All ARCH Publications

Past Publications Using ARCH Technology

    • Weber, G., Adams, W., Bernstam, E., Bickel, J., Fox, K., Marsolo, K., Raghavan, V., Turchin, A., Zhou, X., Murphy, S. and Mandl, K. (2017). Biases introduced by filtering electronic health records for patients with “complete data”. Journal of the American Medical Informatics Association. Available from: https://academic.oup.com/jamia/article-abstract/doi/10.1093/jamia/ocx071/4057688/Biases-introduced-by-filtering-electronic-health?redirectedFrom=fulltext.
    • Gupta, S., Zabarovskaya, C., Romine, B., Vianello, D., Hudson Vitale, C. and McIntosh, L. (2017). Incorporating Data Citation in a Biomedical Repository: An Implementation Use Case. AMIA Jt Summits Transl Sci Proc.. [online] Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543373/.
    • Klann, J., Abend, A., Raghavan, V., Mandl, K. and Murphy, S. (2016). Data interchange using i2b2. Journal of the American Medical Informatics Association, [online] 23(5), pp.909-915. Available at: https://www.ncbi.nlm.nih.gov/pubmed/26911824.
    • Geva, A., Gronsbell, J., Cai, T., Cai, T., Murphy, S., Lyons, J., Heinz, M., Natter, M., Patibandla, N., Bickel, J., Mullen, M., Mandl, K., Abman, S., Adatia, I., Austin, E., Feinstein, J., Fineman, J., Hanna, B., Hopper, R., Ivy, D., Keller, R., Krishnan, U., Kulik, T., Mullen, M., Raj, U. and Rosenzweig, E. (2017). A Computable Phenotype Improves Cohort Ascertainment in a Pediatric Pulmonary Hypertension Registry. The Journal of Pediatrics, [online] 188(5), pp.224-231.e5. Available at: https://www.ncbi.nlm.nih.gov/pubmed/28625502.
    • McMurry, A.J., Murphy, S.N., MacFadden, D., Weber, G., Simons, W.W., Orechia, J., Bickel, J., Wattanasin, N., Gilbert, C., Trevvett, P., Churchill, S., Kohane, I.S.  SHRINE: Enabling nationally scalable multi-site disease studies. PLoS One. 2013;8(3):e55811. doi: 10.1371/journal.pone.0055811. Epub 2013 Mar 7. PMID: 3591385
    • Klann, J.G., McCoy, A.B., Wright, A., Wattanasin, N., Sittig, D.F., Murphy, S.N. Health Care Transformation Through Collaboration on Open-Source Informatics Projects: Integrating a Medical Applications Platform, Research Data Repository, and Patient Summarization.  Interact J Med Res 2013;2. Doi:10.2196/ijmr.2454 PMID: 23722634.
    • Klann, J.G., Murphy, S.N.  Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside.  J Med Internet Res 2013;15. Doi:10.2196/jmir.2493  PMID: 23603227.
    • Liao, K.P., Diogo, D., Cui, J., Cai, T., Okada, Y., Gainer, V.S., Murphy, S.N., Gupta, N., Mirel, D., Ananthakrishnan, A.N., Szolovits, P., Shaw, S.Y., Raychaudhuri, S., Churchill, S., Kohane, I., Karlson, E.W., Plenge, R.M.  Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls.  Ann Rheum Dis. 2013 May 28 (Epub ahead of print). PMID: 23716066.
    • Liao KP, Kurreeman F, Li G, Duclos G, Murphy SN, P RG, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM.  Autoantibodies, autoimmune risk alleles and clinical associations in rheumatoid arthritis cases and non-RA controls in the electronic medical records.  Arthritis Rheum. 2012 Dec 10. doi: 10.1002/art.37801.
    • Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP.  Similar Risk of Depression and Anxiety Following Surgery or Hospitalization for Crohn’s Disease and Ulcerative Colitis. Am J Gastroenterol. 2013 Jan 22. doi: 10.1038/ajg.2012.471.
    • Castro VM, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.  QT interval and antidepressant use: a cross sectional study of electronic health records. BMJ 2013;346:f288. Doi: 10.1136/bmj.f288.
    • Bellazzi, R., Masseroli, M., Murphy, S.N., Shabo, A., Romano, P.  Clinical Bioinformatics: challenges and opportunities.  BMC Bioinformatics. 2012;13 Suppl 14:S1. doi; 10.1186/1471-2105-13-S14-S!. Epub 2012 Sep 7.
    • Ananthakrishnan, A.N., Gainer, V.S., Guzman-Perez, R., Cai, T., Cheng, S-C., Savova, G., Chen, P., Szolovits, P., Xia, Z., De Jager, P.L., Shaw, S.Y., Churchill, S., Karlson, E.W., Kohane, I., Perlis, R.H., Plenge, R.M., Murphy, S.N., Liao, K.P.  Psychiatric co-morbidity is associated with increased risk of surgery in Crohn’s disease.  Alimentary Pharmacology and Therapeutics. 2013 Feb;37(4):445-54. Doi: 10.1111/apt.12195. Epub 2013 Jan 7.
    • Wattanasin, N., Porter, A., Ubaha, S., Mendis, M., Phillips, L., Mandel, J., Ramoni, R., Mandl, K., Kohane, I., Murphy, S.N.  Apps to display patient data, making SMART available in the i2b2 platform.  AMIA Annu Symp Proc. 2012; 2012:960-9. Epub 2012 Nov 3.
    • Gallagher, P.J., Castro, V., Fava, M., Weilburg, J.B., Murphy, S.N., Gainer, V.S., Churchill, S.E., Kohane, I.S., Iosifescu, D.V., Smoller, J.W., Perlis, R.H.  Antidepressant response in individuals with major depressive disorder exposed to NSAIDs: a pharmacovigilance study.  Am J. Psychiatry 2012;169:1065-1072.
    • Hoogenboom, W.S., Perlis, R. H., Smoller, J.W., Zeng-Treitler, Q., Gainer, V.S., Murphy, S.N., Churchill, S.E., Kohane, I.S., Shenton, M.E., Iosifescu, D.V.  Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: A pilot study.  Psychiatry Research. 2013 Mar 30;211(3):202-13. Doi: 10.1016/j.psychresns.2012.07.007. Epub 2012 Nov 11.
    • Murphy, S.N., Dubey, A., Embi, P.J., Harris, P.A., Richter, B.G., Turisco, F., Weber, G.M., Tcheng, J.E., Keogh, D.  Current state of information technologies for the clinical research enterprise across academic medical centers.  Clin Transl Sci. 2012 June;5(3):281-4. doi: 10.1111/j.1752-8062.2011.00387.x. Epub 2012 Feb 23.
    • Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV. Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: A pilot study.  Psych Res.  2012: accepted.
    • Gallagher PJ, Castro V, Fava M, Weilburg JB, Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. Antidepressant response in individuals with major depressive disorder exposed to NSAIDs: a pharmacovigilance study. Am J Psychiatry (in press).
    • Sittig DF, Hazlehurst BL, Brown J, Murphy SN, Rosenman M, Tarczy-Hornoch P, Wilcox AD.  A survey of informatics platforms that enable distributed comparative effectiveness research using multiinstitutional heterogenous clinical data.  Med Care.  2012 July;50(P):S49-59.  doi:10.1097/MLR.obo13e318259co2b.  PMID:22692259.
    • Kurreeman FA, Stahl EA, Okada Y, Liao K, Diogo D, Raychaudhuri S, Freudenberg J, Kochi Y, Patsopoulos NA, Gupta N; CLEAR investigators, Sandor C, Bang SY, Lee HS, Padyukov L, Suzuki A, Siminovitch K, Worthington J, Gregersen PK, Hughes LB, Reynolds RJ, Bridges SL Jr, Bae SC, Yamamoto K, Plenge RM.  Use of a multiethnic approach to identify rheumatoid- arthritis-susceptibility loci, 1p36 and 17q12. Am J Hum Genet. 2012 Mar 9;90(3):524-32. Epub 2012 Feb 23.  PMID: 22365150.
    • Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC.  Portability of an algorithm to identify rheumatoid arthritis in electronic health records.  J Am Med Inform Assoc. 2012 Jun 1;19(e1):e162-e169. Epub 2012 Feb 28.  PMID: 22374935.
    • Harpaz R, Dumouchel W, Shah NH, Madigan D, Ryan P, Friedman C. Novel data-mining methodologies for adverse drug event discovery and analysis.  Clin Pharm Ther  2012 May 2. PMID: 22549283.
    • Wu ST, Liu H, Tao C, Musen MA, Chute GG, and Shah NH. Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J Am Med Inform Assoc.  2012 Jun 1;19(e1):e149-e156. PMID:22493050
    • Mandl KD, Mandel JC, Murphy SN, Bernstam EV, Ramoni RL, Kreda DA, McCoy JM, Adida B, Kohane IS.  The SMART Platform: early experience enabling substitutable applications for electronic health records.  J Am Med Inform Assoc. 2012 Mar 17.  (Epub ahead of print)  PMID:22427539. ]
    • Kohane IS, Churchill SE, Murphy SN.  A translational engine at the national scale: informatics for integrating biology and the bedside.  J Am Med Inform Assoc.  2012;19(2)181-5.  Epub 2011 Nov 10.  PMID:22081225.
    • Castro V, Gallagher PJ, Clements CC, Murphy SN, Gainer VS, Weilburg JB, Fava M, Churchill SE, Kohane IS, Smoller JW, Iosifescu DV, Perlis RH. Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with Major Depressive Disorder treated with antidepressants. Brit Med J Open. 2012 Mar 30;2(2):e000544.  PMID:22466034.
    • Perlis RH, Iosifescu DV, Castro VM, Murphy SN, Gainer VS, Minnier J, Cai T, Goryachev S, Zeng Q, Gallagher PJ, Fava M, Weilburg JB, Churchill SE, Kohane IS, Smoller JW. Using electronic medical records to enable large-scale studies in psychiatry: Treatment Resistant Depression as a model. Psychol Med. 2012 Jan;42(1):41-50.  PMID: 21682950
    • Ananthakrishnan AN, Guzman-Perez R, Gainer V, Cai T, Churchill S, Kohane I, Plenge RM and  Murphy S.  Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease.  Aliment Pharmacol Ther.  2012;1-7.  PMID:22360370.
    • Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, and Iosifescu DV.  Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: A diffusion tensor imaging study using legacy data.  World J Biol Psychiatry.  2012 Apr 30. PMID: 22540406.
    • Pestian JP, Matykiewicz P, Linn-Gust M, South B, Uzuner Ö, Wiebe J, Cohen K, Hurdle J, Brew C. Sentiment analysis of suicide notes: A Shared Task.  Biomed Inform Insights. 2012;5 (Suppl. 1):1–14PMID: 22419877.
    • Uzuner Ö, Bodnari A, Shen S, Forbush T, Pestian J, South B.  Evaluating the state of the art in coreference resolution for electronic medical records.  J Am Med Inform Assoc.  2012;19(5):786-91. doi:10.1136/amiajnl-2011-000784.   PMID: 22366294.
    • Bodnari A, Szolovits P, Uzuner Ö.  MCORES: A system for noun phrase coreference resolution for clinical records.  J Am Med Inform Assoc. 2012.  doi:10.1136/amiajnl-2011-000591.   PMID:22419739.
    • Xia Z, Savova G. Leveraging electronic health records for research in Multiple Sclerosis. American Neurological Association (ANA). 2012. Pediatrics in NLP. Edited by Dr. Hutton. Chapter contributions: (1) NLP basics, (2) Applications of NLP in Pediatrics Research.
    • Xia  Z, Savova G. Leveraging electronic health records for research in Multiple Sclerosis. European Committee for Treatment and Research in Multiple Sclerosis (ECTRIMS). 2012.
    • Zheng J, Chapman W, Miller T, Lin C, Crowley R, Savova, G.   A system for coreference resolution for the clinical narrative.  J Am Med Inform Assoc. 2012 Jul 1;9(4):660-7.  PMID: 22298565.
    • Lin C, Canhao H, Miller T, Dligach D, Plenge Rm, Karlson EW, Savova G.  Feature engineering and selection for Rheumatoid Arthritis disease activity classification using electronic medical records.  Proceedings of the 29th International Conference of Machine Learning (ICML) Workshop on Machine Learning for Clinical Data.  2012.
    • Miller T, Dligach D, Savova G. Active learning for coreference resolution in the biomedical domain. BioNLP Workshop at the Conference of the North American Association of Computational Linguistics. 2012.
    • Kohane IS, Valtchinov V.  Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome.  Bioinformatics.  2012 Feb 15;28(4):538-45.  Erratum in: Bioinformatics. 2012 Mar 15;28(6):905.  PMID:22219206.
    • Masys DR, Jarvik GP, Aabernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN, Hoffman MA, Kohane IS, Levy HP.  Technical desiderata for the integration of genomic data into Electronic Health Records.  J Biomed Inform. 2012 Jun;45(3):419-22.  Epub 2011 Dec 27.  PMID:22223081.
    • Murphy SN, Dubey A, Embi PJ, Harris PA, Richter BG, Turisco F, Weber GM, Tcheng JE, Keogh D. Current state of information technologies for the cinical research enterprise across Academic Medical Centers. Clin Transl Sci. 2012 Jun;5(3):281-284. doi: 10.1111/j.1752-8062.2011.00387.x. Epub 2012 Feb 23. PMID:22686207.
    • Valtchinov VI , Kohane IS.  Quantifying the white blood cell transcriptome as an accessible window to the multi-organ transcriptome.  Bioinfomatics.  2012;28(4):538-545.
    • Natter MD, Quan J, Ortiz DM, Bousvaros A, Ilowite NT, Inman CJ, Marsolo K, McMurry AJ, Sandborg CI, Schanberg LE, Wallace CA, Warren RW, Weber GM, Mandl KD. An i2b2-based, generalizable, open source, self-scaling chronic disease registry. J Am Med Inform Assoc. 2012 Jun 25. PMID:22733975.
    • Kohane IS.  (Mis)treating the pharmacogenetic incidentalome.  Nat Rev Drug Discov. 2012 Feb 1;11(2):89-90.  doi: 10.1038/nrd3659.  PMID:22293554.
    • Kohane IS, Hsing M, Kong SW.  Taxonomizing, sizing, and overcoming the incidentalome.  Genet Med. 2012 Apr;14(4)399-404. doi: 10.1038/gim.2011.68. Epub 2012 Feb 9.  PMID:22323072.
    • Wolf SM, Crock BN, Van Ness B, Lawrenz F, Kahn JP, Beskow LM, Cho MK, Christman MF, Green RC, Hall R, Illes J, Keane M, Knoppers BM, Koenig BA, Kohane IS, Leroy B, Maschke KJ, McGeveran W, Ossorio P, Parker LS, Petersen GM, Richardson HS, Scott JA, Tery SF, Wiolfond BS, Wolf WA.  Managing incidental findings and research results in genomic research involving biobanks and archived data sets.  Genet Med. 2012 Apr;14(4):361-84. doi:10.1038/gim.2012.23 PMID:22436882 (PubMed – in process).
    • Schmid PR, Palmer NP, Kohane IS, Berger B.  Making sense out of massive data by going beyond differential expression.  Proc Natl Acad Sci USA.  2012 Apr 10;109(15):5594-9.  Epub 2012 Mar 23.  PMID:22447773 (PubMed – indexed for MEDLINE).
    • Kohane IS, McMurry A, Weber G, MacFadden D, Rappaport L, Kunkel L, Bickel J, Wattanasin N, Spence S, Murphy S, Churchill S.  The co-mordibidy burden of children and young adults with Autism Spectrum Disorders.  PLoS One. 2012;7(4):e33224.  Epub 2012 Apr 12.  PMID:22511918.
    • Kohane IS, Shendure J.  What’s a Genome Worth?  Sci Transl Med. 2012 May 9;4(133):133fs13.  PMID:22572879.
    • Mandl KD, Khorasani R, Kohane IS.  Meaningful use of electronic health records.  Health Aff (Millwood).  2012 Jun;31(6):1365.  PMID:22665650.
    • Mandl KD, Kohane IS.  Escaping the EHR trap-the future of health IT.  N Engl J Med. 2012 Jun 14;366(24):2240-2.  PMID:22693995.
    • Lin C, Miller T, Dligach D, Plenge RM, Karlson EW, Savova G.  Maximal information coefficient for feature selection for clinical document classification. Proceedings of the 28th International Conference on Machine Learning Workshop on Machine Learning for Clinical Data.  2011.
    • Murphy SN, Gainer V, Mendis M, Churchill S, Kohane I.  Strategies for maintaining patient privacy in i2b2.  J Am Med Inform Assoc.  2011 Dec;18 Suppl 1:i103-8.  Epub 2011 Oct 7.  PMID:21984588.
    • Gong T, Hartmann N, Kohane IS, Brinkmann V, Staedtler F, Letzkus M, Bongiovanni S, Szustakowski JD.  Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.  PLosOne.  2011;6(11):e27156.  Epub 2011 Nov 16.  PMID:22110609.
    • Castro V, Gallagher P, Murphy SN, Gainer V, Fava M, Weilburg J, Churchill S, Kohane I, Iosifescu D, Smoller J, Perlis R.  Using electronic medical records to enable large-scale studies in Psychiatry: Treatment Resistant Depression as a model.  Psychological Med.  2011 June; 10:1-10.
    • Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, Li G, Bry L, Mahan S, Ardlie K, Thomson B, Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge R.  Genetic basis of autoanitbody positive and negative Rheumatoid Arthritis risk in a multi-ethnic cohort derived from Electronic Health Records.  Am J Human Gen.  2011;88:57-69.  doi:10.1016/j.ajhg.2010.12.007.
    • Alexandrov BS, Valtchinov VI, Alexandrov LB, Gelev V, Dagon,Block J, Kohane IS, Rasmussen K, Bishop AR, Usheva A.  DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.  PLoS One 2011;6(5):e19800.  PMID:21625483..
    • Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsau PS, Kohane IS, Roden DM, Altman RB.  Detecting drug interactions from adverse-event reports: Interaction between paroxetine and pravastatin increases blood glucose levels.  Clin Pharm Therapeutics.  2011 Jun;90:133-42.   PMID: 21613990.
    • Kohane, IS.  Using electronic health records to drive discovery in disease genomics.  Nature Review Genetics.  2011;12:417-428.  doi:10.1038/nrg2999.
    • Himes BE, Klanderman B, Kohane IS, Weiss ST.  Assessing the reproducibility of asthma genome-wide association studies in a general clinical population.  J Allergy Clin Immunol.  2011 Apr;127(4)1067-9.  Epub 2011 Jan 26.
    • Jacobsen JC, Gregory GC, Wode JM, Thompson MN, Coser KR, Murthy V, Kohane IS, Gusella JF, Seong IS, MacDonald ME, Shioda T, Lee JM.  HD CAG-correlated gene expression changes support a simple dominant gain of function.  Hum Mol Genet. 2011 Jul 15;20(14)2846-60.  Epub 2011 May 2.  PMID:21536587.
    • Fossale E, Seong IS, Coser KR, Shioda T, Kohane IS, Wheeler VC, Gusella JF, MacDonald ME, Lee JM.  Differential effects of the Huntington’s disease CAG mutation in striatum and cerebellum are quantitative not qualitative.  Hum Mol Genet.  2011 Nov 1;20(21):4258-67.  Epub 2011 Aug 12.  PMID:21840924.
    • Parast L, Cheng S, Cai T. Incorporating short-term outcome information to predict long-term survival with discrete markers.   Biomet J.  2011 Mar;53(2):294–307.  PMID: 2133760.
    • Minnier J, Tian L, Cai .  A perturbation method for inference on regularized regression estimates. J Am Stat Assoc. 2011;106(496):1371-1382. PMCID: 22844171.
    • Li J, Tian L, Wei LJ.  Estimating subject-specific dependent competing risk profile with censored event time observations.  Biometrics.  2011;67: 427-35. PMCID:PMC2970653.
    • Forbush T, Shen S, Thibault J, Weir C, Uzuner Ö, South BR. Using the UMLS as a semantic priming mechanism for co-reference resolution in annotation of clinical texts. AMIA Annu Symp Proc.  2011.
    • South BR, Shen S, Barrus R, DuVall SL, Uzuner Ö, Weir C. Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA Challenge.  AMIA Annu Symp Proc. 2011:1232-1251  PMID: 22195185.
    • Chapman WW, Nadkarni PM, Hirschman L, D’Avolio L, Savova G, Uzuner Ö.  Overcoming barriers to NLP for clinical text: The role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc. 2011 Sep-Oct;18 (5):540-543.  PMID: 21846785.
    • Uzuner Ö, South B, Shen S, DuVall S.  2010 i2b2/VA Challenge on Concepts, Assertions, and Relations in clinical text.  J Am Med Inform Assoc. 2011 Sep-Oct;18(5):552-556.  Published Online First: 16 June 2011 doi:10.1136/amiajnl-2011-000203.     PMID: 21685143.
    • Cai T, Gerds T, Zheng Y, Chen J. Robust prediction of t-year survival with data from multiple studies.  Biometrics.  2011;67(2):436-444. published online 28 June 2010.  doi:10.1111/j.1541-0420.2010.
    • Zhao L, Cai T, Tian L, Uno H, Solomon S, Wei LJ.  Stratifying subjects for treatment selection with censored event time data from a comparative study.  Harvard University Biostatics Working Paper Series, #122, 2011.
    • Uno H, Cai T, Tian L, Wei LJ.  Graphical procedures for evaluating overall and subject-specific incremental values from new predictors with censored event time data.  Biometrics.  2011;67(4):1389-96.  PMID:21504421.
    • Cai T, Tian L, Wong P, Wei LJ.  Analysis of randomized comparative clinical trial data for personalized treatment selections.  Biostatistics. 2011;12(2):270-282.
    • Patti ME, Corvera S.  The role of mitochondria in the pathogenesis of Type 2 Diabetes.  Endocrine Reviews.  2010;31(3)364-95.  PMID:20156986.
    • Liao KP, Cai T, Gainer V, Goryachev, Zeng-Treitler Q, Raychaudhuri S, Szolovits, Churchill S, Murphy S, Kohane IS, Karlson E, Plenge R.  Utilizing electronic medical records for discovery research in rheumatoid arthritis.  Arthritis Care Res. 2010;62(8):1120-1127.
    • Tian L, Wang R, Cai T, Wei LJ.  The highest confidence density region and its usage for inferences about the survival function with censored data.  Biometrics.  2010;67:604-10.
    • Wang R, Tian L, Cai T, Wei LJ.   Nonparametric inference procedure for percentiles of the random effect distribution in meta analysis. Annals of Applied Statistics. 2010;4(1):520-532.  doi:10.1214/09-AOAS280SVPP.
    • Cai T, Tian L, Uno H, Solomon D, Wei LJ.  Calibrating parametric subject-specific risk estimation.  Biometrika.  2010;97(2):389-404.  doi:1093/biomet/asq012.
    • L. Ryan L, Cai T, Parast L. Meta-analysis for rare events. Statistics in Medicine,2010;29(20):2078-89.
    • Pearson JF, Brownstein CA, Brownstein JS.  The potential for electronic health records and health social networking to redefine medical research.  Clin Chem.  2010;57(2):196-204.   PMID:21159898.
    • Pearson JF, Bachireddy C, Shyamprasad S, Goldfine AB, Brownstein JS.  Association between fine particular matter and diabetes prevalence.  Diabetes Care.  2010;33(10):2196-201.   PMID:20628090.
    • Brownstein J, Murphy S, Goldfine A, Grant R, Sordo M, Gainer V, Colecchi J, Dubey A, Nathan, D, Glaser J, Kohane I.  Rapid identification of myocardial infarction risk associated with diabetic medications using electronic medical records.  Diabetes Care. 2010;33(3):526-31.  PMID:20009093.
    • Turchin A, Shubina M, Murphy SN.  I am not dead yet: Identification of false-posivite matches to death Master file.  AMIA Annu Symp Proc.  2010: 807-811.  PMID:21347090.
    • Murphy SN, Weber G, Mendis M, Chueh HC, Churchill S, Glaser JP, Kohane IS.  Serving the Enterprise and beyond with Informatics for Integrating Biology and the Bedside (i2b2).  J Am Med Inform Assoc.  2010;17(2):124-30.  PMID:20190053.
    • Jin W, Patti ME.  Genetic determinants and molecular pathways in the pathogenesis of diabetes.  Clinical Science. 2009;116 (2):99-111.  PMID:19076063.
    • Pihlajamaki J, Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I, Park PJ, Bianco AC, Goldfine AB, Patti ME.  Thyroid hormone-related regulation of gene expression in human fatty liver.  J Clin Endo Metab. 2009;94:3521-8.  PMID:19549744.
    • Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M, Kasif S, Zavacki AM, Leshan RL, Myers MG, Patti ME.  Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice.  Diabetes. 2009 May;58(5):1192-200. PMID: 19208909,
    • Himes BE, Dai Y, Kohane IS, Weiss ST, Ramoni MF. Prediction of Chronic Obstructive Pulmonary Disease (COPD) in Asthma Patients using Electronic Medical Records. J Am Med Inform Assoc. 2009;16(3):371-9.  PMID:19261943.
    • Wunderlich Z, Mirny LA. An optimized energy potential can predict domain-peptide interactions. Nucleic Acids Res.  2009;7:1-13.
    •  Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T,  Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R,  Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J,  Mirny L, Lander ES, Dekker J.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.  Science.  2009;326(5950):289-93.  PMID:19815776.
    • Mirny L, Slutsky M, Wunderlich Z, Tafvizi A, Leith J, Kosmrlj A. How a protein searches for its site on DNA: The mechanism of facilitated diffusion J. Phys. A: Math. Theor. 2009 Cotober 30;42(43):434013.  doi:10.1088;1751-8113/42/43/43401.
    • Wunderlich Z., Mirny LA.  Different strategies for transcriptional regulation are revealed by information-theoretical analysis of binding motifs. Trends Genet. 2009;25(10):434-40.   PMID:19815308.
    • Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Bio. 2009;541:421-48.
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