Papers that used NIH HPC Systems resources

Papers that used NIH HPC (Biowulf) resources

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

2021 to date (102 papers)

The structure, function and evolution of a complete human chromosome 8 Logsdon, GA; Vollger, MR; Hsieh, P et al. Nature, DOI://10.1038/s41586-021-03420-7 (2021)
A comprehensive macaque fMRI pipeline and hierarchical atlas Jung, B; Taylor, PA; Seidlitz, J et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.117997 (2021)
Functional Anatomy of the Trimer Apex Reveals Key Hydrophobic Constraints That Maintain the HIV-1 Envelope Spike in a Closed State Zhang, P; Kwon, AL; Guzzo, C et al. mBio, DOI://10.1128/mBio.00090-21 (2021)
Beyond linearity in neuroimaging: Capturing nonlinear relationships with application to longitudinal studies Chen, G; Nash, TA; Cole, KM et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.117891 (2021)

CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning Conrad, R; Narayan, K; Elife, DOI://10.7554/eLife.65894 (2021)
Martini 3: a general purpose force field for coarse-grained molecular dynamics Souza, PCT; Alessandri, R; Barnoud, J et al. Nat Methods, DOI://10.1038/s41592-021-01098-3 (2021)
SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation Yan, B; Freiwald, T; Chauss, D et al. Sci Immunol, DOI://10.1126/sciimmunol.abg0833 (2021)
A transcription-centric model of SNP-age interaction Wang, K; Basu, M; Malin, J; Hannenhalli, S; , PLoS Genet, DOI://10.1371/journal.pgen.1009427 (2021)
Conception by fertility treatment and offspring deoxyribonucleic acid methylation Yeung, EH; Mendola, P; Sundaram, R et al. Fertil Steril, DOI://10.1016/j.fertnstert.2021.03.011 (2021)
Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection Singh, K; Chen, YC; Hassanzadeh, S et al. Front Genet, DOI://10.3389/fgene.2021.599261 (2021)

Genome-wide binding potential and regulatory activity of the glucocorticoid receptor's monomeric and dimeric forms Johnson, TA; Paakinaho, V; Kim, S; Hager, GL; Presman, DM; , Nat Commun, DOI://10.1038/s41467-021-22234-9 (2021)
Predicting tissue-specific gene expression from whole blood transcriptome Basu, M; Wang, K; Ruppin, E; Hannenhalli, S; , Sci Adv, DOI://10.1126/sciadv.abd6991 (2021)
Movie-watching outperforms rest for functional connectivity-based prediction of behavior Finn, ES; Bandettini, PA; , Neuroimage, DOI://10.1016/j.neuroimage.2021.117963 (2021)
Structure-Activity Relationship of Heterocyclic P2Y 14 Receptor Antagonists: Removal of the Zwitterionic Character with Piperidine Bioisosteres Jung, YH; Salmaso, V; Wen, Z et al. J Med Chem, DOI://10.1021/acs.jmedchem.1c00164 (2021)
Nascent Prostate Cancer Heterogeneity Drives Evolution and Resistance to Intense Hormonal Therapy Wilkinson, S; Ye, H; Karzai, F et al. Eur Urol, DOI://10.1016/j.eururo.2021.03.009 (2021)
Thousands of previously unknown phages discovered in whole-community human gut metagenomes Benler, S; Yutin, N; Antipov, D et al. Microbiome, DOI://10.1186/s40168-021-01017-w (2021)

Genomic insights into the host specific adaptation of the Pneumocystis genus Cissé, OH; Ma, L; Dekker, JP et al. Commun Biol, DOI://10.1038/s42003-021-01799-7 (2021)
New insights into modeling exposure measurements below the limit of detection Ortega-Villa, AM; Liu, D; Ward, MH; Albert, PS; , Environ Epidemiol, DOI://10.1097/EE9.0000000000000116 (2021)
The Structural Basis of Akt PH Domain Interaction with Calmodulin Weako, J; Jang, H; Keskin, O; Nussinov, R; Gursoy, A; , Biophys J, DOI://10.1016/j.bpj.2021.03.018 (2021)
The NIMH Intramural Longitudinal Study of the Endocrine and Neurobiological Events Accompanying Puberty: Protocol and Rationale for Methods and Measures Cole, KM; Wei, SM; Martinez, PE et al. Neuroimage, DOI://10.1016/j.neuroimage.2021.117970 (2021)
Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis Taumoefolau, GH; Best, RB; , J Chem Phys, DOI://10.1063/5.0040949 (2021)
A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse Chen, L; Chou, CL; Knepper, MA; , J Am Soc Nephrol, DOI://10.1681/ASN.2020101406 (2021)
Integrative analysis of multiple case-control studies Zhang, H; Deng, L; Wheeler, W; Qin, J; Yu, K; , Biometrics, DOI://10.1111/biom.13461 (2021)
Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis Kaczanowska, S; Beury, DW; Gopalan, V et al. Cell, DOI://10.1016/j.cell.2021.02.048 (2021)
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2 Ghorbani, M; Brooks, BR; Klauda, JB; , Biophys J, DOI://10.1016/j.bpj.2021.02.047 (2021)
Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area Thielen, PM; Wohl, S; Mehoke, T et al. JCI Insight, DOI://10.1172/jci.insight.144350 (2021)
Conformational Ensemble of Tte AdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition Ma, B; Bai, G; Nussinov, R; Ding, J; Wang, YX; , J Phys Chem B, DOI://10.1021/acs.jpcb.1c00038 (2021)
Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity Rouf Banday, A; Onabajo, OO; Lin, SH et al. Commun Biol, DOI://10.1038/s42003-021-01844-5 (2021)

Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation Guan, R; Lian, T; Zhou, BR et al. Nat Commun, DOI://10.1038/s41467-021-21985-9 (2021)
Iterative epigenomic analyses in the same single cell Ohnuki, H; Venzon, DJ; Lobanov, A; Tosato, G; , Genome Res, DOI://10.1101/gr.269068.120 (2021)
Ancestral haplotype reconstruction in endogamous populations using identity-by-descent Finke, K; Kourakos, M; Brown, G et al. PLoS Comput Biol, DOI://10.1371/journal.pcbi.1008638 (2021)
Chloride-dependent conformational changes in the GlyT1 glycine transporter Zhang, YW; Uchendu, S; Leone, V et al. Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2017431118 (2021)
Death agonist antibody against TRAILR2/DR5/TNFRSF10B enhances birinapant anti-tumor activity in HPV-positive head and neck squamous cell carcinomas An, Y; Jeon, J; Sun, L et al. Sci Rep, DOI://10.1038/s41598-021-85589-5 (2021)
Structure of membrane diacylglycerol kinase in lipid bilayers Li, J; Shen, Y; Chen, Y et al. Commun Biol, DOI://10.1038/s42003-021-01802-1 (2021)
Genetically inferred telomere length and testicular germ cell tumor risk Brown, DW; Lan, Q; Rothman, N et al. Cancer Epidemiol Biomarkers Prev, DOI://10.1158/1055-9965.EPI-20-1775 (2021)
Fully automated CT imaging biomarkers of bone, muscle, and fat: correcting for the effect of intravenous contrast Perez, AA; Pickhardt, PJ; Elton, DC; Sandfort, V; Summers, RM; , Abdom Radiol (NY), DOI://10.1007/s00261-020-02755-5 (2021)
B-Raf autoinhibition in the presence and absence of 14-3-3 Zhang, M; Jang, H; Li, Z; Sacks, DB; Nussinov, R; , Structure, DOI://10.1016/j.str.2021.02.005 (2021)
Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord Nguyen, TH; Vicidomini, R; Choudhury, SD et al. Curr Protoc, DOI://10.1002/cpz1.38 (2021)
Dose conversion coefficients for neutron external exposures with five postures: walking, sitting, bending, kneeling, and squatting Yeom, YS; Griffin, K; Han, H et al. Radiat Environ Biophys, DOI://10.1007/s00411-021-00900-2 (2021)
Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells Gao, W; Ku, WL; Pan, L et al. Nucleic Acids Res, DOI://10.1093/nar/gkab102 (2021)

MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23 Mikami, Y; Philips, RL; Sciumè, G et al. Immunity, DOI://10.1016/j.immuni.2021.02.015 (2021)
CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids Yu, Y; Krämer, A; Venable, RM et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.0c01327 (2021)
Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion Yu, Y; Krämer, A; Venable, RM et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.0c01326 (2021)
Mechanism of membrane-tethered mitochondrial protein synthesis Itoh, Y; Andréll, J; Choi, A et al. Science, DOI://10.1126/science.abe0763 (2021)
Gene-based analysis of bi-variate survival traits via functional regressions with applications to eye diseases Zhang, B; Chiu, CY; Yuan, F et al. Genet Epidemiol, DOI://10.1002/gepi.22381 (2021)
BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8 + T cells Yao, C; Lou, G; Sun, HW et al. Nat Immunol, DOI://10.1038/s41590-021-00868-7 (2021)

Lysosome-associated membrane protein 3 misexpression in salivary glands induces a Sjögren's syndrome-like phenotype in mice Nakamura, H; Tanaka, T; Pranzatelli, T et al. Ann Rheum Dis, DOI://10.1136/annrheumdis-2020-219649 (2021)
Structure of an activated DNA-PK and its implications for NHEJ Chen, X; Xu, X; Chen, Y et al. Mol Cell, DOI://10.1016/j.molcel.2020.12.015 (2021)
Does the ATP-bound EQ mutant reflect the pre- or post-ATP hydrolysis state in the catalytic cycle of human P-glycoprotein (ABCB1)? Lusvarghi, S; Durell, SR; Ambudkar, SV; , FEBS Lett, DOI://10.1002/1873-3468.14054 (2021)
Audiovisual integration in macaque face patch neurons Khandhadia, AP; Murphy, AP; Romanski, LM; Bizley, JK; Leopold, DA; , Curr Biol, DOI://10.1016/j.cub.2021.01.102 (2021)
A Genome-First Approach to Characterize DICER1 Pathogenic Variant Prevalence, Penetrance, and Phenotype Mirshahi, UL; Kim, J; Best, AF et al. JAMA Netw Open, DOI://10.1001/jamanetworkopen.2021.0112 (2021)
The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization Xiao, T; Li, X; Felsenfeld, G; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2023127118 (2021)

The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution Eriksson, PR; Clark, DJ; , Sci Rep, DOI://10.1038/s41598-021-82842-9 (2021)
Smoking modifies pancreatic cancer risk loci on 2q21.3 Mocci, E; Kundu, P; Wheeler, W et al. Cancer Res, DOI://10.1158/0008-5472.CAN-20-3267 (2021)
Exome Sequencing of 21 Bardet-Biedl Syndrome (BBS) Genes to Identify Obesity Variants in 6,851 American Indians Day, SE; Muller, YL; Koroglu, C et al. Obesity (Silver Spring), DOI://10.1002/oby.23115 (2021)
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community Lee, HK; Knabl, L; Pipperger, L et al. Sci Rep, DOI://10.1038/s41598-021-83110-6 (2021)
The NF-κB regulator Bcl-3 restricts terminal differentiation and promotes memory cell formation of CD8+ T cells during viral infection Jaiswal, H; Ciucci, T; Wang, H et al. PLoS Pathog, DOI://10.1371/journal.ppat.1009249 (2021)
Gene Therapy of Dominant CRX-Leber Congenital Amaurosis using Patient Stem Cell-Derived Retinal Organoids Kruczek, K; Qu, Z; Gentry, J et al. Stem Cell Reports, DOI://10.1016/j.stemcr.2020.12.018 (2021)

Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes Maruyama, SR; Rogerio, LA; Freitas, PD; Teixeira, MMG; Ribeiro, JMC; , Sci Rep, DOI://10.1038/s41598-021-81926-w (2021)
Dynamic sex chromosome expression in Drosophila male germ cells Mahadevaraju, S; Fear, JM; Akeju, M et al. Nat Commun, DOI://10.1038/s41467-021-20897-y (2021)
Admixture mapping identifies African and Amerindigenous local ancestry loci associated with fetal growth Tekola-Ayele, F; Ouidir, M; Shrestha, D et al. Hum Genet, DOI://10.1007/s00439-021-02265-4 (2021)
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture Chia, R; Sabir, MS; Bandres-Ciga, S et al. Nat Genet, DOI://10.1038/s41588-021-00785-3 (2021)
Genome-wide transcriptome study using deep RNA sequencing for myocardial infarction and coronary artery calcification Zhang, X; van Rooij, JGJ; Wakabayashi, Y et al. BMC Med Genomics, DOI://10.1186/s12920-020-00838-2 (2021)
Assessment of assumptions underlying models of prokaryotic pangenome evolution Sela, I; Wolf, YI; Koonin, EV; , BMC Biol, DOI://10.1186/s12915-021-00960-2 (2021)

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets Kia, DA; Zhang, D; Guelfi, S et al. JAMA Neurol, DOI://10.1001/jamaneurol.2020.5257 (2021)
Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue Ghosh, U; Thurber, KR; Yau, WM; Tycko, R; , Proc Natl Acad Sci U S A, DOI://10.1073/pnas.2023089118 (2021)
An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing Montemayor, C; Simone, A; Long, J et al. Vox Sang, DOI://10.1111/vox.13035 (2021)
On the Role of a Conserved Methionine in the Na+-Coupling Mechanism of a Neurotransmitter Transporter Homolog Zhou, W; Trinco, G; Slotboom, DJ; Forrest, LR; Faraldo-Gómez, JD; , Neurochem Res, DOI://10.1007/s11064-021-03253-w (2021)
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning Kim, JH; Noskov, VN; Ogurtsov, AY et al. Sci Rep, DOI://10.1038/s41598-021-82565-x (2021)
Deep transcriptome sequencing of subgenual anterior cingulate cortex reveals cross-diagnostic and diagnosis-specific RNA expression changes in major psychiatric disorders Akula, N; Marenco, S; Johnson, K et al. Neuropsychopharmacology, DOI://10.1038/s41386-020-00949-5 (2021)

An examination of the relationships between attention/deficit hyperactivity disorder symptoms and functional connectivity over time Norman, LJ; Sudre, G; Bouyssi-Kobar, M; Sharp, W; Shaw, P; , Neuropsychopharmacology, DOI://10.1038/s41386-021-00958-y (2021)
Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers Zhao, J; Mohan, N; Nussinov, R; Ma, B; Wu, WJ; , Antibodies (Basel), DOI://10.3390/antib10010007 (2021)
Infection trains the host for microbiota-enhanced resistance to pathogens Stacy, A; Andrade-Oliveira, V; McCulloch, JA et al. Cell, DOI://10.1016/j.cell.2020.12.011 (2021)
Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics Haspel, N; Jang, H; Nussinov, R; , Biophys J, DOI://10.1016/j.bpj.2020.12.007 (2021)
Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation Beck, DB; Basar, MA; Asmar, AJ et al. Sci Adv, DOI://10.1126/sciadv.abe2116 (2021)
Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity Cheng, K; Nair, NU; Lee, JS; Ruppin, E; , Sci Adv, DOI://10.1126/sciadv.abc2100 (2021)

Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types Saez-Atienzar, S; Bandres-Ciga, S; Langston, RG et al. Sci Adv, DOI://10.1126/sciadv.abd9036 (2021)
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements Eicher, T; Chan, J; Luu, H; Machiraju, R; Mathé, EA; , BMC Bioinformatics, DOI://10.1186/s12859-021-03976-1 (2021)
Associations of maternal blood pressure-raising polygenic risk scores with fetal weight Workalemahu, T; Rahman, ML; Ouidir, M; Wu, J; Zhang, C; Tekola-Ayele, F; , J Hum Hypertens, DOI://10.1038/s41371-021-00483-x (2021)
Dense cellular segmentation for EM using 2D-3D neural network ensembles Guay, MD; Emam, ZAS; Anderson, AB et al. Sci Rep, DOI://10.1038/s41598-021-81590-0 (2021)
An optimized protocol for acquiring and processing cryo-EM data of human 26S proteasome with M1-Ub6 Chen, X; Shi, D; Zhang, P; Walters, KJ; , STAR Protoc, DOI://10.1016/j.xpro.2020.100278 (2021)
A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication Hattori, SI; Higashi-Kuwata, N; Hayashi, H et al. Nat Commun, DOI://10.1038/s41467-021-20900-6 (2021)

Whole-exome sequencing reveals germline-mutated small cell lung cancer subtype with favorable response to DNA repair-targeted therapies Tlemsani, C; Takahashi, N; Pongor, L et al. Sci Transl Med, DOI://10.1126/scitranslmed.abc7488 (2021)
Cenote-Taker 2 democratizes virus discovery and sequence annotation Tisza, MJ; Belford, AK; Domínguez-Huerta, G; Bolduc, B; Buck, CB; , Virus Evol, DOI://10.1093/ve/veaa100 (2021)
Glycolytic metabolism of pathogenic T cells enables early detection of GVHD by 13C-MRI Assmann, JC; Farthing, DE; Saito, K et al. Blood, DOI://10.1182/blood.2020005770 (2021)
TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization Brown, MA; Dotson, GA; Ronquist, S; Emons, G; Rajapakse, I; Ried, T; , Neoplasia, DOI://10.1016/j.neo.2020.12.010 (2021)
Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA Patterson-West, J; Tai, CH; Son, B; Hsieh, ML; Iben, JR; Hinton, DM; , Viruses, DOI://10.3390/v13010084 (2021)
Regulatory roles of Escherichia coli 5'UTR and ORF-internal RNAs detected by 3'end mapping Adams, PP; Baniulyte, G; Esnault, C et al. Elife, DOI://10.7554/eLife.62438 (2021)

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

Pleiotropic genetic influence on birth weight and childhood obesity Chatterjee, S; Ouidir, M; Tekola-Ayele, F; , Sci Rep, DOI://10.1038/s41598-020-80084-9 (2021)
A population scale analysis of rare SNCA variation in the UK Biobank Blauwendraat, C; Makarious, MB; Leonard, HL et al. Neurobiol Dis, DOI://10.1016/j.nbd.2020.105182 (2021)
Platypus and echidna genomes reveal mammalian biology and evolution Zhou, Y; Shearwin-Whyatt, L; Li, J et al. Nature, DOI://10.1038/s41586-020-03039-0 (2021)
Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux Castellano, S; Claxton, DP; Ficici, E et al. J Biol Chem, DOI://10.1074/jbc.RA120.016792 (2021)
Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake Schureck, MA; Darling, JE; Merk, A et al. Elife, DOI://10.7554/eLife.65282 (2021)
Automated assessment of longitudinal biomarker changes at abdominal CT: correlation with subsequent cardiovascular events in an asymptomatic adult screening cohort Graffy, PM; Summers, RM; Perez, AA; Sandfort, V; Zea, R; Pickhardt, PJ; , Abdom Radiol (NY), DOI://10.1007/s00261-020-02885-w (2021)

Great Expectations: A Critical Review of and Suggestions for the Study of Reward Processing as a Cause and Predictor of Depression Nielson, DM; Keren, H; O'Callaghan, G et al. Biol Psychiatry, DOI://10.1016/j.biopsych.2020.06.012 (2021)
END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells Wong, N; John, S; Nussenzweig, A; Canela, A; , Methods Mol Biol, DOI://10.1007/978-1-0716-0644-5_2 (2021)

2020 (431 papers)

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 Zhang, Q; Bastard, P; Liu, Z et al. Science, DOI://10.1126/science.abd4570 (2020)
Scale-Free Dynamics in Animal Groups and Brain Networks Ribeiro, TL; Chialvo, DR; Plenz, D; , Front Syst Neurosci, DOI://10.3389/fnsys.2020.591210 (2020)
Case Report: Single-Cell Transcriptomic Analysis of an Anaplastic Oligodendroglioma Post Immunotherapy Yu, G; Butler, MK; Abdelmaksoud, A et al. Front Oncol, DOI://10.3389/fonc.2020.601452 (2020)
G-Protein biased opioid agonists: 3-hydroxy- N-phenethyl-5-phenylmorphans with three-carbon chain substituents at C9 Gutman, ES; Bow, E; Li, F et al. RSC Med Chem, DOI://10.1039/d0md00104j (2020)

Emx2 regulates hair cell rearrangement but not positional identity within neuromasts Ohta, S; Ji, YR; Martin, D; Wu, DK; , Elife, DOI://10.7554/eLife.60432 (2020)
NCINM: organ dose calculator for patients undergoing nuclear medicine procedures Villoing, D; Cuthbert, TA; Kitahara, CM; Lee, C; , Biomed Phys Eng Express, DOI://10.1088/2057-1976/aba41e (2020)
Genetic determinants of survival in progressive supranuclear palsy: a genome-wide association study Jabbari, E; Koga, S; Valentino, RR et al. Lancet Neurol, DOI://10.1016/S1474-4422(20)30394-X (2020)
Assessment of LIN28A variants in Parkinson's disease in large European cohorts Diez-Fairen, M; Makarious, MB; Bandres-Ciga, S; Blauwendraat, C; , ; , Neurobiol Aging, DOI://10.1016/j.neurobiolaging.2020.12.002 (2020)
Longitudinal changes in network homogeneity in presymptomatic C9orf72 mutation carriers Waugh, RE; Danielian, LE; Shoukry, RFS; Floeter, MK; , Neurobiol Aging, DOI://10.1016/j.neurobiolaging.2020.11.014 (2020)
Progressive multifocal leukoencephalopathy lesion and brain parenchymal segmentation from MRI using serial deep convolutional neural networks Al-Louzi, O; Roy, S; Osuorah, I et al. Neuroimage Clin, DOI://10.1016/j.nicl.2020.102499 (2020)

Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis Dewan, R; Chia, R; Ding, J et al. Neuron, DOI://10.1016/j.neuron.2020.11.005 (2020)
The Evolutionary Dynamics of Influenza A Viruses Circulating in Mallards in Duck Hunting Preserves in Maryland, USA Trovão, NS; Nolting, JM; Slemons, RD; Nelson, MI; Bowman, AS; , Microorganisms, DOI://10.3390/microorganisms9010040 (2020)
Enhancing Question Answering by Injecting Ontological Knowledge through Regularization Goodwin, TR; Demner-Fushman, D; , Proc Conf Empir Methods Nat Lang Process, DOI://10.18653/v1/2020.deelio-1.7 (2020)
Towards Zero-Shot Conditional Summarization with Adaptive Multi-Task Fine-Tuning Goodwin, TR; Savery, ME; Demner-Fushman, D; , Proc Conf Empir Methods Nat Lang Process (2020)
Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations Zheng, W; Dignon, GL; Jovic, N et al. J Phys Chem B, DOI://10.1021/acs.jpcb.0c10489 (2020)
Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration Hargrove-Grimes, P; Mondal, AK; Gumerson, J et al. PLoS Genet, DOI://10.1371/journal.pgen.1009259 (2020)

Evolving schema representations in orbitofrontal ensembles during learning Zhou, J; Jia, C; Montesinos-Cartagena, M; Gardner, MPH; Zong, W; Schoenbaum, G; , Nature, DOI://10.1038/s41586-020-03061-2 (2020)
Seeker: alignment-free identification of bacteriophage genomes by deep learning Auslander, N; Gussow, AB; Benler, S; Wolf, YI; Koonin, EV; , Nucleic Acids Res, DOI://10.1093/nar/gkaa856 (2020)
Disseminated Mycobacterium marinum in HIV unmasked by Immune Reconstitution Inflammatory Syndrome Manion, M; Dulanto Chiang, A; Pei, L et al. J Infect Dis, DOI://10.1093/infdis/jiaa769 (2020)
Resting State Functional Connectivity Is Decreased Globally Across the C9orf72 Mutation Spectrum Smallwood Shoukry, RF; Clark, MG; Floeter, MK; , Front Neurol, DOI://10.3389/fneur.2020.598474 (2020)
An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development Chopp, LB; Gopalan, V; Ciucci, T et al. Immunity, DOI://10.1016/j.immuni.2020.10.024 (2020)
Identification of a novel long-acting 4'-modified nucleoside reverse transcriptase inhibitor against HBV Higashi-Kuwata, N; Hayashi, S; Kumamoto, H et al. J Hepatol, DOI://10.1016/j.jhep.2020.12.006 (2020)

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Integrative analysis suggests cell type-specific decoding of NF-κB dynamics Martin, EW; Pacholewska, A; Patel, H; Dashora, H; Sung, MH; Sci Signal, DOI://10.1126/scisignal.aax7195 (2020)
Distribution and evolution of the serine/aspartate racemase family in plants Uda, K; Edashige, Y; Nishimura, R et al. Phytochemistry, DOI://10.1016/j.phytochem.2019.112164 (2020)

Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation Lee, SY; Hung, S; Esnault, C et al. Cell Rep, DOI://10.1016/j.celrep.2020.01.094 (2020)
Low Serum Insulinlike Growth Factor II Levels Correlate with High BMI in American Indian Adults Muller, YL; Hanson, RL; Mahkee, D et al. Obesity (Silver Spring), DOI://10.1002/oby.22741 (2020)
CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG Liu, Z; Zhang, X; Lei, H et al. Nat Commun, DOI://10.1038/s41467-020-14684-4 (2020)
A case report of multiple primary prostate tumors with differential drug sensitivity Wilkinson, S; Harmon, SA; Terrigino, NT et al. Nat Commun, DOI://10.1038/s41467-020-14657-7 (2020)
A resource for the detailed 3D mapping of white matter pathways in the marmoset brain Liu, C; Ye, FQ; Newman, JD et al. Nat. Neurosci., DOI://10.1038/s41593-019-0575-0 (2020)
The Pharmacopea within Triatomine Salivary Glands Santiago, PB; de Araújo, CN; Charneau, S et al. Trends Parasitol., DOI://10.1016/j.pt.2019.12.014 (2020)

MY-5445, a phosphodiesterase type 5 inhibitor, resensitizes ABCG2-overexpressing multidrug-resistant cancer cells to cytotoxic anticancer drugs Wu, CP; Lusvarghi, S; Tseng, PJ et al. Am J Cancer Res, 2156-6976 (2020)
The Glu102 mutation disrupts higher-order oligomerization of the sigma 1 receptor Abramyan, AM; Yano, H; Xu, M et al. Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2019.12.012 (2020)
High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1 Liao, TJ; Jang, H; Nussinov, R; Fushman, D; J. Am. Chem. Soc., DOI://10.1021/jacs.9b10710 (2020)
Placental DNA methylation changes associated with maternal prepregnancy BMI and gestational weight gain Shrestha, D; Ouidir, M; Workalemahu, T; Zeng, X; Tekola-Ayele, F; Int J Obes (Lond), DOI://10.1038/s41366-020-0546-2 (2020)
Refining genome-wide associated loci for serum uric acid in individuals with African ancestry Chen, G; Shriner, D; Doumatey, AP et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddz272 (2020)
A customizable deep learning model for nosocomial risk prediction from critical care notes with indirect supervision Goodwin, TR; Demner-Fushman, D; J Am Med Inform Assoc, DOI://10.1093/jamia/ocaa004 (2020)

Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes Pascini, TV; Ramalho-Ortigão, M; Ribeiro, JM; Jacobs-Lorena, M; Martins, GF; BMC Genomics, DOI://10.1186/s12864-020-6543-y (2020)
Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans Mitchell, KA; Nichols, N; Tang, W et al. Nat Commun, DOI://10.1038/s41467-020-14448-0 (2020)
Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study Smith, JL; Ries, RE; Hylkema, T et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-19-1800 (2020)
TCR Repertoires of Thymic Conventional and Regulatory T Cells: Identification and Characterization of Both Unique and Shared TCR Sequences Ko, A; Watanabe, M; Nguyen, T et al. J. Immunol., DOI://10.4049/jimmunol.1901006 (2020)
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 (521 papers)

A novel HIV-1 protease inhibitor, GRL-044, has potent activity against various HIV-1s with an extremely high genetic barrier to the emergence of HIV-1 drug resistance Aoki, M; Chang, SB; Das, D et al. Glob Health Med, DOI://10.35772/ghm.2019.01003 (2019)
MAIT cells are imprinted by the microbiota in early life and promote tissue repair Constantinides, MG; Link, VM; Tamoutounour, S et al. Science, DOI://10.1126/science.aax6624 (2019)
Amphetamines signal through intracellular TAAR1 receptors coupled to Gα13 and GαS in discrete subcellular domains Underhill, SM; Hullihen, PD; Chen, J et al. Mol. Psychiatry, DOI://10.1038/s41380-019-0469-2 (2019)
GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia Belver, L; Yang, AY; Albero, R et al. Cancer Discov, DOI://10.1158/2159-8290.CD-19-0471 (2019)
Sptlc1 is essential for myeloid differentiation and hematopoietic homeostasis Parthibane, V; Acharya, D; Srideshikan, SM et al. Blood Adv, DOI://10.1182/bloodadvances.2019000729 (2019)
Genome-Wide Association Study in Irradiated Childhood Cancer Survivors Identifies HTR2A for Subsequent Basal Cell Carcinoma Sapkota, Y; Turcotte, LM; Ehrhardt, MJ et al. J. Invest. Dermatol., DOI://10.1016/j.jid.2019.02.029 (2019)
Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq) Carter, B; Ku, WL; Kang, JY et al. Nat Commun, DOI://10.1038/s41467-019-11559-1 (2019)
Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex Pillon, MC; Hsu, AL; Krahn, JM et al. Nat. Struct. Mol. Biol., DOI://10.1038/s41594-019-0289-8 (2019)
Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer Magen, A; Das Sahu, A; Lee, JS et al. Cell Rep, DOI://10.1016/j.celrep.2019.06.067 (2019)
ATP-dependent thermostabilization of human P-glycoprotein (ABCB1) is blocked by modulators Lusvarghi, S; Ambudkar, SV; , Biochem. J., DOI://10.1042/BCJ20190736 (2019)
Organ Doses from Chest Radiographs in Tuberculosis Patients in Canada and Their Uncertainties in Periods from 1930 to 1969 Kocher, DC; Apostoaei, AI; Thomas, BA; Borrego, D; Lee, C; Zablotska, LB; , Health Phys, DOI://10.1097/HP.0000000000001171 (2019)
Association of dietary folate and vitamin B-12 intake with genome-wide DNA methylation in blood: a large-scale epigenome-wide association analysis in 5841 individuals Mandaviya, PR; Joehanes, R; Brody, J et al. Am. J. Clin. Nutr., DOI://10.1093/ajcn/nqz031 (2019)
PARP1 inhibition alleviates injury in ARH3-deficient mice and human cells Mashimo, M; Bu, X; Aoyama, K et al. JCI Insight, DOI://10.1172/jci.insight.124519 (2019)
Placental malaria vaccine candidate antigen VAR2CSA displays atypical domain architecture in some Plasmodium falciparum strains Doritchamou, JYA; Morrison, R; Renn, JP et al. Commun Biol, DOI://10.1038/s42003-019-0704-z (2019)
The Selective Class IIa Histone Deacetylase Inhibitor TMP195 Resensitizes ABCB1- and ABCG2-Overexpressing Multidrug-Resistant Cancer Cells to Cytotoxic Anticancer Drugs Wu, CP; Lusvarghi, S; Wang, JC et al. Int J Mol Sci, DOI://10.3390/ijms21010238 (2019)
Assessment of APOE in atypical parkinsonism syndromes Sabir, MS; Blauwendraat, C; Ahmed, S et al. Neurobiol. Dis., DOI://10.1016/j.nbd.2019.02.016 (2019)
SLC35A2-CDG: Functional characterization, expanded molecular, clinical, and biochemical phenotypes of 30 unreported Individuals Ng, BG; Sosicka, P; Agadi, S et al. Hum. Mutat., DOI://10.1002/humu.23731 (2019)
Association between epigenetic age acceleration and depressive symptoms in a prospective cohort study of urban-dwelling adults Beydoun, MA; Hossain, S; Chitrala, KN et al. J Affect Disord, DOI://10.1016/j.jad.2019.06.032 (2019)
Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons Sheng, C; Javed, U; Rosenthal, J; Yin, J; Qin, B; Yuan, Q; J Vis Exp, DOI://10.3791/60287 (2019)
The Genetic Architecture of Parkinson Disease in Spain: Characterizing Population-Specific Risk, Differential Haplotype Structures, and Providing Etiologic Insight Bandres-Ciga, S; Ahmed, S; Sabir, MS et al. Mov. Disord., DOI://10.1002/mds.27864 (2019)
Gene signature predictive of hepatocellular carcinoma patient response to transarterial chemoembolization Fako, V; Martin, SP; Pomyen, Y et al. Int. J. Biol. Sci., DOI://10.7150/ijbs.39534 (2019)
Assessment of the Association of D2 Dopamine Receptor Gene and Reported Allele Frequencies With Alcohol Use Disorders: A Systematic Review and Meta-analysis Jung, Y; Montel, RA; Shen, PH; Mash, DC; Goldman, D; JAMA Netw Open, DOI://10.1001/jamanetworkopen.2019.14940 (2019)
Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies Nalls, MA; Blauwendraat, C; Vallerga, CL et al. Lancet Neurol, DOI://10.1016/S1474-4422(19)30320-5 (2019)

Resistin-like Molecule α Provides Vitamin-A-Dependent Antimicrobial Protection in the Skin Harris, TA; Gattu, S; Propheter, DC et al. Cell Host Microbe, DOI://10.1016/j.chom.2019.04.004 (2019)
Complementary Task Structure Representations in Hippocampus and Orbitofrontal Cortex during an Odor Sequence Task Zhou, J; Montesinos-Cartagena, M; Wikenheiser, AM; Gardner, MPH; Niv, Y; Schoenbaum, G; Curr. Biol., DOI://10.1016/j.cub.2019.08.040 (2019)
Negative-Stain Transmission Electron Microscopy of Molecular Complexes for Image Analysis by 2D Class Averaging Gallagher, JR; Kim, AJ; Gulati, NM; Harris, AK; Curr Protoc Microbiol, DOI://10.1002/cpmc.90 (2019)
NAA10 polyadenylation signal variants cause syndromic microphthalmia Johnston, JJ; Williamson, KA; Chou, CM et al. J. Med. Genet., DOI://10.1136/jmedgenet-2018-105836 (2019)
Immunoelectron Microscopy of Viral Antigens Gulati, NM; Torian, U; Gallagher, JR; Harris, AK; Curr Protoc Microbiol, DOI://10.1002/cpmc.86 (2019)
The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity Jevtić, P; Schibler, AC; Wesley, CC; Pegoraro, G; Misteli, T; Levy, DL; , EMBO Rep., DOI://10.15252/embr.201847283 (2019)

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma Gryder, BE; Pomella, S; Sayers, C et al. Nat. Genet., DOI://10.1038/s41588-019-0534-4 (2019)
Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma Yeung, C; Gibson, AE; Issaq, SH et al. Cancer Res., DOI://10.1158/0008-5472.CAN-19-0217 (2019)
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire Shinoda, K; Maman, Y; Canela, A; Schatz, DG; Livak, F; Nussenzweig, A; , Cell Rep, DOI://10.1016/j.celrep.2019.11.088 (2019)
Targeting the Chromosomal Passenger Complex Subunit INCENP Induces Polyploidization, Apoptosis, and Senescence in Neuroblastoma Sun, M; Veschi, V; Bagchi, S et al. Cancer Res., DOI://10.1158/0008-5472.CAN-19-0695 (2019)
Meta-analysis of Chromatin Programming by Steroid Receptors Paakinaho, V; Swinstead, EE; Presman, DM; Grøntved, L; Hager, GL; , Cell Rep, DOI://10.1016/j.celrep.2019.08.039 (2019)
Sympathetic activity contributes to the fMRI signal Özbay, PS; Chang, C; Picchioni, D et al. Commun Biol, DOI://10.1038/s42003-019-0659-0 (2019)
Evidence for a Causal Role of the SH2B3-β 2 M Axis in Blood Pressure Regulation Keefe, JA; Hwang, SJ; Huan, T et al. Hypertension, DOI://10.1161/HYPERTENSIONAHA.118.12094 (2019)
Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus Mistry, P; Nakabo, S; O'Neil, L et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1908576116 (2019)
The Bone Marrow Protects and Optimizes Immunological Memory during Dietary Restriction Collins, N; Han, SJ; Enamorado, M et al. Cell, DOI://10.1016/j.cell.2019.07.049 (2019)
Relationship between human leukocyte antigen alleles and risk of Kaposi's sarcoma in Cameroon Cornejo Castro, EM; Morrison, BJ; Marshall, VA et al. Genes Immun., DOI://10.1038/s41435-019-0077-9 (2019)
Integration of TGF-β-induced Smad signaling in the insulin-induced transcriptional response in endothelial cells Budi, EH; Hoffman, S; Gao, S; Zhang, YE; Derynck, R; , Sci Rep, DOI://10.1038/s41598-019-53490-x (2019)
Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling Adikaram, PR; Zhang, JH; Kittock, CM et al. Commun Biol, DOI://10.1038/s42003-019-0585-1 (2019)
Differential expression and subcellular localization of Copines in mouse retina Goel, M; Li, T; Badea, TC; J. Comp. Neurol., DOI://10.1002/cne.24684 (2019)
Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1 Martin, KB; Williams, IM; Cluzeau, CV et al. Int J Mol Sci, DOI://10.3390/ijms21010292 (2019)
A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers El Khattabi, L; Zhao, H; Kalchschmidt, J et al. Cell, DOI://10.1016/j.cell.2019.07.011 (2019)
Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae Kulkarni, SD; Zhou, F; Sen, ND; Zhang, H; Hinnebusch, AG; Lorsch, JR; BMC Biol., DOI://10.1186/s12915-019-0718-5 (2019)
A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity Bradfield, JP; Vogelezang, S; Felix, JF et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddz161 (2019)
Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in mice Wang, Z; Xu, X; Li, JL; Palmer, C; Maric, D; Dean, J; Nat Commun, DOI://10.1038/s41467-019-13193-3 (2019)

A Peripheral Blood DNA Methylation Signature of Hepatic Fat Reveals a Potential Causal Pathway for Nonalcoholic Fatty Liver Disease Ma, J; Nano, J; Ding, J et al. Diabetes, DOI://10.2337/DB18-1193 (2019)
Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival Tang, W; Putluri, V; Ambati, CR; Dorsey, TH; Putluri, N; Ambs, S; , Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-19-0094 (2019)
ARSA variants in α-synucleinopathies Makarious, MB; Diez-Fairen, M; Krohn, L et al. Brain, DOI://10.1093/brain/awz340 (2019)
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands Farrer, RA; Chang, M; Davis, MJ et al. mBio, DOI://10.1128/mBio.02306-19 (2019)
Contribution of SLC22A12 on hypouricemia and its clinical significance for screening purposes Cha, DH; Gee, HY; Cachau, R et al. Sci Rep, DOI://10.1038/s41598-019-50798-6 (2019)
Dose coefficients of mesh-type ICRP reference computational phantoms for external exposures of neutrons, protons, and helium ions Yeom YS, Choi C, et al. Nuc. Engg. Tech., doi://10.1016/j.net.2019.12.020 (2019)

White Blood Cell Count and Risk of Incident Lung Cancer in the UK Biobank Wong JYY, Bassig BA et al. JNCI Cancer Spectrum, doi://10.1093/jncics/pkz102 (2019)
Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery Botos I, Lountos GT et al. Cur. Res. Struct. Biol. , doi://0.1016/j.crstbi.2019.10.001 (2019)
Dosimetric impact of voxel resolutions of computational human phantoms for external photon exposure Choonsik Lee, Andreu Badal, Yeon Soo Yeom, Keith T Griffin and Dayton McMillan Biomed. Phys. Engg. Exp. , doi://10.1088/2057-1976/ab2850 (2019)
Joint modelling of competing risks and current status data: an application to a spontaneous labour study Youjin Lee Mei; Cheng Wang; Katherine L. Grantz; Rajeshwari Sundaram Royal Statistical Society, doi://10.1111/rssc.12351 (2019)
Keratinocyte-intrinsic MHCII expression controls microbiota-induced Th1 cell responses Tamoutounour, S; Han, SJ; Deckers, J et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1912432116 (2019)
Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women Jones, GS; Spencer Feigelson, H; Falk, RT et al. PLoS ONE, DOI://10.1371/journal.pone.0216114 (2019)

NMR Analysis of Apo Glutamine-Binding Protein Exposes Challenges in the Study of Interdomain Dynamics Kooshapur, H; Ma, J; Tjandra, N; Bermejo, GA; Angew. Chem. Int. Ed. Engl., DOI://10.1002/anie.201911015 (2019)
Proteomics Pipeline for Identifying Variant Proteins in Plasmodium falciparum Parasites Isolated from Children Presenting with Malaria Gonzales Hurtado, PA; Morrison, R; Ribeiro, JMC et al. J. Proteome Res., DOI://10.1021/acs.jproteome.9b00169 (2019)
Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry Guven-Maiorov, E; Tsai, CJ; Nussinov, R; , Front Oncol, DOI://10.3389/fonc.2019.01236 (2019)
Rat Orbitofrontal Ensemble Activity Contains Multiplexed but Dissociable Representations of Value and Task Structure in an Odor Sequence Task Zhou, J; Gardner, MPH; Stalnaker, TA et al. Curr. Biol., DOI://10.1016/j.cub.2019.01.048 (2019)
Non-Leishmania Parasite in Fatal Visceral Leishmaniasis-Like Disease, Brazil Maruyama, SR; de Santana, AKM; Takamiya, NT et al. Emerging Infect. Dis., DOI://10.3201/eid2511.181548 (2019)
A Phase II Study of Tumor-infiltrating Lymphocyte Therapy for Human Papillomavirus-associated Epithelial Cancers Stevanovic, S; Helman, SR; Wunderlich, JR et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-18-2722 (2019)

Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans Mitchell, KA; Nichols, N; Tang, W et al. Nat Commun, DOI://10.1038/s41467-019-13732-y (2019)
The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease Bandres-Ciga, S; Saez-Atienzar, S; Bonet-Ponce, L et al. Mov. Disord., DOI://10.1002/mds.27614 (2019)
The GATOR complex regulates an essential response to meiotic double-stranded breaks in Drosophila Wei, Y; Bettedi, L; Ting, CY et al. Elife, DOI://10.7554/eLife.42149 (2019)
Autosomal recessive congenital cataracts linked to HSF4 in a consanguineous Pakistani family Jiao, X; Khan, SY; Kaul, H et al. PLoS ONE, DOI://10.1371/journal.pone.0225010 (2019)
White Matter Microstructure in Pediatric Bipolar Disorder and Disruptive Mood Dysregulation Disorder Linke, JO; Adleman, NE; Sarlls, J et al. J Am Acad Child Adolesc Psychiatry, DOI://10.1016/j.jaac.2019.05.035 (2019)
DENND5B Regulates Intestinal Triglyceride Absorption and Body Mass Gordon, SM; Neufeld, EB; Yang, Z et al. Sci Rep, DOI://10.1038/s41598-019-40296-0 (2019)
Reply to Spreng et al.: Multiecho fMRI denoising does not remove global motion-associated respiratory signals Power, JD; Lynch, CJ; Gilmore, AW; Gotts, SJ; Martin, A; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1909852116 (2019)
Single molecule analysis of lamin dynamics Serebryannyy, LA; Ball, DA; Karpova, TS; Misteli, T; , Methods, DOI://10.1016/j.ymeth.2018.08.009 (2019)
HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction Neckles, C; Boer, RE; Aboreden, N et al. RNA, DOI://10.1261/rna.072454.119 (2019)
Head and Neck Cancers Promote an Inflammatory Transcriptome Through Coactivation of Classic and Alternative NF-κB Pathways Yang, X; Cheng, H; Chen, J et al. Cancer Immunol Res, DOI://10.1158/2326-6066.CIR-18-0832 (2019)
Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3 Wang, S; Chim, B; Su, Y et al. Genes Dev., DOI://10.1101/gad.325100.119 (2019)
Genome-Wide Profiling of Cervical RNA-Binding Proteins Identifies Human Papillomavirus Regulation of RNASEH2A Expression by Viral E7 and E2F1 Xu, J; Liu, H; Yang, Y et al. mBio, DOI://10.1128/mBio.02687-18 (2019)
Classification of GBA Variants and Their Effects in Synucleinopathies Gan-Or, Z; Alcalay, RN; Makarious, MB; Scholz, SW; Blauwendraat, C; , ; Mov. Disord., DOI://10.1002/mds.27803 (2019)
H3.3K4M destabilizes enhancer H3K4 methyltransferases MLL3/MLL4 and impairs adipose tissue development Jang, Y; Broun, A; Wang, C et al. Nucleic Acids Res., DOI://10.1093/nar/gky982 (2019)
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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)
Secondary Metabolites from the Fungus Dictyosporium sp. and Their MALT1 Inhibitory Activities Tran, TD; Wilson, BAP; Henrich, CJ et al. J. Nat. Prod., DOI://10.1021/acs.jnatprod.8b00871 (2019)
The phenotypic landscape of a Tbc1d24 mutant mouse includes convulsive seizures resembling human early infantile epileptic encephalopathy Tona, R; Chen, W; Nakano, Y et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy445 (2019)
Hydrogen-bond dependent conformational switching: a computational challenge from experimental thermochemistry Luccarelli, J; Paton, RS; J. Org. Chem., DOI://10.1021/acs.joc.8b02436 (2019)

Early infantile-onset epileptic encephalopathy 28 due to a homozygous microdeletion involving the WWOX gene in a region of uniparental disomy Davids, M; Markello, T; Wolfe, LA et al. Hum. Mutat., DOI://10.1002/humu.23675 (2019)
A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics Bachu, M; Tamura, T; Chen, C et al. J. Biol. Chem., DOI://10.1074/jbc.RA118.005550 (2019)
Genetic analysis of neurodegenerative diseases in a pathology cohort Blauwendraat C, Pletnikova O, Geiger, JT et al Neurobiology of Aging, 10.1016/j.neurobiolaging.2018.11.007 (2019)
Conformational stability and dynamics of the cancer-associated isoform δ133p53β are modulated by p53 peptides and p53-specific DNA Lei, J; Qi, R; Tang, Y et al. FASEB J., DOI://10.1096/fj.201801973R (2019)
hnRNP L-dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma Kishor, A; Ge, Z; Hogg, JR; EMBO J., DOI://10.15252/embj.201899128 (2019)
Linear mixed models for association analysis of quantitative traits with next-generation sequencing data Chiu, CY; Yuan, F; Zhang, BS et al. Genet. Epidemiol., DOI://10.1002/gepi.22177 (2019)

Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements Marinelli, F; Fiorin, G; Structure, DOI://10.1016/j.str.2018.10.013 (2019)
Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury Harrison, OJ; Linehan, JL; Shih, HY et al. Science, DOI://10.1126/science.aat6280 (2019)
Mosaic Y loss is moderately associated with solid tumor risk Loftfield, E; Zhou, W; Yeager, M; Chanock, SJ; Freedman, ND; Machiela, MJ; Cancer Res., DOI://10.1158/0008-5472.CAN-18-2566 (2019)
Targeted deletion of an NRL- and CRX-regulated alternative promoter specifically silences FERM and PDZ domain containing 1 (Frmpd1) in rod photoreceptors Campla, CK; Mast, H; Dong, L et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddy388 (2019)
Practical issues in using generalized estimating equations for inference on transitions in longitudinal data: What is being estimated Bible, J; Albert, PS; Simons-Morton, BG; Liu, D; Stat Med, DOI://10.1002/sim.8014 (2019)
Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation Michael, DG; Pranzatelli, TJF; Warner, BM; Yin, H; Chiorini, JA; J. Dent. Res., DOI://10.1177/0022034518806518 (2019)

Organ Dose Estimation accounting for uncertainty for pediatric and young adult CT scans in the United Kingdom Lee, C; Journy, N; Moroz, BE et al. Radiat Prot Dosimetry, DOI://10.1093/rpd/ncy184 (2019)
Optimizing and evaluating biomarker combinations as trial-level general surrogates Gabriel, EE; Sachs, MC; Daniels, MJ; Halloran, ME; Stat Med, DOI://10.1002/sim.7996 (2019)
Interface-Based Structural Prediction of Novel Host-Pathogen Interactions Guven-Maiorov, E; Tsai, CJ; Ma, B; Nussinov, R; Methods Mol. Biol., DOI://10.1007/978-1-4939-8736-8_18 (2019)
QuagmiR: A Cloud-based Application for IsomiR Big Data Analytics Bofill-De Ros, X; Chen, K; Chen, S et al. Bioinformatics, DOI://10.1093/bioinformatics/bty843 (2019)
Early life disadvantage and adult adiposity: tests of sensitive periods during childhood and behavioural mediation in adulthood Gilman, SE; Huang, YT; Jimenez, MP et al. Int J Epidemiol, DOI://10.1093/ije/dyy199 (2019)
A Bayesian multi-dimensional couple-based latent risk model with an application to infertility Hwang, BS; Chen, Z; Louis, GMB; Albert, PS; Biometrics, DOI://10.1111/biom.12972 (2019)

Half blind superiority tests for clinical trials of anti-infective drugs Follmann, D; Brittain, E; Lumbard, K; Stat Med, DOI://10.1002/sim.7954 (2019)
Time-varying whole-brain functional network connectivity coupled to task engagement Xie H, Gonzalez-Castillo J, Handwerker D, Bandettini P Network Neuro Science, doi://10.1162/netn_a_00051 (2019)
Neurophysiological Changes Associated with Antidepressant Response to Ketamine Not Observed in a Negative Trial of Scopolamine in Major Depressive Disorder Park, L; Furey, M; Nugent, AC et al. Int. J. Neuropsychopharmacol., DOI://10.1093/ijnp/pyy051 (2019)
Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia Dillon, LW; Hayati, S; Roloff, GW et al. Haematologica, DOI://10.3324/haematol.2018.203133 (2019)
Whole Blood Gene Expression Associated with Clinical Biological Age Lin, H; Lunetta, KL; Zhao, Q et al. J. Gerontol. A Biol. Sci. Med. Sci., DOI://10.1093/gerona/gly164 (2019)
Deep-learning-assisted Volume Visualization Cheng, HC; Cardone, A; Jain, S et al. IEEE Trans Vis Comput Graph, DOI://10.1109/TVCG.2018.2796085 (2019)

A feasibility study to reduce misclassification error in occupational dose estimates for epidemiological studies using body size-dependent computational phantoms Sarah Kim, Lienard Chang, Elizabeth Mosher, Choonik Lee, and Choonsik IEEE Transactions on Radiation and Plasma Medical Sciences, 0.1109/TRPMS.2018.2847227 (2019)
Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium Merino, J; Dashti, HS; Li, SX et al. Mol. Psychiatry, DOI://10.1038/s41380-018-0079-4 (2019)
Tightly Integrated Genomic and Epigenomic Data Mining Using Tensor Decomposition Fang, J Bioinformatics, DOI://10.1093/bioinformatics/bty513 (2019)
Mapping the neuroanatomic substrates of cognition in familial attention deficit hyperactivity disorder Muster, R; Choudhury, S; Sharp, W; Kasparek, S; Sudre, G; Shaw, P; Psychol Med, DOI://10.1017/S0033291718001241 (2019)
A joint spatial factor analysis model to accommodate data from misaligned areal units with application to Louisiana social vulnerability Nethery, RC; Sandler, DP; Zhao, S; Engel, LS; Kwok, RK; Biostatistics, DOI://10.1093/biostatistics/kxy016 (2019)
Ketamine has distinct electrophysiological and behavioral effects in depressed and healthy subjects Nugent, AC; Ballard, ED; Gould, TD et al. Mol. Psychiatry, DOI://10.1038/s41380-018-0028-2 (2019)

2018 (494 papers)

An approximate joint model for multiple paired longitudinal outcomes and time-to-event data Elmi, AF; Grantz, KL; Albert, PS; , Biometrics, DOI://10.1111/biom.12862 (2018)
Methylomic profiling and replication implicates deregulation of PCSK9 in alcohol use disorder Lohoff, FW; Sorcher, JL; Rosen, AD et al. Mol. Psychiatry, DOI://10.1038/mp.2017.168 (2018)
Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates Zhang, M; Zheng, J; Nussinov, R; Ma, B; Antibodies (Basel), DOI://10.3390/antib7030025 (2018)
Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water" Best, RB; Zheng, W; Borgia, A et al. Science, DOI://10.1126/science.aar7101 (2018)
Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA Tagawa, T; Gao, S; Koparde, VN et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1816183115 (2018)
Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism Burke, EA; Frucht, SJ; Thompson, K et al. Clin. Genet., DOI://10.1111/cge.13172 (2018)
Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures Lee, JS; Adler, L; Karathia, H et al. Cell, DOI://10.1016/j.cell.2018.07.019 (2018)
Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells Bodogai, M; O'Connell, J; Kim, K et al. Sci Transl Med, DOI://10.1126/scitranslmed.aat4271 (2018)
Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits Evangelou, E; Warren, HR; Mosen-Ansorena, D et al. Nat. Genet., DOI://10.1038/s41588-018-0205-x (2018)
Fully automated segmentation and quantification of visceral and subcutaneous fat at abdominal CT: application to a longitudinal adult screening cohort Lee, SJ; Liu, J; Yao, J; Kanarek, A; Summers, RM; Pickhardt, PJ; Br J Radiol, DOI://10.1259/bjr.20170968 (2018)
Analysis of type 2 diabetes and obesity genetic variants in Mexican Pima Indians: Marked allelic differentiation among Amerindians at HLA Hsueh, WC; Bennett, PH; Esparza-Romero, J et al. Ann. Hum. Genet., DOI://10.1111/ahg.12252 (2018)
A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation Ferreira, CR; Xia, ZJ; Clément, A et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.09.003 (2018)
Reservoir pH replica exchange Damjanovic, A; Miller, BT; Okur, A; Brooks, BR; J Chem Phys, DOI://10.1063/1.5027413 (2018)
Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides Narayan, B; Herbert, C; Yuan, Y; Rodriguez, BJ; Brooks, BR; Buchete, NV; J Chem Phys, DOI://10.1063/1.5027580 (2018)
EXP2 is a nutrient-permeable channel in the vacuolar membrane of Plasmodium and is essential for protein export via PTEX Garten, M; Nasamu, AS; Niles, JC; Zimmerberg, J; Goldberg, DE; Beck, JR; Nat Microbiol, DOI://10.1038/s41564-018-0222-7 (2018)
Non-classical monocytes as mediators of tissue destruction in arthritis Puchner, A; Saferding, V; Bonelli, M et al. Ann. Rheum. Dis., DOI://10.1136/annrheumdis-2018-213250 (2018)
Abruptio placentae risk and genetic variations in mitochondrial biogenesis and oxidative phosphorylation: replication of a candidate gene association study Workalemahu, T; Enquobahrie, DA; Gelaye, B et al. Am. J. Obstet. Gynecol., DOI://10.1016/j.ajog.2018.08.042 (2018)
Activation of Th1 Immunity within the Tumor Microenvironment Is Associated with Clinical Response to Lenalidomide in Chronic Lymphocytic Leukemia Aue, G; Sun, C; Liu, D et al. J. Immunol., DOI://10.4049/jimmunol.1800570 (2018)
Comparison of normal tissue dose calculation methods for epidemiological studies of radiotherapy patients Mille, MM; Jung, JW; Lee, C; Kuzmin, GA; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aabd4f (2018)
Novel variants in SPTAN1 without epilepsy: An expansion of the phenotype Gartner, V; Markello, TC; Macnamara, E et al. Am. J. Med. Genet. A, DOI://10.1002/ajmg.a.40628 (2018)
Novel truncating mutation in TENM3 in siblings with motor developmental delay, ocular coloboma, oval cornea, without microphthalmia Stephen, J; Nampoothiri, S; Kuppa, S et al. Am. J. Med. Genet. A, DOI://10.1002/ajmg.a.40658 (2018)
Exogenous ghrelin administration increases alcohol self-administration and modulates brain functional activity in heavy-drinking alcohol-dependent individuals Farokhnia, M; Grodin, EN; Lee, MR et al. Mol. Psychiatry, DOI://10.1038/mp.2017.226 (2018)
Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase Hickman, AB; Voth, AR; Ewis, H; Li, X; Craig, NL; Dyda, F; Nucleic Acids Res., DOI://10.1093/nar/gky838 (2018)
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila Wang, Y; Cho, DY; Lee, H; Fear, J; Oliver, B; Przytycka, TM; Nat Commun, DOI://10.1038/s41467-018-06382-z (2018)
High density lipoprotein proteome is associated with cardiovascular risk factors and atherosclerosis burden as evaluated by coronary CT angiography Gordon, SM; Chung, JH; Playford, MP et al. Atherosclerosis, DOI://10.1016/j.atherosclerosis.2018.09.032 (2018)
Agreement in Histological Assessment of Mitotic Activity Between Microscopy and Digital Whole Slide Images Informs Conversion for Clinical Diagnosis Wei, BR; Halsey, CH; Hoover, SB et al. Acad Pathol, DOI://10.1177/2374289519859841 (2018)
Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy Norouzi, D; Zhurkin, VB; Biophys. J., DOI://10.1016/j.bpj.2018.06.032 (2018)
GCN5L1 interacts with αTAT1 and RanBP2 to regulate hepatic α-tubulin acetylation and lysosome trafficking Wu, K; Wang, L; Chen, Y et al. J. Cell. Sci., DOI://10.1242/jcs.221036 (2018)
Sequential loss of tumor surface antigens following chimeric antigen receptor T-cell therapies in diffuse large B-cell lymphoma Shalabi, H; Kraft, IL; Wang, HW et al. Haematologica, DOI://10.3324/haematol.2017.183459 (2018)
GATA2 deficiency and human hematopoietic development modeled using induced pluripotent stem cells Jung, M; Cordes, S; Zou, J et al. Blood Adv, DOI://10.1182/bloodadvances.2018017137 (2018)

Interdomain Stabilization Impairs CD4 Binding and Improves Immunogenicity of the HIV-1 Envelope Trimer Zhang, P; Gorman, J; Geng, H et al. Cell Host Microbe, DOI://10.1016/j.chom.2018.05.002 (2018)
Genetic variations and risk of placental abruption: A genome-wide association study and meta-analysis of genome-wide association studies Workalemahu, T; Enquobahrie, DA; Gelaye, B et al. Placenta, DOI://10.1016/j.placenta.2018.04.008 (2018)
Role of humoral immunity against hepatitis B virus core antigen in the pathogenesis of acute liver failure Chen, Z; Diaz, G; Pollicino, T et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1809028115 (2018)
Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism Stephen, J; Maddirevula, S; Nampoothiri, S et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2018.11.001 (2018)
Using Devices to Assess Physical Activity and Sedentary Behavior in a Large Cohort Study, the Women's Health Study Lee, IM; Shiroma, EJ; Evenson, KR; Kamada, M; LaCroix, AZ; Buring, JE; J Meas Phys Behav, DOI://10.1123/jmpb.2018-0005 (2018)
Co-activation patterns in resting-state fMRI signals Liu, X; Zhang, N; Chang, C; Duyn, JH; Neuroimage, DOI://10.1016/j.neuroimage.2018.01.041 (2018)
Using mobile location data in biomedical research while preserving privacy Goldenholz, DM; Goldenholz, SR; Krishnamurthy, KB et al. J Am Med Inform Assoc, DOI://10.1093/jamia/ocy071 (2018)
Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease Splinter, K; Adams, DR; Bacino, CA et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1714458 (2018)
GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes Franceschini, N; Giambartolomei, C; de Vries, PS et al. Nat Commun, DOI://10.1038/s41467-018-07340-5 (2018)
Hallmarks of primate lentiviral immunodeficiency infection recapitulate loss of innate lymphoid cells Mudd, JC; Busman-Sahay, K; DiNapoli, SR et al. Nat Commun, DOI://10.1038/s41467-018-05528-3 (2018)
The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage Brady, OA; Jeong, E; Martina, JA; Pirooznia, M; Tunc, I; Puertollano, R; Elife, DOI://10.7554/eLife.40856 (2018)
Tenectin recruits integrin to stabilize bouton architecture and regulate vesicle release at the Drosophila neuromuscular junction Wang, Q; Han, TH; Nguyen, P; Jarnik, M; Serpe, M; Elife, DOI://10.7554/eLife.35518 (2018)

CD22-targeted CAR T cells induce remission in B-ALL that is naive or resistant to CD19-targeted CAR immunotherapy Fry, TJ; Shah, NN; Orentas, RJ et al. Nat. Med., DOI://10.1038/nm.4441 (2018)
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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)
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)
Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation Meng, F; Bellaiche, MMJ; Kim, JY; Zerze, GH; Best, RB; Chung, HS; Biophys. J., DOI://10.1016/j.bpj.2017.12.025 (2018)
Identification of Casz1 as a Regulatory Protein Controlling T Helper Cell Differentiation, Inflammation, and Immunity Bhaskaran, N; Liu, Z; Saravanamuthu, SS et al. Front Immunol, DOI://10.3389/fimmu.2018.00184 (2018)
GRL-079, a Novel HIV-1 Protease Inhibitor, Is Extremely Potent against Multidrug-Resistant HIV-1 Variants and Has a High Genetic Barrier against the Emergence of Resistant Variants Delino NS, Aoki M, Hayashi H, Hattori SI, Chang SB, Takamatsu Y, Martyr CD, Das D, Ghosh AK, Mitsuya H Antimicrob Agents Chemother. , doi: 10.1128/AAC.02060-17 (2018)

Design and statistical considerations for studies evaluating the efficacy of a single dose of the human papillomavirus (HPV) vaccine Sampson, JN; Hildesheim, A; Herrero, R; Gonzalez, P; Kreimer, A; Gail, MH; Contemp Clin Trials, DOI://10.1016/j.cct.2018.02.010 (2018)
Transcriptional regulation by NR5A2 links differentiation and inflammation in the pancreas Cobo, I; Martinelli, P; Flández, M et al. Nature, DOI://10.1038/nature25751 (2018)
Estimating recurrence and incidence of preterm birth subject to measurement error in gestational age: A hidden Markov modeling approach Albert, PS Stat Med, DOI://10.1002/sim.7624 (2018)
Extreme disorder in an ultrahigh-affinity protein complex Borgia, A; Borgia, MB; Bugge, K et al. Nature, DOI://10.1038/nature25762 (2018)
Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology Howard, BH; Hirai, TH; Russanova, VR; PLoS ONE, DOI://10.1371/journal.pone.0191033 (2018)
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells Hu, G; Cui, K; Fang, D et al. Immunity, DOI://10.1016/j.immuni.2018.01.013 (2018)

Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations Tofoleanu, F; Yuan, Y; Pickard, FC; Tywoniuk, B; Brooks, BR; Buchete, NV; J Phys Chem B, DOI://10.1021/acs.jpcb.7b12083 (2018)
Assessment of PCXMC for patients with different body size in chest and abdominal x ray examinations: a Monte Carlo simulation study Borrego, D; Lowe, EM; Kitahara, CM; Lee, C; Phys Med Biol, DOI://10.1088/1361-6560/aab13e (2018)
Dose coefficients for children and young adolescents exposed to external neutron fields Griffin, KT; Mille, M; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aab126 (2018)
CD63, MHC class 1, and CD47 identify subsets of extracellular vesicles containing distinct populations of noncoding RNAs Kaur, S; Elkahloun, AG; Arakelyan, A et al. Sci Rep, DOI://10.1038/s41598-018-20936-7 (2018)
Transient Receptor Potential Channels TRPM4 and TRPC3 Critically Contribute to Respiratory Motor Pattern Formation but not Rhythmogenesis in Rodent Brainstem Circuits Koizumi, H; John, TT; Chia, JX et al. eNeuro, DOI://10.1523/ENEURO.0332-17.2018 (2018)
Ridding fMRI data of motion-related influences: Removal of signals with distinct spatial and physical bases in multiecho data Power, JD; Plitt, M; Gotts, SJ et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1720985115 (2018)

The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance Yoshimura, T; McLean, MH; Dzutsev, AK et al. J. Immunol., DOI://10.4049/jimmunol.1602073 (2018)
Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance Weingarten, RA; Johnson, RC; Conlan, S et al. MBio, DOI://10.1128/mBio.02011-17 (2018)
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox Müller, F; Cunningham, T; Stookey, S et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1714512115 (2018)
Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling Li, S; Jang, H; Zhang, J; Nussinov, R; Structure, DOI://10.1016/j.str.2018.01.011 (2018)
Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho Brown, JL; Sun, MA; Kassis, JA; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1716299115 (2018)
Precise genome-wide mapping of single nucleosomes and linkers in vivo Chereji, RV; Ramachandran, S; Bryson, TD; Henikoff, S; Genome Biol., DOI://10.1186/s13059-018-1398-0 (2018)

Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer Klein, AP; Wolpin, BM; Risch, HA et al. Nat Commun, DOI://10.1038/s41467-018-02942-5 (2018)
The klotho-related protein KLPH (lctl) has preferred expression in lens and is essential for expression of clic5 and normal lens suture formation Fan, J; Lerner, J; Wyatt, MK et al. Exp. Eye Res., DOI://10.1016/j.exer.2018.02.001 (2018)
Self-reported executive function and hoarding in adults with obsessive-compulsive disorder Samuels, J; Bienvenu, OJ; Krasnow, J et al. Compr Psychiatry, DOI://10.1016/j.comppsych.2017.11.009 (2018)
Sequence determinants of protein phase behavior from a coarse-grained model Dignon, GL; Zheng, W; Kim, YC; Best, RB; Mittal, J; PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1005941 (2018)
Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy VanderWeele, DJ; Finney, R; Katayama, K et al. Eur Urol Focus, DOI://10.1016/j.euf.2018.01.006 (2018)
Extended amygdala connectivity changes during sustained shock anticipation Torrisi, S; Gorka, AX; Gonzalez-Castillo, J et al. Transl Psychiatry, DOI://10.1038/s41398-017-0074-6 (2018)

Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2 Ozdemir, ES; Jang, H; Gursoy, A et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001596 (2018)
Binding kinetics of ultrasmall gold nanoparticles with proteins André Lira, Rodrigo Ferreira, Ricardo Torquato, Huaying Zhao, Maria Luiza Oliva, Sergio A. Hassan, Peter Schuck and Alioscka A Sousa Nanoscale, DOI: 10.1039/C7NR06810G (2018)
Cleavage of TL1A Differentially Regulates Its Effects on Innate and Adaptive Immune Cells Ferdinand, JR; Richard, AC; Meylan, F; Al-Shamkhani, A; Siegel, RM; J. Immunol., DOI://10.4049/jimmunol.1700891 (2018)
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads Eccles, D; Chandler, J; Camberis, M et al. BMC Biol., DOI://10.1186/s12915-017-0473-4 (2018)
Accelerometer-Measured Physical Activity and Sedentary Behavior in Relation to All-Cause Mortality: The Women's Health Study Lee, IM; Shiroma, EJ; Evenson, KR; Kamada, M; LaCroix, AZ; Buring, JE; Circulation, DOI://10.1161/CIRCULATIONAHA.117.031300 (2018)
Altered avalanche dynamics in a developmental NMDAR hypofunction model of cognitive impairment Seshadri, S; Klaus, A; Winkowski, DE; Kanold, PO; Plenz, D; Transl Psychiatry, DOI://10.1038/s41398-017-0060-z (2018)

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma Zheng, H; Pomyen, Y; Hernandez, MO et al. Hepatology, DOI://10.1002/hep.29778 (2018)
Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis Gill, T; Asquith, M; Brooks, SR; Rosenbaum, JT; Colbert, RA; Arthritis Rheumatol., DOI://10.1002/art.40405 (2018)

2017 (409 papers)

Flexible risk prediction models for left or interval-censored data from electronic health records Hyun, N; Cheung, LC; Pan, Q; Schiffman, M; Katki, HA; , Ann Appl Stat, DOI://10.1214/17-AOAS1036 (2017)
Phantoms models to characterize influenza hemagglutinin-based vaccines McCraw, DM; Harris, AK; , Microsc. Microanal., DOI://10.1017/S1431927617007279 (2017)
Inhibitors of the Histone Methyltransferases EZH2/1 Induce a Potent Antiviral State and Suppress Infection by Diverse Viral Pathogens Arbuckle, JH; Gardina, PJ; Gordon, DN et al. mBio, DOI://10.1128/mBio.01141-17 (2017)
Social influence on 5-year survival in a longitudinal chemotherapy ward co-presence network Lienert, J; Marcum, CS; Finney, J; Reed-Tsochas, F; Koehly, L; , Netw Sci (Camb Univ Press), DOI://10.1017/nws.2017.16 (2017)

SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches Gudla, PR; Nakayama, K; Pegoraro, G; Misteli, T; Cold Spring Harb. Symp. Quant. Biol., DOI://10.1101/sqb.2017.82.033761 (2017)
Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs vonHoldt, BM; Shuldiner, E; Koch, IJ et al. Sci Adv, DOI://10.1126/sciadv.1700398 (2017)
Structural deficits in salience network regions are associated with increased impulsivity and compulsivity in alcohol dependence Grodin, EN; Cortes, CR; Spagnolo, PA; Momenan, R; , Drug Alcohol Depend, DOI://10.1016/j.drugalcdep.2017.06.014 (2017)
Regulation of chromatin folding by conformational variations of nucleosome linker DNA Buckwalter, JM; Norouzi, D; Harutyunyan, A; Zhurkin, VB; Grigoryev, SA; , Nucleic Acids Res., DOI://10.1093/nar/gkx562 (2017)
La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis Blewett, NH; Iben, JR; Gaidamakov, S; Maraia, RJ; , Mol. Cell. Biol., DOI://10.1128/MCB.00588-16 (2017)
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)
Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans Mitchell, KA; Zingone, A; Toulabi, L; Boeckelman, J; Ryan, BM; , Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-17-0527 (2017)
Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells Rivero-Hinojosa, S; Kang, S; Lobanenkov, VV; Zentner, GE; Sci Rep, DOI://10.1038/srep41279 (2017)
Preparation of a Conditional RNA Switch Zakrevsky, P; Parlea, L; Viard, M; Bindewald, E; Afonin, KA; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_20 (2017)
Computational Generation of RNA Nanorings Sharan, R; Bindewald, E; Kasprzak, WK; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_2 (2017)
Protocols for Molecular Dynamics Simulations of RNA Nanostructures Kim, T; Kasprzak, WK; Shapiro, BA; , Methods Mol. Biol., DOI://10.1007/978-1-4939-7138-1_3 (2017)
Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma Chaisaingmongkol, J; Budhu, A; Dang, H et al. Cancer Cell, DOI://10.1016/j.ccell.2017.05.009 (2017)
Visualizing abnormalities in chest radiographs through salient network activations in Deep Learning Rajaraman S, Antani SK, Xue Z, Candemir S, Jaeger S, Thoma GR Proc. IEEE Life Sciences Conference (LSC), Sydney, Australia, 10.1109/LSC.2017.826814 (2017)
PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability Gryder, BE; Yohe, ME; Chou, HC et al. Cancer Discov, DOI://10.1158/2159-8290.CD-16-1297 (2017)
Parental bonding and hoarding in obsessive-compulsive disorder Chen, D; Bienvenu, OJ; Krasnow, J et al. Compr Psychiatry, DOI://10.1016/j.comppsych.2016.11.004 (2017)
Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer Assadipour, Y; Zacharakis, N; Crystal, JS et al. Clin. Cancer Res., DOI://10.1158/1078-0432.CCR-16-1423 (2017)
Systems-level identification of PKA-dependent signaling in epithelial cells Isobe, K; Jung, HJ; Yang, CR et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1709123114 (2017)
Association of red cell distribution width with all-cause and cardiovascular-specific mortality in African American and white adults: a prospective cohort study Tajuddin, SM; Nalls, MA; Zonderman, AB; Evans, MK; J Transl Med, DOI://10.1186/s12967-017-1313-6 (2017)
Sieve analysis using the number of infecting pathogens Follmann, D; Huang, CY; Biometrics, DOI://10.1111/biom.12833 (2017)
Meat Consumption During Pregnancy and Substance Misuse Among Adolescent Offspring: Stratification of TCN2 Genetic Variants Hibbeln, JR; SanGiovanni, JP; Golding, J et al. Alcohol. Clin. Exp. Res., DOI://10.1111/acer.13494 (2017)

A Systems Biology Approach to Investigating Sex Differences in Cardiac Hypertrophy Harrington, J; Fillmore, N; Gao, S et al. J Am Heart Assoc, DOI://10.1161/JAHA.117.005838 (2017)
Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation Agbor-Enoh, S; Tunc, I; De Vlaminck, I et al. J. Heart Lung Transplant., DOI://10.1016/j.healun.2017.05.026 (2017)
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Untangling the relatedness among correlations, Part II: Inter-subject correlation group analysis through linear mixed-effects modeling Chen, G; Taylor, PA; Shin, YW; Reynolds, RC; Cox, RW; Neuroimage, DOI://10.1016/j.neuroimage.2016.08.029 (2017)
Topographical and physiological differences of the skin mycobiome in health and disease Jo, JH; Kennedy, EA; Kong, HH; Virulence, DOI://10.1080/21505594.2016.1249093 (2017)
Empirically derived patterns of psychiatric symptoms in youth: A latent profile analysis Kircanski, K; Zhang, S; Stringaris, A et al. J Affect Disord, DOI://10.1016/j.jad.2016.09.016 (2017)
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge Lee, J; Tofoleanu, F; Pickard, FC et al. J. Comput. Aided Mol. Des., DOI://10.1007/s10822-016-9968-2 (2017)
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)

Can dielectric spheres accurately model atomic-scale interactions Obolensky, OI; Doerr, TP; Ogurtsov, AY; Yu, YK; Europhys Lett, DOI://10.1209/0295-5075/116/24003 (2016)
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)
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)
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Redox-induced activation of the proton pump in the respiratory complex I Vivek Sharma, Galina Belevich, Ana P. Gamiz-Hernandez, Tomasz Ròg, Ilpo Vattulainen, Marina L. Verkhovskaya Mårten Wikström, Gerhard Hummer, and Ville R. I. Kaila PNAS, doi://10.1073/pnas.1503761112 (2016)
High-level expression and characterization of a novel serine protease in Pichia pastoris by multi-copy integration Min Shu, Wei Shen, Shihui Yang , Xiaojuan Wang , Fei Wang , Yaping Wang , Lixin Ma Enzyme and Microbioal Technology, doi:10.1016/j.enzmictec.2016.06.007 (2016)

NMDA Receptors Multiplicatively Scale Visual Signals and Enhance Directional Motion Discrimination in Retinal Ganglion Cells Poleg-Polsky A, Diamond JS Neuron, DOI://10.1016/j.neuron.2016.02.013 (2016)
MEGSA: A Powerful and Flexible Framework for Analyzing Mutual Exclusivity of Tumor Mutations Xing Hua, Paula L. Hyland, Jing Huang, Lei Song, Bin Zhu, Neil E. Caporaso, Maria Teresa Landi, Nilanjan Chatterjee, and Jianxin Shi Am J. Hum. Genet. , doi://10.1016/j.ajhg.2015.12.021 (2016)
Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300 Shrimp JH, Sorum AW, Garlick JM, Guasch L, Nicklaus MC, Meier JL ACS Med Chem Lett, DOI://10.1021/acsmedchemlett.5b00385 (2016)
Plasticity of Sensorimotor Networks: Multiple Overlapping Mechanisms Buch, ER; Liew, SL; Cohen, LG; Neuroscientist, DOI://10.1177/1073858416638641 (2016)
Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q ACS Chem Neurosci, DOI://10.1021/acschemneuro.5b00242 (2016)
Seeking Optimal Region-Of-Interest (ROI) Single-Value Summary Measures for fMRI Studies in Imaging Genetics Tong, Y; Chen, Q; Nichols, TE et al. PLoS ONE, DOI://10.1371/journal.pone.0151391 (2016)

Microscopic interpretation of folding φ-values using the transition path ensemble Robert B. Best and Gerhard Hummer PNAS, doi: 10.1073/pnas.1520864113 (2016)
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold Takako Takeda, Yanli Wang , Stephen H. Bryant J. Computer-Aided Molecular Design, doi://10.1007/s10822-016-9905-4 (2016)
Modulation of Folding Internal Friction by Local and Global Barrier Heights Wenwei Zheng, David de Sancho, and Robert B. Best J. Phys. Chem. Letters, DOI: 10.1021/acs.jpclett.6b00329 (2016)
The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo Josefina Ocampo, Razvan V. Chereji, Peter R. Eriksson and David J. Clark Nucleic Acids Research, doi://10.1093/nar/gkw068 (2016)
Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations Alioscka A. Sousa, Sergio A. Hassan, Luiza L. Knittel, Andrea Balbo, Maria A. Aronova, Patrick H. Brown, Peter Schuck and Richard D. Leapman Nanoscale, DOI: 10.1039/C5NR07642K (2016)
The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes Rinschen, MM; Bharill, P; Wu, X et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddw016 (2016)

Mucolipidosis types II and III and non-syndromic stuttering are associated with different variants in the same genes Raza, MH; Domingues, CE; Webster, R et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2015.154 (2016)
The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities Afonin, KA; Viard, M; Tedbury, P et al. Nano Lett., DOI://10.1021/acs.nanolett.5b04676 (2016)
Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning Hoo-Chang Shin Holger R. Roth ; Mingchen Gao ; Le Lu ; Ziyue Xu ; Isabella Nogues ; Jianhua Yao ; Daniel Mollura ; Ronald M. Summers IEEE Transactions on Medical Imaging, 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)

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Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain Pilar Donado-Godoy, Johan F. Bernal, Fernando Rodrìguez, Yolanda Gomez, Richa Agarwala, David Landsman, Leonardo Mariño-Ramìrez Genome Announc., doi: 10.1128/genomeA.01265-15 (2015)
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Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor Brennan Decker, Brian W Davis, Maud Rimbault, Adrienne H Long, Eric Karlins, Heidi G Parker, Vidhya Jagannathan, Rebecca Reiman, Cord Drögemüller, Jason J Corneveaux, Erica S Chapman, Jeffery M Trent, Tosso Leeb, Matthew J Huentelman, Robert K Wayne, Danielle M Karyadi and Elaine A Ostrander Genome Research, doi: 10.1101/gr.190314.115 (2015)
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Tautomerism of Warfarin: Combined Chemoinformatics, Quantum Chemical, and NMR Investigation Laura Guasch, Megan L. Peach, and Marc C Nicklaus J. Org. Chem. , DOI: 10.1021/acs.joc.5b01370 (2015)
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Cerebro-cerebellar connectivity is increased in primary lateral sclerosis Meoded A, Morrissette AE, Katipally R, Schanz O, Gotts SJ, Floeter MK Neuroimage Clin, DOI://10.1016/j.nicl.2014.12.009 (2015)
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Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups. Tofoleanu F, Brooks BR, Buchete NV. ACS Chem Neurosci., doi://abs/10.1021/cn500277f (2015)
Insights into the Mechanism of Inhibition of CXCR4: Identification of Piperidinylethanamine Analogs as Anti-HIV-1 Inhibitors Das D, Maeda K, Hayashi Y, Gavande N, Desai DV, Chang SB, Ghosh AK, Mitsuya H Antimicrob Agents Chemother., pii: AAC.04654-14. (2015)
Variable selection method for the identification of epistatic models Holzinger ER, Szymczak S, Dasgupta A, Malley J, Li Q, Bailey-Wilson JE Pac Symp Biocomput, 2335-6936 (2015)
CDD: NCBI's conserved domain database Marchler-Bauer, A; Derbyshire, MK; Gonzales, NR et al. Nucleic Acids Res., DOI://10.1093/nar/gku1221 (2015)
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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A novel role of CDX1 in embryonic epicardial development Chu M, Wang L, Wang H, Shen T, Yang Y, Sun Y, Tang N, Ni T, Zhu J, Mailman RB, Wang Y PLoS One, doi: 10.1371/journal.pone.0103271 (2014)

Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy Alberto Bartesaghi, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam Nat Struct Mol Biol., doi: 10.1038/nsmb.2711 (2014)
Clinical correlates and genetic linkage of social and communication difficulties in families with obsessive-compulsive disorder: Results from the OCD Collaborative Genetics Study Samuels, J; Shugart, YY; Wang, Y et al. Am. J. Med. Genet. B Neuropsychiatr. Genet., DOI://10.1002/ajmg.b.32235 (2014)
The spatial structure of resting state connectivity stability on the scale of minutes Javier Gonzalez-Castillo, Daniel A Handwerker, Meghan E. Robinson, Colin Wier Hoy, Laura Cathleen Buchanan, Ziad S Saad and Peter A Bandettini Frontiers in Neuroscience, DOI://10.3389/fnins.2014.00138 (2014)
The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. King MR, Matzat LH, Dale RK, Lim SJ, Lei EP J. Cell. Sci., doi: 10.1242/jcs.151126 (2014)
Use of LC-MS/MS and Bayes' Theorem to Identify Protein Kinases That Phosphorylate Aquaporin-2 at Ser256 Davis Bradford, Viswanathan Raghuram, Justin L.L. Wilson, Chung-Lin Chou, Jason D. Hoffert, Mark A. Knepper, Trairak Pisitkun Am. J. Physiol. - Cell Physiol. , DOI: 10.1152/ajpcell.00377.2012 (2014)
Nill-Schiff base complex as an enzyme inhibitor of hen egg white lysozyme: a crystallographic and spectroscopic study Banabithi Koley Seth, Aurkie Ray, Sampa Biswas and Samita Basu Metallomics, DOI: 10.1039/C4MT00098F (2014)

Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing Yun Ji, Natalie Abrams, Wei Zhu, Eddie Salinas, Zhiya Yu, Douglas C. Palmer, Parthav Jailwala, Zulmarie Franco, Rahul Roychoudhuri, Eric Stahlberg, Luca Gattinoni, Nicholas P. Restifo PLoS One, DOI: 10.1371/journal.pone.0096650 (2014)
Combination of longitudinal biomarkers in predicting binary events Danping Liu and Paul S Albert Biostatistics, doi: 10.1093/biostatistics/kxu020 (2014)
Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma Shi J, Yang XR, Ballew B Nature Genetics, doi: 10.1038/ng.2941 (2014)
Pleiotropic genes for metabolic syndrome and inflammation Kraja AT, Chasman DI, North KE et al. Molecular Genetics & Metabolism, doi://10.1016/j.ymgme.2014.04.007 (2014)
Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves Kent R. Thurber and Robert Tycko J. Chem. Phys. , DOI: 10.1063/1.4874341 (2014)
Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome Yudkin, D; Hayward, BE; Aladjem, MI; Kumari, D; Usdin, K; Hum. Mol. Genet., DOI://10.1093/hmg/ddu006 (2014)

Rhythmic Bursting in the Pre-Bötzinger Complex: Mechanisms and Models Ilya A. Rybak, Yaroslav I. Molkov, Patrick E. Jasinski, Natalia A. Shevtsova, Jeffrey C. Smith Progress in Brain Research, doi://10.1016/B978-0-444-63274-6.00001-1 (2014)
Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2 Francesco Trepiccione, Trairak Pisitkun, Jason D Hoffert, Søren B Poulsen, Giovambattista Capasso, Søren Nielsen, Mark A Knepper, Robert A Fenton and Birgitte M Christensen Kidney International, doi: 10.1038/ki.2014.107 (2014)
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I Ville R. I. Kaila, Mârten Wikström and Gerhard Hummer PNAS, doi: 10.1073/pnas.1319156111 (2014)
Hierarchical clustering of ryanodine receptors enables emergence of a calcium clock in sinoatrial node cells Michael D. Stern, Larissa A. Maltseva, Magdalena Juhaszova, Steven J. Sollott, Edward G. Lakatta, and Victor A. Maltsev J. Gen. Physiol. , doi: 10.1085/jgp.201311123 (2014)
Conserved hydrogen-bonding network of P2 bis-tetrahydrofuran containing HIV-1 protease inhibitors (PI) with protease active site amino acid-backbone aid in their activity against PI-resistant HIV Ravikiran S. Yedidi, Harisha Garimella, Manabu Aoki, Hiromi Aoki, Darshan V. Desai, Simon B. Chang, David A. Davis, W. Sean Fyvie, Joshua D. Kaufman, David W. Smith, Debananda Das, Paul T. Wingfield, Kenji Maeda, Arun K. Ghosh and Hiroaki Mitsuya Antimicrob Agents Chemother., doi://10.1128/AAC.00107-14 (2014)
Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer Ewy A Mathe, Andrew D Patterson, Majda Haznadar, Soumen K Manna, Kristopher W. Krausz, Elise D Bowman, Peter G. Shields, Jeffrey R. Idle, Philip B Smith, Katsuhiro Anami, Dickran Kazandjian, Emmanuel Hatzakis, Frank J Gonzalez, and Curtis C. Harris Cancer Res., doi:10.1158/0008-5472.CAN-14-0109 (2014)

Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin J.-H. Kang, S.A. Hassan, 1, P. Zhao, C.H. Tsai-Morris, M.L. Dufau Biochim. et Biophys. Acta, doi://10.1016/j.bbagen.2014.04.006 (2014)
A Fast and Powerful Tree-Based Association Test for Detecting Complex Joint Effects in Case-Control Studies Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor and Kai Yu Bioinformatics, doi://10.1093/bioinformatics/btu186 (2014)
Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain David N. Hauser, Allissa A. Dillman, Jinhui Ding, Yan Li, Mark R. Cookson PLoS One, DOI: 10.1371/journal.pone.0094646 (2014)
Studies on Inhibition of Respiratory Cytochrome bc1 Complex by the Fungicide Pyrimorph Suggest a Novel Inhibitory Mechanism Yu-Mei Xiao, Lothar Esser, Fei Zhou, Chang Li, Yi-Hui Zhou, Chang-An Yu, Zhao-Hai Qin, Di Xia PLoS One, DOI: 10.1371/journal.pone.0093765 (2014)
Regulation of a novel isoform of Receptor Expression Enhancing Protein REEP6 in rod photoreceptors by bZIP transcription factor NRL Hong Hao, Shobi Veleri, Bo Sun, Douglas S. Kim, Patrick W. Keeley, Jung-Woong Kim, Hyun-Jin Yang, Sharda P. Yadav, Souparnika H. Manjunath, Raman Sood, Paul Liu, Benjamin E. Reese and Anand Swaroop Human Molecular Genetics, doi: 10.1093/hmg/ddu143 (2014)
Distributed MRI reconstruction using gadgetron-based cloud computing Hui Xue, Souheil Inati, Thomas Sangild Sørensen, Peter Kellman and Michael S. Hansen Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25213 (2014)

Hemoglobinopathic erythrocytes affect the intraerythrocytic multiplication of Plasmodium falciparum in vitro Svetlana Glushakova, Amanda Balaban, Philip G. McQueen, Rosane Coutinho, Jeffery L. Miller, Ralph Nossal, Rick M. Fairhurst, Joshua Zimmerberg J. Infectious Diseases, doi:10.1093/infdis/jiu203 (2014)
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface Guntur Fibriansah, Joanne L Tan,Scott A Smith, Adamberage R Alwis, Thiam-Seng Ng, Victor A Kostyuchenko, Kristie D Ibarra, Jiaqi Wang, Eva Harris, Aravinda Silva, James E Crowe, and Shee-Mei Lok EMBO Molecular Medicine, doi: 10.1002/emmm.201303404 (2014)
A mixture of transition models for heterogeneous longitudinal ordinal data: with applications to longitudinal bacterial vaginosis data Kyeongmi Cheon, Marie E. Thoma, Xiangrong Kong and Paul S. Albert Statistics in Medicine, DOI: 10.1002/sim.6151 (2014)
Abdominal lymphadenopathy detection using random forest Kevin M. Cherry, Shijun Wang, Evrim B. Turkbey, Ronald M. Summers SPIE Proceedings, Volume 9035, Lung, Chest, and Abdomen II, doi:10.1117/12.2043837 (2014)
VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions Jianxin Shi, Xiaohong R. Yang, Neil E. Caporaso, Maria T. Landi, and Peng Li Frontiers in Genetics, doi://10.3389/fgene.2014.00053 (2014)
Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values Gelio Alves and Yi-Kuo Yu PLoS One, doi: 10.1371/journal.pone.0091225 (2014)

Differential Coding of Conspecific Vocalizations in the Ventral Auditory Cortical Stream Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck J. Neuroscience, doi: 10.1523/JNEUROSCI.3969-13.2014 (2014)
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein Ville R. I. Kaila, Friedrich Schotte, Hyun Sun Cho, Gerhard Hummer & Philip A. Anfinrud Nature Chemistry, doi:10.1038/nchem.1898 (2014)
Practice and sleep form different aspects of skill Sunbin Song & Leonardo G. Cohen Nature Communications, doi:10.1038/ncomms4407 (2014)
Temperature-dependent solvation modulates the dimensions of disordered proteins René Wuttke, Hagen Hofmann, Daniel Nettels, Madeleine B. Borgia, Jeetain Mittal, Robert B. Best, and Benjamin Schuler PNAS, doi: 10.1073/pnas.1313006111 (2014)
Hypoosmotic Expression of Dunaliella bardawil ζ-Carotene Desaturase Is Attributed to a Hypoosmolarity-Responsive Element Different from Other Key Carotenogenic Genes Yong-Min Lao, Lan Xiao, Li-Xin Luo and Jian-Guo Jiang Plant Physiology, doi://10.1104/pp.114.235390 (2014)
Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Jianxin Shi, Crystal N. Marconett, Jubao Duan et al. Nature Communications, doi:10.1038/ncomms4365 (2014)

Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal and Ruth Nussinov Chem. Soc. Rev., doi://10.1039/C3CS60459D (2014)
Abnormal cortical growth in schizophrenia targets normative modules of synchronized development Aaron F. Alexander-Bloch, Philip T. Reiss, Judith Rapoport, Harry McAdams, Jay N. Giedd, Ed T. Bullmore, Nitin Gogtay Biological Psychiatry, doi://10.1016/j.biopsych.2014.02.010 (2014)
Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis Edina Rosta, Wei Yang, and Gerhard Hummer JACS, DOI: 10.1021/ja411408x (2014)
Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes Gerhard König, Phillip Stephen Hudson, Stefan Boresch, and H. Lee Woodcock J. Chem. Theory & Computation, DOI: 10.1021/ct401118k (2014)
A Network Characteristic That Correlates Environmental and Genetic Robustness Zeina Shreif, Vipul Periwal PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1003474 (2014)
A GCH1 haplotype confers sex-specific susceptibility to pain crises and altered endothelial function in adults with sickle cell anemia Inna Belfer, Victoria Youngblood et al. Am. J. Hematology, DOI: 10.1002/ajh.23613 (2014)

Meta-analysis of Loci Associated with Age at Natural Menopause in African-American Women CTL Chen, C-T Liu, GK Chen, et al Human Molecular Genetics, doi: 10.1093/hmg/ddu041 (2014)
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks J. Computer-Aided Molecular Design, doi://10.1007/s10822-014-9708-4 (2014)
Predicting Stroke Through Genetic Risk Functions CA Ibrahim-Verbaas,M Fornage, JC Bis, et al Stroke, doi: 10.1161/STROKEAHA.113.003044 (2014)
Multilocus Genetic Risk Score Associates With Ischemic Stroke in Case-Control and Prospective Cohort Studies R Malik, S Bevan, M Nalls et al Stroke, doi: 10.1161/STROKEAHA.113.002938 (2014)
Reverse regression: A method for joint analysis of multiple endpoints in randomized clinical trials Zhiwei Zhang Statistica Sinica, doi://10.5705/ss.2010.111 (2014)
Using single cell sequencing data to model the evolutionary history of a tumor Kyung In Kim and Richard Simon BMC Bioinformatics :27, doi: 10.1186/1471-2105-15-27 (2014)

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

2013 (180 papers)

Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains Chuang, GY; Acharya, P; Schmidt, SD et al. J. Virol., DOI://10.1128/JVI.00984-13 (2013)
Integrated strategy for improving functional connectivity mapping using multiecho fMRI Kundu, P; Brenowitz, ND; Voon, V et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301725110 (2013)

Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia Wang, E; Kawaoka, S; Yu, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1301045110 (2013)
Correlated biomarker measurement error: an important threat to inference in environmental epidemiology Pollack, AZ; Perkins, NJ; Mumford, SL; Ye, A; Schisterman, EF; Am. J. Epidemiol., DOI://10.1093/aje/kws209 (2013)
Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies Zhou, T; Zhu, J; Wu, X et al. Immunity, DOI://10.1016/j.immuni.2013.04.012 (2013)
Effective Preprocessing Procedures Vi