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2014 Published Papers

1. Zhang XY, Birtwistle MR, Gallo JM. A General Network Pharmacodynamic Model-Based Design Pipeline for Customized Cancer Therapy Applied to the VEGFR Pathway. CPT: pharmacometrics & systems pharmacology. 2014;3(1):e92-e. doi: 10.1038/psp.2013.65. PubMed PMID: 24429593.
2. Yoo S, Huang T, Campbell JD, Lee E, Tu Z, Geraci MW, et al. MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis. PLOS Computational Biology. 2014;10(8):e1003790. doi: 10.1371/journal.pcbi.1003790.
3. Ye F, Wang L, Castillo-Martin M, McBride R, Galsky MD, Zhu J, et al. Biomarkers for bladder cancer management: present and future. American Journal of Clinical and Experimental Urology. 2014;2(1):1-14. PubMed PMID: PMC4219291.
4. Wu M, Peng S, Yang J, Tu Z, Cai X, Cai C-L, et al. Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node. Cell Research. 2014;24(10):1201-13. doi: 10.1038/cr.2014.113. PubMed PMID: PMC4185344.
5. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature genetics. 2014;46(11):1173-86. doi: 10.1038/ng.3097. PubMed PMID: PMC4250049.
6. Wei Y, Peng S, Wu M, Sachidanandam R, Tu Z, Zhang S, et al. Multifaceted roles of miR-1s in repressing the fetal gene program in the heart. Cell Research. 2014;24:278. doi: 10.1038/cr.2014.12 - supplementary-information.
7. Wang Q, Chikina MD, Pincas H, Sealfon SC. Homer1 Alternative Splicing Is Regulated by Gonadotropin-Releasing Hormone and Modulates Gonadotropin Gene Expression. Molecular and Cellular Biology. 2014;34(10):1747-56. doi: 10.1128/MCB.01401-13. PubMed PMID: PMC4019030.
8. Varble A, Albrecht RA, Backes S, Crumiller M, Bouvier NM, Sachs D, et al. Influenza A virus transmission bottlenecks are defined by infection route and recipient host. Cell host & microbe. 2014;16(5):691-700. doi: 10.1016/j.chom.2014.09.020. PubMed PMID: PMC4272616.
9. Toki D, Zhang W, Hor KLM, Liuwantara D, Alexander SI, Yi Z, et al. The Role of Macrophages in the Development of Human Renal Allograft Fibrosis in the First Year After Transplantation. American Journal of Transplantation. 2014;14(9):2126-36. doi: 10.1111/ajt.12803.
10. Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, et al. Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting. Antimicrobial Agents and Chemotherapy. 2014;58(12):7347-57. doi: 10.1128/AAC.03900-14. PubMed PMID: PMC4249533.
11. Skinner MK, Savenkova MI, Zhang B, Gore AC, Crews D. Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology. BMC Genomics. 2014;15(1):377. doi: 10.1186/1471-2164-15-377. PubMed PMID: PMC4073506.
12. Shi J, Wang Y, Zeng L, Wu Y, Deng J, Zhang Q, et al. Disrupting the Interaction of BRD4 with Di-acetylated Twist Suppresses Tumorigenesis in Basal-like Breast Cancer. Cancer cell. 2014;25(2):210-25. doi: 10.1016/j.ccr.2014.01.028. PubMed PMID: PMC4004960.
13. Shen L, Shao N, Liu X, Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284. Epub 2014/04/17. doi: 10.1186/1471-2164-15-284. PubMed PMID: 24735413; PubMed Central PMCID: PMCPMC4028082.
14. Shapiro JS, Schmid S, Aguado LC, Sabin LR, Yasunaga A, Shim JV, et al. Drosha as an interferon-independent antiviral factor. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(19):7108-13. doi: 10.1073/pnas.1319635111. PubMed PMID: PMC4024876.
15. Shang Y, LeRouzic V, Schneider S, Bisignano P, Pasternak GW, Filizola M. Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions. Biochemistry. 2014;53(31):5140-9. doi: 10.1021/bi5006915.
16. Shabman RS, Jabado OJ, Mire CE, Stockwell TB, Edwards M, Mahajan M, et al. Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells. mBio. 2014;5(6):e02011-14. doi: 10.1128/mBio.02011-14.
17. Scobie KN, Damez-Werno D, Sun H, Shao N, Gancarz A, Panganiban CH, et al. Essential role of poly(ADP-ribosyl)ation in cocaine action. Proc Natl Acad Sci U S A. 2014;111(5):2005-10. Epub 2014/01/23. doi: 10.1073/pnas.1319703111. PubMed PMID: 24449909; PubMed Central PMCID: PMCPMC3918779.
18. Schmid S, Sachs D, tenOever BR. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus. The Journal of Biological Chemistry. 2014;289(1):299-311. doi: 10.1074/jbc.M113.519934. PubMed PMID: PMC3879553.
19. Scarabelli G, Provasi D, Negri A, Filizola M. Bioactive Conformations of Two Seminal Delta Opioid Receptor Penta-peptides Inferred from Free-Energy Profiles. Biopolymers. 2014;101(1):10.1002/bip.22251. doi: 10.1002/bip.22251. PubMed PMID: PMC3812360.
20. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014;2:e545. doi: 10.7717/peerj.545.
21. Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature. 2014;506:185. doi: 10.1038/nature12975 - supplementary-information.
22. Provasi D, Negri A, Coller BS, Filizola M. Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multimicrosecond, all-atom molecular dynamics simulations. Proteins. 2014;82(12):3231-40. doi: 10.1002/prot.24540. PubMed PMID: PMC5156318.
23. Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, et al. Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders. The American Journal of Human Genetics. 2014;94(5):677-94. doi: 10.1016/j.ajhg.2014.03.018.
24. Peloso Gina M, Auer Paul L, Bis Joshua C, Voorman A, Morrison Alanna C, Stitziel Nathan O, et al. Association of Low-Frequency and Rare Coding-Sequence Variants with Blood Lipids and Coronary Heart Disease in 56,000 Whites and Blacks. American Journal of Human Genetics. 2014;94(2):223-32. doi: 10.1016/j.ajhg.2014.01.009. PubMed PMID: PMC3928662.
25. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Frontiers in Microbiology. 2014;5:298. doi: 10.3389/fmicb.2014.00298. PubMed PMID: PMC4063188.
26. Pandey G, Arora S, Manocha S, Whalen S. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks. PLOS ONE. 2014;9(10):e109130. doi: 10.1371/journal.pone.0109130.
27. Ng MCY, Shriner D, Chen BH, Li J, Chen W-M, Guo X, et al. Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes. PLoS Genetics. 2014;10(8):e1004517. doi: 10.1371/journal.pgen.1004517. PubMed PMID: PMC4125087.
28. Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, et al. Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Molecular Systems Biology. 2014;10(7):743-. doi: 10.15252/msb.20145304. PubMed PMID: PMC4299500.
29. Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, et al. Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci. 2014;17(11):1476-90. Epub 2014/10/29. doi: 10.1038/nn.3816. PubMed PMID: 25349914; PubMed Central PMCID: PMCPMC4262187.
30. Maze I, Chaudhury D, Dietz DM, Von Schimmelmann M, Kennedy PJ, Lobo MK, et al. G9a influences neuronal subtype specification in striatum. Nat Neurosci. 2014;17(4):533-9. Epub 2014/03/04. doi: 10.1038/nn.3670. PubMed PMID: 24584053; PubMed Central PMCID: PMCPMC3972624.
31. Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 2014;63(3):401-8. doi: 10.1136/gutjnl-2012-303013. PubMed PMID: PMC3933177.
32. Mäkinen V-P, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, et al. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease. PLOS Genetics. 2014;10(7):e1004502. doi: 10.1371/journal.pgen.1004502.
33. Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, et al. Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Medical Genomics. 2014;7:20-. doi: 10.1186/1755-8794-7-20. PubMed PMID: PMC4022392.
34. Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, et al. Disease Risk Factors Identified through Shared Genetic Architecture and Electronic Medical Records. Science translational medicine. 2014;6(234):234ra57-ra57. doi: 10.1126/scitranslmed.3007191. PubMed PMID: PMC4323098.
35. Li J, Vootukuri S, Shang Y, Negri A, Jiang J-K, Nedelman M, et al. RUC-4: a novel αIIbβ3 antagonist for prehospital therapy of myocardial infarction. Arteriosclerosis, thrombosis, and vascular biology. 2014;34(10):2321-9. Epub 2014/08/21. doi: 10.1161/ATVBAHA.114.303724. PubMed PMID: 25147334.
36. Li J, Vootukuri S, Shang Y, Negri A, Jiang J-k, Nedelman M, et al. RUC-4: A Novel αIIbβ3 Antagonist for Pre-hospital Therapy of Myocardial Infarction. Arteriosclerosis, thrombosis, and vascular biology. 2014;34(10):2321-9. doi: 10.1161/ATVBAHA.114.303724. PubMed PMID: PMC4180209.
37. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang Z-Z, et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. American journal of human genetics. 2014;94(2):233-45. doi: 10.1016/j.ajhg.2014.01.010. PubMed PMID: 24507775.
38. Kozlenkov A, Roussos P, Timashpolsky A, Barbu M, Rudchenko S, Bibikova M, et al. Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Research. 2014;42(1):109-27. doi: 10.1093/nar/gkt838. PubMed PMID: PMC3874157.
39. Johnston JM, Filizola M. Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors. PLOS ONE. 2014;9(2):e90694. doi: 10.1371/journal.pone.0090694.
40. Johnston JM, Filizola M. Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods. Advances in experimental medicine and biology. 2014;796:95-125. doi: 10.1007/978-94-007-7423-0_6. PubMed PMID: PMC4074508.
41. Jiang J-k, McCoy JG, Shen M, LeClair CA, Huang W, Negri A, et al. A novel class of ion displacement ligands as antagonists of the αIIbβ3 receptor that limit conformational reorganization of the receptor. Bioorganic & medicinal chemistry letters. 2014;24(4):1148-53. doi: 10.1016/j.bmcl.2013.12.122. PubMed PMID: PMC3951875.
42. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, et al. Advancing the Microbiome Research Community. Cell. 2014;159(2):227-30. doi: 10.1016/j.cell.2014.09.022. PubMed PMID: PMC4221798.
43. Hoffman GE, Mezey JG, Schadt EE. lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R. Bioinformatics. 2014;30(21):3134-5. doi: 10.1093/bioinformatics/btu435.
44. Heller EA, Cates HM, Pena CJ, Sun H, Shao N, Feng J, et al. Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors. Nat Neurosci. 2014;17(12):1720-7. Epub 2014/10/28. doi: 10.1038/nn.3871. PubMed PMID: 25347353; PubMed Central PMCID: PMCPMC4241193.
45. Heaton NS, Langlois RA, Sachs D, Lim JK, Palese P, tenOever BR. Long-term survival of influenza virus infected club cells drives immunopathology. The Journal of Experimental Medicine. 2014;211(9):1707-14. doi: 10.1084/jem.20140488. PubMed PMID: PMC4144728.
46. Gaugler T, Klei L, Sanders SJ, Bodea CA, Goldberg AP, Lee AB, et al. Most genetic risk for autism resides with common variation. Nature Genetics. 2014;46:881. doi: 10.1038/ng.3039 - supplementary-information.
47. Gacias M, Gerona-Navarro G, Plotnikov AN, Zhang G, Zeng L, Kaur J, et al. Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage Progression. Chemistry & biology. 2014;21(7):841-54. doi: 10.1016/j.chembiol.2014.05.009. PubMed PMID: PMC4104156.
48. Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, et al. De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014;506:179. doi: 10.1038/nature12929 - supplementary-information.
49. Ferré S, Casadó V, Devi LA, Filizola M, Jockers R, Lohse MJ, et al. G Protein–Coupled Receptor Oligomerization Revisited: Functional and Pharmacological Perspectives. Pharmacological Reviews. 2014;66(2):413-34. doi: 10.1124/pr.113.008052. PubMed PMID: PMC3973609.
50. Feng J, Wilkinson M, Liu X, Purushothaman I, Ferguson D, Vialou V, et al. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol. 2014;15(4):R65. Epub 2014/04/25. doi: 10.1186/gb-2014-15-4-r65. PubMed PMID: 24758366; PubMed Central PMCID: PMCPMC4073058.
51. Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, et al. Mutations in NGLY1 Cause an Inherited Disorder of the Endoplasmic Reticulum-Associated Degradation (ERAD) Pathway. Genetics in medicine : official journal of the American College of Medical Genetics. 2014;16(10):751-8. doi: 10.1038/gim.2014.22. PubMed PMID: PMC4243708.
52. Dias C, Feng J, Sun H, Shao NY, Mazei-Robison MS, Damez-Werno D, et al. beta-catenin mediates stress resilience through Dicer1/microRNA regulation. Nature. 2014;516(7529):51-5. Epub 2014/11/11. doi: 10.1038/nature13976. PubMed PMID: 25383518; PubMed Central PMCID: PMCPMC4257892.
53. Di Narzo AF, Kozlenkov A, Roussos P, Hao K, Hurd Y, Lewis DA, et al. A unique gene expression signature associated with serotonin 2C receptor RNA editing in the prefrontal cortex and altered in suicide. Human Molecular Genetics. 2014;23(18):4801-13. doi: 10.1093/hmg/ddu195. PubMed PMID: PMC4140462.
54. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Ercument Cicek A, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209. doi: 10.1038/nature13772 - supplementary-information.
55. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, et al. Synaptic, transcriptional, and chromatin genes disrupted in autism. Nature. 2014;515(7526):209-15. doi: 10.1038/nature13772. PubMed PMID: PMC4402723.
56. Consortium S. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium. Nature biotechnology. 2014;32(9):903-14. doi: 10.1038/nbt.2957. PubMed PMID: PMC4321899.
57. Chikina MD, Sealfon SC. Increasing Consistency of Disease Biomarker Prediction Across Datasets. PLOS ONE. 2014;9(4):e91272. doi: 10.1371/journal.pone.0091272.
58. Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, et al. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. BMC Medical Genomics. 2014;7(1):48. doi: 10.1186/1755-8794-7-48.
59. Brennand K, Savas JN, Kim Y, Tran N, Simone A, Hashimoto-Torii K, et al. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Molecular Psychiatry. 2014;20:361. doi: 10.1038/mp.2014.22 - supplementary-information.
60. Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, et al. Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. The Journal of Experimental Medicine. 2014;211(3):457.
61. Bichoupan K, Martel-Laferriere V, Sachs D, Ng M, Schonfeld EA, Pappas A, et al. Costs of Telaprevir-based Triple Therapy for Hepatitis C: $189,000 per Sustained Virologic Response. Hepatology (Baltimore, Md). 2014;60(4):1187-95. doi: 10.1002/hep.27340. PubMed PMID: PMC4190678.
62. Backes S, Langlois RA, Schmid S, Varble A, Shim JV, Sachs D, et al. The mammalian response to virus infection is independent of small RNA silencing. Cell reports. 2014;8(1):114-25. doi: 10.1016/j.celrep.2014.05.038. PubMed PMID: PMC4096324.
63. Altman DR, Sebra R, Hand J, Attie O, Deikus G, Carpini KWD, et al. Transmission of Methicillin-Resistant Staphylococcus aureus via Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2014;14(11):2640-4. doi: 10.1111/ajt.12897. PubMed PMID: PMC4651443.
64. Loss-of-Function Mutations in APOC3, Triglycerides, and Coronary Disease. New England Journal of Medicine. 2014;371(1):22-31. doi: 10.1056/NEJMoa1307095.

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