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Last Name

profileIsaac Samuel Kohane, M.D.,Ph.D.

TitleMarion V. Nelson Professor of Biomedical Informatics
InstitutionHarvard Medical School
DepartmentBiomedical Informatics
AddressHarvard Medical School
Center for Biomedical Informatics
10 Shattuck St
Boston MA 02115
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Other Positions
TitleHead of the Department of Biomedical Informatics
InstitutionHarvard Medical School
DepartmentBiomedical Informatics

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

TitleProfessor of Pediatrics
InstitutionBoston Children's Hospital

Collapse Research 
Collapse research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
OT3HL142480     (KOHANE, ISAAC S.)Sep 30, 2017 - Sep 29, 2020
Patient-Centric Information Commons under FAIR Principles (PIC-FAIR)
Role: Principal Investigator

OT3OD025466     (KOHANE, ISAAC S.)Sep 30, 2017 - Jun 30, 2018
Patient-Centric Information Commons under FAIR Principles (PIC-FAIR)
Role: Principal Investigator

R21ES025052     (PATEL, CHIRAG JAGDISH)Jan 1, 2015 - Nov 30, 2017
Increasing the power of GxE detection by using multi-locus genome-wide predictors
Role: Principal Investigator

U54HG007963     (KOHANE, ISAAC S.)Sep 29, 2014 - Aug 31, 2018
Patient-Centered Information Commons
Role: Principal Investigator

P50MH106933     (KOHANE, ISAAC S.)Sep 19, 2014 - Jul 31, 2019
Neuropsychiatric Genome-Scale and RDOC Individualized Domains (N-GRID)
Role: Principal Investigator

Collapse Bibliographic 
Collapse 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. Brat GA, Agniel D, Beam A, Yorkgitis B, Bicket M, Homer M, Fox KP, Knecht DB, McMahill-Walraven CN, Palmer N, Kohane I. Postsurgical prescriptions for opioid naive patients and association with overdose and misuse: retrospective cohort study. BMJ. 2018 01 17; 360:j5790. PMID: 29343479.
    View in: PubMed
  2. Yu S, Ma Y, Gronsbell J, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Liao KP, Cai T. Enabling phenotypic big data with PheNorm. J Am Med Inform Assoc. 2018 Jan 01; 25(1):54-60. PMID: 29126253.
    View in: PubMed
  3. Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ, Kohane IS, Avillach P. Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. Bioinformatics. 2017 Dec 18. PMID: 29267850.
    View in: PubMed
  4. Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W. Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 2017 Dec 08; 35(12):1128-1132. PMID: 29220033.
    View in: PubMed
  5. Fried I, Beam AL, Kohane IS, Palmer NP. Utilization, Cost, and Outcome of Branded vs Compounded 17-Alpha Hydroxyprogesterone Caproate in Prevention of Preterm Birth. JAMA Intern Med. 2017 Nov 01; 177(11):1689-1690. PMID: 28973537.
    View in: PubMed
  6. Palmer N, Beam A, Agniel D, Eran A, Manrai A, Spettell C, Steinberg G, Mandl K, Fox K, Nelson SF, Kohane I. Association of Sex With Recurrence of Autism Spectrum Disorder Among Siblings. JAMA Pediatr. 2017 Nov 01; 171(11):1107-1112. PMID: 28973142.
    View in: PubMed
  7. Miron O, Beam AL, Kohane IS. Auditory brainstem response in infants and children with autism spectrum disorder: A meta-analysis of wave V. Autism Res. 2017 Oct 31. PMID: 29087045.
    View in: PubMed
  8. Deverka PA, Majumder MA, Villanueva AG, Anderson M, Bakker AC, Bardill J, Boerwinkle E, Bubela T, Evans BJ, Garrison NA, Gibbs RA, Gentleman R, Glazer D, Goldstein MM, Greely H, Harris C, Knoppers BM, Koenig BA, Kohane IS, La Rosa S, Mattison J, O'Donnell CJ, Rai AK, Rehm HL, Rodriguez LL, Shelton R, Simoncelli T, Terry SF, Watson MS, Wilbanks J, Cook-Deegan R, McGuire AL. Creating a data resource: what will it take to build a medical information commons? Genome Med. 2017 Sep 22; 9(1):84. PMID: 28938910.
    View in: PubMed
  9. Kothari C, Wack M, Hassen-Khodja C, Finan S, Savova G, O'Boyle M, Bliss G, Cornell A, Horn EJ, Davis R, Jacobs J, Kohane I, Avillach P. Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. Am J Med Genet B Neuropsychiatr Genet. 2017 Sep 01. PMID: 28862395.
    View in: PubMed
  10. Feiglin A, Allen BK, Kohane IS, Kong SW. Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst. 2017 Aug 23; 5(2):140-148.e2. PMID: 28822752.
    View in: PubMed
  11. Mandl KD, Kohane IS. A 21st-Century Health IT System - Creating a Real-World Information Economy. N Engl J Med. 2017 May 18; 376(20):1905-1907. PMID: 28514623.
    View in: PubMed
  12. Murphy SN, Avillach P, Bellazzi R, Phillips L, Gabetta M, Eran A, McDuffie MT, Kohane IS. Combining clinical and genomics queries using i2b2 - Three methods. PLoS One. 2017; 12(4):e0172187. PMID: 28388645.
    View in: PubMed
  13. Yu S, Chakrabortty A, Liao KP, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T. Surrogate-assisted feature extraction for high-throughput phenotyping. J Am Med Inform Assoc. 2017 Apr 01; 24(e1):e143-e149. PMID: 27632993.
    View in: PubMed
  14. Beam AL, Kartoun U, Pai JK, Chatterjee AK, Fitzgerald TP, Shaw SY, Kohane IS. Predictive Modeling of Physician-Patient Dynamics That Influence Sleep Medication Prescriptions and Clinical Decision-Making. Sci Rep. 2017 Feb 09; 7:42282. PMID: 28181568.
    View in: PubMed
  15. Patel CJ, Manrai AK, Corona E, Kohane IS. Systematic correlation of environmental exposure and physiological and self-reported behaviour factors with leukocyte telomere length. Int J Epidemiol. 2017 Feb 01; 46(1):44-56. PMID: 27059547.
    View in: PubMed
  16. Beam AL, Kohane IS. Translating Artificial Intelligence Into Clinical Care. JAMA. 2016 12 13; 316(22):2368-2369. PMID: 27898974.
    View in: PubMed
  17. Nazeen S, Palmer NP, Berger B, Kohane IS. Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biol. 2016 11 14; 17(1):228. PMID: 27842596.
    View in: PubMed
  18. Patel CJ, Pho N, McDuffie M, Easton-Marks J, Kothari C, Kohane IS, Avillach P. A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey. Sci Data. 2016 10 25; 3:160096. PMID: 27779619.
    View in: PubMed
  19. Brady CC, Thaker VV, Lingren T, Woo JG, Kennebeck SS, Namjou-Khales B, Roach A, Bickel JP, Patibandla N, Savova GK, Solti I, Holm IA, Harley JB, Kohane IS, Crimmins NA. Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers. Int J Pediatr. 2016; 2016:4068582. PMID: 27698673.
    View in: PubMed
  20. Manrai AK, Funke BH, Rehm HL, Olesen MS, Maron BA, Szolovits P, Margulies DM, Loscalzo J, Kohane IS. Genetic Misdiagnoses and the Potential for Health Disparities. N Engl J Med. 2016 Aug 18; 375(7):655-65. PMID: 27532831.
    View in: PubMed
  21. Somekh J, Peleg M, Eran A, Koren I, Feiglin A, Demishtein A, Shiloh R, Heiner M, Kong SW, Elazar Z, Kohane I. A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. J Biomed Inform. 2016 Oct; 63:366-378. PMID: 27522000.
    View in: PubMed
  22. Beauchemin KJ, Wells JM, Kho AT, Philip VM, Kamir D, Kohane IS, Graber JH, Bult CJ. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ. 2016; 4:e2318. PMID: 27602285; PMCID: PMC4991849.
  23. Lingren T, Chen P, Bochenek J, Doshi-Velez F, Manning-Courtney P, Bickel J, Wildenger Welchons L, Reinhold J, Bing N, Ni Y, Barbaresi W, Mentch F, Basford M, Denny J, Vazquez L, Perry C, Namjou B, Qiu H, Connolly J, Abrams D, Holm IA, Cobb BA, Lingren N, Solti I, Hakonarson H, Kohane IS, Harley J, Savova G. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. PLoS One. 2016; 11(7):e0159621. PMID: 27472449; PMCID: PMC4966969.
  24. Lingren T, Thaker V, Brady C, Namjou B, Kennebeck S, Bickel J, Patibandla N, Ni Y, Van Driest SL, Chen L, Roach A, Cobb B, Kirby J, Denny J, Bailey-Davis L, Williams MS, Marsolo K, Solti I, Holm IA, Harley J, Kohane IS, Savova G, Crimmins N. Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl Clin Inform. 2016 Jul 20; 7(3):693-706. PMID: 27452794.
    View in: PubMed
  25. Perakslis ED, Kohane IS. Treating the enigmatic "exceptional responders" as patients with undiagnosed diseases. Sci Transl Med. 2016 05 25; 8(340):340ed8. PMID: 27225181.
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  26. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN. Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis. 2016 Apr; 22(4):880-5. PMID: 26933751; PMCID: PMC4792716 [Available on 04/01/17].
  27. Warner JL, Rioth MJ, Mandl KD, Mandel JC, Kreda DA, Kohane IS, Carbone D, Oreto R, Wang L, Zhu S, Yao H, Alterovitz G. SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care. J Am Med Inform Assoc. 2016 Jul; 23(4):701-10. PMID: 27018265.
    View in: PubMed
  28. Manrai AK, Ioannidis JP, Kohane IS. Clinical Genomics: From Pathogenicity Claims to Quantitative Risk Estimates. JAMA. 2016 Mar 22-29; 315(12):1233-4. PMID: 26925924.
    View in: PubMed
  29. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I. Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2016 Jul; 14(7):973-9. PMID: 26905907; PMCID: PMC4912917 [Available on 07/01/17].
  30. Mandel JC, Kreda DA, Mandl KD, Kohane IS, Ramoni RB. SMART on FHIR: a standards-based, interoperable apps platform for electronic health records. J Am Med Inform Assoc. 2016 Sep; 23(5):899-908. PMID: 26911829; PMCID: PMC4997036 [Available on 09/01/17].
  31. Brown AS, Kong SW, Kohane IS, Patel CJ. ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics. 2016 Feb 09; 17:78. PMID: 26860211; PMCID: PMC4746802.
  32. Mandl KD, Kohane IS. Time for a Patient-Driven Health Information Economy? N Engl J Med. 2016 Jan 21; 374(3):205-8. PMID: 26789868.
    View in: PubMed
  33. Castro VM, Kong SW, Clements CC, Brady R, Kaimal AJ, Doyle AE, Robinson EB, Churchill SE, Kohane IS, Perlis RH. Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Transl Psychiatry. 2016 Jan 05; 6:e708. PMID: 26731445.
    View in: PubMed
  34. Manrai AK, Wang BL, Patel CJ, Kohane IS. REPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY. Pac Symp Biocomput. 2016; 21:231-42. PMID: 26776189; PMCID: PMC4720982.
  35. Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS. METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:180-2. PMID: 26776184.
    View in: PubMed
  36. Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JP, Kohane IS. METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 2016; 21:180-182. PMID: 28004011.
    View in: PubMed
  37. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I. Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. Inflamm Bowel Dis. 2016 Jan; 22(1):151-8. PMID: 26332313; PMCID: PMC4772891 [Available on 01/01/17].
  38. Prilutsky D, Kho AT, Palmer NP, Bhakar AL, Smedemark-Margulies N, Kong SW, Margulies DM, Bear MF, Kohane IS. Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism. 2015; 6:66. PMID: 26697163; PMCID: PMC4687343.
  39. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ. Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. Inflamm Bowel Dis. 2015 Nov; 21(11):2507-14. PMID: 26241000; PMCID: PMC4615315 [Available on 11/01/16].
  40. Doshi-Velez F, Avillach P, Palmer N, Bousvaros A, Ge Y, Fox K, Steinberg G, Spettell C, Juster I, Kohane I. Prevalence of Inflammatory Bowel Disease Among Patients with Autism Spectrum Disorders. Inflamm Bowel Dis. 2015 Oct; 21(10):2281-8. PMID: 26218138.
    View in: PubMed
  41. Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Cobb BL, Denny JC, Hakonarson H, Hartzler AL, Hripcsak G, Kannry J, Kohane IS, Kullo IJ, Lin S, Manzi S, Marsolo K, Overby CL, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden DM, Tromp G, Uphoff T, Weng C, Wolf W, Williams MS, Starren J. Practical considerations in genomic decision support: The eMERGE experience. J Pathol Inform. 2015; 6:50. PMID: 26605115; PMCID: PMC4629307.
  42. Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Denny J, Freimuth RR, Hartzler A, Kannry J, Kohane IS, Kullo IJ, Lin S, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden D, Tromp G, Williams MS, Starren J. A conceptual model for translating omic data into clinical action. J Pathol Inform. 2015; 6:46. PMID: 26430534; PMCID: PMC4584438.
  43. Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T. Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts. PLoS One. 2015; 10(8):e0136651. PMID: 26301417; PMCID: PMC4547801.
  44. McCoy TH, Castro VM, Cagan A, Roberson AM, Kohane IS, Perlis RH. Sentiment Measured in Hospital Discharge Notes Is Associated with Readmission and Mortality Risk: An Electronic Health Record Study. PLoS One. 2015; 10(8):e0136341. PMID: 26302085; PMCID: PMC4547711.
  45. Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D, Kohane IS. SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. J Am Med Inform Assoc. 2015 Nov; 22(6):1173-8. PMID: 26198304.
    View in: PubMed
  46. Kohane IS. HEALTH CARE POLICY. Ten things we have to do to achieve precision medicine. Science. 2015 Jul 03; 349(6243):37-8. PMID: 26138968.
    View in: PubMed
  47. Mandl KD, Mandel JC, Kohane IS. Driving Innovation in Health Systems through an Apps-Based Information Economy. Cell Syst. 2015 Jul; 1(1):8-13. PMID: 26339683.
    View in: PubMed
  48. Yu S, Liao KP, Shaw SY, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T. Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. J Am Med Inform Assoc. 2015 Sep; 22(5):993-1000. PMID: 25929596; PMCID: PMC4986664.
  49. Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I. Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ. 2015 Apr 24; 350:h1885. PMID: 25911572; PMCID: PMC4707569.
  50. Ni Y, Wright J, Perentesis J, Lingren T, Deleger L, Kaiser M, Kohane I, Solti I. Increasing the efficiency of trial-patient matching: automated clinical trial eligibility pre-screening for pediatric oncology patients. BMC Med Inform Decis Mak. 2015 Apr 14; 15:28. PMID: 25881112; PMCID: PMC4407835.
  51. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases. Aliment Pharmacol Ther. 2015 Jun; 41(11):1141-8. PMID: 25864945; PMCID: PMC4420684.
  52. Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJ, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JB, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One. 2015; 10(4):e0122271. PMID: 25849893; PMCID: PMC4388675.
  53. McCoy TH, Castro VM, Rosenfield HR, Cagan A, Kohane IS, Perlis RH. A clinical perspective on the relevance of research domain criteria in electronic health records. Am J Psychiatry. 2015 Apr; 172(4):316-20. PMID: 25827030.
    View in: PubMed
  54. Mandl KD, Kohane IS. Federalist principles for healthcare data networks. Nat Biotechnol. 2015 Apr; 33(4):360-3. PMID: 25850061; PMCID: PMC4392383.
  55. Roger VL, Boerwinkle E, Crapo JD, Douglas PS, Epstein JA, Granger CB, Greenland P, Kohane I, Psaty BM. Strategic transformation of population studies: recommendations of the working group on epidemiology and population sciences from the National Heart, Lung, and Blood Advisory Council and Board of External Experts. Am J Epidemiol. 2015 Mar 15; 181(6):363-8. PMID: 25743324; PMCID: PMC4375403.
  56. Roger VL, Boerwinkle E, Crapo JD, Douglas PS, Epstein JA, Granger CB, Greenland P, Kohane I, Psaty BM. Roger et al. respond to "future of population studies". Am J Epidemiol. 2015 Mar 15; 181(6):372-3. PMID: 25743323; PMCID: PMC4397156.
  57. Wang F, Remke M, Bhat K, Wong ET, Zhou S, Ramaswamy V, Dubuc A, Fonkem E, Salem S, Zhang H, Hsieh TC, O'Rourke ST, Wu L, Li DW, Hawkins C, Kohane IS, Wu JM, Wu M, Taylor MD, Wu E. A microRNA-1280/JAG2 network comprises a novel biological target in high-risk medulloblastoma. Oncotarget. 2015 Feb 20; 6(5):2709-24. PMID: 25576913; PMCID: PMC4413612.
  58. Vassy JL, McLaughlin HM, McLaughlin HL, MacRae CA, Seidman CE, Lautenbach D, Krier JB, Lane WJ, Kohane IS, Murray MF, McGuire AL, Rehm HL, Green RC. A one-page summary report of genome sequencing for the healthy adult. Public Health Genomics. 2015; 18(2):123-9. PMID: 25612602; PMCID: PMC4348325.
  59. McLaughlin HM, Ceyhan-Birsoy O, Christensen KD, Kohane IS, Krier J, Lane WJ, Lautenbach D, Lebo MS, Machini K, MacRae CA, Azzariti DR, Murray MF, Seidman CE, Vassy JL, Green RC, Rehm HL. A systematic approach to the reporting of medically relevant findings from whole genome sequencing. BMC Med Genet. 2014 Dec 14; 15:134. PMID: 25714468; PMCID: PMC4342199.
  60. Castro VM, Minnier J, Murphy SN, Kohane I, Churchill SE, Gainer V, Cai T, Hoffnagle AG, Dai Y, Block S, Weill SR, Nadal-Vicens M, Pollastri AR, Rosenquist JN, Goryachev S, Ongur D, Sklar P, Perlis RH, Smoller JW. Validation of electronic health record phenotyping of bipolar disorder cases and controls. Am J Psychiatry. 2015 Apr; 172(4):363-72. PMID: 25827034; PMCID: PMC4441333.
  61. Namjou B, Marsolo K, Caroll RJ, Denny JC, Ritchie MD, Verma SS, Lingren T, Porollo A, Cobb BL, Perry C, Kottyan LC, Rothenberg ME, Thompson SD, Holm IA, Kohane IS, Harley JB. Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis. Front Genet. 2014; 5:401. PMID: 25477900; PMCID: PMC4235428.
  62. Castro VM, McCoy TH, Cagan A, Rosenfield HR, Murphy SN, Churchill SE, Kohane IS, Perlis RH. Stratification of risk for hospital admissions for injury related to fall: cohort study. BMJ. 2014 Oct 24; 349:g5863. PMID: 25954985; PMCID: PMC4208628.
  63. Kong SW, Lee IH, Leshchiner I, Krier J, Kraft P, Rehm HL, Green RC, Kohane IS, MacRae CA. Summarizing polygenic risks for complex diseases in a clinical whole-genome report. Genet Med. 2015 Jul; 17(7):536-44. PMID: 25341114; PMCID: PMC4547452.
  64. 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. 2015 Feb; 60(2):471-7. PMID: 25213079; PMCID: PMC4304947.
  65. Clements CC, Castro VM, Blumenthal SR, Rosenfield HR, Murphy SN, Fava M, Erb JL, Churchill SE, Kaimal AJ, Doyle AE, Robinson EB, Smoller JW, Kohane IS, Perlis RH. Prenatal antidepressant exposure is associated with risk for attention-deficit hyperactivity disorder but not autism spectrum disorder in a large health system. Mol Psychiatry. 2015 Jun; 20(6):727-34. PMID: 25155880; PMCID: PMC4427538.
  66. Blumenthal SR, Castro VM, Clements CC, Rosenfield HR, Murphy SN, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Smoller JW, Perlis RH. An electronic health records study of long-term weight gain following antidepressant use. JAMA Psychiatry. 2014 Aug; 71(8):889-96. PMID: 24898363.
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  67. 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. PMID: 25062868; PMCID: PMC4185241.
  68. 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 diseases. Clin Gastroenterol Hepatol. 2015 Feb; 13(2):322-329.e1. PMID: 25041865; PMCID: PMC4297589.
  69. D'Amore JD, Mandel JC, Kreda DA, Swain A, Koromia GA, Sundareswaran S, Alschuler L, Dolin RH, Mandl KD, Kohane IS, Ramoni RB. Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative. J Am Med Inform Assoc. 2014 Nov-Dec; 21(6):1060-8. PMID: 24970839; PMCID: PMC4215060.
  70. Weber GM, Mandl KD, Kohane IS. Finding the missing link for big biomedical data. JAMA. 2014 Jun 25; 311(24):2479-80. PMID: 24854141.
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  71. Hwang KB, Lee IH, Park JH, Hambuch T, Choe Y, Kim M, Lee K, Song T, Neu MB, Gupta N, Kohane IS, Green RC, Kong SW. Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods. Hum Mutat. 2014 Aug; 35(8):936-44. PMID: 24829188; PMCID: PMC4112476.
  72. Kohane IS. An autism case history to review the systematic analysis of large-scale data to refine the diagnosis and treatment of neuropsychiatric disorders. Biol Psychiatry. 2015 Jan 01; 77(1):59-65. PMID: 25034947; PMCID: PMC4260993.
  73. Manrai AK, Bhatia G, Strymish J, Kohane IS, Jain SH. Medicine's uncomfortable relationship with math: calculating positive predictive value. JAMA Intern Med. 2014 Jun; 174(6):991-3. PMID: 24756486; PMCID: PMC4955674.
  74. Mandl KD, Kohane IS, McFadden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, Ge Y, Zhou X, 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-Aug; 21(4):615-20. PMID: 24821734; PMCID: PMC4078286.
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  90. 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. PMID: 23925980; PMCID: PMC4060244.
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  93. Manrai AK, Kohane IS, Szolovits P. Urinary-cell mRNA and acute kidney-transplant rejection. N Engl J Med. 2013 Nov 07; 369(19):1859. PMID: 24195557.
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  136. 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. PMID: 22447773; PMCID: PMC3326474.
  137. 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. PMID: 22427539; PMCID: PMC3384120.
  138. 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. PMID: 22360370; PMCID: PMC3716251.
  139. Kohane IS, Hsing M, Kong SW. Taxonomizing, sizing, and overcoming the incidentalome. Genet Med. 2012 Apr; 14(4):399-404. PMID: 22323072; PMCID: PMC3821385.
  140. Kohane IS. Interview with Isaac S. Kohane conducted by Sarah Miller. Pharmacogenomics. 2012 Feb; 13(3):257-60. PMID: 22304577.
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  141. Kohane IS. (Mis)treating the pharmacogenetic incidentalome. Nat Rev Drug Discov. 2012 Feb 01; 11(2):89-90. PMID: 22293554.
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  142. 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. PMID: 22219206; PMCID: PMC3288749.
  143. 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. PMID: 22223081; PMCID: PMC3328607.
  144. Jung JY, Kohane IS, Wall DP. Identification of autoimmune gene signatures in autism. Transl Psychiatry. 2011 Dec 13; 1:e63. PMID: 22832355; PMCID: PMC3309496.
  145. 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. PMID: 22110609; PMCID: PMC3217948.
  146. 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. PMID: 22081225; PMCID: PMC3277623.
  147. 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. PMID: 21984588; PMCID: PMC3241166.
  148. Kohane IS. No small matter: qualitatively distinct challenges of pediatric genomic studies. Genome Med. 2011 Sep 30; 3(9):62. PMID: 21961648; PMCID: PMC3239237.
  149. 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 01; 20(21):4258-67. PMID: 21840924; PMCID: PMC3188996.
  150. Helman E, Naxerova K, Kohane IS. DNA hypermethylation in lung cancer is targeted at differentiation-associated genes. Oncogene. 2012 Mar 01; 31(9):1181-8. PMID: 21804601.
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  151. 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. PMID: 21712951; PMCID: PMC3119700.
  152. Perlis RH, Iosifescu DV, Castro VM, Murphy SN, Gainer VS, Minnier J, Cai T, Goryachev S, Zeng Q, Gallagher PJ, Fava M, Weilburg JB, Churchill SE, Kohane IS, Smoller JW. Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model. Psychol Med. 2012 Jan; 42(1):41-50. PMID: 21682950; PMCID: PMC3837420.
  153. 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. PMID: 21613990; PMCID: PMC3216673.
  154. 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. PMID: 21625483; PMCID: PMC3098838.
  155. Kohane IS. Using electronic health records to drive discovery in disease genomics. Nat Rev Genet. 2011 Jun; 12(6):417-28. PMID: 21587298.
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  156. 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. PMID: 21536587; PMCID: PMC3118763.
  157. Kohane IS, Szolovits P. Marco Ramoni: an appreciation of academic achievement. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):367-9. PMID: 21474623; PMCID: PMC3128413.
  158. Kohane IS, Margulies DM. Counterpoint: Do not opine before it's time. Nat Biotechnol. 2011 Mar; 29(3):218-9. PMID: 21390023.
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  159. 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. PMID: 21310265; PMCID: PMC3143236.
  160. 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. PMID: 21269672.
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  161. 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. PMID: 21258063; PMCID: PMC3051330.
  162. 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 07; 88(1):57-69. PMID: 21211616; PMCID: PMC3014362.
  163. Lee K, Brownstein JS, Mills RG, Kohane IS. Does collocation inform the impact of collaboration? PLoS One. 2010 Dec 15; 5(12):e14279. PMID: 21179507; PMCID: PMC3002263.
  164. 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. PMID: 21115113; PMCID: PMC3139687.
  165. 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 Nov 13; 2010:6-10. PMID: 21346930; PMCID: PMC3041305.
  166. 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. PMID: 20235204; PMCID: PMC3121049.
  167. Kohane IS, Taylor PL. Multidimensional results reporting to participants in genomic studies: getting it right. Sci Transl Med. 2010 Jun 23; 2(37):37cm19. PMID: 20574066.
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  168. 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 Mar 19; 4:29. PMID: 20302627; PMCID: PMC2856555.
  169. 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. PMID: 20190053; PMCID: PMC3000779.
  170. 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. PMID: 20009093; PMCID: PMC2827502.
  171. 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. PMID: 19830811; PMCID: PMC3208255.
  172. 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 01; 181(1):54-63. PMID: 19815808; PMCID: PMC2797628.
  173. Reis BY, Kohane IS, Mandl KD. Longitudinal histories as predictors of future diagnoses of domestic abuse: modelling study. BMJ. 2009 Sep 29; 339:b3677. PMID: 19789406; PMCID: PMC2755036.
  174. 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 01; 25(23):3121-7. PMID: 19786482; PMCID: PMC2778339.
  175. 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. PMID: 19628477; PMCID: PMC2748894.
  176. 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. PMID: 19602638; PMCID: PMC2752136.
  177. 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. PMID: 19567788; PMCID: PMC2744712.
  178. 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 Jun 02; 7:27. PMID: 19490605; PMCID: PMC2697174.
  179. 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. PMID: 19415117; PMCID: PMC2673043.
  180. 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. PMID: 19381341; PMCID: PMC2668177.
  181. 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. PMID: 19339759; PMCID: PMC2662571.
  182. Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009 Mar 26; 360(13):1278-81. PMID: 19321867.
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  183. 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. PMID: 19303403; PMCID: PMC2717893.
  184. 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. PMID: 19261943; PMCID: PMC2732240.
  185. Kohane IS. The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med. 2009 Jan 20; 1(1):4. PMID: 19348691.
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  186. Kohane I. Ten thousand views of bioinformatics: a bibliome perspective. Yearb Med Inform. 2009; 113-6. PMID: 19855883.
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  187. 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. PMID: 19030102; PMCID: PMC2582946.
  188. 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. PMID: 18950700.
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  189. 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 Nov 06; 1054. PMID: 18999021.
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  190. 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 06; 308-12. PMID: 18999057; PMCID: PMC2655929.
  191. 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. PMID: 18836721; PMCID: PMC3709019.
  192. 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. PMID: 18664640; PMCID: PMC2606946.
  193. Cassa CA, Schmidt B, Kohane IS, Mandl KD. My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics. 2008 Jul 25; 1:32. PMID: 18655711; PMCID: PMC2503988.
  194. 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. PMID: 18611264; PMCID: PMC2530866.
  195. 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 May 28; 3(5):e2265. PMID: 18509477; PMCID: PMC2386255.
  196. Mandl KD, Kohane IS. Tectonic shifts in the health information economy. N Engl J Med. 2008 Apr 17; 358(16):1732-7. PMID: 18420506.
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  197. 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 01; 122(1):31-8. PMID: 17847033.
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  198. 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. PMID: 18044979; PMCID: PMC2082639.
  199. 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 Nov 23; 8:430. PMID: 18034909; PMCID: PMC2258306.
  200. 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. PMID: 17947624; PMCID: PMC2274873.
  201. 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. PMID: 17942673; PMCID: PMC2040449.
  202. 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 Oct 11; 548-52. PMID: 18693896; PMCID: PMC2655844.
  203. 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. PMID: 17903520.
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  204. 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 Sep 05; 2(9):e840. PMID: 17786211; PMCID: PMC1950690.
  205. 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. PMID: 17625512; PMCID: PMC1948102.
  206. 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. PMID: 17708681; PMCID: PMC1950164.
  207. 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. PMID: 17541859.
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  208. Reis BY, Kohane IS, Mandl KD. An epidemiological network model for disease outbreak detection. PLoS Med. 2007 Jun; 4(6):e210. PMID: 17593895; PMCID: PMC1896205.
  209. 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. PMID: 17571924; PMCID: PMC1904360.
  210. 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. PMID: 17495156.
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  211. 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. PMID: 17490722.
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  212. 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. PMID: 17460129; PMCID: PMC2244902.
  213. 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. PMID: 17360362; PMCID: PMC1820821.
  214. 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 Mar 10; 8:68. PMID: 17349058; PMCID: PMC1828730.
  215. 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 Feb 28; 7:37. PMID: 17386082; PMCID: PMC1810540.
  216. 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. PMID: 17916252; PMCID: PMC2246284.
  217. 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 Dec 08; 5:56. PMID: 17156451; PMCID: PMC1702538.
  218. Saxena V, Orgill D, Kohane I. Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res. 2006; 34(22):e151. PMID: 17130162; PMCID: PMC1702493.
  219. 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. PMID: 17090523.
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  220. 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 09; 175(1):99-110. PMID: 17015616; PMCID: PMC2064502.
  221. 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. PMID: 16921376.
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  222. 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. PMID: 16889408.
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  223. Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006 Jul 12; 296(2):212-5. PMID: 16835427.
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  224. 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. PMID: 16800721; PMCID: PMC1483910.
  225. 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. PMID: 16794260; PMCID: PMC2643292.
  226. 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. PMID: 16645996; PMCID: PMC4128871.
  227. 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. PMID: 16741228; PMCID: PMC3372914.
  228. Adida B, Kohane IS. GenePING: secure, scalable management of personal genomic data. BMC Genomics. 2006 Apr 26; 7:93. PMID: 16638151; PMCID: PMC1524750.
  229. 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. PMID: 16601137.
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  230. 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 Mar 07; 7:23. PMID: 16522209; PMCID: PMC1525166.
  231. Inaoka H, Fukuoka Y, Kohane IS. Lower expression of genes near microRNA in C. elegans germline. BMC Bioinformatics. 2006 Mar 06; 7:112. PMID: 16519803; PMCID: PMC1420334.
  232. 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. PMID: 16500934.
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  233. Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan; 24(1):55-62. PMID: 16404398; PMCID: PMC2716377.
  234. Hackett KL, Kohane IS, Chueh HC, Murphy SN. Mapping tool for maintaining vocabulary relationships. AMIA Annu Symp Proc. 2006; 939. PMID: 17238558; PMCID: PMC1839260.
  235. 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. PMID: 17238718; PMCID: PMC1839527.
  236. 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. PMID: 17238659; PMCID: PMC1839291.
  237. 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 Nov 27; 6:168. PMID: 16309559; PMCID: PMC1310621.
  238. Kohane IS, Altman RB. Health-information altruists--a potentially critical resource. N Engl J Med. 2005 Nov 10; 353(19):2074-7. PMID: 16282184.
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  239. 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. PMID: 16261416.
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  240. Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics. 2005 Sep 14; 6:227. PMID: 16162296; PMCID: PMC1239911.
  241. 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. PMID: 16174746; PMCID: PMC1200092.
  242. 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. PMID: 16133046; PMCID: PMC1343534.
  243. 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. PMID: 15983338.
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  244. 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 Apr 25; 6:107. PMID: 15850491; PMCID: PMC1127107.
  245. 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 Mar 30; 6:79. PMID: 15799782; PMCID: PMC1131891.
  246. 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 01; 21(9):2116-7. PMID: 15684227; PMCID: PMC2819168.
  247. 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. PMID: 15684133; PMCID: PMC1090456.
  248. 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. PMID: 15684127; PMCID: PMC1090461.
  249. 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. PMID: 16779139; PMCID: PMC1560516.
  250. 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. PMID: 16779192; PMCID: PMC1560748.
  251. Marinescu VD, Kohane IS, Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D91-7. PMID: 15608292; PMCID: PMC540057.
  252. 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. PMID: 15652349.
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  253. 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. PMID: 15492031; PMCID: PMC543826.
  254. 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. PMID: 15467014.
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  255. 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. PMID: 15364876.
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  256. 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. PMID: 15161964.
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  257. 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. PMID: 15298999; PMCID: PMC524636.
  258. 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. PMID: 15241800.
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  259. 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. PMID: 15153803.
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  260. 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. PMID: 15190254.
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  261. 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 May 25; 32(9):e74. PMID: 15161944; PMCID: PMC419626.
  262. 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. PMID: 15056467.
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  263. Riva A, Kohane IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. 2004 Mar 26; 5:33. PMID: 15046636; PMCID: PMC395999.
  264. 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. PMID: 15075291; PMCID: PMC387239.
  265. Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004 Feb 25; 5:18. PMID: 15053845; PMCID: PMC375525.
  266. 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. PMID: 14764617; PMCID: PMC400513.
  267. 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):248-253. PMID: 14727015.
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  268. 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. PMID: 14718066; PMCID: PMC331401.
  269. 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. PMID: 15361017.
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  270. 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. PMID: 17270926.
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  271. 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. PMID: 14688207.
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  272. 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. PMID: 14666028.
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  273. 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. PMID: 12900503; PMCID: PMC187880.
  274. 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 08; 100(14):8466-71. PMID: 12832613; PMCID: PMC166252.
  275. 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. PMID: 12823866; PMCID: PMC165600.
  276. 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. PMID: 12698323.
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  277. 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. PMID: 12691993.
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  278. 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. PMID: 12677001; PMCID: PMC153613.
  279. 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. PMID: 12548269.
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  280. 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. PMID: 14728497; PMCID: PMC1480323.
  281. Turchin A, Kohane IS. Gene homology resources on the World Wide Web. Physiol Genomics. 2002 Dec 03; 11(3):165-77. PMID: 12464690.
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  282. Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84. PMID: 12490441.
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  283. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002 Dec; 18(12):1681-5. PMID: 12490454.
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  284. 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. PMID: 12415109; PMCID: PMC137534.
  285. 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. PMID: 12391344.
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  286. Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A. 2002 Jul 09; 99(14):9121-6. PMID: 12082179; PMCID: PMC123104.
  287. 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. PMID: 11960025; PMCID: PMC122835.
  288. 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. PMID: 11934739.
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  289. Kohane IS. The contributions of biomedical informatics to the fight against bioterrorism. J Am Med Inform Assoc. 2002 Mar-Apr; 9(2):116-9. PMID: 11861623; PMCID: PMC344565.
  290. 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. PMID: 12415724.
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  291. 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. PMID: 11826206.
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  292. Riva A, Kohane IS. Accessing genomic data through XML-based remote procedure calls. Proc AMIA Symp. 2002; 662-6. PMID: 12463907; PMCID: PMC2244329.
  293. 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. PMID: 12463793; PMCID: PMC2244345.
  294. 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. PMID: 12169539.
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  295. Schachter AD, Kohane IS. An unsupervised self-optimizing gene clustering algorithm. Proc AMIA Symp. 2002; 682-6. PMID: 12463911; PMCID: PMC1357234.
  296. 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. PMID: 12463937; PMCID: PMC2244364.
  297. 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. PMID: 12198759.
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  298. 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. PMID: 11735308.
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  299. 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. PMID: 11340004.
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  300. Kohane IS. The ever imminent electronic medical record. J Med Pract Manage. 2001 Mar-Apr; 16(5):264-5. PMID: 11345886.
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  301. Mandl KD, Szolovits P, Kohane IS. Public standards and patients' control: how to keep electronic medical records accessible but private. BMJ. 2001 Feb 03; 322(7281):283-7. PMID: 11157533; PMCID: PMC1119527.
  302. Reis BY, Butte AS, Kohane IS. Extracting knowledge from dynamics in gene expression. J Biomed Inform. 2001 Feb; 34(1):15-27. PMID: 11376539.
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  303. Riva A, Kohane IS. A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp. 2001; 558-62. PMID: 11825250; PMCID: PMC2243317.
  304. Tsien CL, Libermann TA, Gu X, Kohane IS. On reporting fold differences. Pac Symp Biocomput. 2001; 496-507. PMID: 11262967.
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  305. 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. PMID: 11262977.
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  306. 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. PMID: 11604722.
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  307. Tsien CL, Kohane IS, McIntosh N. Building ICU artifact detection models with more data in less time. Proc AMIA Symp. 2001; 706-10. PMID: 11825277; PMCID: PMC2243686.
  308. Kim JH, Ohno-Machado L, Kohane IS. Unsupervised learning from complex data: the matrix incision tree algorithm. Pac Symp Biocomput. 2001; 30-41. PMID: 11262950.
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  309. 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. PMID: 11027309; PMCID: PMC17315.
  310. 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. PMID: 11063357.
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  311. Kohane IS. Bioinformatics and clinical informatics: the imperative to collaborate. J Am Med Inform Assoc. 2000 Sep-Oct; 7(5):512-6. PMID: 10984470; PMCID: PMC79046.
  312. 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. PMID: 10961567.
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  313. 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. PMID: 10906612.
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  314. 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. PMID: 10807304.
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  315. 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. PMID: 10736120.
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  316. 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. PMID: 10730599; PMCID: PMC61469.
  317. Nigrin DJ, Kohane IS. Glucoweb: a case study of secure, remote biomonitoring and communication. Proc AMIA Symp. 2000; 610-4. PMID: 11079956; PMCID: PMC2243912.
  318. Butte AJ, Weinstein DA, Kohane IS. Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 2000; 111-5. PMID: 11079855; PMCID: PMC2244056.
  319. Kohane IS, Altman RB. The new peer review. Proc AMIA Symp. 2000; 433-7. PMID: 11079920; PMCID: PMC2244085.
  320. Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000; 418-29. PMID: 10902190.
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  321. 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. PMID: 12578032.
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  322. 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. PMID: 10094227.
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  323. Nigrin DJ, Kohane IS. Scaling a data retrieval and mining application to the enterprise-wide level. Proc AMIA Symp. 1999; 901-5. PMID: 10566491; PMCID: PMC2232595.
  324. Cao C, Kohane IS, McIntosh N. Artifact detection in cardiovascular time series monitoring data from preterm infants. Proc AMIA Symp. 1999; 207-11. PMID: 10566350; PMCID: PMC2232725.
  325. Mandl KD, Kohane IS. Healthconnect: clinical grade patient-physician communication. Proc AMIA Symp. 1999; 849-53. PMID: 10566480; PMCID: PMC2232826.
  326. 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. PMID: 10351590.
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  327. Butte AJ, Kohane IS. Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 1999; 711-5. PMID: 10566452; PMCID: PMC2232846.
  328. Mandl KD, Kohane IS, Brandt AM. Electronic patient-physician communication: problems and promise. Ann Intern Med. 1998 Sep 15; 129(6):495-500. PMID: 9735088.
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  329. 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. PMID: 9929248; PMCID: PMC2232068.
  330. 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. PMID: 9929213; PMCID: PMC2232108.
  331. Kohane IS, Dong H, Szolovits P. Health information identification and de-identification toolkit. Proc AMIA Symp. 1998; 356-60. PMID: 9929241; PMCID: PMC2232117.
  332. Nigrin DJ, Kohane IS. Data mining by clinicians. Proc AMIA Symp. 1998; 957-61. PMID: 9929360; PMCID: PMC2232327.
  333. Kohane IS. Computer-based Patient Records. Yearb Med Inform. 1998; (1):227-229. PMID: 27699340.
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  334. 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. PMID: 9403660.
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  335. 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. PMID: 9230004.
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  336. 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. PMID: 10169476.
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  337. 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. PMID: 9186174; PMCID: PMC2126819.
  338. Kohane IS. Patient assessment systems using the World Wide Web. Behav Healthc Tomorrow. 1997 Feb; 6(1):77-9. PMID: 10164823.
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  339. 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. PMID: 9357684; PMCID: PMC2233350.
  340. Haimowitz IJ, Kohane IS. Managing temporal worlds for medical trend diagnosis. Artif Intell Med. 1996 Jul; 8(3):299-321. PMID: 8830926.
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  341. Kohane IS. Exploring the functions of World Wide Web-based electronic medical record systems. MD Comput. 1996 Jul-Aug; 13(4):339-46. PMID: 8754243.
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  342. 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. PMID: 8723610; PMCID: PMC116301.
  343. 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. PMID: 8860795.
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  344. 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. PMID: 8947738; PMCID: PMC2233175.
  345. 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. PMID: 8947761; PMCID: PMC2233054.
  346. 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. PMID: 8947745; PMCID: PMC2233237.
  347. Kohane IS. Editorial. Artif Intell Med. 1995 Dec; 7(6):471-2. PMID: 8963371.
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  348. Gordon CM, Rowitch DH, Mitchell ML, Kohane IS. Topical iodine and neonatal hypothyroidism. Arch Pediatr Adolesc Med. 1995 Dec; 149(12):1336-9. PMID: 7489070.
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  349. Haimowitz IJ, Le PP, Kohane IS. Clinical monitoring using regression-based trend templates. Artif Intell Med. 1995 Dec; 7(6):473-96. PMID: 8963372.
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  350. 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. PMID: 8563248; PMCID: PMC2579067.
  351. 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. PMID: 8563410; PMCID: PMC2579212.
  352. Waisel DB, Fackler JC, Brunner JX, Kohane I. PEFIOS: an expert closed-loop oxygenation algorithm. Medinfo. 1995; 8 Pt 2:1132-6. PMID: 8591387.
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  353. Szolovits P, Kohane I. Against simple universal health-care identifiers. J Am Med Inform Assoc. 1994 Jul-Aug; 1(4):316-9. PMID: 7719815; PMCID: PMC116211.
  354. 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. PMID: 8137526.
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  355. 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. PMID: 7950026; PMCID: PMC2247890.
  356. 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. PMID: 7949852; PMCID: PMC2247809.
  357. Fackler J, Kohane I. Monitor-driven data visualization: SmartDisplay. Proc Annu Symp Comput Appl Med Care. 1994; 939-43. PMID: 7950062; PMCID: PMC2247908.
  358. 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. PMID: 7949969; PMCID: PMC2247935.
  359. Kohane IS, Haimowitz IJ. Hypothesis-driven data abstraction with trend templates. Proc Annu Symp Comput Appl Med Care. 1993; 444-8. PMID: 8130513; PMCID: PMC2248548.
  360. Haimowitz IJ, Kohane IS. Influences on the performance of hospital clinical event monitoring. Proc Annu Symp Comput Appl Med Care. 1991; 614-8. PMID: 1807675; PMCID: PMC2247604.
  361. 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. PMID: 6863893.
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