You are here

2016 Published Papers

1. Zubair N, Graff M, Luis Ambite J, Bush WS, Kichaev G, Lu Y, et al. Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Human Molecular Genetics. 2016;25(24):5500-12. doi: 10.1093/hmg/ddw358. PubMed PMID: PMC5721937.
2. Zhou F, Wang W, Shen C, Li H, Zuo X, Zheng X, et al. Epigenome-Wide Association Analysis Identified Nine Skin DNA Methylation Loci for Psoriasis. Journal of Investigative Dermatology. 2016;136(4):779-87. doi:
3. Zhao Y, Song W-M, Zhang F, Zhou M-M, Zhang W, Walsh MJ, et al. Distinct distributions of genomic features of the 5' and 3' partners of coding somatic cancer gene fusions: arising mechanisms and functional implications. Oncotarget. 2016;8(40):66769-83. doi: 10.18632/oncotarget.10734. PubMed PMID: 28977995.
4. Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and Genetic Inflammation Networks in Major Human Diseases. Molecular bioSystems. 2016;12(8):2318-41. doi: 10.1039/c6mb00240d. PubMed PMID: PMC4955784.
5. Zhao W, Ho L, Wang J, Bi W, Yemul S, Ward L, et al. In Silico Modelling of Novel Drug Ligands Associated with Abnormal Tau Phosphorylation: Implications for Concussion Associated Tauopathy Intervention(). Journal of cellular biochemistry. 2016;117(10):2241-8. doi: 10.1002/jcb.25521. PubMed PMID: PMC4988328.
6. Zhang F, Ren C, Lau KK, Zheng Z, Lu G, Yi Z, et al. A network medicine approach to build a comprehensive atlas for the prognosis of human cancer. Briefings in Bioinformatics. 2016;17(6):1044-59. doi: 10.1093/bib/bbw076.
7. Zhang DY, Goossens N, Guo J, Tsai M-c, Chou H-I, Altunkaynak C, et al. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. Gut. 2016;65(10):1754-64. doi: 10.1136/gutjnl-2015-309655. PubMed PMID: PMC4848165.
8. Zhang DY, Goossens N, Guo J, Tsai M-C, Chou H-I, Altunkaynak C, et al. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. Gut. 2016;65(10):1754-64. Epub 2015/06/04. doi: 10.1136/gutjnl-2015-309655. PubMed PMID: 26045137.
9. Zhang B, Tran L, Emilsson V, Zhu J. Characterization of Genetic Networks Associated with Alzheimer’s Disease. In: Castrillo JI, Oliver SG, editors. Systems Biology of Alzheimer's Disease. New York, NY: Springer New York; 2016. p. 459-77.
10. Yuan H, Liu H, Liu Z, Owzar K, Han Y, Su L, et al. A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer. Scientific Reports. 2016;6:34234. doi: 10.1038/srep34234. PubMed PMID: PMC5054367.
11. Yang X, Li F, Konze KD, Meslamani J, Ma A, Brown PJ, et al. Structure–Activity Relationship Studies for Enhancer of Zeste Homologue 2 (EZH2) and Enhancer of Zeste Homologue 1 (EZH1) Inhibitors. Journal of Medicinal Chemistry. 2016;59(16):7617-33. doi: 10.1021/acs.jmedchem.6b00855.
12. Yang J, Huang T, Song W-m, Petralia F, Mobbs CV, Zhang B, et al. Discover the network mechanisms underlying the connections between aging and age-related diseases. Scientific Reports. 2016;6:32566. doi: 10.1038/srep32566 - supplementary-information.
13. Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, et al. Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports. 2016;6:19384. doi: 10.1038/srep19384.
14. Whalen S, Pandey OP, Pandey G. Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Methods (San Diego, Calif). 2016;93:92-102. doi: 10.1016/j.ymeth.2015.08.016. PubMed PMID: PMC4718788.
15. Watson CT, Roussos P, Garg P, Ho DJ, Azam N, Katsel PL, et al. Genome-wide12 DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease. Genome Medicine. 2016;8:5. doi: 10.1186/s13073-015-0258-8. PubMed PMID: PMC4719699.
16. Wardman JH, Gomes I, Bobeck EN, Stockert JA, Kapoor A, Bisignano P, et al. Identification of a small-molecule ligand that activates the neuropeptide receptor GPR171 and increases food intake. Science signaling. 2016;9(430):ra55-ra. doi: 10.1126/scisignal.aac8035. PubMed PMID: PMC5150984.
17. Wang T, Santos JH, Feng J, Fargo DC, Shen L, Riadi G, et al. A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq. PLoS ONE. 2016;11(7):e0159028. doi: 10.1371/journal.pone.0159028. PubMed PMID: PMC4945064.
18. Wang Q, Lin L, Yoo S, Wang W, Blank S, Fiel MI, et al. Impact of non-neoplastic vs intratumoural hepatitis B viral DNA and replication on hepatocellular carcinoma recurrence. British Journal of Cancer. 2016;115(7):841-7. doi: 10.1038/bjc.2016.239. PubMed PMID: PMC5046201.
19. Wang M, Roussos P, McKenzie A, Zhou X, Kajiwara Y, Brennand KJ, et al. Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease. Genome Medicine. 2016;8(1):104. doi: 10.1186/s13073-016-0355-3.
20. Wang L, Oh WK, Zhu J. Disease-specific classification using deconvoluted whole blood gene expression. Scientific Reports. 2016;6:32976. doi: 10.1038/srep32976 - supplementary-information.
21. Vedanthan R, Bansilal S, Soto AV, Kovacic JC, Latina J, Jaslow R, et al. Family-Based Approaches to Cardiovascular Health Promotion. Journal of the American College of Cardiology. 2016;67(14):1725-37. doi:
22. Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, et al. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Medicine. 2016;8:62. doi: 10.1186/s13073-016-0313-0. PubMed PMID: PMC4888213.
23. Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Readhead B, et al. Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells. Cell reports. 2016;15(5):1024-36. doi: 10.1016/j.celrep.2016.03.090. PubMed PMID: PMC4856588.
24. Tignor N, Wang PEI, Genes N, Rogers L, Hershman SG, Scott ER, et al. METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS. Biocomputing 2017: WORLD SCIENTIFIC; 2016. p. 300-11.
25. Tan PS, Nakagawa S, Goossens N, Venkatesh A, Huang T, Ward SC, et al. Clinicopathological indices to predict hepatocellular carcinoma molecular classification. Liver international : official journal of the International Association for the Study of the Liver. 2016;36(1):108-18. Epub 2015/06/29. doi: 10.1111/liv.12889. PubMed PMID: 26058462.
26. Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nature Medicine. 2016;22:713. doi: 10.1038/nm.4142.
27. Tamburini S, Clemente JC. Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments. Cellular and Molecular Gastroenterology and Hepatology. 2016;2(5):540-1. doi: 10.1016/j.jcmgh.2016.07.001. PubMed PMID: PMC5042882.
28. Tajuddin Salman M, Schick Ursula M, Eicher John D, Chami N, Giri A, Brody Jennifer A, et al. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. American Journal of Human Genetics. 2016;99(1):22-39. doi: 10.1016/j.ajhg.2016.05.003. PubMed PMID: PMC5005433.
29. Sung YJ, Winkler TW, Manning AK, Aschard H, Gudnason V, Harris TB, et al. An Empirical Comparison of Joint and Stratified Frameworks for Studying G × E Interactions: Systolic Blood Pressure and Smoking in the CHARGE Gene-Lifestyle Interactions Working Group. Genetic Epidemiology. 2016;40(5):404-15. doi: 10.1002/gepi.21978.
30. Sun H, Martin JA, Werner CT, Wang ZJ, Damez-Werno DM, Scobie KN, et al. BAZ1B in Nucleus Accumbens Regulates Reward-Related Behaviors in Response to Distinct Emotional Stimuli. J Neurosci. 2016;36(14):3954-61. Epub 2016/04/08. doi: 10.1523/jneurosci.3254-15.2016. PubMed PMID: 27053203; PubMed Central PMCID: PMCPMC4821908.
31. Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Wasserstein M, Kasarskis A, et al. Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project. Journal of Genetic Counseling. 2016;25(5):1044-53. doi: 10.1007/s10897-016-9935-z.
32. Stoesser N, Sheppard AE, Peirano G, Sebra RP, Lynch T, Anson LW, et al. First Report of bla(IMP-14) on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131. Antimicrobial Agents and Chemotherapy. 2016;60(8):5068-71. doi: 10.1128/AAC.00840-16. PubMed PMID: PMC4958194.
33. Stoesser N, Sheppard AE, Peirano G, Sebra R, Lynch T, Anson L, et al. Complete Sequencing of Plasmids Containing bla(OXA-163) and bla(OXA-48) in Escherichia coli Sequence Type 131. Antimicrobial Agents and Chemotherapy. 2016;60(11):6948-51. doi: 10.1128/AAC.01130-16. PubMed PMID: PMC5075115.
34. Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, et al. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. mBio. 2016;7(2).
35. Stanescu ANA, Pandey G. LEARNING PARSIMONIOUS ENSEMBLES FOR UNBALANCED COMPUTATIONAL GENOMICS PROBLEMS. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:288-99. PubMed PMID: PMC5147733.
36. Smith SG, Zhou M-M. Bromodomains as targets for therapeutic intervention. Drug Discovery Today: Technologies. 2016;19:1-2. doi:
37. Shukla-Dave A, Castillo-Martin M, Chen M, Lobo J, Gladoun N, Collazo-Lorduy A, et al. Ornithine Decarboxylase Is Sufficient for Prostate Tumorigenesis via Androgen Receptor Signaling. The American Journal of Pathology. 2016;186(12):3131-45. doi:
38. Shoemaker LD, Clark MJ, Patwardhan A, Chandratillake G, Garcia S, Chen R, et al. Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing. G3: Genes|Genomes|Genetics. 2016;6(1):41-9. doi: 10.1534/g3.115.020321. PubMed PMID: PMC4704723.
39. Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, et al. Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. Antimicrobial Agents and Chemotherapy. 2016;60(6):3767-78.
40. Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, et al. Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193. Genome Announcements. 2016;4(1):e01649-15. doi: 10.1128/genomeA.01649-15. PubMed PMID: PMC4732343.
41. Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YE, Ma Q, et al. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology. 2016;41(13):3103-13. Epub 2016/08/04. doi: 10.1038/npp.2016.144. PubMed PMID: 27485686; PubMed Central PMCID: PMCPMC5101561.
42. Shang Y, Yeatman HR, Provasi D, Alt A, Christopoulos A, Canals M, et al. Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors. ACS Chemical Biology. 2016;11(5):1220-9. doi: 10.1021/acschembio.5b00712.
43. Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, et al. PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:276-87. PubMed PMID: PMC5362124.
44. Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, et al. Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Thorax. 2016.
45. Segal LN, Clemente JC, Tsay J-CJ, Koralov SB, Keller BC, Wu BG, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nature microbiology. 2016;1:16031-. doi: 10.1038/nmicrobiol.2016.31. PubMed PMID: PMC5010013.
46. Schneider S, Provasi D, Filizola M. How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways. Biochemistry. 2016;55(46):6456-66. doi: 10.1021/acs.biochem.6b00948.
47. Schmidt B, Wei L, DePeralta DK, Hoshida Y, Tan PS, Sun X, et al. Molecular subclasses of hepatocellular carcinoma predict sensitivity to fibroblast growth factor receptor inhibition. International journal of cancer. 2016;138(6):1494-505. Epub 2015/11/09. doi: 10.1002/ijc.29893. PubMed PMID: 26481559.
48. Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, et al. Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington’s Disease. PLOS Genetics. 2016;12(7):e1006137. doi: 10.1371/journal.pgen.1006137.
49. Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, et al. Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. European Journal of Human Genetics. 2016;24(1):14-20. doi: 10.1038/ejhg.2015.118. PubMed PMID: PMC4795230.
50. Salmon H, Idoyaga J, Rahman A, Leboeuf M, Remark R, Jordan S, et al. Expansion and activation of CD103(+) dendritic cell progenitors at the tumor site enhances tumor responses to therapeutic PD-L1 and BRAF inhibition. Immunity. 2016;44(4):924-38. doi: 10.1016/j.immuni.2016.03.012. PubMed PMID: PMC4980762.
51. Roussos P, Guennewig B, Kaczorowski DC, Barry G, Brennand KJ. Activity-Dependent Changes in Gene Expression in Schizophrenia Human-Induced Pluripotent Stem Cell Neurons. JAMA psychiatry. 2016;73(11):1180-8. doi: 10.1001/jamapsychiatry.2016.2575. PubMed PMID: PMC5437975.
52. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JSY, et al. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science (New York, NY). 2016;352(6289):aad7993-aad. doi: 10.1126/science.aad7993. PubMed PMID: PMC5193222.
53. Ren C, Smith SG, Yap K, Li S, Li J, Mezei M, et al. Structure-Guided Discovery of Selective Antagonists for the Chromodomain of Polycomb Repressive Protein CBX7. ACS Medicinal Chemistry Letters. 2016;7(6):601-5. doi: 10.1021/acsmedchemlett.6b00042.
54. Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, et al. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Research. 2016;44(8):3750-62. doi: 10.1093/nar/gkw219. PubMed PMID: PMC4857002.
55. Qiao W, Yang Y, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, et al. Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6. Human mutation. 2016;37(3):315-23. Epub 2015/12/18. doi: 10.1002/humu.22936. PubMed PMID: 26602992.
56. Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA. The CYP2D6 VCF Translator. The Pharmacogenomics Journal. 2016;17:301. doi: 10.1038/tpj.2016.14.
57. Pfau ML, Purushothaman I, Feng J, Golden SA, Aleyasin H, Lorsch ZS, et al. Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens. Frontiers in Molecular Neuroscience. 2016;9:144. doi: 10.3389/fnmol.2016.00144. PubMed PMID: PMC5179560.
58. Petralia F, Song W-M, Tu Z, Wang P. New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer. Journal of Proteome Research. 2016;15(3):743-54. doi: 10.1021/acs.jproteome.5b00925.
59. Perumal D, Kuo P-Y, Leshchenko VV, Jiang Z, Divakar SKA, Cho HJ, et al. Dual Targeting of CDK4 and ARK5 Using a Novel Kinase Inhibitor ON123300 Exerts Potent Anticancer Activity against Multiple Myeloma. Cancer Research. 2016;76(5):1225.
60. Pattaro C, Teumer A, Gorski M, Chu AY, Li M, Mijatovic V, et al. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nature communications. 2016;7:10023-. doi: 10.1038/ncomms10023. PubMed PMID: PMC4735748.
61. Pak TR, Kasarskis A. Reply to Lesho. Clinical Infectious Diseases. 2016;62(8):1053-. doi: 10.1093/cid/ciw010.
62. Osman R, Mezei M, Engel S. The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone-receptor complex. Journal of Computational Chemistry. 2016;37(10):913-9. doi: 10.1002/jcc.24276.
63. O'Connell PJ, Zhang W, Menon MC, Yi Z, Schröppel B, Gallon L, et al. Biopsy transcriptome expression profiling to identify kidney transplants at risk of chronic injury: a multicentre, prospective study. The Lancet. 2016;388(10048):983-93. doi:
64. Nakagawa S, Wei L, Song WM, Higashi T, Ghoshal S, Kim RS, et al. Molecular liver cancer prevention in cirrhosis by organ transcriptome analysis and lysophosphatidic acid pathway inhibition. Cancer cell. 2016;30(6):879-90. doi: 10.1016/j.ccell.2016.11.004. PubMed PMID: PMC5161110.
65. Moyon S, Huynh JL, Dutta D, Zhang F, Ma D, Yoo S, et al. Functional characterization of DNA methylation in the oligodendrocyte lineage. Cell reports. 2016;15(4):748-60. doi: 10.1016/j.celrep.2016.03.060. PubMed PMID: PMC5063656.
66. Mezei M. Use of an interface contact statistics to rescore protein‐protein docked ensembles2016.
67. Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534:55. doi: 10.1038/nature18003 - supplementary-information.
68. Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, et al. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016;7:157-66. doi: 10.1016/j.ebiom.2016.04.008. PubMed PMID: PMC4909610.
69. Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, et al. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife. 2016;5:e16777. doi: 10.7554/eLife.16777. PubMed PMID: PMC4957980.
70. Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, et al. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences. 2016;17(8):1215. doi: 10.3390/ijms17081215. PubMed PMID: PMC5000613.
71. McKenzie AT, Katsyv I, Song W-M, Wang M, Zhang B. DGCA: A comprehensive R package for Differential Gene Correlation Analysis. BMC Systems Biology. 2016;10:106. doi: 10.1186/s12918-016-0349-1. PubMed PMID: PMC5111277.
72. Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 2016;7:12522. doi: 10.1038/ncomms12522 - supplementary-information.
73. Marino KA, Prada-Gracia D, Provasi D, Filizola M. Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model. PLOS Computational Biology. 2016;12(12):e1005240. doi: 10.1371/journal.pcbi.1005240.
75. Luo W, Obeidat Me, Di Narzo AF, Chen R, Sin DD, Paré PD, et al. Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. American Journal of Respiratory Cell and Molecular Biology. 2016;54(2):177-87. doi: 10.1165/rcmb.2014-0381OC. PubMed PMID: PMC4821039.
76. Lu AT, Hannon E, Levine ME, Hao K, Crimmins EM, Lunnon K, et al. Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum. Nature Communications. 2016;7:10561. doi: 10.1038/ncomms10561. PubMed PMID: PMC4740877.
77. Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, et al. Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. Genome Medicine. 2016;8:15. doi: 10.1186/s13073-016-0268-1. PubMed PMID: PMC4746932.
78. Loley C, Alver M, Assimes TL, Bjonnes A, Goel A, Gustafsson S, et al. No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis. Scientific Reports. 2016;6:35278. doi: 10.1038/srep35278 - supplementary-information.
79. Loh YH, Shen L. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. Methods Mol Biol. 2016;1415:371-83. Epub 2016/04/27. doi: 10.1007/978-1-4939-3572-7_18. PubMed PMID: 27115642.
80. Liu P, Ping Y, Ma M, Zhang D, Liu C, Zaidi S, et al. Anabolic actions of Notch on mature bone. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(15):E2152-E61. doi: 10.1073/pnas.1603399113. PubMed PMID: PMC4839423.
81. Liu C-T, Raghavan S, Maruthur N, Kabagambe Edmond K, Hong J, Ng Maggie C, et al. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. American Journal of Human Genetics. 2016;99(1):56-75. doi: 10.1016/j.ajhg.2016.05.006. PubMed PMID: PMC5005440.
82. Liu C, Kraja AT, Smith JA, Brody JA, Franceschini N, Bis JC, et al. Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. Nature genetics. 2016;48(10):1162-70. doi: 10.1038/ng.3660. PubMed PMID: PMC5320952.
83. Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, et al. Variants in TRIM22 that Affect NOD2 Signaling Are Associated With Very Early Onset Inflammatory Bowel Disease. Gastroenterology. 2016;150(5):1196-207. doi: 10.1053/j.gastro.2016.01.031. PubMed PMID: PMC4842103.
84. Li CW, Menconi F, Osman R, Mezei M, Jacobson EM, Concepcion E, et al. Identifying a Small Molecule Blocking Antigen Presentation in Autoimmune Thyroiditis. The Journal of Biological Chemistry. 2016;291(8):4079-90. doi: 10.1074/jbc.M115.694687. PubMed PMID: PMC4759184.
85. Lessard S, Manning AK, Low-Kam C, Auer PL, Giri A, Graff M, et al. Testing the role of predicted gene knockouts in human anthropometric trait variation. Human Molecular Genetics. 2016;25(10):2082-92. doi: 10.1093/hmg/ddw055. PubMed PMID: PMC5062577.
86. Lepack AE, Bagot RC, Pena CJ, Loh YE, Farrelly LA, Lu Y, et al. Aberrant H3.3 dynamics in NAc promote vulnerability to depressive-like behavior. Proc Natl Acad Sci U S A. 2016;113(44):12562-7. Epub 2016/11/03. doi: 10.1073/pnas.1608270113. PubMed PMID: 27791098; PubMed Central PMCID: PMCPMC5098673.
87. Lee E, Ito K, Zhao Y, Schadt EE, Irie HY, Zhu J. Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. Bioinformatics. 2016;32(1):96-105. doi: 10.1093/bioinformatics/btv531. PubMed PMID: PMC5006235.
88. Latif R, Realubit RB, Karan C, Mezei M, Davies TF. TSH Receptor Signaling Abrogation by a Novel Small Molecule. Frontiers in Endocrinology. 2016;7:130. doi: 10.3389/fendo.2016.00130. PubMed PMID: PMC5037132.
89. Laitman BM, Asp L, Mariani JN, Zhang J, Liu J, Sawai S, et al. The Transcriptional Activator Krüppel-like Factor-6 Is Required for CNS Myelination. PLOS Biology. 2016;14(5):e1002467. doi: 10.1371/journal.pbio.1002467.
90. Kruegel AC, Gassaway MM, Kapoor A, Váradi A, Majumdar S, Filizola M, et al. Synthetic and Receptor Signaling Explorations of the Mitragyna Alkaloids: Mitragynine as an Atypical Molecular Framework for Opioid Receptor Modulators. Journal of the American Chemical Society. 2016;138(21):6754-64. doi: 10.1021/jacs.6b00360.
91. Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, et al. Substantial DNA methylation differences between two major neuronal subtypes in human brain. Nucleic Acids Research. 2016;44(6):2593-612. doi: 10.1093/nar/gkv1304. PubMed PMID: PMC4824074.
92. Kosoy R, Agashe C, Grishin A, Leung DY, Wood RA, Sicherer SH, et al. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype. PLOS ONE. 2016;11(10):e0163831. doi: 10.1371/journal.pone.0163831.
93. Kocabayoglu P, Zhang DY, Kojima K, Hoshida Y, Friedman SL. Induction and contribution of beta platelet-derived growth factor signalling by hepatic stellate cells to liver regeneration after partial hepatectomy in mice. Liver international : official journal of the International Association for the Study of the Liver. 2016;36(6):874-82. Epub 2015/09/21. doi: 10.1111/liv.12933. PubMed PMID: 26256287.
94. Kilpeläinen TO, Carli JFM, Skowronski AA, Sun Q, Kriebel J, Feitosa MF, et al. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels. Nature Communications. 2016;7:10494. doi: 10.1038/ncomms10494 - supplementary-information.
95. Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, et al. Mapping the effects of drugs on the immune system. Nature biotechnology. 2016;34(1):47-54. doi: 10.1038/nbt.3367. PubMed PMID: PMC4706827.
96. Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, et al. Fetal liver hematopoietic stem cell niches associate with portal vessels. Science (New York, NY). 2016;351(6269):176-80. doi: 10.1126/science.aad0084. PubMed PMID: PMC4706788.
97. Katsyv I, Wang M, Song WM, Zhou X, Zhao Y, Park S, et al. EPRS is a critical regulator of cell proliferation and estrogen signaling in ER(+) breast cancer. Oncotarget. 2016;7(43):69592-605. doi: 10.18632/oncotarget.11870. PubMed PMID: PMC5342500.
98. Kapoor M, Chou YL, Edenberg HJ, Foroud T, Martin NG, Madden PAF, et al. Genome-wide polygenic scores for age at onset of alcohol dependence and association with alcohol-related measures. Translational Psychiatry. 2016;6(3):e761. doi: 10.1038/tp.2016.27. PubMed PMID: PMC4872451.
99. Kamlesh KY, Khader S, Ben R, Shalini SY, Li L, Andrew K, et al. Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer. Current Pharmaceutical Design. 2016;22(34):5234-48. doi:
100. Kajiwara Y, McKenzie A, Dorr N, Gama Sosa MA, Elder G, Schmeidler J, et al. The human-specific CASP4 gene product contributes to Alzheimer-related synaptic and behavioural deficits. Human Molecular Genetics. 2016;25(19):4315-27. doi: 10.1093/hmg/ddw265. PubMed PMID: PMC5291199.
101. Hoffman KW, Sachs D, Bardina SV, Michlmayr D, Rodriguez CA, Sum J, et al. Differences in Early Cytokine Production Are Associated With Development of a Greater Number of Symptoms Following West Nile Virus Infection. The Journal of Infectious Diseases. 2016;214(4):634-43. doi: 10.1093/infdis/jiw179. PubMed PMID: PMC4957436.
102. Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, et al. Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio. 2016;7(5):e01250-16. doi: 10.1128/mBio.01250-16. PubMed PMID: PMC5030358.
103. Heck MM, Thalgott M, Schmid SC, Oh WK, Gong Y, Wang L, et al. A 2-Gene Panel Derived From Prostate Cancer-Enhanced Transcripts in Whole Blood Is Prognostic for Survival and Predicts Treatment Benefit in Metastatic Castration-Resistant Prostate Cancer. The Prostate. 2016;76(13):1160-8. doi: 10.1002/pros.23202.
104. Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, et al. Limiting influenza virus, HIV and dengue virus infection by targeting viral proteostasis. Immunity. 2016;44(1):46-58. doi: 10.1016/j.immuni.2015.12.017. PubMed PMID: PMC4878455.
105. Haro C, Garcia-Carpintero S, Alcala-Diaz JF, Gomez-Delgado F, Delgado-Lista J, Perez-Martinez P, et al. The gut microbial community in metabolic syndrome patients is modified by diet. The Journal of Nutritional Biochemistry. 2016;27:27-31. doi:
106. Hamilton JR, Sachs D, Lim JK, Langlois RA, Palese P, Heaton NS. Club cells surviving influenza A virus infection induce temporary nonspecific antiviral immunity. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(14):3861-6. doi: 10.1073/pnas.1522376113. PubMed PMID: PMC4833272.
107. Halene TB, Kozlenkov A, Jiang Y, Mitchell A, Javidfar B, Dincer A, et al. NeuN(+) Neuronal Nuclei in Non-Human Primate Prefrontal Cortex and Subcortical White Matter After Clozapine Exposure. Schizophrenia research. 2016;170(0):235-44. doi: 10.1016/j.schres.2015.12.016. PubMed PMID: PMC4740223.
108. Hakenberg J, Cheng W-Y, Thomas P, Wang Y-C, Uzilov AV, Chen R. Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics. 2016;17:24. doi: 10.1186/s12859-015-0865-9. PubMed PMID: PMC4706706.
109. Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, et al. Nonalcoholic Steatohepatitis Is Associated With Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2016;14(11):1619-28. Epub 2015/10/20. doi: 10.1016/j.cgh.2015.10.010. PubMed PMID: 26492845.
110. Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, et al. Non-alcoholic Steatohepatitis is Associated with Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2016;14(11):1619-28. doi: 10.1016/j.cgh.2015.10.010. PubMed PMID: PMC4838546.
111. Gonzalo B, Dusan B-B, Marcelo Cortez San M, Víctor N, Harm van B, Michele T, et al. Avian Influenza Virus H5 Strain with North American and Eurasian Lineage Genes in an Antarctic Penguin. Emerging Infectious Disease journal. 2016;22(12):2221. doi: 10.3201/eid2212.161076.
112. Gong Y, Wang L, Chippada-Venkata U, Dai X, Oh WK, Zhu J. Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. Oncotarget. 2016;7(42):68688-707. doi: 10.18632/oncotarget.11925. PubMed PMID: PMC5356583.
113. Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, et al. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics. 2016;32(12):i101-i10. doi: 10.1093/bioinformatics/btw282. PubMed PMID: PMC4908366.
114. Gajzer D, Ross J, Winder L, Navada S, Zhang W, Silverman L, et al. Epigenetic and molecular signatures of cord blood CD34+ cells treated with histone deacetylase inhibitors. Vox Sanguinis. 2016;110(1):79-89. doi: 10.1111/vox.12303.
115. Gacias M, Gaspari S, Santos P-MG, Tamburini S, Andrade M, Zhang F, et al. Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior. eLife. 2016;5:e13442. doi: 10.7554/eLife.13442. PubMed PMID: PMC4880443.
116. Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, et al. The genetic architecture of type 2 diabetes. Nature. 2016;536(7614):41-7. doi: 10.1038/nature18642. PubMed PMID: PMC5034897.
117. Fu J, Wei C, Lee K, Zhang W, He W, Chuang P, et al. Comparison of Glomerular and Podocyte mRNA Profiles in Streptozotocin-Induced Diabetes. Journal of the American Society of Nephrology : JASN. 2016;27(4):1006-14. Epub 2015/08/11. doi: 10.1681/ASN.2015040421. PubMed PMID: 26264855.
118. Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, et al. Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia. Nature neuroscience. 2016;19(11):1442-53. doi: 10.1038/nn.4399. PubMed PMID: PMC5083142.
119. Franzén O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, et al. Cardiometabolic Risk Loci Share Downstream Cis- and Trans-Gene Regulation Across Tissues and Diseases. Science (New York, NY). 2016;353(6301):827-30. doi: 10.1126/science.aad6970. PubMed PMID: PMC5534139.
120. Franceschini N, Carty CL, Lu Y, Tao R, Sung YJ, Manichaikul A, et al. Variant Discovery and Fine Mapping of Genetic Loci Associated with Blood Pressure Traits in Hispanics and African Americans. PLOS ONE. 2016;11(10):e0164132. doi: 10.1371/journal.pone.0164132.
121. Epel ES, Puterman E, Lin J, Blackburn EH, Lum PY, Beckmann ND, et al. Meditation and vacation effects have an impact on disease-associated molecular phenotypes. Translational Psychiatry. 2016;6:e880. doi: 10.1038/tp.2016.164 - supplementary-information.
122. Ely BA, Xu J, Goodman WK, Lapidus KA, Gabbay V, Stern ER. Resting-State Functional Connectivity of the Human Habenula in Healthy Individuals: Associations with Subclinical Depression. Human brain mapping. 2016;37(7):2369-84. doi: 10.1002/hbm.23179. PubMed PMID: PMC4905808.
123. Eicher John D, Chami N, Kacprowski T, Nomura A, Chen M-H, Yanek Lisa R, et al. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals. American Journal of Human Genetics. 2016;99(1):40-55. doi: 10.1016/j.ajhg.2016.05.005. PubMed PMID: PMC5005441.
124. E Cahill M, Bagot R, Gancarz A, Walker D, Sun H, Wang Z, et al. Bidirectional Synaptic Structural Plasticity after Chronic Cocaine Administration Occurs through Rap1 Small GTPase Signaling2016. 566-82 p.
125. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature medicine. 2016;22(3):250-3. doi: 10.1038/nm.4039. PubMed PMID: PMC5062956.
126. Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, et al. Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci. Clinical and Translational Gastroenterology. 2016;7(6):e177. doi: 10.1038/ctg.2016.34. PubMed PMID: PMC4931595.
127. Di Cecilia S, Zhang F, Sancho A, Li S, Aguiló F, Sun Y, et al. <em>RBM5-AS1</em> Is Critical for Self-Renewal of Colon Cancer Stem-like Cells. Cancer Research. 2016;76(19):5615. doi: 10.1158/0008-5472.CAN-15-1824.
128. Damez-Werno DM, Sun H, Scobie KN, Shao N, Rabkin J, Dias C, et al. Histone arginine methylation in cocaine action in the nucleus accumbens. Proc Natl Acad Sci U S A. 2016;113(34):9623-8. Epub 2016/08/11. doi: 10.1073/pnas.1605045113. PubMed PMID: 27506785; PubMed Central PMCID: PMCPMC5003250.
129. Crowley RS, Riley AP, Sherwood AM, Groer CE, Shivaperumal N, Biscaia M, et al. Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability. Journal of Medicinal Chemistry. 2016;59(24):11027-38. doi: 10.1021/acs.jmedchem.6b01235.
130. Collazo-Lorduy A, Castillo-Martin M, Wang L, Patel V, Iyer G, Jordan E, et al. Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition. European urology. 2016;70(5):771-5. doi: 10.1016/j.eururo.2016.04.037. PubMed PMID: PMC5489411.
131. Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, et al. EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:120-31. PubMed PMID: PMC5161348.
132. Clemente JC, Dominguez-Bello MG. Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes. BMJ. 2016;352.
133. Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, et al. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome. Cell. 2016;167(2):444-56.e14. doi: 10.1016/j.cell.2016.08.076. PubMed PMID: PMC5129837.
134. Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, et al. Characterization of Gonadotrope Secretoproteome Identifies Neurosecretory Protein VGF-derived Peptide Suppression of Follicle-stimulating Hormone Gene Expression. The Journal of Biological Chemistry. 2016;291(40):21322-34. doi: 10.1074/jbc.M116.740365. PubMed PMID: PMC5076536.
135. Cheng W-Y, Hakenberg J, Li SD, Chen R. DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. Bioinformatics. 2016;32(1):151-3. doi: 10.1093/bioinformatics/btv511. PubMed PMID: PMC4681987.
136. Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, et al. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology. 2016;34:531. doi: 10.1038/nbt.3514 - supplementary-information.
137. Chen P, Yi Z, Zhang W, Klotman ME, Chen BK. HIV infection-induced transcriptional program in renal tubular epithelial cells activates a CXCR2-driven CD4+ T-cell chemotactic response. AIDS (London, England). 2016;30(12):1877-88. doi: 10.1097/QAD.0000000000001153. PubMed PMID: 27163710.
138. Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, et al. Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease. Human mutation. 2016;37(11):1215-22. doi: 10.1002/humu.23067. PubMed PMID: PMC5063710.
139. Chami N, Chen M-H, Slater Andrew J, Eicher John D, Evangelou E, Tajuddin Salman M, et al. Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits. American Journal of Human Genetics. 2016;99(1):8-21. doi: 10.1016/j.ajhg.2016.05.007. PubMed PMID: PMC5005438.
140. Bunyavanich S, Shen N, Grishin A, Wood R, Burks A, Dawson P, et al. Early-life gut microbiome composition and milk allergy resolution2016.
141. Bien SA, Wojcik GL, Zubair N, Gignoux CR, Martin AR, Kocarnik JM, et al. Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array. PLOS ONE. 2016;11(12):e0167758. doi: 10.1371/journal.pone.0167758.
142. Below JE, Parra EJ, Gamazon ER, Torres J, Krithika S, Candille S, et al. Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs. Scientific Reports. 2016;6:19429. doi: 10.1038/srep19429 - supplementary-information.
143. Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, et al. The Great Migration and African-American Genomic Diversity. PLOS Genetics. 2016;12(5):e1006059. doi: 10.1371/journal.pgen.1006059.
144. Bagot RC, Cates HM, Purushothaman I, Lorsch ZS, Walker DM, Wang J, et al. Circuit-wide transcriptional profiling reveals brain region-specific gene networks regulating depression susceptibility. Neuron. 2016;90(5):969-83. doi: 10.1016/j.neuron.2016.04.015. PubMed PMID: PMC4896746.
145. Bagot R, Cates H, Purushothaman I, Vialou V, Heller E, Yieh L, et al. Ketamine and Imipramine Reverse Transcriptional Signatures of Susceptibility and Induce Resilience-Specific Gene Expression Profiles2016.
146. Bagot R, Cates H, Purushothaman I, Lorsch Zachary S, Walker D, Wang J, et al. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility2016.
147. Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, et al. EHDViz: clinical dashboard development using open-source technologies. BMJ Open. 2016;6(3):e010579. doi: 10.1136/bmjopen-2015-010579. PubMed PMID: PMC4809078.
148. Ayers KL, Mirshahi UL, Wardeh AH, Murray MF, Hao K, Glicksberg BS, et al. A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers. BMC Genomics. 2016;17(Suppl 2):445. doi: 10.1186/s12864-016-2725-z. PubMed PMID: PMC4928152.
149. Argmann CA, Houten SM, Zhu J, Schadt EE. A next generation multiscale view of inborn errors of metabolism. Cell metabolism. 2016;23(1):13-26. doi: 10.1016/j.cmet.2015.11.012. PubMed PMID: PMC4715559.
150. Aguilo F, Li S, Balasubramaniyan N, Sancho A, Benko S, Zhang F, et al. Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α. Cell reports. 2016;14(3):479-92. Epub 2016/01/07. doi: 10.1016/j.celrep.2015.12.043. PubMed PMID: 26774474.
151. Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease. New England Journal of Medicine. 2016;374(12):1134-44. doi: 10.1056/NEJMoa1507652.

Theme by Danetsoft and Danang Probo Sayekti inspired by Maksimer