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Keywords
Last Name
Institution

Isaac Samuel Kohane, M.D.,Ph.D.

TitleLawrence J. Henderson Professor of Pediatrics
InstitutionChildren's Hospital Boston
DepartmentPediatrics
AddressChildrens Hospital
Informatics Program
300 Longwood Ave
Boston MA 02115
Phone617/919-2182
Fax206/333-1182
Other Positions
TitleDirector, Countway Library of Medicine
InstitutionHarvard Medical School
DepartmentCountway Library of Medicine

TitleAssociate Professor of Medicine
InstitutionBrigham and Women's Hospital
DepartmentMedicine
DivisionChanning Division of Network Medicine


 Research 
 research resources
This researcher has shared information about their research resources
in the eagle-i Network. To update or add resource records, contact
eagle-i@hms.harvard.edu.
Children's Hospital Informatics Program - Core services (1) and Software (6)

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Kolker E, Ozdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS. 2014 Jan; 18(1):10-4.
    View in: PubMed
  2. Doshi-Velez F, Ge Y, Kohane I. Comorbidity clusters in autism spectrum disorders: an electronic health record time-series analysis. Pediatrics. 2014 Jan; 133(1):e54-63.
    View in: PubMed
  3. Namjou B, Keddache M, Marsolo K, Wagner M, Lingren T, Cobb B, Perry C, Kennebeck S, Holm IA, Li R, Crimmins NA, Martin L, Solti I, Kohane IS, Harley JB. EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children. Front Genet. 2013; 4:268.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL. Modeling disease severity in multiple sclerosis using electronic health records. PLoS One. 2013; 8(11):e78927.
    View in: PubMed
  6. Manrai AK, Kohane IS, Szolovits P. Urinary-cell mRNA and acute kidney-transplant rejection. N Engl J Med. 2013 Nov 7; 369(19):1859.
    View in: PubMed
  7. Zimolzak AJ, Spettell CM, Fernandes J, Fusaro VA, Palmer NP, Saria S, Kohane IS, Jonikas MA, Mandl KD. Early detection of poor adherers to statins: applying individualized surveillance to pay for performance. PLoS One. 2013; 8(11):e79611.
    View in: PubMed
  8. Kohane IS, Eran A. Can we measure autism? Sci Transl Med. 2013 Oct 30; 5(209):209ed18.
    View in: PubMed
  9. Kohane IS. Secondary use of health information: are we asking the right question? JAMA Intern Med. 2013 Oct 28; 173(19):1806-7.
    View in: PubMed
  10. McMurry AJ, Fitch B, Savova G, Kohane IS, Reis BY. Improved de-identification of physician notes through integrative modeling of both public and private medical text. BMC Med Inform Decis Mak. 2013; 13:112.
    View in: PubMed
  11. Campbell MG, Kohane IS, Kong SW. Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome. BMC Med Genomics. 2013; 6:34.
    View in: PubMed
  12. Overby CL, Kohane I, Kannry JL, Williams MS, Starren J, Bottinger E, Gottesman O, Denny JC, Weng C, Tarczy-Hornoch P, Hripcsak G. Opportunities for genomic clinical decision support interventions. Genet Med. 2013 Oct; 15(10):817-23.
    View in: PubMed
  13. 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 Aug; 19(9):1921-7.
    View in: PubMed
  14. Bosl W, Mandel J, Jonikas M, Ramoni RB, Kohane IS, Mandl KD. Scalable decision support at the point of care: a substitutable electronic health record app for monitoring medication adherence. Interact J Med Res. 2013; 2(2):e13.
    View in: PubMed
  15. Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, Crosslin D, Denny JC, Gallego CJ, Haines JL, Hakonarson H, Harley J, Jarvik GP, Kohane I, Kullo IJ, Larson EB, McCarty C, Ritchie MD, Roden DM, Smith ME, Böttinger EP, Williams MS. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med. 2013 Oct; 15(10):761-71.
    View in: PubMed
  16. 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):1411-20.
    View in: PubMed
  17. Weber GM, Kohane IS. Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS One. 2013; 8(5):e64933.
    View in: PubMed
  18. Kong SW, Shimizu-Motohashi Y, Campbell MG, Lee IH, Collins CD, Brewster SJ, Holm IA, Rappaport L, Kohane IS, Kunkel LM. Peripheral blood gene expression signature differentiates children with autism from unaffected siblings. Neurogenetics. 2013 May; 14(2):143-52.
    View in: PubMed
  19. Lee JM, Galkina EI, Levantovsky RM, Fossale E, Anne Anderson M, Gillis T, Srinidhi Mysore J, Coser KR, Shioda T, Zhang B, Furia MD, Derry J, Kohane IS, Seong IS, Wheeler VC, Gusella JF, Macdonald ME. Dominant effects of the Huntington's disease HTT CAG repeat length are captured in gene-expression data sets by a continuous analysis mathematical modeling strategy. Hum Mol Genet. 2013 Aug 15; 22(16):3227-38.
    View in: PubMed
  20. Chute CG, Kohane IS. Genomic medicine, health information technology, and patient care. JAMA. 2013 Apr 10; 309(14):1467-8.
    View in: PubMed
  21. 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.
    View in: PubMed
  22. Kohane IS. Automating the study of population variation of electrocardiographic features. Circulation. 2013 Apr 2; 127(13):1357-8.
    View in: PubMed
  23. 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.
    View in: PubMed
  24. Altman RB, Clayton EW, Kohane IS, Malin BA, Roden DM. Data re-identification: societal safeguards. Science. 2013 Mar 1; 339(6123):1032-3.
    View in: PubMed
  25. Castro VM, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. QT interval and antidepressant use: a cross sectional study of electronic health records. BMJ. 2013; 346:f288.
    View in: PubMed
  26. 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.
    View in: PubMed
  27. 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.
    View in: PubMed
  28. Kohane IS, Drazen JM, Campion EW. A glimpse of the next 100 years in medicine. N Engl J Med. 2012 Dec 27; 367(26):2538-9.
    View in: PubMed
  29. Kong SW, Collins CD, Shimizu-Motohashi Y, Holm IA, Campbell MG, Lee IH, Brewster SJ, Hanson E, Harris HK, Lowe KR, Saada A, Mora A, Madison K, Hundley R, Egan J, McCarthy J, Eran A, Galdzicki M, Rappaport L, Kunkel LM, Kohane IS. Characteristics and predictive value of blood transcriptome signature in males with autism spectrum disorders. PLoS One. 2012; 7(12):e49475.
    View in: PubMed
  30. Saxena V, Ramdas S, Ochoa CR, Wallace D, Bhide P, Kohane I. Structural, genetic, and functional signatures of disordered neuro-immunological development in autism spectrum disorder. PLoS One. 2012; 7(12):e48835.
    View in: PubMed
  31. 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.
    View in: PubMed
  32. Wattanasin N, Porter A, Ubaha S, Mendis M, Phillips L, Mandel J, Ramoni R, Mandl K, Kohane I, Murphy SN. Apps to display patient data, making SMART available in the i2b2 platform. AMIA Annu Symp Proc. 2012; 2012:960-9.
    View in: PubMed
  33. Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R. Next-generation sequencing in the clinic: are we ready? Nat Rev Genet. 2012 Nov; 13(11):818-24.
    View in: PubMed
  34. Uno H, Tian L, Cai T, Kohane IS, Wei LJ. A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data. Stat Med. 2013 Jun 30; 32(14):2430-42.
    View in: PubMed
  35. 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 patients with major depression exposed to NSAIDs: a pharmacovigilance study. Am J Psychiatry. 2012 Oct; 169(10):1065-72.
    View in: PubMed
  36. Masys DR, Harris PA, Fearn PA, Kohane IS. Designing a public square for research computing. Sci Transl Med. 2012 Aug 29; 4(149):149fs32.
    View in: PubMed
  37. Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS, Kunkel LM. Comparative RNA editing in autistic and neurotypical cerebella. Mol Psychiatry. 2013 Sep; 18(9):1041-8.
    View in: PubMed
  38. Mandl KD, Kohane IS. Escaping the EHR trap--the future of health IT. N Engl J Med. 2012 Jun 14; 366(24):2240-2.
    View in: PubMed
  39. Mandl KD, Khorasani R, Kohane IS. Meaningful use of electronic health records. Health Aff (Millwood). 2012 Jun; 31(6):1365.
    View in: PubMed
  40. Kohane IS, Shendure J. What's a Genome Worth? Sci Transl Med. 2012 May 9; 4(133):133fs13.
    View in: PubMed
  41. Kohane IS, McMurry A, Weber G, MacFadden D, Rappaport L, Kunkel L, Bickel J, Wattanasin N, Spence S, Murphy S, Churchill S. The co-morbidity burden of children and young adults with autism spectrum disorders. PLoS One. 2012; 7(4):e33224.
    View in: PubMed
  42. Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G, Byrne EM, Blackwood DH, Boomsma DI, Cichon S, Heath AC, Holsboer F, Lucae S, Madden PA, Martin NG, McGuffin P, Muglia P, Noethen MM, Penninx BP, Pergadia ML, Potash JB, Rietschel M, Lin D, Müller-Myhsok B, Shi J, Steinberg S, Grabe HJ, Lichtenstein P, Magnusson P, Perlis RH, Preisig M, Smoller JW, Stefansson K, Uher R, Kutalik Z, Tansey KE, Teumer A, Viktorin A, Barnes MR, Bettecken T, Binder EB, Breuer R, Castro VM, Churchill SE, Coryell WH, Craddock N, Craig IW, Czamara D, De Geus EJ, Degenhardt F, Farmer AE, Fava M, Frank J, Gainer VS, Gallagher PJ, Gordon SD, Goryachev S, Gross M, Guipponi M, Henders AK, Herms S, Hickie IB, Hoefels S, Hoogendijk W, Hottenga JJ, Iosifescu DV, Ising M, Jones I, Jones L, Jung-Ying T, Knowles JA, Kohane IS, Kohli MA, Korszun A, Landen M, Lawson WB, Lewis G, Macintyre D, Maier W, Mattheisen M, McGrath PJ, McIntosh A, McLean A, Middeldorp CM, Middleton L, Montgomery GM, Murphy SN, Nauck M, Nolen WA, Nyholt DR, O'Donovan M, Oskarsson H, Pedersen N, Scheftner WA, Schulz A, Schulze TG, Shyn SI, Sigurdsson E, Slager SL, Smit JH, Stefansson H, Steffens M, Thorgeirsson T, Tozzi F, Treutlein J, Uhr M, van den Oord EJ, Van Grootheest G, Völzke H, Weilburg JB, Willemsen G, Zitman FG, Neale B, Daly M, Levinson DF, Sullivan PF. A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry. 2013 Apr; 18(4):497-511.
    View in: PubMed
  43. 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, Terry SF, Wilfond 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.
    View in: PubMed
  44. Castro VM, Gallagher PJ, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants. BMJ Open. 2012; 2(2):e000544.
    View in: PubMed
  45. Schmid PR, Palmer NP, Kohane IS, Berger B. Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci U S A. 2012 Apr 10; 109(15):5594-9.
    View in: PubMed
  46. 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 Jul-Aug; 19(4):597-603.
    View in: PubMed
  47. Ananthakrishnan AN, Guzman-Perez R, Gainer V, Cai T, Churchill S, Kohane I, Plenge RM, Murphy S. Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease. Aliment Pharmacol Ther. 2012 Apr; 35(7):789-95.
    View in: PubMed
  48. Kohane IS, Hsing M, Kong SW. Taxonomizing, sizing, and overcoming the incidentalome. Genet Med. 2012 Apr; 14(4):399-404.
    View in: PubMed
  49. Kohane IS. Interview with Isaac S. Kohane conducted by Sarah Miller. Pharmacogenomics. 2012 Feb; 13(3):257-60.
    View in: PubMed
  50. Kohane IS. (Mis)treating the pharmacogenetic incidentalome. Nat Rev Drug Discov. 2012 Feb; 11(2):89-90.
    View in: PubMed
  51. Kohane IS, Valtchinov VI. Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. Bioinformatics. 2012 Feb 15; 28(4):538-45.
    View in: PubMed
  52. Masys DR, Jarvik GP, Abernethy 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.
    View in: PubMed
  53. Jung JY, Kohane IS, Wall DP. Identification of autoimmune gene signatures in autism. Transl Psychiatry. 2011; 1:e63.
    View in: PubMed
  54. 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. PLoS One. 2011; 6(11):e27156.
    View in: PubMed
  55. 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 Mar-Apr; 19(2):181-5.
    View in: PubMed
  56. 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.
    View in: PubMed
  57. Kohane IS. No small matter: qualitatively distinct challenges of pediatric genomic studies. Genome Med. 2011; 3(9):62.
    View in: PubMed
  58. 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.
    View in: PubMed
  59. Helman E, Naxerova K, Kohane IS. DNA hypermethylation in lung cancer is targeted at differentiation-associated genes. Oncogene. 2012 Mar 1; 31(9):1181-8.
    View in: PubMed
  60. Tian Z, Shen J, Wang F, Xiao P, Yang J, Lei H, Kazlauskas A, Kohane IS, Wu E. Cambogin is preferentially cytotoxic to cells expressing PDGFR. PLoS One. 2011; 6(6):e21370.
    View in: PubMed
  61. 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.
    View in: PubMed
  62. Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Tsau PS, Kohane I, Roden DM, Altman RB. Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Clin Pharmacol Ther. 2011 Jul; 90(1):133-42.
    View in: PubMed
  63. Alexandrov BS, Valtchinov VI, Alexandrov LB, Gelev V, Dagon Y, Bock J, Kohane IS, Rasmussen KØ, 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.
    View in: PubMed
  64. Kohane IS. Using electronic health records to drive discovery in disease genomics. Nat Rev Genet. 2011 Jun; 12(6):417-28.
    View in: PubMed
  65. Jacobsen JC, Gregory GC, Woda 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.
    View in: PubMed
  66. Kohane IS, Szolovits P. Marco Ramoni: an appreciation of academic achievement. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):367-9.
    View in: PubMed
  67. Kohane IS, Margulies DM. Counterpoint: Do not opine before it's time. Nat Biotechnol. 2011 Mar; 29(3):218-9.
    View in: PubMed
  68. Ferrazzi F, Engel FB, Wu E, Moseman AP, Kohane IS, Bellazzi R, Ramoni MF. Inferring cell cycle feedback regulation from gene expression data. J Biomed Inform. 2011 Aug; 44(4):565-75.
    View in: PubMed
  69. 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.
    View in: PubMed
  70. Tong MY, Cassa CA, Kohane IS. Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. Bioinformatics. 2011 Mar 15; 27(6):891-3.
    View in: PubMed
  71. 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 RM. Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Am J Hum Genet. 2011 Jan 7; 88(1):57-69.
    View in: PubMed
  72. Lee K, Brownstein JS, Mills RG, Kohane IS. Does collocation inform the impact of collaboration? PLoS One. 2010; 5(12):e14279.
    View in: PubMed
  73. Schachter AD, Kohane IS. Drug target-gene signatures that predict teratogenicity are enriched for developmentally related genes. Reprod Toxicol. 2011 May; 31(4):562-9.
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  74. Adida B, Sanyal A, Zabak S, Kohane IS, Mandl KD. Indivo x: developing a fully substitutable personally controlled health record platform. AMIA Annu Symp Proc. 2010; 2010:6-10.
    View in: PubMed
  75. Liao KP, Cai T, Gainer V, Goryachev S, Zeng-treitler Q, Raychaudhuri S, Szolovits P, Churchill S, Murphy S, Kohane I, Karlson EW, Plenge RM. Electronic medical records for discovery research in rheumatoid arthritis. Arthritis Care Res (Hoboken). 2010 Aug; 62(8):1120-7.
    View in: PubMed
  76. Kohane IS, Taylor PL. Multidimensional results reporting to participants in genomic studies: getting it right. Sci Transl Med. 2010 Jun 23; 2(37):37cm19.
    View in: PubMed
  77. Lee JM, Zhang J, Su AI, Walker JR, Wiltshire T, Kang K, Dragileva E, Gillis T, Lopez ET, Boily MJ, Cyr M, Kohane I, Gusella JF, MacDonald ME, Wheeler VC. A novel approach to investigate tissue-specific trinucleotide repeat instability. BMC Syst Biol. 2010; 4:29.
    View in: PubMed
  78. Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc. 2010 Mar-Apr; 17(2):124-30.
    View in: PubMed
  79. Brownstein JS, Murphy SN, Goldfine AB, Grant RW, Sordo M, Gainer V, Colecchi JA, Dubey A, Nathan DM, Glaser JP, Kohane IS. Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records. Diabetes Care. 2010 Mar; 33(3):526-31.
    View in: PubMed
  80. Roach KL, King KR, Uygun BE, Kohane IS, Yarmush ML, Toner M. High throughput single cell bioinformatics. Biotechnol Prog. 2009 Nov-Dec; 25(6):1772-9.
    View in: PubMed
  81. Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ. Transcriptomic analysis of human lung development. Am J Respir Crit Care Med. 2010 Jan 1; 181(1):54-63.
    View in: PubMed
  82. Reis BY, Kohane IS, Mandl KD. Longitudinal histories as predictors of future diagnoses of domestic abuse: modelling study. BMJ. 2009; 339:b3677.
    View in: PubMed
  83. 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 Dec 1; 25(23):3121-7.
    View in: PubMed
  84. Davis AR, Kohane IS. Expression differences by continent of origin point to the immortalization process. Hum Mol Genet. 2009 Oct 15; 18(20):3864-75.
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  85. Murphy S, Churchill S, Bry L, Chueh H, Weiss S, Lazarus R, Zeng Q, Dubey A, Gainer V, Mendis M, Glaser J, Kohane I. Instrumenting the health care enterprise for discovery research in the genomic era. Genome Res. 2009 Sep; 19(9):1675-81.
    View in: PubMed
  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 Sep-Oct; 16(5):624-30.
    View in: PubMed
  87. Oriol NE, Cote PJ, Vavasis AP, Bennet J, Delorenzo D, Blanc P, Kohane I. Calculating the return on investment of mobile healthcare. BMC Med. 2009; 7:27.
    View in: PubMed
  88. Liu H, Kohane IS, Kohane IS. Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy. PLoS One. 2009; 4(5):e5436.
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  89. Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M, Berger B, Wu E, Kohane IS. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood. PLoS One. 2009; 4(4):e5157.
    View in: PubMed
  90. Eran A, Graham KR, Vatalaro K, McCarthy J, Collins C, Peters H, Brewster SJ, Hanson E, Hundley R, Rappaport L, Holm IA, Kohane IS, Kunkel LM. Comment on "Autistic-like phenotypes in Cadps2-knockout mice and aberrant CADPS2 splicing in autistic patients". J Clin Invest. 2009 Apr; 119(4):679-80; author reply 680-1.
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  91. Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009 Mar 26; 360(13):1278-81.
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  92. Roach KL, King KR, Uygun K, Hand SC, Kohane IS, Yarmush ML, Toner M. High-throughput single cell arrays as a novel tool in biopreservation. Cryobiology. 2009 Jun; 58(3):315-21.
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  93. 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 May-Jun; 16(3):371-9.
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  94. Kohane IS. The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med. 2009; 1(1):4.
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  95. Kohane I. Ten thousand views of bioinformatics: a bibliome perspective. Yearb Med Inform. 2009; 113-6.
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  96. Wu E, Palmer N, Tian Z, Moseman AP, Galdzicki M, Wang X, Berger B, Zhang H, Kohane IS. Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells. PLoS One. 2008; 3(11):e3794.
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  97. Wall DP, Esteban FJ, Deluca TF, Huyck M, Monaghan T, Velez de Mendizabal N, Goñí J, Kohane IS. Comparative analysis of neurological disorders focuses genome-wide search for autism genes. Genomics. 2009 Feb; 93(2):120-9.
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  98. Mendis M, Phillips LC, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc. 2008; 1054.
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  99. 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; 308-12.
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  100. Tian Z, An N, Zhou B, Xiao P, Kohane IS, Wu E. Cytotoxic diarylheptanoid induces cell cycle arrest and apoptosis via increasing ATF3 and stabilizing p53 in SH-SY5Y cells. Cancer Chemother Pharmacol. 2009 May; 63(6):1131-9.
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  101. Kho AT, Bhattacharya S, Mecham BH, Hong J, Kohane IS, Mariani TJ. Expression profiles of the mouse lung identify a molecular signature of time-to-birth. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):47-57.
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  102. Cassa CA, Schmidt B, Kohane IS, Mandl KD. My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics. 2008; 1:32.
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  103. 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.
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  104. 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.
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  105. Mandl KD, Kohane IS. Tectonic shifts in the health information economy. N Engl J Med. 2008 Apr 17; 358(16):1732-7.
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  106. Tian Z, Shen J, Moseman AP, Yang Q, Yang J, Xiao P, Wu E, Kohane IS. Dulxanthone A induces cell cycle arrest and apoptosis via up-regulation of p53 through mitochondrial pathway in HepG2 cells. Int J Cancer. 2008 Jan 1; 122(1):31-8.
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  107. Levine M, Adida B, Mandl K, Kohane I, Halamka J. What are the benefits and risks of fitting patients with radiofrequency identification devices. PLoS Med. 2007 Nov 27; 4(11):e322.
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  108. Saxena V, Orgill D, Kohane I. A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. BMC Genomics. 2007; 8:430.
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  109. Uzuner O, Goldstein I, Luo Y, Kohane I. Identifying patient smoking status from medical discharge records. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):14-24.
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  110. Eisenberg I, Eran A, Nishino I, Moggio M, Lamperti C, Amato AA, Lidov HG, Kang PB, North KN, Mitrani-Rosenbaum S, Flanigan KM, Neely LA, Whitney D, Beggs AH, Kohane IS, Kunkel LM. Distinctive patterns of microRNA expression in primary muscular disorders. Proc Natl Acad Sci U S A. 2007 Oct 23; 104(43):17016-21.
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  111. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips LC, Gainer V, Berkowicz D, Glaser JP, Kohane I, Chueh HC. Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. AMIA Annu Symp Proc. 2007; 548-52.
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  112. Ramlawi B, Otu H, Rudolph JL, Mieno S, Kohane IS, Can H, Libermann TA, Marcantonio ER, Bianchi C, Sellke FW. Genomic expression pathways associated with brain injury after cardiopulmonary bypass. J Thorac Cardiovasc Surg. 2007 Oct; 134(4):996-1005.
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  113. Brownstein JS, Sordo M, Kohane IS, Mandl KD. The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarction. PLoS One. 2007; 2(9):e840.
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  114. Loscalzo J, Kohane I, Barabasi AL. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol. 2007; 3:124.
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  115. 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 Aug; 3(8):e135.
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  116. 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 Jun; 32(2):93-102.
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  117. Reis BY, Kohane IS, Mandl KD. An epidemiological network model for disease outbreak detection. PLoS Med. 2007 Jun; 4(6):e210.
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  118. Liu M, Liberzon 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 Jun; 3(6):e96.
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  119. Kohane IS, Mandl KD, Taylor PL, Holm IA, Nigrin DJ, Kunkel LM. Medicine. Reestablishing the researcher-patient compact. Science. 2007 May 11; 316(5826):836-7.
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  120. Drake TA, Braun J, Marchevsky A, Kohane IS, Fletcher C, Chueh H, Beckwith B, Berkowicz D, Kuo F, Zeng QT, Balis U, Holzbach A, McMurry A, Gee CE, McDonald CJ, Schadow G, Davis M, Hattab EM, Blevins L, Hook J, Becich M, Crowley RS, Taube SE, Berman J. A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network. Hum Pathol. 2007 Aug; 38(8):1212-25.
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  121. McMurry AJ, Gilbert CA, Reis BY, Chueh HC, Kohane IS, Mandl KD. A self-scaling, distributed information architecture for public health, research, and clinical care. J Am Med Inform Assoc. 2007 Jul-Aug; 14(4):527-33.
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  122. Inaoka H, Fukuoka Y, Kohane IS. Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):5020-5.
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  123. 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.
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  124. Patel AA, Gupta D, Seligson D, Hattab EM, Balis UJ, Ulbright TM, Kohane IS, Berman JJ, Gilbertson JR, Dry S, Schirripa O, Yu H, Becich MJ, Parwani AV. Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN). BMC Cancer. 2007; 7:37.
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  125. Cohen J, Van Marter LJ, Sun Y, Allred E, Leviton A, Kohane IS. Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia. Genome Biol. 2007; 8(10):R210.
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  126. Brownstein JS, Cassa CA, Kohane IS, Mandl KD. An unsupervised classification method for inferring original case locations from low-resolution disease maps. Int J Health Geogr. 2006; 5:56.
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  127. Saxena V, Orgill D, Kohane I. Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res. 2006; 34(22):e151.
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  128. Liu F, Park PJ, Lai W, Maher E, Chakravarti A, Durso L, Jiang X, Yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane I, Carroll RS, Black PM, Johnson MD. A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. Cancer Res. 2006 Nov 15; 66(22):10815-23.
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  129. Frank NY, Kho AT, Schatton T, Murphy GF, Molloy MJ, Zhan Q, Ramoni MF, Frank MH, Kohane IS, Gussoni E. Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin. J Cell Biol. 2006 Oct 9; 175(1):99-110.
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  130. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006 Sep; 38(9):1043-8.
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  131. Hung KE, Kho AT, Sarracino D, Richard LG, Krastins B, Forrester S, Haab BB, Kohane IS, Kucherlapati R. Mass spectrometry-based study of the plasma proteome in a mouse intestinal tumor model. J Proteome Res. 2006 Aug; 5(8):1866-78.
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  132. Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006 Jul 12; 296(2):212-5.
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  133. Liu H, Kho AT, Kohane IS, Sun Y. Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. PLoS Med. 2006 Jul; 3(7):e232.
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  134. Chu EK, Cheng J, Foley JS, Mecham BH, Owen CA, Haley KJ, Mariani TJ, Kohane IS, Tschumperlin DJ, Drazen JM. Induction of the plasminogen activator system by mechanical stimulation of human bronchial epithelial cells. Am J Respir Cell Mol Biol. 2006 Dec; 35(6):628-38.
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  135. Sebastiani P, Mandl KD, Szolovits P, Kohane IS, Ramoni MF. A Bayesian dynamic model for influenza surveillance. Stat Med. 2006 Jun 15; 25(11):1803-16; discussion 1817-25.
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  136. Gazda HT, Kho AT, Sanoudou D, Zaucha JM, Kohane IS, Sieff CA, Beggs AH. Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia. Stem Cells. 2006 Sep; 24(9):2034-44.
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  137. Adida B, Kohane IS. GenePING: secure, scalable management of personal genomic data. BMC Genomics. 2006; 7:93.
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  138. Turchin A, Guo CZ, Adler GK, Ricchiuti V, Kohane IS, Williams GH. Effect of acute aldosterone administration on gene expression profile in the heart. Endocrinology. 2006 Jul; 147(7):3183-9.
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  139. Kho AT, Kang PB, Kohane IS, Kunkel LM. Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes. BMC Musculoskelet Disord. 2006; 7:23.
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  140. Inaoka H, Fukuoka Y, Kohane IS. Lower expression of genes near microRNA in C. elegans germline. BMC Bioinformatics. 2006; 7:112.
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  141. Marinescu VD, Kohane IS, Kim TK, Harmin DA, Greenberg ME, Riva A. START: an automated tool for serial analysis of chromatin occupancy data. Bioinformatics. 2006 Apr 15; 22(8):999-1001.
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  142. Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan; 24(1):55-62.
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  143. Hackett KL, Kohane IS, Chueh HC, Murphy SN. Mapping tool for maintaining vocabulary relationships. AMIA Annu Symp Proc. 2006; 939.
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  144. Simons WW, Halamka JD, Kohane IS, Nigrin D, Finstein N, Mandl KD. Integration of the personally controlled electronic medical record into regional inter-regional data exchanges: a national demonstration. AMIA Annu Symp Proc. 2006; 1099.
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  145. Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh HC. Integration of clinical and genetic data in the i2b2 architecture. AMIA Annu Symp Proc. 2006; 1040.
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  146. 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.
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  147. Kohane IS, Altman RB. Health-information altruists--a potentially critical resource. N Engl J Med. 2005 Nov 10; 353(19):2074-7.
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  148. Haslett JN, Kang PB, Han M, Kho AT, Sanoudou D, Volinski JM, Beggs AH, Kohane IS, Kunkel LM. The influence of muscle type and dystrophin deficiency on murine expression profiles. Mamm Genome. 2005 Oct; 16(10):739-48.
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  149. Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics. 2005; 6:227.
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  150. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9.
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  151. Schachter AD, Ichimura T, Kohane IS. Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats. Pediatr Nephrol. 2005 Dec; 20(12):1717-23.
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  152. Turchin A, Kohane IS, Pendergrass ML. Identification of patients with diabetes from the text of physician notes in the electronic medical record. Diabetes Care. 2005 Jul; 28(7):1794-5.
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  153. Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. 2005; 6:107.
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  154. Marinescu VD, Kohane IS, Riva A. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics. 2005; 6:79.
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  155. Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. 2005 May 1; 21(9):2116-7.
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  156. Sax U, Kohane I, Mandl KD. Wireless technology infrastructures for authentication of patients: PKI that rings. J Am Med Inform Assoc. 2005 May-Jun; 12(3):263-8.
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  157. Porter SC, Kohane IS, Goldmann DA. Parents as partners in obtaining the medication history. J Am Med Inform Assoc. 2005 May-Jun; 12(3):299-305.
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  158. Turchin A, Pendergrass ML, Kohane IS. DITTO - a tool for identification of patient cohorts from the text of physician notes in the electronic medical record. AMIA Annu Symp Proc. 2005; 744-8.
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  159. Brownstein JS, Cassa CA, Kohane IS, Mandl KD. Reverse geocoding: concerns about patient confidentiality in the display of geospatial health data. AMIA Annu Symp Proc. 2005; 905.
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  160. Marinescu VD, Kohane IS, Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D91-7.
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  161. Liadaki K, Kho AT, Sanoudou D, Schienda J, Flint A, Beggs AH, Kohane IS, Kunkel LM. Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. Exp Cell Res. 2005 Feb 15; 303(2):360-74.
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  162. Simons WW, Mandl KD, Kohane IS. The PING personally controlled electronic medical record system: technical architecture. J Am Med Inform Assoc. 2005 Jan-Feb; 12(1):47-54.
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  163. Adam RM, Eaton SH, Estrada C, Nimgaonkar A, Shih SC, Smith LE, Kohane IS, Bägli D, Freeman MR. Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells. Physiol Genomics. 2004 Dec 15; 20(1):36-44.
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  164. Voisine P, Ruel M, Khan TA, Bianchi C, Xu SH, Kohane I, Libermann TA, Otu H, Saltiel AR, Sellke FW. Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest. Circulation. 2004 Sep 14; 110(11 Suppl 1):II280-6.
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  165. Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004 Aug 11; 18(3):308-15.
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  166. Porter SC, Cai Z, Gribbons W, Goldmann DA, Kohane IS. The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department. J Am Med Inform Assoc. 2004 Nov-Dec; 11(6):458-67.
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  167. Cai Z, Tsung EF, Marinescu VD, Ramoni MF, Riva A, Kohane IS. Bayesian approach to discovering pathogenic SNPs in conserved protein domains. Hum Mutat. 2004 Aug; 24(2):178-84.
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  168. Lader AS, Ramoni MF, Zetter BR, Kohane IS, Kwiatkowski DJ. Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell lines. Cancer Biol Ther. 2004 Jul; 3(7):624-31.
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  169. Lu T, Pan Y, Kao SY, Li C, Kohane I, Chan J, Yankner BA. Gene regulation and DNA damage in the ageing human brain. Nature. 2004 Jun 24; 429(6994):883-91.
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  170. Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 2004; 32(9):e74.
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  171. Sanoudou D, Frieden LA, Haslett JN, Kho AT, Greenberg SA, Kohane IS, Kunkel LM, Beggs AH. Molecular classification of nemaline myopathies: "nontyping" specimens exhibit unique patterns of gene expression. Neurobiol Dis. 2004 Apr; 15(3):590-600.
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  172. Riva A, Kohane IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. 2004 Mar 26; 5:33.
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  173. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. 2004 Mar 15; 18(6):629-40.
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  174. Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004 Feb 25; 5:18.
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  175. Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH, Stormo GD, Szczepaniak MC, Tuck D, Williamson J. Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc. 2004 May-Jun; 11(3):167-72.
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  176. Nimgaonkar A, Karnad DR, Sudarshan S, Ohno-Machado L, Kohane I. Prediction of mortality in an Indian intensive care unit. Comparison between APACHE II and artificial neural networks. Intensive Care Med. 2004 Feb; 30(2):248-53.
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  177. Fukuoka Y, Inaoka H, Kohane IS. Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics. 2004 Jan 13; 5(1):4.
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  178. Namini AH, Berkowicz DA, Kohane IS, Chueh H. A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens. Stud Health Technol Inform. 2004; 107(Pt 2):1264-7.
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  179. Alterovitz G, Aivado M, Spentzos D, Libermann TA, Ramoni M, Kohane IS. Analysis and robot pipelined automation for SELDI-TOF mass spectrometry. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:3068-71.
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  180. Tomczak KK, Marinescu VD, Ramoni MF, Sanoudou D, Montanaro F, Han M, Kunkel LM, Kohane IS, Beggs AH. Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J. 2004 Feb; 18(2):403-5.
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  181. Ruel M, Bianchi C, Khan TA, Xu S, Liddicoat JR, Voisine P, Araujo E, Lyon H, Kohane IS, Libermann TA, Sellke FW. Gene expression profile after cardiopulmonary bypass and cardioplegic arrest. J Thorac Cardiovasc Surg. 2003 Nov; 126(5):1521-30.
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  182. Sebastiani P, Lazarus R, Weiss ST, Kunkel LM, Kohane IS, Ramoni MF. Minimal haplotype tagging. Proc Natl Acad Sci U S A. 2003 Aug 19; 100(17):9900-5.
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  183. Patti ME, Butte AJ, Crunkhorn S, Cusi K, Berria R, Kashyap S, Miyazaki Y, Kohane I, Costello M, Saccone R, Landaker EJ, Goldfine AB, Mun E, DeFronzo R, Finlayson J, Kahn CR, Mandarino LJ. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A. 2003 Jul 8; 100(14):8466-71.
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  184. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics. 2003 Jun 25; 4:27.
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  185. Haslett JN, Sanoudou D, Kho AT, Han M, Bennett RR, Kohane IS, Beggs AH, Kunkel LM. Gene expression profiling of Duchenne muscular dystrophy skeletal muscle. Neurogenetics. 2003 Aug; 4(4):163-71.
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  186. Lee K, Kohane IS, Butte AJ. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics. 2003 Apr 12; 19(6):778-9.
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  187. Sanoudou D, Haslett JN, Kho AT, Guo S, Gazda HT, Greenberg SA, Lidov HG, Kohane IS, Kunkel LM, Beggs AH. Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle. Proc Natl Acad Sci U S A. 2003 Apr 15; 100(8):4666-71.
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  188. Porter SC, Fleisher GR, Kohane IS, Mandl KD. The value of parental report for diagnosis and management of dehydration in the emergency department. Ann Emerg Med. 2003 Feb; 41(2):196-205.
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  189. Saluja SK, Kohane I. Localization and characterization of mouse-human alignments within the human genome. Does evolutionary conservation suggest functional importance? AMIA Annu Symp Proc. 2003; 994.
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  190. Turchin A, Kohane IS. Gene homology resources on the World Wide Web. Physiol Genomics. 2002 Dec 3; 11(3):165-77.
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  191. Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84.
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  192. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002 Dec; 18(12):1681-5.
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  193. Haslett JN, Sanoudou D, Kho AT, Bennett RR, Greenberg SA, Kohane IS, Beggs AH, Kunkel LM. Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):15000-5.
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  194. Greenberg SA, Sanoudou D, Haslett JN, Kohane IS, Kunkel LM, Beggs AH, Amato AA. Molecular profiles of inflammatory myopathies. Neurology. 2002 Oct 22; 59(8):1170-82.
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  195. Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A. 2002 Jul 9; 99(14):9121-6.
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  196. Zhao Q, Kho A, Kenney AM, Yuk Di DI, Kohane I, Rowitch DH. Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5704-9.
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  197. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002 Mar; 18(3):405-12.
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  198. Kohane IS. The contributions of biomedical informatics to the fight against bioterrorism. J Am Med Inform Assoc. 2002 Mar-Apr; 9(2):116-9.
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  199. Kim JH, Kohane IS, Ohno-Machado L. Visualization and evaluation of clusters for exploratory analysis of gene expression data. J Biomed Inform. 2002 Feb; 35(1):25-36.
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  200. Mandl KD, Feit S, Larson C, Kohane IS. Newborn screening program practices in the United States: notification, research, and consent. Pediatrics. 2002 Feb; 109(2):269-73.
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  201. Riva A, Kohane IS. Accessing genomic data through XML-based remote procedure calls. Proc AMIA Symp. 2002; 662-6.
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  202. Cai Z, Kohane I, Fleisher GR, Greenes DS. Computerized reminders to physicians in the emergency department: a web-based system to report late-arriving abnormal laboratory results. Proc AMIA Symp. 2002; 91-5.
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  203. Park PJ, Tian L, Kohane IS. Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 2002; 18 Suppl 1:S120-7.
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  204. Schachter AD, Kohane IS. An unsupervised self-optimizing gene clustering algorithm. Proc AMIA Symp. 2002; 682-6.
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  205. Tsien CL, Libermann TA, Gu X, Kho A, Kohane IS. CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery. Proc AMIA Symp. 2002; 810-4.
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  206. Butte AJ, Bao L, Reis BY, Watkins TW, Kohane IS. Comparing the similarity of time-series gene expression using signal processing metrics. J Biomed Inform. 2001 Dec; 34(6):396-405.
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  207. Gonzalez-Heydrich J, Steingard RJ, Putnam FW, De Bellis MD, Beardslee W, Kohane IS. Corticotropin releasing hormone increases apparent potency of adrenocorticotropic hormone stimulation of cortisol secretion. Med Hypotheses. 2001 Nov; 57(5):544-8.
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  208. Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS. The personal internetworked notary and guardian. Int J Med Inform. 2001 Jun; 62(1):27-40.
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  209. Kohane IS. The ever imminent electronic medical record. J Med Pract Manage. 2001 Mar-Apr; 16(5):264-5.
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  210. Mandl KD, Szolovits P, Kohane IS. Public standards and patients' control: how to keep electronic medical records accessible but private. BMJ. 2001 Feb 3; 322(7281):283-7.
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  211. Reis BY, Butte AS, Kohane IS. Extracting knowledge from dynamics in gene expression. J Biomed Inform. 2001 Feb; 34(1):15-27.
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  212. Riva A, Kohane IS. A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp. 2001; 558-62.
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  213. Tsien CL, Libermann TA, Gu X, Kohane IS. On reporting fold differences. Pac Symp Biocomput. 2001; 496-507.
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  214. Butte AJ, Ye J, Häring HU, Stumvoll M, White MF, Kohane IS. Determining significant fold differences in gene expression analysis. Pac Symp Biocomput. 2001; 6-17.
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  215. Porter SC, Kohane IS. Optimal data entry by patients: effects of interface structure and design. Stud Health Technol Inform. 2001; 84(Pt 1):141-5.
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  216. Tsien CL, Kohane IS, McIntosh N. Building ICU artifact detection models with more data in less time. Proc AMIA Symp. 2001; 706-10.
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  217. Kim JH, Ohno-Machado L, Kohane IS. Unsupervised learning from complex data: the matrix incision tree algorithm. Pac Symp Biocomput. 2001; 30-41.
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  218. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):12182-6.
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  219. Greenes DS, Fleisher GR, Kohane I. Potential impact of a computerized system to report late-arriving laboratory results in the emergency department. Pediatr Emerg Care. 2000 Oct; 16(5):313-5.
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  220. Kohane IS. Bioinformatics and clinical informatics: the imperative to collaborate. J Am Med Inform Assoc. 2000 Sep-Oct; 7(5):512-6.
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  221. Gonzalez-Heydrich J, DeMaso DR, Irwin C, Steingard RJ, Kohane IS, Beardslee WR. Implementation of an electronic medical record system in a pediatric psychopharmacology program. Int J Med Inform. 2000 Jul; 57(2-3):109-16.
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  222. Tsien CL, Kohane IS, McIntosh N. Multiple signal integration by decision tree induction to detect artifacts in the neonatal intensive care unit. Artif Intell Med. 2000 Jul; 19(3):189-202.
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  223. Mandl KD, Feit S, Peña BM, Kohane IS. Growth and determinants of access in patient e-mail and Internet use. Arch Pediatr Adolesc Med. 2000 May; 154(5):508-11.
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  224. Porter SC, Silvia MT, Fleisher GR, Kohane IS, Homer CJ, Mandl KD. Parents as direct contributors to the medical record: validation of their electronic input. Ann Emerg Med. 2000 Apr; 35(4):346-52.
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  225. Nigrin DJ, Kohane IS. Temporal expressiveness in querying a time-stamp--based clinical database. J Am Med Inform Assoc. 2000 Mar-Apr; 7(2):152-63.
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  226. Nigrin DJ, Kohane IS. Glucoweb: a case study of secure, remote biomonitoring and communication. Proc AMIA Symp. 2000; 610-4.
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  227. Butte AJ, Weinstein DA, Kohane IS. Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 2000; 111-5.
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  228. Kohane IS, Altman RB. The new peer review. Proc AMIA Symp. 2000; 433-7.
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  229. Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000; 418-29.
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  230. Cao C, McIntosh N, Kohane IS, Wang K. Artifact detection in the PO2 and PCO2 time series monitoring data from preterm infants. J Clin Monit Comput. 1999 Aug; 15(6):369-78.
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  231. Gonzalez-Heydrich J, Steingard RJ, Putnam F, Beardslee W, Kohane IS. Using 'off the shelf', computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed. Comput Methods Programs Biomed. 1999 Mar; 58(3):227-38.
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  232. Nigrin DJ, Kohane IS. Scaling a data retrieval and mining application to the enterprise-wide level. Proc AMIA Symp. 1999; 901-5.
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  233. Cao C, Kohane IS, McIntosh N. Artifact detection in cardiovascular time series monitoring data from preterm infants. Proc AMIA Symp. 1999; 207-11.
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  234. Mandl KD, Kohane IS. Healthconnect: clinical grade patient-physician communication. Proc AMIA Symp. 1999; 849-53.
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  235. Sun Y, van Wingerde FJ, Kohane IS, Harary O, Mandl KD, Salem-Schatz SR, Homer CJ. The challenges of automating a real-time clinical practice guideline. Clin Perform Qual Health Care. 1999 Jan-Mar; 7(1):28-35.
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  236. Butte AJ, Kohane IS. Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 1999; 711-5.
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  237. Mandl KD, Kohane IS, Brandt AM. Electronic patient-physician communication: problems and promise. Ann Intern Med. 1998 Sep 15; 129(6):495-500.
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  238. van Wingerde FJ, Sun Y, Harary O, Mandl KD, Salem-Schatz S, Homer CJ, Kohane IS. Linking multiple heterogeneous data sources to practice guidelines. Proc AMIA Symp. 1998; 391-5.
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  239. Mandl KD, Katz SB, Kohane IS. Social equity and access to the World Wide Web and E-mail: implications for design and implementation of medical applications. Proc AMIA Symp. 1998; 215-9.
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  240. Kohane IS, Dong H, Szolovits P. Health information identification and de-identification toolkit. Proc AMIA Symp. 1998; 356-60.
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  241. Nigrin DJ, Kohane IS. Data mining by clinicians. Proc AMIA Symp. 1998; 957-61.
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  242. Sun Y, Kohane IS, Stark AR. Computer-assisted adjustment of inspired oxygen concentration improves control of oxygen saturation in newborn infants requiring mechanical ventilation. J Pediatr. 1997 Nov; 131(5):754-6.
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  243. Rind DM, Kohane IS, Szolovits P, Safran C, Chueh HC, Barnett GO. Maintaining the confidentiality of medical records shared over the Internet and the World Wide Web. Ann Intern Med. 1997 Jul 15; 127(2):138-41.
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  244. Kohane I. Physician pushes for the use of technology. Interview by Tyler L. Chin. Health Data Manag. 1997 Jul; 5(7):30, 32, 34-6.
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  245. Fraser HS, Kohane IS, Long WJ. Using the technology of the World Wide Web to manage clinical information. BMJ. 1997 May 31; 314(7094):1600-3.
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  246. Kohane IS. Patient assessment systems using the World Wide Web. Behav Healthc Tomorrow. 1997 Feb; 6(1):77-9.
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  247. Wang K, van Wingerde FJ, Bradshaw K, Szolovits P, Kohane I. A Java-based multi-institutional medical information retrieval system. Proc AMIA Annu Fall Symp. 1997; 538-42.
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  248. Haimowitz IJ, Kohane IS. Managing temporal worlds for medical trend diagnosis. Artif Intell Med. 1996 Jul; 8(3):299-321.
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  249. Kohane IS. Exploring the functions of World Wide Web-based electronic medical record systems. MD Comput. 1996 Jul-Aug; 13(4):339-46.
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  250. Kohane IS, Greenspun P, Fackler J, Cimino C, Szolovits P. Building national electronic medical record systems via the World Wide Web. J Am Med Inform Assoc. 1996 May-Jun; 3(3):191-207.
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  251. Miller D, Emans SJ, Kohane I. Follow-up study of adolescent girls with a history of premature pubarche. J Adolesc Health. 1996 Apr; 18(4):301-5.
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  252. Kohane IS, van Wingerde FJ, Fackler JC, Cimino C, Kilbridge P, Murphy S, Chueh H, Rind D, Safran C, Barnett O, Szolovits P. Sharing electronic medical records across multiple heterogeneous and competing institutions. Proc AMIA Annu Fall Symp. 1996; 608-12.
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  253. Wang K, Kohane I, Bradshaw KL, Fackler J. A real time patient monitoring system on the World Wide Web. Proc AMIA Annu Fall Symp. 1996; 729-32.
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  254. van Wingerde FJ, Schindler J, Kilbridge P, Szolovits P, Safran C, Rind D, Murphy S, Barnett GO, Kohane IS. Using HL7 and the World Wide Web for unifying patient data from remote databases. Proc AMIA Annu Fall Symp. 1996; 643-7.
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  255. Kohane IS. Editorial. Artif Intell Med. 1995 Dec; 7(6):471-2.
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  256. Gordon CM, Rowitch DH, Mitchell ML, Kohane IS. Topical iodine and neonatal hypothyroidism. Arch Pediatr Adolesc Med. 1995 Dec; 149(12):1336-9.
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  257. Haimowitz IJ, Le PP, Kohane IS. Clinical monitoring using regression-based trend templates. Artif Intell Med. 1995 Dec; 7(6):473-96.
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  258. Hinds A, Greenspun P, Kohane IS. WHAM!: a forms constructor for medical record access via the World Wide Web. Proc Annu Symp Comput Appl Med Care. 1995; 116-20.
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  259. Le PP, Kohane IS, Weeks JC. Using a pen-based computer to collect health-related quality of life and utilities information. Proc Annu Symp Comput Appl Med Care. 1995; 839-43.
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  260. Waisel DB, Fackler JC, Brunner JX, Kohane I. PEFIOS: an expert closed-loop oxygenation algorithm. Medinfo. 1995; 8 Pt 2:1132-6.
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  261. Szolovits P, Kohane I. Against simple universal health-care identifiers. J Am Med Inform Assoc. 1994 Jul-Aug; 1(4):316-9.
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  262. Emanuel RL, Robinson BG, Seely EW, Graves SW, Kohane I, Saltzman D, Barbieri R, Majzoub JA. Corticotrophin releasing hormone levels in human plasma and amniotic fluid during gestation. Clin Endocrinol (Oxf). 1994 Feb; 40(2):257-62.
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  263. Sun Y, Kohane I, Stark AR. Fuzzy logic assisted control of inspired oxygen in ventilated newborn infants. Proc Annu Symp Comput Appl Med Care. 1994; 757-61.
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  264. Gonzalez-Heydrich J, Steingard RJ, Kohane I. A computer simulation of the hypothalamic-pituitary-adrenal axis. Proc Annu Symp Comput Appl Med Care. 1994; 1010.
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  265. Fackler J, Kohane I. Monitor-driven data visualization: SmartDisplay. Proc Annu Symp Comput Appl Med Care. 1994; 939-43.
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  266. Kohane IS. Getting the data in: three year experience with a pediatric electronic medical record system. Proc Annu Symp Comput Appl Med Care. 1994; 457-61.
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  267. Kohane IS, Haimowitz IJ. Hypothesis-driven data abstraction with trend templates. Proc Annu Symp Comput Appl Med Care. 1993; 444-8.
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  268. Haimowitz IJ, Kohane IS. Influences on the performance of hospital clinical event monitoring. Proc Annu Symp Comput Appl Med Care. 1991; 614-8.
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  269. Kohane I, Kidwell JF. Effect of selection, mutation, and linkage on the equilibrium structure of selfing systems. J Hered. 1983 May-Jun; 74(3):175-80.
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