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Isaac S. Kohane, MD, PhD

Publications

  • 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;21(4):615-20.
    24821734
  • Weber GM, Mandl KD, Kohane IS.Finding the Missing Link for Big Biomedical Data.JAMA. 2014 May 22.
    24854141
  • 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 May 14.
    24829188
  • 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 May;35(5):537-47.
    24478219
  • Manrai AK, Bhatia G, Strymish J, Kohane IS, Jain SH.Medicine's Uncomfortable Relationship With Math: Calculating Positive Predictive Value.JAMA Intern Med. 2014 Apr 21.
    24756486
  • 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 Mar 25;15(3):R53.
    24667040
  • 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(1):16.
    24564913
  • Weber GM, Kohane IS.Extracting physician group intelligence from electronic health records to support evidence based medicine.PLoS ONE. 2013;8(5):e64933.
    23734227
  • Chute CG, Kohane IS.Genomic medicine, health information technology, and patient care.JAMA. 2013 Apr 10;309(14):1467-8.
    23571583
  • Altman RB, Clayton EW, Kohane IS, Malin BA, Roden DM.Data re-identification: societal safeguards.Science. 2013 Mar 1;339(6123):1032-3.
    23449577
  • 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 Oct 5.
    23037800
  • 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 Aug 21;13(8):R71.
    22909066
  • 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.
    21258063
  • Kohane IS, Margulies DM.COUNTERPOINT: Do not opine before it's time.Nat Biotechnol. 2011 Mar;29(3):218-9.
    21390023
  • 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 Feb 16.
    21310265
  • Schachter AD, Kohane IS.Drug target-gene signatures that predict teratogenicity are enriched for developmentally related genes.Reprod Toxicol. 2010 Nov 27.
    21115113
  • Kohane IS, Taylor PL.Multidimensional results reporting to participants in genomic studies: getting it right.Sci Transl Med. 2010 Jun 23;2(37):37cm19.
    20574066
  • 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(1):29.
    20302627
  • 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.
    20009093
  • Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ.Transcriptomic analysis of human lung development.Am J Respir Crit Care Med. 2010 Jan 1;181(1):54-63.
    19815808
  • Roach KL, King KR, Uygun BE, Kohane IS, Yarmush ML, Toner M.High throughput single cell bioinformatics.Biotechnol. Prog.;25(6):1772-9.
    19830811
  • 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.
    19628477
  • 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.;16(5):624-30.
    19567788
  • 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.
    19381341
  • 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.
    19348691
  • 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.
    19339759
  • 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.
    19030102
  • 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.
    18836721
  • The Cancer Genome Atlas Research Network.Comprehensive genomic characterization defines human glioblastoma genes and core pathways.Nature.;455(7216):1061-8.
  • 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.
    18655711
  • 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.
    18611264
  • Kohane I, Uzuner O.No Structure Before Its Time.J Am Med Inform Assoc. 2008 Apr 24.
    18436893
  • Mandl KD, Kohane IS.Tectonic shifts in the health information economy.N Engl J Med. 2008 Apr 17;358(16):1732-7.
    18420506
  • 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.
    18044979
  • 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.
    17947624
  • 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.
    17942673
  • Tian Z, Shen J, Moseman AP, Yang Q, Yang J, Xiao P, Wu E, Kohane IS.Dulxanthone A induces cell cycle arrest and apoptosis via up-regulation of p53 through mitochondrial pathway in HepG2 cells.Int J Cancer. 2008 Jan 1;122(1):31-8.
    17847033
  • 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.
    17708681
  • 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.
    17490722
  • 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.
    17625512
  • 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.;14(4):527-33.
    17460129
  • 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.
    17541859
  • 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.
    17495156
  • 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.
    17386082
  • 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.
    17360362
  • 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.
    17349058
  • Hackett KL, Kohane IS, Chueh HC, Murphy SN.Mapping tool for maintaining vocabulary relationships.AMIA Annu Symp Proc. 2006:939.
    17238558
  • Murphy SN, Mendis ME, Berkowicz DA, Kohane IS, Chueh HC.Integration of Clinical and Genetic Data in the i2b2 Architecture.AMIA Annu Symp Proc. 2006:1040.
    17238659
  • 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. 2006:1099.
    17238718
  • 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.
    17156451
  • 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.
    17090523
  • Frank NY, Kho AT, Schatton T, Murphy GF, Molloy MJ, Zhan Q, Ramoni MF, Frank MH, Kohane IS, Gussoni E.Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin.J Cell Biol. 2006 Oct 9;175(1):99-110.
    17015616
  • 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.
    16741228
  • 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.
    16921376
  • 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.
    16889408
  • Kohane IS, Masys DR, Altman RB.The incidentalome: a threat to genomic medicine.JAMA. 2006 Jul 12;296(2):212-5.
    16835427
  • 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 4;3(7):e232.
    16800721
  • 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.
    16779192
  • 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.
    16779139
  • Sebastiani P, Mandl KD, Szolovits P, Kohane IS, Ramoni MF.A Bayesian dynamic model for influenza surveillance.Stat Med. 2006 Jun 15;25(11):1823-5.
    16680805
  • Adida B, Kohane IS.GenePING: secure, scalable management of personal genomic data.BMC Genomics. 2006;7:93.
    16638151
  • 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 7;7(1):23.
    16522209
  • Inaoka H, Fukuoka Y, Kohane IS.Lower expression of genes near microRNA in C. elegans germline.BMC Bioinformatics. 2006;7:112.
    16519803
  • 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.
    16500934
  • Butte AJ, Kohane IS.Creation and implications of a phenome-genome network.Nat Biotechnol. 2006 Jan;24(1):55-62.
    16404398
  • 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.
    15153803
  • 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.
    15075291
  • 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.
    11960025
  • 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.
    11027309