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2013 Published Papers

1. Zhang B, Gaiteri C, Bodea L-G, Wang Z, McElwee J, Podtelezhnikov AA, et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell. 2013;153(3):707-20. doi: 10.1016/j.cell.2013.03.030. PubMed PMID: PMC3677161.
2. Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, et al. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics. 2013;14(Suppl 6):S1-S. doi: 10.1186/1471-2105-14-S6-S1. PubMed PMID: PMC3633009.
3. Wu C, Zhu J, Zhang X. Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. BMC Bioinformatics. 2013;14(1):365. doi: 10.1186/1471-2105-14-365.
4. Whalen S, Pandey G. A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics. eprint arXiv:13095047. 2013:arXiv:1309.5047.
5. Warren BL, Vialou VF, Iniguez SD, Alcantara LF, Wright KN, Feng J, et al. Neurobiological sequelae of witnessing stressful events in adult mice. Biol Psychiatry. 2013;73(1):7-14. Epub 2012/07/17. doi: 10.1016/j.biopsych.2012.06.006. PubMed PMID: 22795644; PubMed Central PMCID: PMCPMC3498570.
6. Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, et al. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics. 2013;29(24):3204-10. Epub 2013/10/01. doi: 10.1093/bioinformatics/btt558. PubMed PMID: 24078702; PubMed Central PMCID: PMCPMC3842760.
7. Wang Q, Chikina M, Zaslavsky E, Pincas H, Sealfon SC. β-Catenin Regulates GnRH-Induced FSHβ Gene Expression. Molecular Endocrinology. 2013;27(2):224-37. doi: 10.1210/me.2012-1310. PubMed PMID: PMC3683805.
8. Vimaleswaran KS, Berry DJ, Lu C, Tikkanen E, Pilz S, Hiraki LT, et al. Causal Relationship between Obesity and Vitamin D Status: Bi-Directional Mendelian Randomization Analysis of Multiple Cohorts. PLOS Medicine. 2013;10(2):e1001383. doi: 10.1371/journal.pmed.1001383.
9. Varble A, Benitez Asiel A, Schmid S, Sachs D, Shim Jaehee V, Rodriguez-Barrueco R, et al. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication. Cell Host & Microbe. 2013;14(3):346-56. doi:
10. van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription. PLOS Genetics. 2013;9(5):e1003479. doi: 10.1371/journal.pgen.1003479.
11. The GC. The Genotype-Tissue Expression (GTEx) project. Nature genetics. 2013;45(6):580-5. doi: 10.1038/ng.2653. PubMed PMID: PMC4010069.
12. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting family members share microbiota with one another and with their dogs. eLife. 2013;2:e00458. doi: 10.7554/eLife.00458. PubMed PMID: PMC3628085.
13. Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, et al. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet Journal of Rare Diseases. 2013;8:45-. doi: 10.1186/1750-1172-8-45. PubMed PMID: PMC3648437.
14. Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One. 2013;8(6):e65598. Epub 2013/06/14. doi: 10.1371/journal.pone.0065598. PubMed PMID: 23762400; PubMed Central PMCID: PMCPMC3677880.
15. Shen L, Choi I, Nestler EJ, Won K-J. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics & Informatics. 2013;11(2):60-7. doi: 10.5808/GI.2013.11.2.60. PubMed PMID: PMC3704928.
16. Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, et al. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Research. 2013;23(1):129-41. doi: 10.1101/gr.136739.111. PubMed PMID: PMC3530673.
17. Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, et al. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Medicine. 2013;5(12):113. doi: 10.1186/gm518.
18. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice. Science. 2013;341(6150).
19. Poultney Christopher S, Goldberg Arthur P, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, et al. Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder. American Journal of Human Genetics. 2013;93(4):607-19. doi: 10.1016/j.ajhg.2013.09.001. PubMed PMID: PMC3791269.
20. Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, et al. Whole genome sequencing in support of wellness and health maintenance. Genome Medicine. 2013;5(6):58-. doi: 10.1186/gm462. PubMed PMID: PMC3967117.
21. Patel CJ, Chen R, Kodama K, Ioannidis JPA, Butte AJ. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Human Genetics. 2013;132(5):495-508. doi: 10.1007/s00439-012-1258-z. PubMed PMID: PMC3625410.
22. Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, et al. Biphasic assembly of the murine intestinal microbiota during early development. The ISME Journal. 2013;7(6):1112-5. doi: 10.1038/ismej.2013.15. PubMed PMID: PMC3660675.
23. Pandey G, Zhang B, Jian L. Predicting submicron air pollution indicators: a machine learning approach. Environmental Science: Processes & Impacts. 2013;15(5):996-1005. doi: 10.1039/C3EM30890A.
24. Nilsson E, Zhang B, Skinner MK. Gene bionetworks that regulate ovarian primordial follicle assembly. BMC Genomics. 2013;14(1):496. doi: 10.1186/1471-2164-14-496.
25. Neto EC, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, et al. Modeling Causality for Pairs of Phenotypes in System Genetics. Genetics. 2013;193(3):1003-13. doi: 10.1534/genetics.112.147124. PubMed PMID: PMC3583988.
26. Negri A, Rives M-L, Caspers MJ, Prisinzano TE, Javitch JA, Filizola M. Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening. Journal of Chemical Information and Modeling. 2013;53(3):521-6. doi: 10.1021/ci400019t.
27. Mondal S, Johnston JM, Wang H, Khelashvili G, Filizola M, Weinstein H. Membrane Driven Spatial Organization of GPCRs. Scientific Reports. 2013;3:2909. doi: 10.1038/srep02909 - supplementary-information.
28. Monda KL, Chen GK, Taylor KC, Palmer C, Edwards TL, Lange LA, et al. A Meta-Analysis Identifies New Loci Associated with Body Mass index in Individuals of African Ancestry. Nature genetics. 2013;45(6):690-6. doi: 10.1038/ng.2608. PubMed PMID: PMC3694490.
29. Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, et al. Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus. PLOS Genetics. 2013;9(7):e1003652. doi: 10.1371/journal.pgen.1003652.
30. Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, et al. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genetics In Medicine. 2013;16:149. doi: 10.1038/gim.2013.84 - supplementary-information.
31. Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, et al. Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution. PLOS Genetics. 2013;9(1):e1003191. doi: 10.1371/journal.pgen.1003191.
32. Leeper Nicholas J, Raiesdana A, Kojima Y, Kundu Ramendra K, Cheng H, Maegdefessel L, et al. Loss of CDKN2B Promotes p53-Dependent Smooth Muscle Cell Apoptosis and Aneurysm Formation. Arteriosclerosis, Thrombosis, and Vascular Biology. 2013;33(1):e1-e10. doi: 10.1161/ATVBAHA.112.300399.
33. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 2013;31:814. doi: 10.1038/nbt.2676 - supplementary-information.
34. Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, et al. Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS ONE. 2013;8(2):e47879. doi: 10.1371/journal.pone.0047879. PubMed PMID: PMC3568148.
35. Karkheiran S, Krebs CE, Makarov V, Nilipour Y, Hubert B, Darvish H, et al. Identification of COL6A2 mutations in progressive myoclonus epilepsy syndrome. Human Genetics. 2013;132(3):275-83. doi: 10.1007/s00439-012-1248-1.
36. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, et al. Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(23):9607-12. doi: 10.1073/pnas.1219099110. PubMed PMID: PMC3677437.
37. Jin Y-J, Cai CY, Mezei M, Ohlmeyer M, Sanchez R, Burakoff SJ. Identification of a Novel Binding Site Between HIV Type 1 Nef C-Terminal Flexible Loop and AP2 Required for Nef-Mediated CD4 Downregulation. AIDS Research and Human Retroviruses. 2013;29(4):725-31. doi: 10.1089/aid.2012.0286. PubMed PMID: PMC3903168.
38. Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD, et al. Epigenome-wide differences in pathology-free regions of multiple sclerosis–affected brains. Nature Neuroscience. 2013;17:121. doi: 10.1038/nn.3588 - supplementary-information.
39. Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, et al. A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease. Arteriosclerosis, thrombosis, and vascular biology. 2013;33(6):1427-34. doi: 10.1161/ATVBAHA.112.300112. PubMed PMID: PMC3752786.
40. Hu Y-J, Berndt Sonja I, Gustafsson S, Ganna A, Berndt Sonja I, Gustafsson S, et al. Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics. The American Journal of Human Genetics. 2013;93(2):236-48. doi:
41. Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, et al. Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). BMC Medical Genetics. 2013;14:62-. doi: 10.1186/1471-2350-14-62. PubMed PMID: PMC3699381.
42. Heaton NS, Sachs D, Chen C-J, Hai R, Palese P. Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(50):20248-53. doi: 10.1073/pnas.1320524110. PubMed PMID: PMC3864309.
43. Gomes I, Fujita W, Gupta A, Saldanha SA, Negri A, Pinello CE, et al. Identification of a μ-δ opioid receptor heteromer-biased agonist with antinociceptive activity. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(29):12072-7. doi: 10.1073/pnas.1222044110. PubMed PMID: PMC3718106.
44. Ganesh SK, Tragante V, Guo W, Guo Y, Lanktree MB, Smith EN, et al. Loci influencing blood pressure identified using a cardiovascular gene-centric array. Human Molecular Genetics. 2013;22(8):1663-78. doi: 10.1093/hmg/dds555.
45. Gandy S, Haroutunian V, DeKosky ST, Sano M, Schadt EE. CR1 and the “Vanishing Amyloid” Hypothesis of Alzheimer’s Disease. Biological Psychiatry. 2013;73(5):393-5. doi:
46. Filizola M, Devi LA. Grand Opening of Structure-Guided Design for Novel Opioids. Trends in pharmacological sciences. 2013;34(1):6-12. doi: 10.1016/ PubMed PMID: PMC3534797.
47. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, et al. Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science. 2013;342(6158):621.
48. Ferguson D, Koo JW, Feng J, Heller E, Rabkin J, Heshmati M, et al. Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action. J Neurosci. 2013;33(41):16088-98. Epub 2013/10/11. doi: 10.1523/jneurosci.1284-13.2013. PubMed PMID: 24107942; PubMed Central PMCID: PMCPMC3792451.
49. Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, et al. Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic. PLOS Computational Biology. 2013;9(3):e1002935. doi: 10.1371/journal.pcbi.1002935.
50. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science (New York, NY). 2013;341(6141):1237439-. doi: 10.1126/science.1237439. PubMed PMID: PMC3791589.
51. Ding Y, Hubert CG, Herman J, Corrin P, Toledo CM, Skutt-Kakaria K, et al. Cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. Cancer discovery. 2013;3(2):198-211. doi: 10.1158/2159-8290.CD-12-0353. PubMed PMID: PMC3632446.
52. Coudray N, Valvo S, Hu M, Lasala R, Kim C, Vink M, et al. Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(6):2140-5. doi: 10.1073/pnas.1215455110. PubMed PMID: PMC3568326.
53. Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, et al. Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration. PLoS Genetics. 2013;9(5):e1003447. doi: 10.1371/journal.pgen.1003447. PubMed PMID: PMC3662561.
54. Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, et al. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. Human Molecular Genetics. 2013;22(12):2529-38. doi: 10.1093/hmg/ddt087. PubMed PMID: PMC3658166.
55. Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, et al. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. The ISME Journal. 2013;7(1):85-95. doi: 10.1038/ismej.2012.81. PubMed PMID: PMC3526177.
56. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, et al. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. PLOS Computational Biology. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047.
57. Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics. 2013;45:501. doi: 10.1038/ng.2606 - supplementary-information.
58. Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, et al. Global biogeography of highly diverse protistan communities in soil. The ISME Journal. 2013;7(3):652-9. doi: 10.1038/ismej.2012.147. PubMed PMID: PMC3578557.
59. Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, et al. Characterization of the human ESC transcriptome by hybrid sequencing. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(50):E4821-E30. doi: 10.1073/pnas.1320101110. PubMed PMID: PMC3864310.

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