Test for Detecting Complex Joint Effects in Case-Control Studies Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor and Kai Yu Bioinformatics, doi://10.1093/bioinformatics/btu186 (2014)
Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain David N. Hauser, Allissa A. Dillman, Jinhui Ding, Yan Li, Mark R. Cookson PLoS One, DOI: 10.1371/journal.pone.0094646 (2014)
Studies on Inhibition of Respiratory Cytochrome bc1 Complex by the Fungicide Pyrimorph Suggest a Novel Inhibitory Mechanism Yu-Mei Xiao, Lothar Esser, Fei Zhou, Chang Li, Yi-Hui Zhou, Chang-An Yu, Zhao-Hai Qin, Di Xia PLoS One, DOI: 10.1371/journal.pone.0093765 (2014)

Regulation of a novel isoform of Receptor Expression Enhancing Protein REEP6 in rod photoreceptors by bZIP transcription factor NRL Hong Hao, Shobi Veleri, Bo Sun, Douglas S. Kim, Patrick W. Keeley, Jung-Woong Kim, Hyun-Jin Yang, Sharda P. Yadav, Souparnika H. Manjunath, Raman Sood, Paul Liu, Benjamin E. Reese and Anand Swaroop Human Molecular Genetics, doi: 10.1093/hmg/ddu143 (2014)
Distributed MRI reconstruction using gadgetron-based cloud computing Hui Xue, Souheil Inati, Thomas Sangild Sørensen, Peter Kellman and Michael S. Hansen Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25213 (2014)
Hemoglobinopathic erythrocytes affect the intraerythrocytic multiplication of Plasmodium falciparum in vitro Svetlana Glushakova, Amanda Balaban, Philip G. McQueen, Rosane Coutinho, Jeffery L. Miller, Ralph Nossal, Rick M. Fairhurst, Joshua Zimmerberg J. Infectious Diseases, doi:10.1093/infdis/jiu203 (2014)
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface Guntur Fibriansah, Joanne L Tan,Scott A Smith, Adamberage R Alwis, Thiam-Seng Ng, Victor A Kostyuchenko, Kristie D Ibarra, Jiaqi Wang, Eva Harris, Aravinda Silva, James E Crowe, and Shee-Mei Lok EMBO Molecular Medicine, doi: 10.1002/emmm.201303404 (2014)
A mixture of transition models for heterogeneous longitudinal ordinal data: with applications to longitudinal bacterial vaginosis data Kyeongmi Cheon, Marie E. Thoma, Xiangrong Kong and Paul S. Albert Statistics in Medicine, DOI: 10.1002/sim.6151 (2014)
Abdominal lymphadenopathy detection using random forest Kevin M. Cherry, Shijun Wang, Evrim B. Turkbey, Ronald M. Summers SPIE Proceedings, Volume 9035, Lung, Chest, and Abdomen II, doi:10.1117/12.2043837 (2014)

VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions Jianxin Shi, Xiaohong R. Yang, Neil E. Caporaso, Maria T. Landi, and Peng Li Frontiers in Genetics, doi://10.3389/fgene.2014.00053 (2014)
Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values Gelio Alves and Yi-Kuo Yu PLoS One, doi: 10.1371/journal.pone.0091225 (2014)
Differential Coding of Conspecific Vocalizations in the Ventral Auditory Cortical Stream Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck J. Neuroscience, doi: 10.1523/JNEUROSCI.3969-13.2014 (2014)
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein Ville R. I. Kaila, Friedrich Schotte, Hyun Sun Cho, Gerhard Hummer & Philip A. Anfinrud Nature Chemistry, doi:10.1038/nchem.1898 (2014)
Practice and sleep form different aspects of skill Sunbin Song & Leonardo G. Cohen Nature Communications, doi:10.1038/ncomms4407 (2014)
Temperature-dependent solvation modulates the dimensions of disordered proteins René Wuttke, Hagen Hofmann, Daniel Nettels, Madeleine B. Borgia, Jeetain Mittal, Robert B. Best, and Benjamin Schuler PNAS, doi: 10.1073/pnas.1313006111 (2014)
Hypoosmotic Expression of Dunaliella bardawil ζ-Carotene Desaturase Is Attributed to a Hypoosmolarity-Responsive Element Different from Other Key Carotenogenic Genes Yong-Min Lao, Lan Xiao, Li-Xin Luo and Jian-Guo Jiang Plant Physiology, doi://10.1104/pp.114.235390 (2014)
Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Jianxin Shi, Crystal N. Marconett, Jubao Duan et al. Nature Communications, doi:10.1038/ncomms4365 (2014)
Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal and Ruth Nussinov Chem. Soc. Rev., doi://10.1039/C3CS60459D (2014)
Abnormal cortical growth in schizophrenia targets normative modules of synchronized development Aaron F. Alexander-Bloch, Philip T. Reiss, Judith Rapoport, Harry McAdams, Jay N. Giedd, Ed T. Bullmore, Nitin Gogtay Biological Psychiatry, doi://10.1016/j.biopsych.2014.02.010 (2014)
Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis Edina Rosta, Wei Yang, and Gerhard Hummer JACS, DOI: 10.1021/ja411408x (2014)
Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes Gerhard König, Phillip Stephen Hudson, Stefan Boresch, and H. Lee Woodcock J. Chem. Theory & Computation, DOI: 10.1021/ct401118k (2014)

A Network Characteristic That Correlates Environmental and Genetic Robustness Zeina Shreif, Vipul Periwal PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1003474 (2014)
A GCH1 haplotype confers sex-specific susceptibility to pain crises and altered endothelial function in adults with sickle cell anemia Inna Belfer, Victoria Youngblood et al. Am. J. Hematology, DOI: 10.1002/ajh.23613 (2014)
Meta-analysis of Loci Associated with Age at Natural Menopause in African-American Women CTL Chen, C-T Liu, GK Chen, et al Human Molecular Genetics, doi: 10.1093/hmg/ddu041 (2014)
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks J. Computer-Aided Molecular Design, doi://10.1007/s10822-014-9708-4 (2014)
Predicting Stroke Through Genetic Risk Functions CA Ibrahim-Verbaas,M Fornage, JC Bis, et al Stroke, doi: 10.1161/STROKEAHA.113.003044 (2014)
Multilocus Genetic Risk Score Associates With Ischemic Stroke in Case-Control and Prospective Cohort Studies R Malik, S Bevan, M Nalls et al Stroke, doi: 10.1161/STROKEAHA.113.002938 (2014)

Reverse regression: A method for joint analysis of multiple endpoints in randomized clinical trials Zhiwei Zhang Statistica Sinica, doi://10.5705/ss.2010.111 (2014)
Using single cell sequencing data to model the evolutionary history of a tumor Kyung In Kim and Richard Simon BMC Bioinformatics :27, doi: 10.1186/1471-2105-15-27 (2014)
Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors Jack F. Shern, Li Chen, Juliann Chmielecki, et al. Cancer Discovery, doi:10.1158/2159-8290.CD-13-0639 (2014)
Fluorescence excitation and ultraviolet absorption spectra and theoretical calculations for benzocyclobutane: Vibrations and structure of its excited S1(π,π*) electronic state Hee Won Shin, Esther J. Ocola, Sunghwan Kim and Jaan Laane J. Chem. Phys., doi://10.1063/1.4858412 (2014)
Spectral Tuning of Rhodopsin and Visual Cone Pigments Xiuwen Zhou , Dage Sundholm , Tomasz Adam Wesolowski , and Ville R. I. Kaila J.Am.Chem.Soc., DOI: 10.1021/ja411864m (2014)
RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder N Akula, J Barb, X Jiang, J R Wendland, K H Choi, S K Sen, L Hou, D T W Chen, G Laje, K Johnson, B K Lipska, J E Kleinman, H Corrada-Bravo, S Detera-Wadleigh, P J Munson and F J McMahon Molecular Psychiatry, doi: 10.1038/mp.2013.170 (2014)

2013 (180 papers)

Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains Chuang, GY; Acharya, P; Schmidt, SD et al. J. Virol., DOI://10.1128/JVI.00984-13 (2013)
Integrated strategy for improving functional connectivity mapping using multiecho fMRI Kundu, P; Brenowitz, ND; Voon, V et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301725110 (2013)
Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia Wang, E; Kawaoka, S; Yu, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301045110 (2013)
Correlated biomarker measurement error: an important threat to inference in environmental epidemiology Pollack, AZ; Perkins, NJ; Mumford, SL; Ye, A; Schisterman, EF; Am. J. Epidemiol., DOI://10.1093/aje/kws209 (2013)
Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies Zhou, T; Zhu, J; Wu, X et al. Immunity, DOI://10.1016/j.immuni.2013.04.012 (2013)
Effective Preprocessing Procedures Virtually Eliminate Distance-Dependent Motion Artifacts in Resting State FMRI Jo, HJ; Gotts, SJ; Reynolds, RC et al. J Appl Math, DOI://10.1155/2013/935154 (2013)

A structural and molecular dynamics approach to understanding the peptide-receptive transition state of MHC-I molecules Mage, MG; Dolan, MA; Wang, R et al. Mol. Immunol., DOI://10.1016/j.molimm.2012.10.021 (2013)
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)
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)
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)
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Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome Yu Xu, Hong Wang, Ruth Nussinov, Buyong Ma Proteomics, DOI: 10.1002/pmic.201100540 (2013)
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly C Park, X Chen, J-R Yang, J Zhang PNAS, doi: 10.1073/pnas.1218066110 (2013)
The Val158Met COMT polymorphism is a modifier of the age at onset in Parkinson's disease with a sexual dimorphism S Klebe, J-L Golmard, MA Nalls et al, French Parkinson's Disease Genetics Study Group and the International Parkinson's Disease Genomics Consortium J Neurol Neurosurg Psychiatry , doi:10.1136/jnnp-2012-304475 (2013)
The Convergence of Maturational Change and Structural Covariance in Human Cortical Networks Aaron Alexander-Bloch, Armin Raznahan, Ed Bullmore, and Jay Giedd J. Neuroscience , doi: 10.1523/JNEUROSCI.3554-12.2013 (2013)
Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer Li-Jun Di, Jung S. Byun, Madeline M. Wong, Clay Wakano, Tara Taylor, Sven Bilke, Songjoon Baek, Kent Hunter, Howard Yang, Maxwell Lee, Cecilia Zvosec, Galina Khramtsova, Fan Cheng, Charles M. Perou, C. Ryan Miller, Rachel Raab, Olufunmilayo I. Olopade & Kevin Gardner Nature Communications, doi:10.1038/ncomms2438 (2013)

Ischemic stroke is associated with the ABO locus: The EuroCLOT study FMK Williams, AM Carter, PG Hysi et al and EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2, MORGAM, MetaStroke and the International Stroke Genetics Consortium Annals of Neurology, DOI: 10.1002/ana.23838 (2013)
Initial Assessment of the Pathogenic Mechanisms of the Recently Identified Alzheimer Risk Loci P Holton, M Ryten, MA Nalls et al. Annals of Human Genetics, DOI: 10.1111/ahg.12000 (2013)
Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin Erica L.W. Majumder, Jeremy D. King, Robert E. Blankenship Biochim. et Biophys. Acta - Bioenergetics, doi://10.1016/j.bbabio.2013.01.008 (2013)
Identification of Early Replicating Fragile Sites that Contribute to Genome Instability JH Barlow, RB Faryabi, E Callen, N Wong, A Malhowski, H Tang Chen, G Gutierrez-Cruz, H-W Sun, P McKinnon, G Wright, R Casellas, DF Robbiani, L Staudt, O Fernandez-Capetillo, A Nussenzweig Cell, doi://10.1016/j.cell.2013.01.006 (2013)
Genetic variation associated with circulating monocyte count in the eMERGE Network DR Crosslin, A McDavid, N Weston et al Hum. Mol. Genetics, doi: 10.1093/hmg/ddt010 (2013)
PI(4,5)P2-Mediated Cell Signaling: Emerging Principles and PTEN as a Paradigm for Regulatory Mechanism Arne Gericke, Nicholas R. Leslie, Mathias Lösche, Alonzo H. Ross Adv Exp Med Biol, doi: 10.1007/978-94-007-6331-9_6 (2013)

2012 (144 papers)

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 byAPOEGenotype 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)

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids Jeetain Mittal, Gerhard Hummer arXiv preprint, arXiv:1202.6039 (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 Conformation and Intermolecular Reactivity of a 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, D