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2012 Published Papers

1. Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, et al. Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation. PLoS Biology. 2012;10(4):e1001301. doi: 10.1371/journal.pbio.1001301. PubMed PMID: PMC3317911.
2. Zhu J, Choi W-S, McCoy JG, Negri A, Zhu J, Naini S, et al. Structure-Guided Design of a High-Affinity Platelet Integrin α(IIb)β(3) Receptor Antagonist That Disrupts Mg(2+) Binding to the MIDAS. Science Translational Medicine. 2012;4(125):125ra32-ra32. doi: 10.1126/scitranslmed.3003576. PubMed PMID: PMC3390238.
3. Zhang G, Sanchez R, Zhou M-M. Scaling the Druggability Landscape of Human Bromodomains, a New Class of Drug Targets. Journal of Medicinal Chemistry. 2012;55(17):7342-5. doi: 10.1021/jm3011977.
4. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7. doi: 10.1038/nature11053. PubMed PMID: PMC3376388.
5. Xia Y, Bin Z, Jun Z. Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics. Current Drug Metabolism. 2012;13(7):952-67. doi:
6. Wu H, Moshkina N, Min J, Zeng H, Joshua J, Zhou M-M, et al. Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(23):8925-30. doi: 10.1073/pnas.1114117109. PubMed PMID: PMC3384170.
7. Wu C, Zhu J, Zhang X. Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. BMC Bioinformatics. 2012;13(1):182. doi: 10.1186/1471-2105-13-182.
8. Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, et al. Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers. Molecular Systems Biology. 2012;8:594-. doi: 10.1038/msb.2012.24. PubMed PMID: PMC3421440.
9. van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, et al. Seventy-five genetic loci influencing the human red blood cell. Nature. 2012;492:369. doi: 10.1038/nature11677 - supplementary-information.
10. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. The Journal of allergy and clinical immunology. 2012;129(5):1204-8. doi: 10.1016/j.jaci.2012.03.010. PubMed PMID: PMC3342686.
11. Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, et al. Integrative Analysis of a Cross-Loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets. PLOS Genetics. 2012;8(12):e1003107. doi: 10.1371/journal.pgen.1003107.
12. The Human Microbiome Project C. Structure, Function and Diversity of the Healthy Human Microbiome. Nature. 2012;486(7402):207-14. doi: 10.1038/nature11234. PubMed PMID: PMC3564958.
13. The CDC, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nature Genetics. 2012;45:25. doi: 10.1038/ng.2480 - supplementary-information.
14. Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, et al. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Research. 2012;22(11):2146-52. doi: 10.1101/gr.140608.112. PubMed PMID: PMC3483544.
15. Smith CC, Wang Q, Chin C-S, Salerno S, Damon LE, Levis MJ, et al. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature. 2012;485:260. doi: 10.1038/nature11016 - supplementary-information.
16. Skinner MK, Manikkam M, Haque MM, Zhang B, Savenkova MI. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions. Genome Biology. 2012;13(10):R91. doi: 10.1186/gb-2012-13-10-r91.
17. Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, et al. Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. PLoS Computational Biology. 2012;8(6):e1002538. doi: 10.1371/journal.pcbi.1002538. PubMed PMID: PMC3369906.
18. Rothbard JB, Kurnellas MP, Brownell S, Adams CM, Su L, Axtell RC, et al. Therapeutic Effects of Systemic Administration of Chaperone αB-Crystallin Associated with Binding Proinflammatory Plasma Proteins. The Journal of Biological Chemistry. 2012;287(13):9708-21. doi: 10.1074/jbc.M111.337691. PubMed PMID: PMC3322989.
19. Patel CJ, Chen R, Butte AJ. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics. 2012;28(12):i121-i6. doi: 10.1093/bioinformatics/bts229. PubMed PMID: PMC3371861.
20. Negri A, Li J, Naini S, Coller BS, Filizola M. Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand. Journal of computer-aided molecular design. 2012;26(9):1005-15. doi: 10.1007/s10822-012-9594-6. PubMed PMID: PMC3496400.
21. Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012;485:242. doi: 10.1038/nature11011 - supplementary-information.
22. Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. Journal of the American Medical Informatics Association : JAMIA. 2012;19(e1):e21-e7. doi: 10.1136/amiajnl-2011-000737. PubMed PMID: PMC3392859.
23. Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, et al. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi: 10.1038/nature11209. PubMed PMID: PMC3377744.
24. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience. 2012;1:7-. doi: 10.1186/2047-217X-1-7. PubMed PMID: PMC3626512.
25. Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants. Bioinformatics. 2012;28(5):724-5. doi: 10.1093/bioinformatics/bts032.
26. Luo MJ, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, Plump A, et al. 11β-HSD1 inhibition reduces atherosclerosis in mice by altering proinflammatory gene expression in the vasculature. Physiological Genomics. 2012;45(1):47-57. doi: 10.1152/physiolgenomics.00109.2012.
27. Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, et al. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. BMC Systems Biology. 2012;6(1):101. doi: 10.1186/1752-0509-6-101.
29. Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, et al. A Common Peripheral Blood Gene Set for Diagnosis of Operational Tolerance in Pediatric and Adult Liver Transplantation. American Journal of Transplantation. 2012;12(5):1218-28. doi: 10.1111/j.1600-6143.2011.03928.x.
30. Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone M, et al. A Five-Gene Peripheral Blood Diagnostic Test for Acute Rejection in Renal Transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2012;12(10):2710-8. doi: 10.1111/j.1600-6143.2012.04253.x. PubMed PMID: PMC4148014.
31. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, et al. Performance comparison of whole-genome sequencing platforms. Nature biotechnology. 2012;30(1):78-82. doi: 10.1038/nbt.2065. PubMed PMID: PMC4076012.
32. Kou Y, Betancur C, Xu H, Buxbaum JD, Ma'ayan A. Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. American Journal of Medical Genetics Part C: Seminars in Medical Genetics. 2012;160C(2):130-42. doi: 10.1002/ajmg.c.31330.
33. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, et al. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(18):7049-54. doi: 10.1073/pnas.1114513109. PubMed PMID: PMC3344989.
34. Kidd Jeffrey M, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, et al. Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation. American Journal of Human Genetics. 2012;91(4):660-71. doi: 10.1016/j.ajhg.2012.08.025. PubMed PMID: PMC3484644.
35. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, et al. Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012;55(8):2205-13. doi: 10.1007/s00125-012-2568-3. PubMed PMID: PMC3390705.
36. Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. AMIA Summits on Translational Science Proceedings. 2012;2012:35-41. PubMed PMID: PMC3392070.
37. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, et al. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119. doi: 10.1038/nature11582 - supplementary-information.
38. Johnston JM, Wang H, Provasi D, Filizola M. Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors. PLOS Computational Biology. 2012;8(8):e1002649. doi: 10.1371/journal.pcbi.1002649.
39. Ionita-Laza I, Makarov V, Buxbaum Joseph D. Scan-Statistic Approach Identifies Clusters of Rare Disease Variants in LRP2, a Gene Linked and Associated with Autism Spectrum Disorders, in Three Datasets. The American Journal of Human Genetics. 2012;90(6):1002-13. doi:
40. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, et al. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012;13:440-. doi: 10.1186/1471-2164-13-440. PubMed PMID: PMC3534380.
41. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature biotechnology. 2012;30(11):10.1038/nbt.2403. doi: 10.1038/nbt.2403. PubMed PMID: PMC3827024.
42. Fromer M, Moran Jennifer L, Chambert K, Banks E, Bergen Sarah E, Ruderfer Douglas M, et al. Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth. The American Journal of Human Genetics. 2012;91(4):597-607. doi:
43. Fitzpatrick K, Winrow CJ, Gotter AL, Millstein J, Arbuzova J, Brunner J, et al. Altered Sleep and Affect in the Neurotensin Receptor 1 Knockout Mouse. Sleep. 2012;35(7):949-56. doi: 10.5665/sleep.1958. PubMed PMID: PMC3369230.
44. Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature Biotechnology. 2012;30:1232. doi: 10.1038/nbt.2432 - supplementary-information.
45. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, et al. Human genomic disease variants: A neutral evolutionary explanation. Genome Research. 2012;22(8):1383-94. doi: 10.1101/gr.133702.111. PubMed PMID: PMC3409252.
46. Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery. Molecular Biology and Evolution. 2012;29(9):2087-94. doi: 10.1093/molbev/mss079. PubMed PMID: PMC3424407.
47. Clemente JC, Ursell LK, Parfrey LW, Knight R. The Impact of the Gut Microbiota on Human Health: An Integrative View. Cell. 2012;148(6):1258-70. doi: 10.1016/j.cell.2012.01.035. PubMed PMID: PMC5050011.
48. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HYK, Chen R, et al. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes. Cell. 2012;148(6):1293-307. doi: 10.1016/j.cell.2012.02.009. PubMed PMID: PMC3341616.
49. Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. AMIA Summits on Translational Science Proceedings. 2012;2012:11-8. PubMed PMID: PMC3392055.
50. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, et al. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases. PLoS Genetics. 2012;8(4):e1002621. doi: 10.1371/journal.pgen.1002621. PubMed PMID: PMC3325177.
51. Carvalho FA, Koren O, Goodrich JK, Johansson MEV, Nalbantoglu I, Aitken JD, et al. Transient Inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell host & microbe. 2012;12(2):139-52. doi: 10.1016/j.chom.2012.07.004. PubMed PMID: PMC4310462.
52. Buxbaum Joseph D, Daly Mark J, Devlin B, Lehner T, Roeder K, State Matthew W. The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders. Neuron. 2012;76(6):1052-6. doi:
53. Bashir A, Klammer A, Robins WP, Chin C-S, Webster D, Paxinos E, et al. A Hybrid Approach for the Automated Finishing of Bacterial Genomes. Nature biotechnology. 2012;30(7):701-7. doi: 10.1038/nbt.2288. PubMed PMID: PMC3731737.
54. Anh Tran V, Carlos Clemente J, Nguyen Duc T, Li J, Dang X, Tu T, et al. IMPACT: A novel clustering algorithm based on attraction2012.

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