Photo of Isaac S. Kohane,  MD, PhD

Isaac S. Kohane, MD, PhD

Boston Children's Hospital

Boston Children's Hospital
Phone: (617) 355-7476
Fax: (617) 734-1369


isaac.kohane@tch.harvard.edu

Isaac S. Kohane, MD, PhD

Boston Children's Hospital

EDUCATIONAL TITLES

  • Lawrence J. Henderson Professor of Pediatrics, Pediatrics, Harvard Medical School
  • Associate Professor, Medicine, Harvard Medical School
  • Director, Countway Library of Medicine, Harvard Medical School
  • Chair, Informatics Program, Boston Children's Hospital

DF/HCC PROGRAM AFFILIATION

Publications

Powered by Harvard Catalyst
  • 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. 2015; 6:2709-24. PubMed
  • 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; 21:615-20. PubMed
  • Weber GM, Mandl KD, Kohane IS. Finding the Missing Link for Big Biomedical Data. JAMA 2014. PubMed
  • Hwang KB, Lee IH, Park JH, Hambuch T, Choi 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. PubMed
  • Lee IH, Lee K, Hsing M, Choe Y, Park JH, Kim SH, Bohn JM, Neu MB, Hwang KB, Green RC, Kohane IS, Kong SW. Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. Hum Mutat 2014; 35:537-47. PubMed
  • Manrai AK, Bhatia G, Strymish J, Kohane IS, Jain SH. Medicine's Uncomfortable Relationship With Math: Calculating Positive Predictive Value. JAMA Intern Med 2014. PubMed
  • Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre I L, Palanda I A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. PubMed
  • Kong SW, Sahin M, Collins CD, Wertz MH, Campbell MG, Leech JD, Krueger D, Bear MF, Kunkel LM, Kohane IS. Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis. Mol Autism 2014; 5:16. PubMed
  • Chute CG, Kohane IS. Genomic medicine, health information technology, and patient care. JAMA 2013; 309:1467-8. PubMed
  • Altman RB, Clayton EW, Kohane IS, Malin BA, Roden DM. Data re-identification: societal safeguards. Science 2013; 339:1032-3. PubMed
  • Weber GM, Kohane IS. Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS ONE 2013; 8:e64933. PubMed
  • 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 2012. PubMed
  • Palmer NP, Schmid PR, Berger B, Kohane IS. A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biol 2012; 13:R71. PubMed
  • 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; 27:891-3. PubMed
  • Kohane IS, Margulies DM. COUNTERPOINT: Do not opine before it's time. Nat Biotechnol 2011; 29:218-9. PubMed
  • 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. PubMed
  • Schachter AD, Kohane IS. Drug target-gene signatures that predict teratogenicity are enriched for developmentally related genes. Reprod Toxicol 2010. PubMed
  • Kohane IS, Taylor PL. Multidimensional results reporting to participants in genomic studies: getting it right. Sci Transl Med 2010; 2:37cm19. PubMed
  • 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. PubMed
  • 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; 33:526-31. PubMed
  • 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 2009; 181:54-63. PubMed
  • Davis AR, Kohane IS. Expression differences by continent of origin point to the immortalization process. Hum Mol Genet 2009; 18:3864-75. PubMed
  • 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 2008; 63:1131-9. PubMed
  • 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; 119:679-80; author reply 680-1. PubMed
  • Kohane IS. The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med 2009; 1:4. PubMed
  • 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:e5157. PubMed
  • Kohane I, Uzuner O. No Structure Before Its Time. J Am Med Inform Assoc 2008. PubMed
  • Mandl KD, Kohane IS. Tectonic shifts in the health information economy. N Engl J Med 2008; 358:1732-7. PubMed
  • 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 2007; 122:31-8. PubMed
  • Uzuner O, Goldstein I, Luo Y, Kohane I. Identifying patient smoking status from medical discharge records. J Am Med Inform Assoc 2007; 15:14-24. PubMed
  • 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. PubMed
  • 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:R108. PubMed
  • 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:e3794. PubMed
  • 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; 4:e322. PubMed
  • 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; 104:17016-21. PubMed
  • 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; 38:1212-25. PubMed
  • Lee JM, Ivanova EV, Seong IS, Cashorali T, Kohane I, Gusella JF, MacDonald ME. Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. PLoS Genet 2007; 3:e135. PubMed
  • Turchin A, Kolatkar NS, Pendergrass ML, Kohane IS. Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record. Med Inform Internet Med 2007; 32:93-102. PubMed
  • Kohane IS, Mandl KD, Taylor PL, Holm IA, Nigrin DJ, Kunkel LM. Medicine. Reestablishing the researcher-patient compact. Science 2007; 316:836-7. PubMed
  • 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; 104:5020-5. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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; 66:10815-23. PubMed
  • 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; 175:99-110. PubMed
  • 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; 38:1043-8. PubMed
  • 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; 24:2034-44. PubMed
  • 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; 5:1866-78. PubMed
  • Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA 2006; 296:212-5. PubMed
  • 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; 3:e232. PubMed
  • Sebastiani P, Mandl KD, Szolovits P, Kohane IS, Ramoni MF. A Bayesian dynamic model for influenza surveillance. Stat Med 2006; 25:1823-5. PubMed
  • 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; 22:999-1001. PubMed
  • 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. PubMed
  • Inaoka H, Fukuoka Y, Kohane IS. Lower expression of genes near microRNA in C. elegans germline. BMC Bioinformatics 2006; 7:112. PubMed
  • Adida B, Kohane IS. GenePING: secure, scalable management of personal genomic data. BMC Genomics 2006; 7:93. PubMed
  • Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol 2006; 24:55-62. PubMed
  • Hackett KL, Kohane IS, Chueh HC, Murphy SN. Mapping tool for maintaining vocabulary relationships. AMIA Annu Symp Proc 2007. PubMed
  • Murphy SN, Mendis ME, Berkowicz DA, Kohane IS, Chueh HC. Integration of Clinical and Genetic Data in the i2b2 Architecture. AMIA Annu Symp Proc 2007. PubMed
  • 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. PubMed
  • Simons W, Halamka J, 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 2007. PubMed
  • 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 2006. PubMed
  • 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 2006. PubMed
  • 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; 3:624-31. PubMed
  • 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; 18:629-40. PubMed
  • 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; 99:5704-9. PubMed
  • 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; 97:12182-6. PubMed
  • McMurry AJ, Gilbert CA, Reis BY, Chueh HC, Kohane IS, Mandl KD. A Self Scaling, Distributed Architecture for Public Health, Research, and Clinical Care. J Am Med Inform Assoc 2007; 14:527-33. PubMed
  • Roach KL, King KR, Uygun BE, Kohane IS, Yarmush ML, Toner M. High throughput single cell bioinformatics. Biotechnol. Prog. 2009; 25:1772-9. PubMed
  • 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; 16:624-30. PubMed
  • The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways Nature 2008; 455:1061-8.
Hide