i2b2: Informatics for Integrating Biology & the Bedside - A National Center for Biomedical Computing
Publications i2b2 Publications

i2b2 PUBLICATIONS 2005-2012

A.  Noteworthy Selection

  • Butte AJ, Kohane IS.  Creation and implications of a phenome-genome network.  Nature Biotechnology.  2006;24(1):55-62.  PMC2716377.

Demonstrated how NLP on experimental labels could be combined with systematic gene expression measurements across public databases to provide useful retaxonomization of disease. In many ways presaged the IOM report on Precision Medicine.

Citations: 90 Impact Factor 23.26

  • Kohane IS, Masys DR, Altman RA.  The incidentalome:  a threat to genomic medicine. J Am Med Assoc. 2006 Jul 12;296(2):212-5.  PMID: 16835427

Opened up the dialog of the clinical consequences of high throughput measurements in the absence of the kind of high-throughput population studies that i2b2 made possible. Widely cited in the lay press (e.g WSJ, NPR) as well as citations in the scholarly publications.

Citations: 73 Impact Factor 30.02

  • Murphy SN, Churchill SE, Bry L, Chueh H, Cai T, Weiss S, et al. Instrumenting the health care enterprise for discovery research in the genomic era.  Genome Res. 2009;360(13)1278-81.  PMC2752136.

Summarized the design features of i2b2 that allowed phenotyping and sample collection to occur two orders magnitude more rapidly and at a tenth of the cost.  In addition to scholarly citations, it helped lead to the adoption of i2b2 at over 72 major academic health centers internationally.

Citations: 23 Impact Factor 13.6

  • Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009 Sep-Oct;16(5):624-30.  PMC2744712.

Described how a distributed query system across multiple i2b2 instances allowed the sharing of patient study data across institutions nationwide in near-real-time while allowing each healthcare institution to maintain autonomous control of their own data.  In doing so, this publication provided the template for multiple SHRINE installations covering 8 to 60 institutions for a variety of large studies.

Citations: 20, Impact Factor 3.6

  • Cai C, Tian L, Lloyd-Jones D, Wei LJ.  Evaluating subject-level incremental values of new markers for risk classification rule. Biometrics. 2009.

In the original i2b2 publication we set ourselves the goal of reframing the evaluation of biomarkers which often, especially early in the genomic era, just described the performance characteristics of the biomarker itself and not with comparison to the best use of existing conventional clinical data. This manuscript is one of several our team published that developed a framework for understanding the incremental contribution to diagnostics (and progrnostics) of novel biomarkers.

Citations: 6 Impact Factor 1.87

  • 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 Mar;33(3):526-31.  PMC2827502.

After an earlier proof of concept publication showing the retrospective identification of Vioxx-associated increased cardiovascular disease burden, this publication demonstrated that i2b2 could be used in the midst of national controversies requiring a “big data” approach to pubic health. We identified and quantified the increased myocardial infarction risk of rosiglitazone (Avandia) relative to other drugs in the same class used for the treatment of diabetes mellitus. This publication was one of a handful cited by the FDA in the “black box”ing of the drug and its subsequent near-disappearance from the market

Citations 17 Impact Factor 8.07

  • 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 leels.  Clin Pharm Therapeutics.  2011 Jun;90:133-42.   PMC3216673.

A demonstration of how EHR-based methods could go from a signal in an FDA database to validation in three academic health centers in less than 3 months.

Citations: 13 Impact Factor 6.04

  • Kohane, IS.  Using electronic health records to drive discovery in disease genomics.  Nat Rev Genet.  2011 Jun;12(6):417-428.  doi:10.1038/nrg2999.  PMID: 21587298

A summary of EHR-driven genomic disease research demonstrating the broad impact that i2b2 has had.

Citations 14  Impact Factor 38.07

  • Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science.  2009;326(5950):289-93.  PMC2858594.

An example from one of many of our core 1 computational biology resarchers (Mirny) that developed  novel biological insights using computational methods.

Citations 357, Impact Factor 31.2

  • 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 autoantibody positive and negative Rheumatoid Arthritis risk in a multi-ethnic cohort derived from Electronic Health Records.  Am J Human Gen.  2011 Jan 7;88(1):57-69.    PMC3014362

Demonstration that not only can i2b2 be used to perform cost-effective genetic studies but they a) reproduce prior studies and b) go beyond prior studies by including under-represented minorities (which are even more underrepresented in traditional cohort studies) and studying the genetics of both antibody positive and negative rheumatoid arthritis

Citations: 12 Impact factor 10.6

B.  Chronologically

  1. Kohane IS, Altman RA. Health-information altruists – a potentially critical resource.  New Engl J Med.  2005;353:2074-7.
  2. Sordo M, Zeng Q.  On sample size and classification accuracy: A performance comparison. Lecture Notes in Computer Science. 2005;3745:193-201.
  3. Fraser HSF, Biodich P, Moodley D, Choi S, Mamlin B, Szolovits P.  Implementing electronic records systems in developing countries.  Informatics in Primary Care.  2005;13:83-95.
  4. Wolfe CJ, Kohane IS, Butte AJ.  Systematic survey reveals general applicability of “guilt-by-association” within gene coexpression networks.  BMC Bioinformatics.  2005;6:227.
  5. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane I, Park P.  Discovering statistically significant pathways in expression profiling studies.  Proc Natl Acad Sci USA.  2005;102(38)13544-9.
  6. Lee S, Kohane I, Kasif S.  Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.  BMC Genomics.  2005;6:168.  PMID: 16309559.
  7. Wu CH,  Kasif S.  GEMS: A web server for biclustering analysis of expression data.  Nucleic Acids Res. 2005;33:W596-9. 
  8. Kryukov GV, Schmidt S, Sunyaev S.  Small fitness effect of mutations in highly conserved non-coding regions.  Human Mol Gen. 2005;4:2221-2229.
  9. Butte AJ, Kohane IS.  Creation and implications of a phenome-genome network.  Nature Biotechnology.  2006;24(1):55-62.
  10. Kohane IS, Masys DR, Altman RA.  The incidentalome:  a threat to genomic medicine. J Am Med Assoc. 2006;296(2):212-5.
  11. Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh H.  Integration of clinical and genetic data in the i2b2 architecture.  AMIA Annu Symp Proc. 2006:1040. PMID:17238659.
  12. Carter SL, Eklund AC, Kohane IS, Haris LN, Szallasi Z.  A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.  Nat Gen. 2006;38(9):1043-48.
  13. Brownstein JS, Cassa CC, Kohane IS, Mandl KD.  An unsupervised classification method for inferring original case locations from low-resolution disease maps.  Internatl J Health Geographics. 2006;5:56.
  14. Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome.  Nature/Embo Molecular Systems Biology. 2006;2:1.
  15. Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge.   Bioinformatics. 2006;22:2373-80. 
  16. Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R.  Extracting principal diagnosis, co-morbidity and smoking status for asthma research: Evaluation of a natural language processing system.  BMC Med Inform Med Decision Making.  2006;6:30.
  17. Goryachev S, Sordo M, Zeng QT.  A suite of natural language processing tools developed for the i2b2 project.  AMIA Annu Symp Proc. 2006:931.
  18. Bramsen P, Deshpande P, Lee YK, Barzilay R.  Finding temporal order in discharge summaries.  AMIA Annu Symp Proc. 2006:81-85.  PMID:17238307.
  19. Sibanda T, He T, Szolovits P, Uzuner Ö.  Syntactically-informed semantic category recognizer for discharge summaries.  AMIA Annu Symp Proc. 2006:714–718.
  20. Uzuner Ö, Szolovits P,  Kohane I. i2b2 Workshop on Natural Language Processing Challenges for Clinical Records.  AMIA Annu Symp Proc. 2006:81-5. PMID:17238307.
  21. Sibanda T, He T, Szolovits P, Uzuner Ö.  Syntactically-informed semantic category recognizer for discharge summaries.  AMIA Annu Symp Proc. 2006:714-718.
  22. Sibanda T, Uzuner Ö.  Role of local context in de-identification of ungrammatical, fragmented text.  Proceedings of the North American Chapter of Association for Computational Linguistics/Human Language Technology (NAACL-HLT 2006), New York, NY, June 5-7, 2006. pp. 65-73.
  23. Gusella JF, Macdonald ME.  Huntington's Disease: Seeing the pathogenic process through a genetic lens. Trends Biochem Sci. 2006 Sept;31(9):533-40.  PMID: 16829072.
  24. McMurry AJ, Gilbert CA, Reis BY, Chueh HC, Kohane IS, Mandl KD. A self scaling, distributed architecture for public health, research, and clinical care. J Am Med Inform Assoc. 2007;14(4):527-33.
  25. Loscalzo J, Kohane IS, Barabasi AL.  Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.  Mol Syst Biol.  2007;3:124.
  26. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips L, et  al. Architecture of  the open-source clinical research chart from Informatics for Integrating Biology and the Bedside.  AMIA Annu Symp Proc. 2007 Oct 11;548-52.  PMID:18693896.
  27. Dubey A, Herrick C, Murphy SN. Mining for associations between categorical data items in a clinical data repository. AMIA Annu Symp Proc. 2007 Oct 11:945.  PMID:18694045.
  28. Gainer V, Hackett K, Mendis M,  Kuttan R, Pan W, Phillips L, Chueh H, Murphy SN. Using the i2b2 Hive for clinical discovery: An example. AMIA Annu Symp Proc. 2007 Oct 11:959. PMID:18694059.
  29. Mendis M, Wattanasin N, Kuttan R, Pan W, Hackett K, Gainer V, Chueh H, Murphy SN.  Integration of Hive and Cell software in the i2b2 architecture. AMIA Annu Symp Proc.  2007 Oct 11:1048.  PMID:18694146.
  30. Evans SR, Li L, Wei LJ.  Data monitoring in clinical trials using predictions.  Drug Information J.  2007;41:733-742.
  31. Tian T, Cai T, Goetghebeur E, Wei LJ.  Model evaluation based on the distribution of estimated absolute prediction error. Biometrika. 2007;94:297-311.
  32. Uno H, Cai T, Tian L, and Wei LJ.  Evaluating prediction rules for t-year survivors with censored regression models.  2007;102:527-37.
  33. Brownstein JS, Sordo M, Kohane IS, Mandl Kl.  Telltale heart: population based surveillance model reveals association with rofecoxib and celecoxib with myocardial infarction.  PlosOne. 2007;9(9):e840.
  34. Reis BY, Kohane IS, Mandl KD. An epidemiological network model for disease outbreak detection. PLoS Med. 2007;4(6):e210.
  35. Goldstein I, Arzrumtsyan A, Uzuner Ö.  Three approaches to automatic assignment of ICD-9-CM codes to radiology reports.  AMIA Annu Symp Proc. 2007 Oct 11:279-83.
  36. Uzuner Ö, Luo Y, Szolovits P.  Evaluating the state-of-the-art in automatic de-identification. J Am Med Inform Assoc. 2007;14(5):550-563.
  37. Turchin A, Kolatkar NS, Pendergrass ML, Kohane IS. Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record. Med Inform Internet Med. 2007;32(2):93-102.
  38. Inaoka H, Fukuoka Y, Kohane I.  Evidence of spatially bound gene regulation in Mus musculus: Decreased gene expression proximal to microRNA genomic location.  Proc Natl Acad Sci. 2007;104(12)5020-5.
  39. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Human Gen.  2007 Apr;80(4):727-39.
  40. Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed non-coding purifying selection in the human genome. Proc Natl Acad Sci. 2007;104(30):12410-5.
  41. Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol. 2007;Dec;3(12):e254.
  42. Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev  SR. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. Am J Hum Genet. 2007 Oct 19;81(6).
  43. Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev  S, Stamatoyannopoulos  JA. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci USA. 2007;104(30):12410-5.
  44. ENCODE Consortium (Sunyaev). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
  45. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio  LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007;80(4):779-91.
  46. Allocco DJ, Song Q, Gibbons GH, Ramoni MF, Kohane IS. Geography and genography: Prediction of continental origin using randomly selected single nucleotide polymorphisms. BMC Genomics. 2007;8:68.
  47. Dotan-Cohen D, Melkman AA, Kasif S.  Hierarchical tree snipping: clustering guided by prior knowledge.  Bioinformatics.  2007;23(24):3335-42.
  48. Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R.  GGtools: analysis of genetics of gene expression in Bioconductor. Bioinformatics. 2007;23(4):522-523.
  49. Kolesov G, Virnau P, Kardar M, Mirny LA.  Protein knot server: Detection of knots in protein structures.  Nucleic Acids Research 2007;35(10):W425-8.
  50. Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, Mirny LA, Reizis B.  Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell. 2007; 129(2):345-57.
  51. Kolesov G, Wunderlich Z, Laikova O., Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci. 2007;104(35):13948-53.
  52. Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol. 2007;3(12):e246.
  53. Lee JM, Ivanova EV, Seong IS, Cashorali T, Kohane I, Gusella JF, MacDonald ME.  Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet. 2007;3(8):e135.  PMID: 17708681
  54. Gusella JF, Macdonald M.  Genetic criteria for Huntington's Disease pathogenesis. Brain Res Bull. 2007 Apr 30;72(2-3):78-82. PMID: 17352930.
  55. Liu M, Liberzon A, Kong SW, Weil RL, Park PJ, Kohane IS, Kasif S.  Network-based analysis of affected biological processes in Type 2 diabetes models.  PLoS Genetics. 2007;3:0001-0015. doi:10.1371/journal.pgen.0030096.
  56. Dubey AK, Gainer V, Murphy SN.  Simulated yields of prospective specimen collection from specific patient cohorts using retrospective data from a research patient data repository.  AMIA Annu Symp Proc. 2008 Nov 6:935.  PMID:18999309.
  57. Mendis M, Phillips L, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc. 2008 Nov 6:1054.  PMID:18999021.
  58. Scheufele EL, Dubey AK, Murphy SN. A study of the age attribute in a query tool for a clinical data warehouse.  AMIA Annu Symp Proc. 2008 Nov 6:1123.  PMID:18999019. 
  59. Sordo M, Colecchi J, Dubey AK, Gainer V, Murphy SN.  STROBE-Based methodology for detection of adverse events across multiple communities. AMIA Annu Symp Proc. 2008 Nov 6:1144.  PMID:18998965.
  60. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW.   iTools: A framework for classification, categorization and integration of computational biology resources. PLoS ONE. 2008;3(5): e2265.  PMC2386255.
  61. Wang T,  Plaisant C,  Quinn A,  Stanchak R, Murphy SN, Shneiderman B.  Aligning temporal data by sentinel events: Discovering patterns in electronic health records, Proc ACM. 2008 April 5;10:457-466.
  62. Cai T, Tian L,Solomon S, Wei LJ.  Predicting future responses based on possibly misspecified working models.  Biometrika.  2008;95(1):75-92.
  63. Uzuner Ö.  Second i2b2 workshop on natural language processing challenges for clinical records.  AMIA Annu Symp Proc. 2008 Nov 6:1252-3.  PMID:18998924.
  64. Uzuner Ö, Goldstein I, Kohane I.  Identifying patient smoking status from medical discharge records.  J Am Med Inform.  2008;15(1):14-24.  PMC2274873.
  65. Zhang Y, Szolovits P.  Patient-specific learning in real time for adaptive monitoring in critical care. J Biomed Inform. 2008;41(3):452-460.  PMID:18463000.
  66. Uzuner Ö,  Sibanda T,  Luo Y,  Szolovits P.  A de-identifier for medical discharge summaries.  Artificial Intelligence Med. 2008;42(1):13-35.   
  67. Uzuner Ö, Zhang X, Sibanda T. Two approaches to assertion classification.  AMIA Annu Symp Proc. 2008 Nov 6:752.  PMID:18990049.
  68. Goryachev S, Kim H, Zeng-Treitler Q.  Identification and extraction of family history information from clinical records.  AMIA Annu Symp Proc. 2008 Nov 6:247-51.  PMC2656021.
  69. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante  CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008 Feb 21;451(7181):994-7.  PMC2923434.
  70. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: Value of rare single-nucleotide polymorphisms. Am J Hum Genet. 2008;82(1):100-12.   PMC2253956.
  71. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS.  Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers.  Genome Biol. 2008;9(7):R108.  PMC2530866.
  72. Beckstead WA, Bjork BC, Stottmann RW, Sunyaev S, Beier DR.  SNP2RFLP: A computational tool to facilitate genetic mapping using benchtop analysis of SNPs. Mammalian Genome. 2008 Oct-Dec;19(10-12):687-90.
  73. Boyko A, Hernandez R, Schmidt S, Sunyaev S, Nielsen R, Clark A, Bustamante C. Assessing the evolutionary impact of amino acid mutations in the human genome.  PLoS Genet. 2008;4(5)e1000083.  PMC2377339.
  74. Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, Sunyaev S.   Hypermutable non-synonymous sites are under stronger negative selection.  PLoS Genet. 2008;Nov;4(11):e1000281.   PMC2583910
  75. Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.   Integration of relational and hierarchical network information for protein function prediction.  BMC Bioinformatics.  2008;9:350.  PMC2535605
  76. Kolesov G, Mirny LA. Using evolutionary information to find specificity determining and co-evolving residues, In Computational Systems Biology, edited by Jason Mcdermott, Springer-Verlag New York Inc, 2008.
  77. Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, van Oijen AM. Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys J. 2008;95(1):L01-2.
  78. Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.   Integration of relational and hierarchical network information for protein function prediction.  BMC Bioinformatics.  2008;9:350.  PMID:18721473.
  79. Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search.  Nucleic Acids Res. 2008;36(11):3570-8.  PMC2441786.
  80. Rahi SJ, Virnau P, Mirny LA, Kardar M. Predicting transcription factor specificity with all-atom models. Nucleic Acids Res. 2008;36(19):6209-17.  PMC2577325.
  81. Himes BE, Kohane IS, Ramoni MF, Weiss ST. Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records. AMIA Annu Symp Proc. 2008 Nov 6:308-12.  PMC2655929.
  82. Doria A, Patti ME, Kahn CR.  The emerging genetic architecture of type 2 diabetes.  Cell Metabolism. 2008;8(3):186-200.  PMID:18762020.
  83. Kohane IS. The twin questions of personalized medicine: Who are you and whom do you most resemble? Genome Med. 2009;1(1):4.  PMC2651581.
  84. Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009;360(13):1278-81.  PMID:19321867 (Pub Med - Indexed for Medline).
  85. Murphy SN, Churchill SE, Bry L, Chueh H, Cai T, Weiss S, et al. Instrumenting the health care enterprise for discovery research in the genomic era.  Genome Res. 2009;360(13)1278-81.  PMC2752136.
  86. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009;6(5):624-30.  PMC2744712.
  87. Lingling LI, Evans SR, Uno H, Wei LJ.  Statistics in Biopharmaceutical Research.  2009;1(4)348-355.
  88. Tian L, Cai T, Pfeffer M, Piankov N, Cremieux P, Wei LJ.  Exact and efficient inference procedures for meta-analysis and its application to the analysis of independent 2 x 2 tables with all available data but without artificial continuity correction.  Biometrics.  2009;67(2):604-10.  PMID:20825392.
  89. Cornelis M, Qi L, Shang C, Kraft P, Manson J, Cai T, Hunter D, Hu F.  Joint effects of common genetic variants on the risk of Type 2 Diabetes in US men and women.  Ann Int Med.  2009;150(8):541-50.  PMC3825275.
  90. Uzuner Ö, Zhang X, Sibanda T. Machine learning and rule-based approaches to
    assertion classification.  J Am Med Inform Assoc. 2009;16(1):109-115.  PMC2605605.
  91. Uzuner Ö. Recognizing obesity and co-morbidities in sparse data. J Am Med Inform Assoc. 2009; 16(4):561-70.  PMID:19390096.
  92. Goldstein I, Uzuner Ö. Specializing for predicting obesity and its co-morbidities.  J Biomed Inform. 2009;42(5):873-86.  PMC3253373.
  93. Uzuner Ö, Mailoa J, Sibanda T. Semantic relations for problem-oriented medical records.  AMIA Annu Symp Proc. 2009:661.   PMC1839398.
  94. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR Human mutation rate associated with DNA replication timing.  Nat Genet. 2009 Apr;41(4):393-5.  PMC2914101.
  95. Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci USA. 2009 Mar; 10:106(10):3871-6.  PMC2656172.
  96. Davis A, Kohane I.  Expression differences by continent of origin point to the immortalization process.   Human Molecular Genetics 2009;18(20):3864-75.  PMC2748894.
  97. Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M, Berger B, Wu E, Kohane I. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood. PLoS ONE. 2009;4(4):e5157.  PMC2668177.
  98. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics.  2009;25:3121-7, 2009.  PMC2778339.
  99. Dreyfuss JD, Johnson MD, Park PJ. Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers.  Molecular Cancer.  2009;8:71.  PMC2743637.
  100. Pihlajamäki 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 Endocrinol Metab. 2009;94:3521-9.  PMC2741713.
  101. Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade B, Lynch AM, Stewart EA, Morton CC. Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis. Genes, Chromosomes, & Cancer. 2009;48:865-85.  PMC2778251.
  102. Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M.  A predictive phosphorylation signature of lung cancer.  PLos One.  2009;4(11):e7994.  PMC2777383.
  103. Molla M, Delcher A, Sunyaev S, Cantor C, Kasif S.  Triplet repeat length bias and variation in the human transcriptome.  Proc Natl Acad Sci USA.  2009;106(40):17095-100.  PMC2746125.
  104. Dotan-Cohen D, Kasif S, Melkman AA.  Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering.  Bioinformatics.  2009;25(14):1789-95.  PMC2705235.
  105. Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S.  Biological process linkage networks.  PLoS One.  2009;4(4):e5313.  PMC2669181.
  106. Carey V, Davis A, Lawrence M, Gentleman R, Raby B.  Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.  Bioinformatics 2009;25(11)1447-8. doi:10.1093/bioinformatics/btp169.  PMC2682516.
  107. Nuzzo A, Riva A.  Genephony: a knowledge management tool for genome-wide research.  BMC Informatics. 2009;10:278.  PMC2744709.
  108. Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions, Nucleic Acids Res. 2009 August;37(4):4629-41.  PMC2724268.
  109. Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Bio. 2009;541:421-48.  PMID:19381538.
  110. 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.   PMC3697852.
  111. 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.
  112. 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.  PMC2858594.
  113. Wunderlich Z, Mirny LA. An optimized energy potential can predict domain-peptide interactions. Nucleic Acids Res.  2009;7:1-13.
  114. 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.  PMC2732240.
  115. 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. PMC2671035.
  116. 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.  PMC2741713.
  117. Jin W, Patti ME.  Genetic determinants and molecular pathways in the pathogenesis of diabetes.  Clinical Science. 2009;116 (2):99-111.  PMID:19076063.
  118. 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.  PMC3000779.
  119. 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.  PMC3041274.
  120. 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.  PMC2827502.
  121. 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.   PMC2945160.
  122. 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.
  123. L. Ryan L, Cai T, Parast L. Meta-analysis for rare events. Statistics in Medicine. 2010;29(20):2078-89.  PMC2932857.
  124. 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.   PMC3412577.
  125. 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.
  126. 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.
  127. 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.
  128. Patti ME, Corvera S.  The role of mitochondria in the pathogenesis of Type 2 Diabetes.  Endocrine Reviews.  2010;31(3)364-95.  PMC3365846.
  129. 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.  PMC3062150.
  130. 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.  PMC3144297.
  131. 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.
  132. 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.
  133. Uzuner O, Mailoa J, Ryan R, Sibanda T.  Semantic relations for problem-oriented medical records.  Artif Intell Med.  2010:50(2):63-73.  PMC2948592.
  134. Uzuner O, Solti I, Xia F, Cadag E.  Community annotation experiment for ground truth generation for the i2b2 Medication Challenge.  J Am Med Inform Assoc.  2010;17:519-523.  PMC2995684.
  135. Uzuner O, Solti I, Cadag E.  Extracting medication information from clinical text. J Am Med Inform Assoc.  2010;17:514-518. PMC2995677.
  136. 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. PMC3168320.
  137. 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.  PMC3168329.
  138. 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  PMC3243132.
  139. 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,
  140. Li J, Tian L, Wei LJ.  Estimating subject-specific dependent competing risk profile with censored event time observations.  Biometrics.  2011;67: 427-35.  PMC2970653.
  141. Minnier J, Tian L, Cai .  A perturbation method for inference on regularized regression estimates. J Am Stat Assoc. 2011;106(496):1371-1382. PMC3404855.
  142. 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.  PMC3472667.
  143. 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.  PMC3188996.
  144. 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.  PMC3118763.
  145. 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.
  146. Kohane, IS.  Using electronic health records to drive discovery in disease genomics.  Nature Review Genetics.  2011;12:417-428.  doi:10.1038/nrg2999.
  147. 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.   PMC3216673.
  148. 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.  PMC3098838.
  149. 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(1):57-69.  PMC3014362.
  150. 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.  PMC3837420.
  151. 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.  PMC3217948.
  152. 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.  PMC3241160.
  153. 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.
  154. 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.
  155. Mandl KD, Khorasani R, Kohane IS.  Meaningful use of electronic health records.  Health Aff (Millwood).  2012 Jun;31(6):1365.  PMID:22665650.
  156. Kohane IS, Shendure J.  What’s a Genome Worth?  Sci Transl Med. 2012 May 9;4(133):133fs13.  PMID:22572879.
  157. 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.  PMC3325235.
  158. 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.  PMC3326474.
  159. 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. PMC3597341.
  160. 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.  PMC3821385.
  161. Kohane IS.  (Mis)treating the pharmacogenetic incidentalome.  Nat Rev Drug Discov. 2012 Feb 1;11(2):89-90.  doi: 10.1038/nrd3659.  PMID:22293554.
  162. 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.  PMC3555330.
  163. 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.   PMC3288749.  Erratum in: Bioinformatics. 2012 Mar 15;28(6):905.  PMC3663292.
  164. 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.
  165. 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.  PMC3328607.
  166. Parast L, Cheng SC, Cai T. Landmark prediction of long term survival incorporating short term event time information. J Am Stat Assoc. 2012;107(500):1492-1501. PMC3535339.
  167. 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.
  168. 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.
  169. 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.  PMC3384116.
  170. 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.   PMC3422821.
  171. 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.   PMC3422835.
  172. 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):1–14PMC3299408.
  173. 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.
  174. 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.  PMC3716251.
  175. 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.  PMC3837420.
  176. 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.  PMC3330255.
  177. 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.  PMC3277623.
  178. Masys DR, Harris PA, Fearn PA, Kohane IS. Designing a public square for research computing. Sci Transl Med. 2012 Aug 29;4(149):149fs32. PMC3725749.
  179. 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)  PMC3384120.
  180. 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. PMC3392861. 
  181. 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. PMC3675775.
  182. 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.  PMC3392871.
  183. 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.  PMC3309197.
  184. 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.  PMC3415281.
  185. Zheng Y, Parast L, Cai T, Brown M. Evaluating incremental values from new predictors with net reclassification improvement in survival analysis. Lifetime Data Anal. 2013 July;19(3):350-370.  PMC3686882.
  186. 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 2012 Oct;169(10):1065-1072.  PMC3787520.
  187. McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS. SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013;8(3):e55811. PMC3591385.  (Collaboration with the Harvard Medical School CTSA Catalyst SHRINE team).
  188. Parast L, Cai T. Landmark risk prediction of residual life for breast cancer survival. Stat Med. 2013 Sept 10;32(20):3459-3471.  PMC3744612.
  189. Zhou QM, Zheng Y, Cai T. Subgroup specific incremental value of new markers for risk prediction. Lifetime Data Anal. 2013 Apr;19(2):142-69. PMC3633735.   
  190. Tian L, Cai T, Zhao L, Wei LJ. On the covariate-adjusted estimation for an overall treatment difference with data from a randomized comparative clinical trial. Biostatistics. 2012 Apr;13(2):256-73. PMC3297822.
  191. Cai T, Lin X, Carroll RJ. Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test. Biostatistics. 2012 Sep;13(4):776-90. PMC3440238. 
  192. Sinnott JA, Cai T.  Omnibus risk assessment via accelerated failure time kernal machine modeling.  Biometrics.  2013 Dec;69(4):861-73.  PMC3869038.
  193. Zhou QM, Sheng Y, Cai T.  Assessment of biomarkers for risk prediction with nested case-control studies.  Clin Trials.  2013 Oct;10(5)677-9.  PMC3800233.
  194. Zheng Y, Cai T, Pepe MS.  Adopting nested case-control quota sampling designs for the evaluation of risk markers. Lifetime Data Anal.  2013 Oct;19(4):568-88.  PMC3903399.
  195. Miller T, Bethard S,Dligach D, Pradhan S, Lin C, and Savova G. 2013. Discovering narrative containers in clinical text. BioNLP workshop at the Association for Computational Linguistics Conference, August 3-9, Sofia, Bulgaria.
  196. Dligach D,. Miller T, Savova G. 2013. Active learning for phenotyping tasks. In Proceedings of the 2013 NLP for Medicine and Biology Workshop held in conjunction with RANLP-2013. September 2013. Hissar, Bulgaria. http://aclweb.org/anthology//W/W13/W13-5101.pdf. 
  197. Pradhan S, Moschitti A, Xue N, Ng H,  Bjorkelund A, Uryupina O, Zhang Y and Zhong Z. In Press. Towards robust linguistic analysis using OntoNotes. Proceedings of the Conference on Natural Language Learning (CoNLL). Sofia, Bulgaria. August, 2013.
  198. Lin C , Karlson EW, Canhao H, Miller TA, Dligach D, et al.    Automatic prediction of Rheumatoid Arthritis disease activity from the electronic medical records. PLoS One.  2013 August 16;8(8):e69932.  doi:10.10.1371/journal.pone.0069932.  PMC3745469.
  199. Weber GM, Kohane IS. Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS One. 2013;8(5):e64933. PMC3666978.
  200. Weber GM. Federated queries of clinical data repositories: the sum of the parts does not equal the whole. J Am Med Inform Assoc. 2013 Jun;20(e1):e155-61. PMC3715334.
  201. Klann JG, Murphy SN.  Computing health quality measures using Informatics for Integrating Biology and the Bedside.  J Med Internet Res.  2013;15.  PMC3636801.
  202. Klann JG, McCoy AB, Wright A, Wattanasin N, Sittig DF, Murphy SN.  Health care transformation through collaboration on open-source informatics projects: Integrating a medical application platform, research data repository and patient summarization.  Interact J Med Res 2013;2.  PMC3668611.
  203. Sun W, Runshisky A, Uzuner O.  Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. J Am Med Inform Assoc.  2013 Apr 5. PMC3756273.
  204. Sun W, Rumshisky A, Uzuner O.  Temporal reasoning over clinical text: the state of the art.  J Am Med Inform Assoc 2013 Sept;20(5); 814-819.  PubMed PMC3756277.
  205. Uzuner O, Stubbs A, Sun W.  Guest Editorial: Chronology of your health events: Approaches to extracting temporal relations from medical narratives.  J Biomed Inform.  2013 Dec;46 Suppl:S104. PMC4193667.
  206. Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP. Normalization of plasma 25-hydroxy vitamin D Is associated with reduced risk of surgery in Crohn's disease. Inflamm Bowel Dis. August 2013;19(9):1921-1927.  PMC3720838.
  207. Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP.  Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. Aliment Pharmacol Ther. 2013 Feb;37(4):445-54.  PMC3552092.
  208. Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP. Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: A novel informatics approach.  Inflamm Bowel Dis. 2013 Jun;19(7):1411-1420. PMC3665760.
  209. 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 Apr;108(4):594-601. PMC3627544.
  210. 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. Psychiatry Res. 2013 Mar 30;211(3):202-13. PMC3574623.
  211. 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 Jan 29;346:f288. PMC3558546. (Collaboration with previous Major Depressive Disorder DBP team on work sponsored by a follow on grant that used the original virtual cohort developed by the i2b2 team).
  212. Liao KP, Diogo D, Cui J, Cai T, Okada Y, Gainer VS, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovits P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM. 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. PMC3815491.
  213. Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis Rheum. 2013 Mar;65(3):571-81. PMC3582761.
  214. Xia Z, Secor E, Chibnik L, Bove R, Cheng S, Chitnis T, Cagan A, Gainer V, Pei C, Liao K, Shaw S, Ananthakrishnan A, Szolovits P, Weinter H, Karlson E, Murphy S, Savova G, Cai T, Churchill S, Plenge R, Kohane I, De Jager P.  Modeling disease severity in multiple sclerosis using electronic health records.  PLoS One.  2013;8(11):e78927.  PMC3823928.
  215. Sun W, Rumshisky A, Uzuner O.   Annotating temporal information in clinical narratives.   J Biomed Inform. 2013 Dec;46 Suppl:S5-12.  PMC3855581.
  216. Chasin R, Rumshisky A, Uzuner O, Szolovits P.  Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods. J Am Med Inform Assoc. 2014 Sep-Oct;20(5)842-9.   PMC4147600.
  217. Uzuner O, Stubbs A, Sun W.  Chronology of your health events: approaches to extracting temporal relations from medical narratives.  J Biomed Inform. 2013 Dec;46 Suppl:S1-4.  PMC4193667.
  218. Liao KP, Cai T, Gainer VS, Cagan A, Murphy SN, Liu C, Churchill S, Shaw SY, Kohane I, Solomon DH, Plenge RM, Karlson EW. Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population. Arthritis Care Res (Hoboken) 2013 Dec;65(12):2046-50. PMC4060244.
  219. Doshi Velez F, Ge Y, Kohane I.  Comorbidity clusters in autism spectrum disorder: an EHR time-series analysis.  Pediatrics 2014 Jan;133(1)e54-63. PMC3876178.
  220. Weber GM.  How many patients are ‘normal’?  Only 1.55%.  AMIA Jt Summits Transl Sci Proc.  2013:79.  PMC3845778.
  221. Matsouaka RA, Li J, Cai T.  Evaluating marker-guided treatment selection strategies.  Biometrics.  2014 Apr 29;. PMC4213325 [Epub ahead of print].
  222. Parast L, Tian l, Cai T.  Landmark estimation of survival and treatment effect in a randomized clinical trial.  J Am Stat Assoc.  2014 Jan 1;109(505):384-394.  PMC3960087.
  223. Minnear J, Yuan M, Liu J, Cai T.  Risk classification with an adaptive naive Bayes Kernel matching model. J Am Stat Assoc.  2014: in press.  DOI: http://www.tandfonline.com/doi/abs/10.1080/01621459.2014.908778#.V19GcfTF9Z8.
  224. Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IS, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, deBakker PIW, Duzkale H, Dworzyski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M.  An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical geniome sequencing results in the CLARITY Challenge.  Genome Bio.  2014;15:R53. PMC4073084.
  225. Velasquez A, Ghassemi M, Szolovits P, Park S, Osorio J, Dejam A, Celi L.  Long-term outcomes of minor troponin elevations in the intensive care unit.  Anaesth Intensive Care.  2014, May;42(3):356-64.  PMID:24794476.
  226. Luo Y, Uzuner O.  Semi-supervised learning to identify UMLS semantic relations.  Proc. AMIA 2014 Jt. Summits on Translational Science, San Francisco, April 7-11, 2014.
  227. Tian L, Zhao L, Wei LJ.  Predicting the restricted mean event time with the subject's baseline covariates in survival analysis.  Biostatistics 2014 Apr;15(2):222-33.   PMC3944973.
  228. Dligach D, Bethard S, Becker L, Miller TA, Savova GK.  Discovering body site and severity modifiers in clinical texts.  J Am Med Inform Assoc.  2014 May;21(3):448-454.   PMC3994852.
  229. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Higher plasma vitamin D is associated with reduced risk of clostridium difficile infection in patients with inflammatory bowel diseases.  Aliment Pharmacol Ther. 2014 May;39(10):1136-42. PMC4187206.
  230. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Scoville E, Lonijeti GG, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 Mar 12.pii:S1542-3565(14)00359-0.  PMC4162859.
  231. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.  J Crohns Colitis.  2014 Feb 18.pii:S1873-9946(14)00038-5.  PMC4136996.
  232. Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 Aug;12(8):1342-48.e1.  PMC4085150.
  233. Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 May;12(5):821-7.  PMC3995841.
  234. Liao KP, Diogo D, Gui J, Cai T, Okada Y, Gainer V, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovitz P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM.  The association between low density lipoprotein (LDL) and RA genetic factors with LDL levels in rheumatoid arthritis and non-RA controls.  Ann Rheum Dis 2014;73:1170-5.  PMC3815491.
  235. Mandl KD, Kohane IS, McFaden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, GeY, Zhou S, Perkins J, Marsolo K, Bernstam E, Showalter J, Quarshie A, Ofili E, Hripcsak G, Murphy SN.  Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture.  J Am Med Inform Assoc.  2014 Jul;21(4):615-20.  PMC4078286.
  236. Klann JG, Buck MD, Brown J, Hadley M, Elmore R, Weber GM, Murphy SN.  Query Health: standards-based, cross-platform population health surveillance.  J Am Med Inform Assoc.  2014 Jul;21(4)650-6. PMC4078284.
  237. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.   Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel disease. Clin Gastroenterol Hepatol. 2014 Jul 17;PubMed PMID: 25041865; NIHMSID:615037. [Epub adhead of print]
  238. Ananthakrishnan AN, Cheng A, Cagan A. Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Mode of childbirth and long-term outcomes in women with inflammatory bowel diseases. Dig Dis Sci. 2014 Sept 12; PubMed PMID:252 13079; NIHMSID:627958. [Epub ahead of print].
  239. Sinnott JA, Dai W, Liao KP, Shaw SY, Ananthakrishnan AN, Gainer VS, Karlson EW, Churchill S, Szolovits P, Murphy S, Kohane I, Plenge R, Cai T.  Improving the power of genetic association tests with imperfect phenotype derived from electronic medical records.  Hum Genet.  2014 Nov;133(11):1369-82.  PMC4185241.
  240. Castro V, Minnier J, Murphy S, Kohane I, ChurchillS, Gainer V, Cai T, Hoffnagle A, Dai Y, Block S, Weill S, Nadal-Vicens M, Pollastri A, Rosenquist J, Goryachev S, Ongur D, Sklar P, Perlis R, Smoller J.  Validation of electronic health record phenotyping of bipolar disorder cases and controls.  Am J Psychiatry.  2014;; AiA:1-10; doi:10.1176/appi.ajp.2014.14030423.
  1.  

 ***********************************

Publications facilitated by i2b2

From the First NLP Challenge (2006: Deidentification and Smoking Status):

  • Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan M, Peshkin L, Yeh A, Hitzeman J, HirschmanL: Rapidly retargetable approaches to de-identification in medical records.  J Am Med Inform Assoc. 2007;14:564-573.  Epub 2007 Jun 28.
  • Szarvas Gy., Farkas R, Busa-Fekete R. State-of-the-art anonymisation of medical records using an iterative machine learning framework. J Am Med Inform Assoc.   2007;14:574-580.  Epub 2007 Jun 28.
  • Savova G, Ogren P, Duffy P, Buntrock J, Chute C. Mayo Clinic NLP System for patient smoking status sdentification. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):25-28.  Epub 2007 Oct 18.  PMC2274870.
  • Wicentowski R, Sydes MR. Using implicit information to iIdentify smoking status in smoke-blind medical discharge summaries.  J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):29-31.  Epub 2007 Oct 18.  PMC2274867.
  • Cohen AM. Five-way smoking status classification using text hot-spot identification and error-correcting output codes. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):32-35.  Epub 2007 Oct 18.  PMC2247879.
  • Clark C, Good K, Jezierny L, Macpherson M, Wilson B, Chajewska U. Identifying smokers with a medical extraction system. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):36-39.  Epub 2007 Oct 18.  PMC2274874.
  • Heinze DT, Morsch ML, Potter BC, Sheffer RE Jr. A‑Life Medical i2b2 NLP Smoking Challenge system architecture & methodology.  J Am Med Inform Assoc. 2008 Jan-Feb;15(1):40-43.  Epub 2007 Oct 18.  PMC2274871.
  • Hara K. Applying a SVM based chunker and a text classifier to the Deid Challenge. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org .
  • Pedersen T. Determining smoker status using supervised and unsupervised learning with lexical features. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org.
  • McMormick PJ, Elhadad N, Stetson PD.  Use of semantic features to classify patient smoking status.  AMIA Annu Symp Proc 2008;6:450-4.  PMC2655942.

From the Second NLP Challenge (2008: Obesity):

  • Farkas R, Szarvas G, Hegedüs I, Almási A, Vincze V, Ormándi R, Busa-Fekete R. “Semi-automated construction of decision rules to predict morbidities from clinical texts.  J Am Med Inform Assoc. July 2009;16(4):601-5.  Epub 2009 Apr 23.  PMC2705267.
  • Yang H, Spasic I, Keane JA, Nenadic G. A text mining approach to the prediction of a disease status from clinical discharge summaries.  J Am Med Informs Assoc. July-Aug 2009;16(4):596-600.  Epub 2009 Apr 23.  PMC2705266.
  • Kyle H. Ambert, Aaron M. Cohen. A system for classifying disease comorbidity status from medical discharge summaries using automated hotspot and negated concept detection.  J Am Med Inform Assoc. July-Aug 2009;16(4):590-5.  Epub 2009 Apr 23.  PMC2705265.
  • Ware H, Mullett CJ, Jagannathan J. Natural Language Processing (NLP) Framework to assess clinical conditions.  J Am Med Inform Assoc. July-Aug 2009;16(4):585-9.  Epub 2009 Apr 23.  PMC2705264.
  • Solt I, Tikk D, Gal V, Kardkovics ZT.  Semantic classification of diseases in discharge summaries using a context-aware rule based classifier.  J Am Med Inform Assoc. July 2009;6(4):580-4.  Epub 2009 Apr 23.  PMC2705263.
  • Mishra NK, Cummo DM, Arnzen JJ, Bonander J. A rule-based approach for identifying obesity and its co-morbidities in medical discharge summaries.  J Am Med Inform Assoc. 2009;16(4): 576-9.  Epub 2009 Apr 23.  PMC2705262.
  • Childs LC, Taylor RJ, Simonsen L, Heintzelman NH, Kowalski KM, Enelow R.  Description of a rule-based system for the i2b2 Challenge in Natural Language Processing for Clinical Data.  J Am Med Inform Assoc. 2009; 16(4):571-5.  Epub 2009 Apr 23.  PMC2705261.

From the Third NLP Challenge (2009: Medication):

From the Fourth NLP Challenge ( 2010: Relations):

  • Manabu Torii, Kavishwar Wagholikar, Hongfang Liu.  Using machine learning for concept extraction on clinical documents from multiple data sources. JAMIA 2011 Sept-Oct;18(5):580-7; Published Online First: 27 June 2011 doi:10.1136/amiajnl-2011-000155.  PMC3168314.
  • Leonard W D'Avolio, Thien M Nguyen, Sergey Goryachev, Louis D Fiore.Automated concept-level information extraction to reduce the need for custom software and rules development.  JAMIA 2011 Sept-Oct;18(5):607-13; Published Online First: 22 June 2011 doi:10.1136/amiajnl-2011-000183.   PMC3168318.
  • Anne-Lyse Minard, Anne-Laure Ligozat, Asma Ben Abacha, Delphine Bernhard, Bruno Cartoni,LouiseDeléger, Brigitte Grau, Sophie Rosset, Pierre Zweigenbaum, Cyril Grouin. Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. JAMIA 2011 Sept-Oct;18(5):558-93; Published Online First: 19 May 2011 doi:10.1136/amiajnl-2011-000154.  PMC3168313.
  • Berry de Bruijn, Colin Cherry, Svetlana Kiritchenko, Joel Martin, Xiaodan Zhu.  Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. JAMIA 2011 Sept-Oct;18(5):557-62; Published Online First: 12 May 2011 doi:10.1136/amiajnl-2011-000150.  PMC3168309.
  • Cheryl Clark, John Aberdeen, Matt Coarr, David Tresner-Kirsch, Ben Wellner, Alexander Yeh,Lynette Hirschman. MITRE system for clinical assertion status classification.   JAMIA 2011 Sept-Oct;18(5)563-7; Published Online First: 22 April 2011 doi:10.1136/amiajnl-2011-000164.   PMC3168316.
  • Kirk Roberts, Sanda Harabagiu.  A flexible framework for deriving assertions from electronic medical records.  JAMIA 2011 Sept-Oct;18(5):568-73; Published Online First:1 July 2011 doi:10.1136/amiahnl-2011-000152.  PMC3168311.
  • Min Jiang, Yukun Chen, Mei Liu, S Trent Rosenbloom, Subramani Mani, Joshua C Denny,HuaXu. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. JAMIA 2011 Sept-Oct;18(5):601-6; Published Online First: 20 April 2011 doi:10.1136/amiajnl-2011-000163.  PMC3168315.

 

From the Fifth NLP Challenge (2011: Co-reference)

  • Siddhartha Reddy Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar Wagholikar, Manabu Torii, Hongfang Liu. Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J Am Med Inform Assoc 2012 Sept-Oct;19:867-874 Published Online First: 16 June 2012 doi:10.1136/amiajnl-2011-000766.  PMC3422831.
  • Bryan Rink, Kirk Roberts, Sanda M Harabagiu.  A supervised framework for resolving coreference in clinical records. J Am Med Inform Assoc 2012 Sept-Oct;19:875-882 Published Online First: 19 May 2012 doi:10.1136/amiajnl-2012-000810.   PMC3244838
  • Henry Ware, Charles J Mullett, Vasudevan Jagannathan, Oussama El-Rawas. Machine learning-based coreference resolution of concepts in clinical documents. J Am Med Inform Assoc 2012 Sept-Oct;19:883-887 Published Online First: 12 May 2012 doi:10.1136/amiajnl-2011-000774.  PMC3422832.
  • Hong-Jie Dai, Chun-Yu Chen, Chi-Yang Wu, Po-Ting Lai, Richard Tzong-Han Tsai, Wen-Lian Hsu. Coreference resolution of medical concepts in discharge summaries by exploiting contextual information. J Am Med Inform Assoc 2012 Sept-Oct;19:888-896 Published Online First: 3 May 2012 doi:10.1136/amiajnl-2012-000808.   PMC3422837.
  • Yan Xu, Jiahua Liu, Jiajun Wu, Yue Wang, Zhuowen Tu, Jian-Tao Sun, Junichi Tsujii, Eric I-Chao Chang. A classification approach to coreference in discharge summaries: 2011 i2b2 challenge. J Am Med Inform Assoc 2012 Sept-Oct;19:897-905 Published Online First: 13 April 2012 doi:10.1136/amiajnl-2011-000734.  PMC3422828.
  • Prateek Jindal, Dan Roth. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives.  J Am Med Inform Assoc 2013 Mar-Apr;20(2):356-362; amiajnl-2011-000767Published Online First: 10 July 2012 doi:10.1136/amiajnl-2011-000767.  PMC3638172.
  • Chen P, Hinote D, Chen G.  A rule based solution to the co-reference resolution in clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):891-7.PMC3756251.
  • Sohn S. Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H.   Comprehensive temporal information detection from clinical text: medical events, time and TLINK identification.  J Am Med Inform Assooc. 2013 Sep-Oct;20(5):836-42.  PMC37565269.

 

From the Sixth NLP Challenge (2012: Temporal Relations)

  • Xu Y, Wang Y, Liu T, Tsujii J, Chang El.  An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 Challenge.   J Am Med Inform Assoc. 2013 Sep-Oct;20(5):849-58.  PMC3756267.
  • Cherry C, Zhu X, Martin J, deBruijn B.  A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP Challenge.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):843-8.  PMC3756270.
  • Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H.   Comprehensive temporal information detection from clinical text: medical events, time and TLINK identification.  J Am Med Inform Assooc. 2013 Sep-Oct;20(5):836-42.  PMC37565269.
  • Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H.  A hybrid system for temporal information extraction from clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):828-36.  PMC3756274.
  • Grouin C, Grabar N, Hamon T, Rosset S, Tannier X, Zweigenbraum P.Eventual situations for timeline extraction from clinical reports.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):820-7.   PMC3756272.
  • Kovacevic A, Dehghan A, Filannino M, Keane JA, Nenadic G.  Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives.   J Am Med Inform Assoc. 2013 Sep-Oct;20(5):859-66.  PMC3756271.
  • Roberts K, Rink B, Harabagiu SM.  A flexible framework for recognizing events, temporal expressions and temporal relations in clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):867-75.  PMC3756268.  
  • D'Souza J, Ng V.  Classifying temporal relations in clonical data: a hybrid, knowledge-rich approch.   J Biomed Inform. 2013 Dec;46 Suppl:S29-39.   PMC3855590.

 

C.  By Interest Area

Systems Medicine: 

  • Kohane IS, Altman RA  Health-information atruists – a potentially critical resource.  New Engl J Med.  2005;353:2074-7.

  • Butte AJ, Kohane IS.  Creation and implications of a phenome-genome network.  Nature Biotechnology.  2006;24(1):55-62.

  • Kohane IS, Masys DR, Altman RA.  The incidentalome:  a threat to genomic medicine. J Am Med Assoc. 2006;296(2):212-5.

  • McMurry AJ, Gilbert CA, Reis BY, Chueh HC, Kohane IS, Mandl KD. A  self scaling, distributed architecture for public health, research, and clinical care. J Am Med Inform Assoc. 2007;14(4):527-33.

  • Loscalzo J, Kohane IS, Barabasi AL.  Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.  Mol Syst Biol.  2007;3:124.

  • Kohane IS. The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med. 2009;1(1):4.   PMC2651581.

  • Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009;360(13):1278-81.  PMID:19321867 [Pub Med - Indexed for MEDLINE]

  • Murphy SN, Churchill SE, Bry L, Chueh H, Cai T, Weiss S, et al. Instrumenting the health care enterprise for discovery research in the genomic era.  Genome Res. 2009;360(13)1278-81.  PMC2752136.

  • Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009;6(5):624-30.   PMC2744712.

  • Valtchinov VI and Kohane IS.  Quantifying the white blood cell transcriptome as an accessible window to the multi-organ transcriptome.  Bioinfomatics 2012 Mar 15;28(6):905.  PMC3663292.

  • 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.
  • Mandl KD, Khorasani R, Kohane IS.  Meaningful use of electronic health records.  Health Aff (Millwood).  2012 Jun;31(6):1365.  PMID:22665650.
  • 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.    PMC3325235.
  • Kohane IS.  (Mis)treating the pharmacogenetic incidentalome.  Nat Rev Drug Discov. 2012 Feb 1;11(2):89-90.  doi: 10.1038/nrd3659.  PMID:22293554.
  • 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.   PMC3328607.
  • 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.  PMC3288749.
  • 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.   PMC3277623.
  • Masys DR, Harris PA, Fearn PA, Kohane IS. Designing a public square for research computing. Sci Transl Med. 2012 Aug 29;4(149):149fs32. PMC3725749.

Informatics Tool Development and Application: 

  • Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh H.  Integration of clinical and genetic data in the i2b2 architecture.  AMIA Annu Symp Proc. 2006;p.1040. PMID:17238659.
    Murphy SN, Mendis M, Hackett K, Kuttan R, Pan; W, Phillips L, et  al. Architecture of  the open-source clinical research chart from Informatics for  Integrating Biology and the Bedside.  AMIA Annu Symp Proc. 2007;p. 548-52.  PMID:18693896.

  • Dubey A, Herrick C, Murphy SN. Mining for associations between categorical data items in a clinical data repository. AMIA Annu Symp Proc. 2007;p.945.

  • Gainer V, Hackett K, Mendis M,  Kuttan R, Pan W, Phillips L, Chueh H, Murphy SN. Using the i2b2 Hive for clinical discovery: an example. AMIA Annu Symp Proc. 2007; p.959. PMID:18694059.

  • Mendis M, Wattanasin N, Kuttan R, Pan W, Hackett K, Gainer V, Chueh H, Murphy SN.  Integration of Hive and Cell software in the i2b2 architecture. AMIA Annu Symp Proc.. 2007;p.1048.  PMID:18694146.

  • Wang T,  Plaisant C,  Quinn A,  Stanchak R, Murphy SN, Shneiderman B.  Aligning temporal data by sentinel events: Discovering patterns in electronic health records, Proceedings of ACM, April 5-10, 2008. pp. 457-466. PMC

  • Dubey AK, Gainer V, Murphy SN.  Simulated yields of prospective specimen collection from specific patient cohorts using retrospective data from a research patient data repository.  AMIA Annu Symp Proc. 2008;p.935. PMC

  • Mendis M, Phillips L, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc. 2008;p.1054.  PMID:18999021.

  • Scheufele EL, Dubey AK, Murphy SN. A study of the age attribute in a query tool for a clinical data warehouse.  AMIA Annu Symp Proc. 2008;p.1123. PMC

  • Sordo M, Colecchi J, Dubey AK, Gainer V, Murphy SN.  STROBE-Based Methodology for Detection of Adverse Events across Multiple Communities. AMIA Annu Symp Proc. 2008;p.1144. PMC

  • Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW.   iTools: A framework for classification, categorization and integration of computational biology resources. PLoS ONE. 2008;3(5): e2265.   PMC2386255.

  • 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.  PMC3000779.

  • Turchin A, Shubina M, Murphy SN.  I am not dead yet: Identification of false-posivite matches to death Master file.  Proc. 2010 AMIA Fall Symposium: 807-811.   PMID:21347090.

  • 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.
  • 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.   PMC3415281.
  • 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.  PMC3555330.
  • 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.   PMC3384120.
  • McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS. SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013;8(3):e55811. PMC3591385.  (Collaboration with the Harvard Medical School CTSA Catalyst SHRINE team).
  • Klann JG, Murphy SN.  Computing health quality measures using informatics for integration biology and the bedside.  J Med Internet Res.  2013;15.  PMC3636801.
  • Klann JG, McCoy AB, Wright A, Wattanasin N, Sittig DF, Murphy SN.  Health Care Transformation through collaboration on open-source informatics projects: Integrating a medical application platform, research data repository and patient summarization.  Interact J Med Res 2013;2.  PMC3668611.
  • Klann JG, Buck MD, Brown J, Hadley M, Elmore R, Weber GM, Murphy SN.  Query Health: standards-based, cross-platform population health surveillance.  J Am Med Inform Assoc.  2014 Jul;21(4)650-6.   PMC4078284.
  • Mandl KD, Kohane IS, McFaden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, GeY, Zhou S, Perkins J, Marsolo K, Bernstam E, Showalter J, Quarshie A, Ofili E, Hripcsak G, Murphy SN.  Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture.  J Am Med Inform Assoc.  2014 Jul;21(4):615-20.   PMC4078286.

Predictive Medicine: 

  • Carter SL, Eklund AC, Kohane IS, Haris LN, Szallasi Z.  A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.  Nat Gen 2006;38(9):1043-48.

  • Evans SR, Li L, Wei LJ.  Data monitoring in clinical trials using predictions.  Drug Information J.  2007;41:733-742.

  • Tian T, Cai T, Goetghebeur E, Wei LJ.  Model evaluation based on the distribution of estimated absolute prediction error. Biometrika. 2007;94:297-311.

  • Uno H, Cai T, Tian L, and Wei LJ.  Evaluating prediction rules for t-year survivors with censored regression models.  2007;102:527-37.

  • Cai T, Tian L, Solomon S, Wei LJ.  Predicting future responses based on possibly misspecified working models.  Biometrika.  2008;95(1):75-92.  PMC

  • Tian L, Cai T , Piankov N,  Cremieux P,Wei LJ.  Effectively combining independent 2 by 2 tables for valid inferences in meta analysis with all available data but no artificial continuity corrections for studies with zero events and its application to the analysis of Rosiglitazone's Cardiovascular disease related event data. Biostatistics,  2009 in press.

  • Cai C, Tian L, Lloyd-Jones D, Wei LJ.  Evaluating subject-level incremental values of new markers for risk classification rule. Biometrics. 2009;in revision.

  • L. Ryan L, Cai T Parast L. Meta-Analysis for rare events. Statistics in Medicine 2010 Sept 10; 29(20):2078-2089.  PMC2932857.

  • Cai T, Tian L, Uno H, Solomon D, Wei LJ. Calibrating parametric subject-specific risk estimation.  Biometrika 2010 June; 97(2):389-404.   PMC3412577.

  • Lingling LI, Evans SR, Uno H, Wei LJ.  Statistics in Biopharmaceutical Research.  2009;1(4)348-355. PMC

  • Cai T, Gerds T, Zheng Y, Chen J. Combining information for robust prediction of survival outcomes. Biometrics.  2009;accepted. 

  • 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, 2009; in press.

  • Cornelis M, Qi L, Shang C, Kraft P, Manson J, Cai T, Hunter D, Hu F.  Joint effects of common genetic variants on the risk of Type 2 Diabetes in US men and women.  Ann Int Med.  2009;accepted.

  • 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, in revision.

  • Cai T, Tian L, Wong P, Wei LJ.  Analysis of randomized comparative clinical trial data for personalized treatent selections.  Biostatistics.  2011;12(2):270-282.  PMC3062150.

  • 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 Dec;67(4):1389-1396.   PMC3144297.

  • 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.

  • Parast L, Cheng SC, Cai T. Landmark prediction of long term survival incorporating short term event time information. J Am Stat Assoc. 2012;107(500):1492-1501. PMC3535339.
  • Zheng Y, Parast L, Cai T, Brown M. Evaluating incremental values from new predictors with net reclassification improvement in survival analysis. Lifetime Data Anal. July 2013;19(3):350-370.  PMC3686882.
  • Parast L, Cai T. Landmark risk prediction of residual life for breast cancer survival. Stat Med. Sept 10, 2013;32(20):3459-3471.  PMC3744612.
  • Zhou QM, Zheng Y, Cai T. Subgroup specific incremental value of new markers for risk prediction. Lifetime Data Anal. 2013 Apr;19(2):142-69. PMC3633735.   
  • Tian L, Cai T, Zhao L, Wei LJ. On the covariate-adjusted estimation for an overall treatment difference with data from a randomized comparative clinical trial. Biostatistics. 2012 Apr;13(2):256-73. PMC3297822.
  • Cai T, Lin X, Carroll RJ. Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test. Biostatistics. 2012 Sep;13(4):776-90. PMC3440238. 
  • Sinnott JA, Cai T.  Omnibus risk assessment via accelerated failure time kernal machine modeling.  Biometrics.  2013 Dec;69(4):861-73.  PMC3869038.
  • Zhou QM, Sheng Y, Cai T.  Assessment of biomarkers for risk prediction with nested case-control studies.  Clin Trials.  2013 Oct;10(5)677-9.  PMC3800233.
  • Zheng Y, Cai T, Pepe MS.  Adopting nested case-control quota sampling designs for the evaluation of risk markers. Lifetime Data Anal.  2013 Oct;19(4):568-88.  PMC3903399.
  • Parast L, Cai T.  Landmark risk prediction of residual life for breast cancer survival.  Stat Med. 2013 Sep 10;32(20):3459-71.  PMC3744612.
  • Parast L, Tian l, Cai T.  Landmark estimation of survival and treatment effect in a randomized clinical trial.  J Am Stat Assoc.  2014 Jan 1;109(505):384-394.  PMC3960087.
  • Minnear J, Yuan M, Liu J, Cai T.  Risk classification with an adaptive naive Bayes Kernel matching model. J Am Stat Assoc.  2014: DOI: http://www.tandfonline.com/doi/abs/10.1080/01621459.2014.908778#.V19GcfTF9Z8.
  • Matsouaka RA, Li J, Cai T.  Evaluating marker-guided treatment selection strategies.  Biometrics.  2014 Apr 29 Published online 10.1111/biom.12179.  PMC4213325.   Available in PMC on 10/29/15. 
  • Tian L, Zhao L, Wei LJ.  Predicting the restricted mean event time with the subject's baseline covariates in survival analysis.  Biostatistics 2014 Apr;15(2):222-33.   PMC3944973.

Population Based Studies (including Pharmacovigilance): 

  • Brownstein JS, Cassa CC, Kohane IS, Mandl KD.  An unsupervised classification method for inferring original case locations from low-resolution disease maps.  Internatl J Health Geographics 2006;5:56.

  • Brownstein JS, Sordo M, Kohane IS, Mandl Kl.  Telltale heart: population based surveillance model reveals association with rofecoxib and celecoxib with myocardial infarction.  PlosOne. 2007;9 (9) e840.

  • Reis BY, Kohane IS, Mandl KD. An epidemiological network model for disease outbreak Detection. PLoS Med. 2007;4(6):e210.

  • 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.   PMC2827502.

  • 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.  PMC2827502.

  • 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.

  • 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 leels.  Clin Pharm Therapeutics.  2011 July;90(1):2133-142.  PMC3216673.

  • Weber GM, Kohane IS. Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS One. 2013;8(5):e64933. PMC3666978.
  • Weber GM. Federated queries of clinical data repositories: the sum of the parts does not equal the whole. J Am Med Inform Assoc. 2013 Jun;20(e1):e155-61. PMC3715334.
  • Doshi Velez F, Ge Y, Kohane I.  Comorbidity clusters in autism spectrum disorder: an EHR time-series analysis.  Pediatrics 2014 Jan;133(1)e54-63. PMC3876178.
  • Weber GM.  How many patients are ‘normal’?  Only 1.55%.  AMIA Jt Summits Transl Sci Proc.  2013:79.  PMC3845778.
  • Velasquez A, Ghassemi M, Szolovits P, Park S, Osorio J, Dejam A, Celi L.  Long-term outcomes of minor troponin elevations in the intensive care unit.  Anaesth Intensive Care.  2014, May;42(3):356-64.  PMID:24794476.

Natural Language Processing: 

  • Sordo M, Zeng Q.  On sample size and classification accuracy: A performance comparison. Lecture Notes in Computer Science. 2005;3745:193-201.

  • Fraser HSF, Biodich P, Moodley D, Choi S, Mamlin B, Szolovits P.  Implementing electronic records systems in developing countries,.  Informatics in Primary Care.  2005; 13:83-95.

  • Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus, R.  Extracting principal diagnosis, co-morbidity and smoking status for asthma research: Evaluation of a natural language processing system.  BMC Med Inform and Med Decision Making. 2006;6:30.

  • Goryachev S, Sordo M, Ngo L, Zeng QT.  Implementation and evaluation of four different methods of negation detection.  Technical report, DSG.

  • Goryachev S, Sordo M, Zeng QT.  A suite of natural language processing tools developed for the i2b2 project.  AMIA Annu Symp Proc 2006:p.931.

  • Bramsen P, Deshpande P, Lee YK, Barzilay R.  Finding temporal order in discharge summaries.  AMIA Annu Symp Proc. 2006.

  • Sibanda T, He T, Szolovits P, Uzuner Ö.  Syntactically-informed semantic category recognizer for discharge summaries.  AMIA Annu Symp Proc. 2006: 714–718

  • Goldstein I, Arzrumtsyan A, Uzuner Ö.  Three approaches to automatic assignment of ICD-9-CM codes to radiology reports.  AMIA Annu Symp Proc. 2007 Oct 11:279-83.

  • Uzuner Ö, Szolovits P,  Kohane I. i2b2 Workshop on Natural Language Processing
    challenges for clinical records.  AMIA Annu Symp Proc. 2006.

  • Sibanda T, Uzuner Ö.  Role of local context in de-identification of ungrammatical, fragmented text.  Proceedings of the North American Chapter of Association for Computational Linguistics/Human Language Technology (NAACL-HLT 2006), New York, NY, June 5-7, 2006. pp. 65-73.

  • Uzuner Ö, Luo Y, Szolovits P.  Evaluating the state-of-the-art in automatic de-identification. J Am Med Inform Assoc. 2007;14(5):550-563.

  • Turchin A, Kolatkar NS, Pendergrass ML, Kohane IS. Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record. Med Inform Internet Med. 2007;32(2):93-102.

  • Uzuner Ö.  Second i2b2 workshop on natural language processing challenges for clinical records.  AMIA Annu Symp Proc. 2008 Nov 6:1252-3. PMC

  • Uzuner Ö, Goldstein I, Kohane I.  Identifying patient smoking status from medical discharge records.  J Am Med Inform.  2008 Jan-Feb;15(1):14-24.  PMC2274873.

  • Zhang Y, Szolovits P.  Patient-specific learning in real time for adaptive monitoring in critical care. J Biomed Inform. 2008;41(3):452-460. PMC

  • Uzuner Ö,  Sibanda T,  Luo Y,  Szolovits P.  A de-identifier for medical discharge summaries.  Artificial intelligence Med. 2008 January;42(1):13-35.   PMC2271040.

  • Uzuner Ö, Zhang X, Sibanda T. Two approaches to assertion classification.  AMIA Annu Symp Proc. 2008;p.6:752.  PMC2656003

  • Goryachev S, Kim H, Zeng-Treitler Q.  Identification and extraction of family history information from clinical records.  AMIA Annu Symp Proc. 2008; pp. 247-51. PMC

  • Uzuner Ö, Zhang X, Sibanda T. Machine learning and rule-based approaches to assertion classification.  J Am Med Inform Assoc. 2009 Jan-Feb;16(1):109-115.  PMC2605605

  • Uzuner Ö. Recognizing obesity and co-morbidities in sparse data. J Am Med Inform Assoc. 2009; 16(4):561-70. PMC

  • Goldstein I, Uzuner Ö. Specializing for predicting obesity and its co-morbidities.  J Biomed Inform. 2009 October;42(5):873-86.    PMC3253373.

  • Uzuner Ö, Mailoa J, Sibanda T. Semantic Relations for Problem-Oriented Medical Records.  AMIA Annu Symp Proc. 2009; p. 661.

  • Sibanda T, He T, Szolovits P, Uzuner Ö.  Syntactically-informed semantic category recognizer for discharge summaries.  AMIA Annu Symp Proc. 2006;pp714-718.  PMC1839398.

  • Uzuner O, Solti I, Xia F, Cadag E.  Community annotation experiment for ground truth generation for the i2b2 Medication Challenge.  J Am Med Inform Assoc.  2010;17:519-523.  PMC2995684.
  • Uzuner O, Solti I, Cadag E.  Extracting Medication Information from clinical text. J Am Med Inform Assoc.  2010;17:514-518. PMC2995677.
  • 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. Sept-Oct;18(5):552-556.   doi:10.1136/amiajnl-2011-000203.   PMC3168320.

  • 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. 
  • 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.
  • 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.   PMC3384116.
  • 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.
  • 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.   PMC3392861.  
  • 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.   PMC3422821.
  • 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.   PMC3422835.
  • 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):1–14.   PMC3299408.
  • Chen L, Karlson E, Canhao H, Miller T, Dligach D, Chen P, Guzman Perez R, Cai T, Weinblatt M, Shadick N, Plenge R, Savova G.  Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. PlosOne 2013;8(8):e69932.  PMC3745469
  • Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Pradhan, Sameer; Lin, Chen; and Savova, Guergana. 2013. Discovering narrative containers in clinical text. BioNLP workshop at the Association for Computational Linguistics conference, August 3-9, Sofia, Bulgaria.
  • Dligach, Dmitriy; Timothy A. Miller, Guergana K. Savova. 2013a. Active learning for phenotyping tasks. In Proceedings of the 2013 NLP for Medicine and Biology workshop held in conjunction with RANLP-2013. September 2013. Hissar, Bulgaria. http://aclweb.org/anthology//W/W13/W13-5101.pdf. 
  • Pradhan S, Moschitti A, Xue N, Ng H,  Bjorkelund A, Uryupina O, Zhang Y and Zhong Z. In Press. Towards robust linguistic analysis using OntoNotes. Proceedings of the Conference on Natural Language Learning (CoNLL). Sofia, Bulgaria. August, 2013.
  • Sun W, Rumshisky A, Uzuner O.  Annotating temporal information in clinical narratives.  J Biomed Inform.  2013 Dec;46 Suppl:S5-12.  PMC3855581.
  • Sun W, Rumshisky A, Uzuner O.  Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. J Am Med Inform Assoc.  2013 Apr 5. PMC3756273.
  • Sun W, Rumshisky A, Uzuner O.  Temporal reasoning over clinical text: the state of the art.  J Am Med Inform Assoc 2013 Sept-Oct;20(5):814-19.   PMC3756277.
  • Uzuner O, Stubbs A, Sun W.  Guest Editorial: Chronology of your health events: Approaches to extracting temporal relations from medical narratives.  J Biomed Inform.  2013 Dec;46 Suppl:S104. PMC4193667.
  • Luo Y, Uzuner O.  Semi-supervised learning to identify UMLS semantic relations.  Proc. AMIA 2014 Jt. Summits on Translational Science, San Francisco, April 7-11, 2014. PMC
  • Dligach D, Bethard S, Becker L, Miller TA, Savova GK.  Discovering body site and severity modifiers in clinical texts.  J Am Med Inform Assoc.  2014;21:438-447.   PMC3994852.
  • Chasin R, Rumshisky A, Uzuner O, Szolovits P.  Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods.  J. Am Med Inform Assoc.  2014, Jan 17.  PMC4147600.
  • D'Souza J, Ng V.  Classifying temporal relations in clonical data: a hybrid, knowledge-rich approch.   J Biomed Inform. 2013 Dec;46 Suppl:S29-39.   PMC3855590.
  • Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan M, Peshkin L, Yeh A, Hitzeman J, HirschmanL: Rapidly retargetable approaches to de-identification in medical records.  J Am Med Inform Assoc. 2007;14:564-573.  Epub 2007 Jun 28.

  • Szarvas Gy., Farkas R, Busa-Fekete R. State-of-the-art anonymisation of medical records using an iterative machine learning framework. J Am Med Inform Assoc.   2007;14:574-580.  Epub 2007 Jun 28.

  • Savova G, Ogren P, Duffy P, Buntrock J, Chute C. Mayo Clinic NLP System for patient smoking status identification. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):25-28.  Epub 2007 Oct 18.  PMC2274870.

  • Wicentowski R, Sydes MR. Using implicit information to identify smoking status in smoke-blind medical discharge summaries.  J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):29-31.  Epub 2007 Oct 18.  PMC2274867.

  • Cohen AM. Five-way smoking status classification using text hot-spot identification and error-correcting output codes. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):32-35.  Epub 2007 Oct 18.  PMC2274879.

  • Clark C, Good K, Jezierny L, Macpherson M, Wilson B, Chajewska U. Identifying smokers with a medical extraction system. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):36-39.  Epub 2007 Oct 18.  PMC2274874.

  • Heinze DT, Morsch ML, Potter BC, Sheffer RE Jr. A‑Life Medical i2b2 NLP Smoking Challenge system architecture & methodology.  J Am Med Inform Assoc. 2008 Jan-Feb;15(1):40-43.  Epub 2007 Oct 18.  PMC2274871.

  • Hara K. Applying a SVM based chunker and a text classifier to the Deid Challenge. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org .     

  • Pedersen T. Determining smoker status using supervised and unsupervised learning with lexical features. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org .

  • McMormick PJ, Elhadad N, Stetson PD.  Use of semantic features to classify patient smoking status.  AMIA Annu Symp Proc 2008;6:450-4.  PMC2655942

  • Chasin R, Rumshisky A, Uzuner O, Szolovits P.  Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods. J Am Med Inform Assoc. 2014 Sep-Oct;20(5)842-9.   PMC4147600.

From the First NLP Challenge (2006: Deidentification and Smoking):

  • Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan M, Peshkin L, Yeh A, Hitzeman J, HirschmanL: Rapidly retargetable approaches to de-identification in medical records.  J Am Med Inform Assoc. 2007;14:564-573.  Epub 2007 Jun 28.
  • Szarvas Gy., Farkas R, Busa-Fekete R. State-of-the-art anonymisation of medical records using an iterative machine learning framework. J Am Med Inform Assoc.   2007;14:574-580.  Epub 2007 Jun 28.
  • Savova G, Ogren P, Duffy P, Buntrock J, Chute C. Mayo Clinic NLP System for patient smoking status sdentification. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):25-28.  Epub 2007 Oct 18.  PMC2274870.
  • Wicentowski R, Sydes MR. Using implicit information to iIdentify smoking status in smoke-blind medical discharge summaries.  J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):29-31.  Epub 2007 Oct 18.  PMC2274867.
  • Cohen AM. Five-way smoking status classification using text hot-spot identification and error-correcting output codes. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):32-35.  Epub 2007 Oct 18.  PMC2247879.
  • Clark C, Good K, Jezierny L, Macpherson M, Wilson B, Chajewska U. Identifying smokers with a medical extraction system. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):36-39.  Epub 2007 Oct 18.  PMC2274874.
  • Heinze DT, Morsch ML, Potter BC, Sheffer RE Jr. A‑Life Medical i2b2 NLP Smoking Challenge system architecture & methodology.  J Am Med Inform Assoc. 2008 Jan-Feb;15(1):40-43.  Epub 2007 Oct 18.  PMC2274871.
  • Hara K. Applying a SVM based chunker and a text classifier to the Deid Challenge. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org .
  • Pedersen T. Determining smoker status using supervised and unsupervised learning with lexical features. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org.
  • McMormick PJ, Elhadad N, Stetson PD.  Use of semantic features to classify patient smoking status.  AMIA Annu Symp Proc 2008;6:450-4.  PMC2655942.

From the Second NLP Challenge (2008: Obesity)  

  • Farkas R, Szarvas G, Hegedüs I, Almási A, Vincze V, Ormándi R, Busa-Fekete R. “Semi-automated construction of decision rules to predict morbidities from clinical texts.  J Am Med Inform Assoc. July 2009 July-Aug;16(4):601-5.  Epub 2009 Apr 23.  PMC2705267.

  • Yang H, Spasic I, Keane JA, Nenadic G. A text mining approach to the prediction of a disease status from clinical discharge summaries.  J Am Med Informs Assoc. July 2009 July-Aug;16(4):596-600.  Epub 2009 Apr 23.  PMC2705266.

  • Kyle H. Ambert, Aaron M. Cohen. A system for classifying disease comorbidity status from medical discharge summaries using automated hotspot and negated concept detection.  J Am Med Inform Assoc. July 2009 July-Aug;16(4):590-5.  Epub 2009 Apr 23.  PMC2705265.

  • Ware H, Mullett CJ, Jagannathan J. Natural Language Processing (NLP) Framework to assess clinical conditions.  J Am Med Inform Assoc. July 2009 July-Aug;16(4):585-9.  Epub 2009 Apr 23.  PMC2705264.

  • Solt I, Tikk D, Gal V, Kardkovics ZT.  Semantic classification of diseases in discharge summaries using a context-aware rule based classifier.  J Am Med Inform Assoc. July 2009 July-Aug;16(4):580-4.  Epub 2009 Apr 23.  PMC2705263.

  • Mishra NK, Cummo DM, Arnzen JJ, Bonander J. A rule-based approach for identifying obesity and its co-morbidities in medical discharge summaries.  J Am Med Inform Assoc. 2009 July-Aug;16(4): 576-9.  Epub 2009 Apr 23.   PMC2705262.

  • Childs LC, Taylor RJ, Simonsen L, Heintzelman NH, Kowalski KM, Enelow R.  Description of a rule-based system for the i2b2 Challenge in Natural Language Processing for Clinical Data.  J Am Med Inform Assoc. 2009 July-Aug; 16(4):571-5.  Epub 2009 Apr 23.  PMC2705261.

From the Third NLP Challenge (2009:Medications):

  • Manabu Torii, Kavishwar Wagholikar, Hongfang Liu.  Using machine learning for concept extraction on clinical documents from multiple data sources. JAMIA 2011 Sept-Oct;18(5):580-7; Published Online First: 27 June 2011 doi:10.1136/amiajnl-2011-000155 .  PMC3168314.

  • Leonard W D'Avolio, Thien M Nguyen, Sergey Goryachev, Louis D Fiore.Automated concept-level information extraction to reduce the need for custom software and rules development.  JAMIA 2011 Sept-Oct;18(5):607-13; Published Online First: 22 June 2011 doi:10.1136/amiajnl-2011-000183.  PMC168318.

  • Anne-Lyse Minard, Anne-Laure Ligozat, Asma Ben Abacha, Delphine Bernhard, Bruno Cartoni,LouiseDeléger, Brigitte Grau, Sophie Rosset, Pierre Zweigenbaum, Cyril Grouin. Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. JAMIA 2011 Sept-Oct;18(5):558-93;Published Online First: 19 May 2011 doi:10.1136/amiajnl-2011-000154.  PMC3168313.

  • Berry de Bruijn, Colin Cherry, Svetlana Kiritchenko, Joel Martin, Xiaodan ZhuMachine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. JAMIA 2011 Sept-Oct;18(5):551-62;  Published Online First: 12 May 2011 doi:10.1136/amiajnl-2011-000150.  PMC3168309.

  • Cheryl Clark, John Aberdeen, Matt Coarr, David Tresner-Kirsch, Ben Wellner, Alexander Yeh,Lynette Hirschman. MITRE system for clinical assertion status classification.  JAMIA 2011 Sept-Oct;18(5):563-7.  Published Online First: 22 April 2011 doi:10.1136/amiajnl-2011-000164.   PMC 3168316.

  • Kirk Roberts, Sanda Harabagiu.  A flexible framework for deriving assertions from electronic medical records.  JAMIA 2011 Sept-Oct;18(5):568-73; Published Online First:1 July 2011 doi:10.1136/amiahnl-2011-000152.   PMC 3168311.

  • Min Jiang, Yukun Chen, Mei Liu, S Trent Rosenbloom, Subramani Mani, Joshua C Denny,HuaXu. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. JAMIA 2011 Sept-Oct;18(5):601-6.  Published Online First: 20 April 2011 doi:10.1136/amiajnl-2011-000163.  PMC3168315.

From the Fourth NLP Challenge (2010:Relations):

  • Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan M, Peshkin L, Yeh A, Hitzeman J, HirschmanL: Rapidly retargetable approaches to de-identification in medical records.  J Am Med Inform Assoc. 2007;14:564-573.  Epub 2007 Jun 28.
  • Szarvas Gy., Farkas R, Busa-Fekete R. State-of-the-art anonymisation of medical records using an iterative machine learning framework. J Am Med Inform Assoc.   2007;14:574-580.  Epub 2007 Jun 28.
  • Savova G, Ogren P, Duffy P, Buntrock J, Chute C. Mayo Clinic NLP System for patient smoking status sdentification. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):25-28.  Epub 2007 Oct 18.  PMC2274870.
  • Wicentowski R, Sydes MR. Using implicit information to iIdentify smoking status in smoke-blind medical discharge summaries.  J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):29-31.  Epub 2007 Oct 18.  PMC2274867.
  • Cohen AM. Five-way smoking status classification using text hot-spot identification and error-correcting output codes. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):32-35.  Epub 2007 Oct 18.  PMC2247879.
  • Clark C, Good K, Jezierny L, Macpherson M, Wilson B, Chajewska U. Identifying smokers with a medical extraction system. J Am Med Inform Assoc. 2008 Jan-Feb;15(1):36-39.  Epub 2007 Oct 18.  PMC2274874.
  • Heinze DT, Morsch ML, Potter BC, Sheffer RE Jr. A‑Life Medical i2b2 NLP Smoking Challenge system architecture & methodology.  J Am Med Inform Assoc. 2008 Jan-Feb;15(1):40-43.  Epub 2007 Oct 18.  PMC2274871.
  • Hara K. Applying a SVM based chunker and a text classifier to the Deid Challenge. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org .
  • Pedersen T. Determining smoker status using supervised and unsupervised learning with lexical features. Available as JAMIA on-line supplement to Uzuner et all at www.jamia.org.
  • McMormick PJ, Elhadad N, Stetson PD.  Use of semantic features to classify patient smoking status.  AMIA Annu Symp Proc 2008;6:450-4.  PMC2655942.

 

From the Fifth NLP Challenge (2011: Co-reference)

  • Siddhartha Reddy Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar Wagholikar, Manabu Torii, Hongfang Liu. Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J Am Med Inform Assoc 2012 Sept-Oct;19:867-874 Published Online First: 16 June 2012 doi:10.1136/amiajnl-2011-000766.  PMC3422831.
  • Bryan Rink, Kirk Roberts, Sanda M Harabagiu.  A supervised framework for resolving coreference in clinical records. J Am Med Inform Assoc 2012 Sept-Oct;19:875-882 Published Online First: 19 May 2012 doi:10.1136/amiajnl-2012-000810.   PMC3244838
  • Henry Ware, Charles J Mullett, Vasudevan Jagannathan, Oussama El-Rawas. Machine learning-based coreference resolution of concepts in clinical documents. J Am Med Inform Assoc 2012 Sept-Oct;19:883-887 Published Online First: 12 May 2012 doi:10.1136/amiajnl-2011-000774.  PMC3422832.
  • Hong-Jie Dai, Chun-Yu Chen, Chi-Yang Wu, Po-Ting Lai, Richard Tzong-Han Tsai, Wen-Lian Hsu. Coreference resolution of medical concepts in discharge summaries by exploiting contextual information. J Am Med Inform Assoc 2012 Sept-Oct;19:888-896 Published Online First: 3 May 2012 doi:10.1136/amiajnl-2012-000808.   PMC3422837.
  • Yan Xu, Jiahua Liu, Jiajun Wu, Yue Wang, Zhuowen Tu, Jian-Tao Sun, Junichi Tsujii, Eric I-Chao Chang. A classification approach to coreference in discharge summaries: 2011 i2b2 challenge. J Am Med Inform Assoc 2012 Sept-Oct;19:897-905 Published Online First: 13 April 2012 doi:10.1136/amiajnl-2011-000734.  PMC3422828.
  • Prateek Jindal, Dan Roth. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives.  J Am Med Inform Assoc 2013 Mar-Apr;20(2):356-362; amiajnl-2011-000767Published Online First: 10 July 2012 doi:10.1136/amiajnl-2011-000767.  PMC3638172.
  • Chen P, Hinote D, Chen G.  A rule based solution to the co-reference resolution in clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):891-7.PMC3756251.
  • Sohn S. Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H.   Comprehensive temporal information detection from clinical text: medical events, time and TLINK identification.  J Am Med Inform Assooc. 2013 Sep-Oct;20(5):836-42.  PMC37565269.

 

From the Sixth NLP Challenge (2012: Temporal Relations)

  • Xu Y, Wang Y, Liu T, Tsujii J, Chang El.  An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 Challenge.   J Am Med Inform Assoc. 2013 Sep-Oct;20(5):849-58.  PMC3756267.
  • Cherry C, Zhu X, Martin J, deBruijn B.  A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP Challenge.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):843-8.  PMC3756270.
  • Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H.   Comprehensive temporal information detection from clinical text: medical events, time and TLINK identification.  J Am Med Inform Assooc. 2013 Sep-Oct;20(5):836-42.  PMC37565269.
  • Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H.  A hybrid system for temporal information extraction from clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):828-36.  PMC3756274.
  • Grouin C, Grabar N, Hamon T, Rosset S, Tannier X, Zweigenbraum P.Eventual situations for timeline extraction from clinical reports.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):820-7.   PMC3756272.
  • Kovacevic A, Dehghan A, Filannino M, Keane JA, Nenadic G.  Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives.   J Am Med Inform Assoc. 2013 Sep-Oct;20(5):859-66.  PMC3756271.
  • Roberts K, Rink B, Harabagiu SM.  A flexible framework for recognizing events, temporal expressions and temporal relations in clinical text.  J Am Med Inform Assoc. 2013 Sep-Oct;20(5):867-75.  PMC3756268.  
  • D'Souza J, Ng V.  Classifying temporal relations in clonical data: a hybrid, knowledge-rich approch.   J Biomed Inform. 2013 Dec;46 Suppl:S29-39.   PMC3855590.

 

Genomics: 

  • Wolfe CJ, Kohane IS, Butte AJ.  Systematic survey reveals general applicability of “guilt-by-association” within gene coexpression networks.  BMC Bioinformatics.  2005;6:227.    

  • Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane I, Park P.  Discovering statistically significant pathways in expression profiling studies.  Proc Natl Acad Sci USA.  2005;102(38)13544-9.

  • Lee S, Kohane I, Kasif S.  Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.  BMC Genomics.  2005;6:168.  PMID: 16309559.

  • Wu CH,  Kasif S.  GEMS: A web server for biclustering analysis of expression data.  Nucleic Acids Res. 2005;33:W596-9. 

  • Kryukov GV, Schmidt S, Sunyaev S.  Small fitness effect of mutations in highly conserved non-coding regions.  Human Mol Gen. 2005;4:2221-2229.

  • Rachlin J, Cohen DD, Cantor C, Kasif S. Biological context networks: a mosaic view of the interactome.  Nature/Embo Molecular Systems Biology. 2006; 2:1.

  • Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge.   Bioinformatics. 2006;22:2373-80. 

  • Inaoka H, Fukuoka Y, Kohane, I.  Evidence of spatially bound gene regulation in Mus musculus: Decreased gene expression proximal to microRNA genomic location.  Proc Natl Acad Sci. 2007;104(12)5020-5.

  • Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS et al.  Network-based analysis of affected biological processes in type 2 diabetes models.  PLoS Genet. 2007;3(6):e96. 

  • Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Human Gen.  2007;Apr;80(4):727-39.

  • Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed non-coding purifying selection in the human genome. Proc Natl Acad Sci. 2007;104(30):12410-5.

  • Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol. 2007;Dec;3(12):e254.

  • Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev  SR. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. Am J Hum Genet. 2007 Oct 19;81(6).

  • Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev  S, Stamatoyannopoulos  JA. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci USA. 2007;104(30):12410-5.

  • Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante  CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008;Feb 21;451(7181):994-7.   PMC2923434.

  • ENCODE Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.

  • Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio  LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007;80(4):779-91.

  • Allocco DJ, Song Q, Gibbons GH, Ramoni MF, Kohane IS. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms. BMC Genomics. 2007;8:68.

  • Dotan-Cohen, Melkman AA, Kasif S.  Hierarchical tree snipping: clustering guided by prior knowledge.  Bioinformatics.  2007;23(24):3335-42.

  • Liu M, Liberson A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S.  Network based analysis of affected biological processes in type 2 diabetes models.  PLoS Genet.  2007;3(6):e96.   PMC

  • Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos  CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet. 2008;82(1):100-12.   PMC2253956.

  • Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS.  Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers.  Genome Biol. 2008;9(7):R108.  PMC2530866.

  • Beckstead WA, Bjork BC, Stottmann RW, Sunyaev S, Beier DR.  SNP2RFLP: Mammal. Genome. A computational tool to facilitate genetic mapping using benchtop analysis of SNPs. 2008; Oct-Dec;19(10-12):687-90.   PMC3001109.

  • Boyko A, Hernandez R, Schmidt S, Sunyaev S, Nielsen R, Clark A, Bustamante C. Assessing the evolutionary impact of amino acid mutations in the human genome.  PLoS Genet. 2008;4(5)e1000083.   PMC2377339.

  • Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, Sunyaev S.   Hypermutable non-synonymous sites are under stronger negative selection.  PLoS Genet. 2008;Nov;4(11):e1000281.  PMC 2583910.

  • Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.   Integration of relational and hierarchical network information for protein function prediction.  BMC Bioinformatics.  2008;9:350.   PMC2535605.

  • Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR.  Human mutation rate associated with DNA replication timing.  Nat Genet. 2009;Apr;41(4):393-5.   PMC2914101.

  • Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci USA. 2009;Mar 10;106(10):3871-6.   PMC2656172.

  • Davis A, Kohane I.  Expression differences by continent of origin point to the immortalization process.   Human Molecular Genetics 2009;18(20):3864-75.   PMC2748894.

  • Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M, Berger B, et al. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood. PLoS ONE. 2009;4(4):e5157. PMC2668177/

  • Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics.  2009;25:3121-7, 2009.   PMC 2778339.

  • Dreyfuss JD, Johnson MD, Park PJ. Meta-analysis of Glioblastoma multiforme versus Anaplastic astrocytoma identifies robust gene markers.  Molecular Cancer.  2009;8:71. PMC

  • Pihlajamäki 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 Endocrinol Metab. 2009;94:3521-9.   PMC 2743637.

  • Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade B, Lynch AM, Stewart EA, Morton CC. Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis. Genes, Chromosomes, & Cancer. 2009;48:865-85.   PMC 2778251.

  • Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M.  PLos One.  2009;4(11):e7994.  PMC2777383.

  • Molla M, Delcher A, Sunyaev S, Cantor C, Kasif S.  Proc Natl Acad Sci USA.  2009;106(40):17095-100. PMC

  • Dotan-Cohen D, Kasif S, Melkman AA.  Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering.  Bioinformatics.  2009;25(14):1789-95.  PMC2705235.

  • Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S.  Biological process linkage networks.  PLoS One.  2009;4(4):e5313.  PMID:19390589.   PMC2669181.

  • Kohane, IS.  Using electronic health records to drive discovery in disease genomics.  Nature Review Genetics.  2011;12:417-428.  doi:10.1038/nrg2999.  PMC

  • Kohane IS, Shendure J.  What’s a Genome Worth?  Sci Transl Med. 2012 May 9;4(133):133fs13.  PMID:22572879.
  • 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.   PMC3326474.
  • 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.  PMC3597341.
  • 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.  PMC3821385.
  • Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IS, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, deBakker PIW, Duzkale H, Dworzyski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M.  An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical geniome sequencing results in the CLARITY Challenge.  Genome Bio.  2014;15:R53. PMC4073084.

Genomics Tools: 

  • Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R.  Ggtools: analysis of genetics of gene expression in Bioconductor. Bioinformatics. 2007;23(4):522-523. 

  • Carey V, Davis A, Lawrence M, Gentleman R, Raby B.  Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.  Bioinformatics 2009;25(11)1447-8. doi:10.1093/bioinformatics/btp169.  PMC2682516.

  • Nuzzo A, Riva A.  Genephony: a knowledge management tool for genome-wide research.  BMC Informatics. 2009;10:278. PMC2744709.

Protein and DNA Biophysics: 

  • Kolesov G, Mirny LA.  Using evolutionary information to find specificity determining and co-evolving residues.  In Computational Systems Biology, Humana Press, 2007.

  • Kolesov G, Virnau P, Kardar M, Mirny LA.  Protein knot server: detection of knots in protein structures.  Nucleic Acids Research 2007;35(10)W425-8.

  • Kolesov G, Mirny LA. Using evolutionary information to find specificity determining and co-evolving residues, In Computational Systems Biology, edited by Jason Mcdermott, Springer-Verlag New York Inc, 2008

  • Galan-Caridad JM, Harel S., Arenzana TL, Hou ZE, Doetsch FK, Mirny LA, Reizis B.  Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell. 2007; 129(2):345-57.  PMC1899089.

  • Kolesov G, Wunderlich Z, Laikova O., Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci. 2007;104(35):13948-53.  PMC1955771.

  • Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol. 2007;3(12):e246.  PMC2230677.

  • Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, van Oijen AM. Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys J. 2008;95(1):L01-2.

  • Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.  Integration of relational and hierarchical network information for protein function prediction.  BMC Bioinformatics. 2008; 9:350. PMC2535605.

  • Rahi SJ, Virnau P, Mirny LA, Kardar M. Predicting transcription factor specificity with all-atom models. Nucleic Acids Res. 2008;36(19):6209-17. PMC2577325.

  • Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res. 2008;6(11):3570-8.   PMC2441786

  • Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions, Nucleic Acids Res. 2009 August;38(14):4629-4641. PMC2724268.

  • Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Bio. 2009;541:421-48.  PMID:19381538. 

  • Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science.  2009;326(5950):289-93.

  • 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.   PMC3697852.

  • 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. 42 No 

  • 43 (30 October 2009) 434013.

  • 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.  PMC2858594.

  • Wunderlich Z, Mirny LA. An optimized energy potential can predict domain-peptide interactions.  Nucleic Acids Res.  2009;7:1-13

  • 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.  doi:10.1371.journal.pone.0019800.   PMC3098838.

From the Asthma DBP: 

  • Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus, R.  Extracting principal diagnosis, co-morbidity and smoking status for asthma research: Evaluation of a natural language processing system.  BMC Med Inform and Med Decision Making. 2006;6:30.
  • 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.  PMC2732240.
  • Himes BE, Kohane IS, Ramoni MF, Weiss ST.  Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records.  AMIA Annu Symp Proc.  2008 Nov 6; 308-12.   PMC2655929.
  • Himes BE, Klanderman B, Kohane IS, Weiss .T.   Assessing the reproducibility of asthma genome-wide association studies in a general clinical population.  J Allergy Clin Immunol.  2011 Apr;127(4):1067-9.   PMID21269672.

From the Huntington’s Disease DBP: 

  • Gusella JF, Macdonald ME.  Huntington's disease: seeing the pathogenic process through a genetic lens. Trends Biochem Sci. 2006;Sep;31(9):533-40.  PMID:16829072.
  • Lee JM, Ivanova EV, Seong IS, Cashorali T, Kohane I, Gusella JF, MacDonald ME.  Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet. 2007;3(8):e135.  PMC19050164.
  • Gusella JF, Macdonald M.  Genetic criteria for Huntington's disease pathogenesis. Brain Res Bull. 2007;Apr 30;72(2-3):78-82. PPMID:17352930.
  • 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;20(14):2846-60.  Epub 2011 May 2.  PMC3118763.
  • 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 cerebullum are quantitative not qualitative.  Hum Mol Genet.  2011;20(21):4258-67.   PMC3188996.

From the Diabetes DBP: 

  • Liu M, Liberzon A, Kong SW, Weil RL, Park PJ, Kohane IS, Kasif S.  Network-based analysis of affected biological processes in Type 2 diabetes models.  PLoS Genetics. 2007;3:0001-0015. doi:10.1371/journal.pgen.0030096.

  • 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.   PMC2671035.

  • 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.   PMC2741713

  • Doria A, Patti ME, Kahn CR.  The emerging genetic architecture of type 2 diabetes.  Cell Metabolism 2008;8(3); 186-200.

  • Pihlajamaki J, Itkonen P, Crunkhorn S, Vänttinen M, Dearie F, Boes T, Jimenez-Chillaron J, Lappalainen T, Miettinen P, Park P, Nasser I, Goldfine AB, Laakso M, Patti ME.  Expression of splicing factor genes is reduced in human obesity:  links to altered Lipin 1 splicing and enhanced lipogenesis.  Cell Metabolism 2011 August 3; 14(2): 208-218.  PMC3167228.

  • Jin W, Patti ME.  Genetic determinants and molecular pathways in the pathogenesis of diabetes.  Clinical Science. 2009;116 (2):  99-111. PMID:19076063.

  • Patti ME, Corvera S.  The role of mitochondria in the pathogenesis of Type 2 Diabetes.  Endocrine Reviews 2010 June; 31(3):364-395.   PMC3365846.

From the Rheumatoid Arthritis DBP: 

  • 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. PMC

  • 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(1):57-69.   PMC3014362.

  • 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.   PMC3392871.
  • Liao KP, Diogo D, Gui J, Cai T, Okada Y, Gainer V, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovitz P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM.  The association between low density lipoprotein (LDL) and RA genetic factors with LDL levels in rheumatoid arthritis and non-RA controls.  Ann Rheum Dis 2014;73:1170-5.  PMC3815491.
  • Liao KP, Diogo D, Cui J, Cai T, Okada Y, Gainer VS, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovits P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM. 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. PMC3815491.
  • Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis Rheum. 2013 Mar;65(3):571-81. PMC3582761.
  • Lin C , Karlson EW, Canhao H, Miller TA, Dligach D, et al. 2013. Automatic prediction of rheumatoid arthritis disease activity from the Electronic Medical Records. PLoS One.  2013;8(8):e69932. PMC3745469
  • Liao KP, Cai T, Gainer VS, Cagan A, Murphy SN, Liu C, Churchill S, Shaw SY, Kohane I, Solomon DH, Plenge RM, Karlson EW. Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population. Arthritis Care Res (Hoboken) 2013 Dec;65(12):2046-50. PMC4060244.

From the Major Depressive Disorder DBP:

  • 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.  PMC3827420.
  • 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.  PMC3330255.
  • Hoogenboom WS, Perlis RH, Smoller JW, Zeng0-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, 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.
  • 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 repressive risorder exposed to NSAIDS: a pharmacovigilance study.  Am J Psychiatry 2012 Oct; 169 (10):1062-72.  PMC 3787520
  • Hoogenboom WS, Perlis RH, smoller JW, Zeng0Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV.  Feasibility of styding brain morphology in major depressive disorder with structural magnetic resonance imagine and clinical data from the electronic medical record: A pilot study.  Psych Res 2013 Mar 30; 211(3):202-213.   PMC3574623.
  • 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.  PMC3837420.
  • 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.  PMC3330255.
  • 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 Jan 29;346:f288. PMC3558546. (Collaboration with previous Major Depressive Disorder DBP team on work sponsored by a follow on grant that used the original virtual cohort developed by the i2b2 team).
  • Castro V, Minnier J, Murphy S, Kohane I, ChurchillS, Gainer V, Cai T, Hoffnagle A, Dai Y, Block S, Weill S, Nadal-Vicens M, Pollastri A, Rosenquist J, Goryachev S, Ongur D, Sklar P, Perlis R, Smoller J.  Validation of electronic health record phenotyping of bipolar disorder cases and controls.  Am J Psychiatry.  2014;; AiA:1-10; doi:10.1176/appi.ajp.2014.14030423.

From the Inflammatory Bowel Disease DBP:

  • 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.  PMC3716251.
  • Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP. Normalization of plasma 25-hydroxy vitamin D Is associated with reduced risk of surgery in Crohn's disease. Inflamm Bowel Dis. 2013 Jun 7.  PMC3720838.
  • Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP.  Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. Aliment Pharmacol Ther. 2013 Feb;37(4):445-54.  PMC3552092.
  • Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP. Improving  case definition of Crohn's disease and ulcerative colitis in electronic medical records using Natural Language Processing: A novel informatics approach.  Inflamm Bowel Dis. 2013 Jun;19(7):1411-1420. PMC3665760.
  • 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 Apr;108(4):594-601. PMC3627544.
  • Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Higher plasma vitamin D is associated with reduced risk of clostridium difficile infection in patients with inflammatory bowel diseases.  Aliment Pharmacol Ther. 2014 May;39(10):1136-42. PMC4187206.
  • Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Scoville E, Lonijeti GG, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 Mar 12.pii:S1542-3565(14)00359-0.  PMC4162859.
  • Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.  J Crohns Colitis.  2014 Feb 18.pii:S1873-9946(14)00038-5.  PMC4136996.
  • Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 Aug;12(8):1342-48.e1.  PMC4085150.
  • Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases.  Clin Gastroenterol Hepatol.  2014 May;12(5):821-7.  PMC3995841.
  • Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.  Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel disease.  Clin Gastroenterol Hepatol. 2014 July 17;PubMed PMID: 25041865:NIHMSID:615037.  [Epub ahead of print]
  • Ananthakrishnan AN, Cheng A, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.   Mode of childbirth and long-term outcomes in women with inflammatory bowel diseases.   Dig Dis Sci. 2014 Sept 12;PubMed PMID: 25213079; NIHMSID:627958.  [Epub ahead of print]

From the Multiple Sclerosis DBP:

  • Xia Z, Secor E, Chibnik L, Bove R, Cheng S, Chitnis T, Cagan A, Gainer V, Pei C, Liao K, Shaw S, Ananthakrishnan A, Szolovits P, Weinter H, Karlson E, Murphy S, Savova G, Cai T, Churchill S, Plenge R, Kohane I, De Jager P.  Modeling disease severity in multiple sclerosis using electronic health records.  PLoS One.  2013;8(11):e78927.  PMC3823928.
[ back to top ]
Home | Contact | Sitemap | Search
©2015 Partners Healthcare