Isaac Kohane in Library

Isaac S. Kohane, MD, PhD

One hundred years ago, the Flexner report provided damning evidence of the sad state of the medical education system, and its implications for the quality of care provided and the lack of quality in biomedical research. Following the publication of that report, half of the medical schools in the US closed. We may be at a similarly pregnant moment in our medical education, medical research, and medical care system. Over the past 30 years, I have focused on twin tracks of research applied to biomedical discovery and clinical care to address this growing challenge.  A synthesis of these tracks can be found in our approach to using healthcare systems as translational research engines that generate genomic-scale knowledge in the routine course of clinical care. This same toolkit, adopted by over 50 academic health centers worldwide and a growing number of commercial organizations, has also allowed studies of drug safety, and quality of care. Along with several colleagues I have developed a system—The Informed Cohort—that makes patients partners in discovery, personally benefiting from breakthrough research while preserving privacy, autonomy, and yet maintaining the role of healthcare providers in filtering the potentially harmful noise inherent in genomic and other biomedical discovery enterprises. Our vision is to make every patient encounter an opportunity for all of biomedicine to progress—alas not the usual modus operandi of medical care.
Biomedical Discovery Clinical Care
It is perhaps in the nature of the bioinformatics discipline that we tend to adopt the macrobiological perspective where systematic mechanisms underlying observed biological processes and diseases are of greater interest rather than ascribing mechanistic primacy to individual genes, gene mutations, or organs. I have found the macrobiological perspective particulary effective as applied to reclassifying disease, and in particular in investigating the processes of development and how they run askew in particular diseases such as cancer. Remarkably, this comprehensive, quantitative approach has served to rediscover, at the molecular scale the observations of more than a century ago of Virchow, Cohnheim and other luminaries of the 19th century. In this spirit, we are now investigating how far the macrobiological perspective will take us in understanding autism spectrum disorder (ASD). That is, to study the molecular and cellular perturbations that cut across classically conceived neurophysiological, developmental and immunological mechanisms. Why is it easier to find out what experience shoppers worldwide have had with the latest digital camera than it is to determine what adverse events patients have had with a particular drug? Why are blood tests and X-rays repeated needlessly? Why can one replace an application on an iPhone with a mouse click and require a team of engineers to do it for an electronic health record system? Mirroring the systems approach taken in biology,we have attempted to answer (through design and implementation) these questions including the pioneering of personal health record systems, distributed clinical query systems, and privacy protection mechanisms and policies. Most recently, we have focused on how to re-engineer electronic health record systems so that they are as easy to manage and customize as other complex but consumer facing systems (e.g. the iPhone) which fundamentally support our notion of substitutability.

Organizational & Academic Reponsibilities

Professor of Pediatrics and Health Sciences Technology, Harvard Medical School

PI, National Center for Biomedical Computing: Informatics for Integrating Biology to the Bedside

Director, Countway Library of Medicine, Harvard Medical School

Director, Children's Hospital Informatics Program

Co-Director, HMS Center for Biomedical Informatics

Co-Director, Bioinformatics and Integrative Genomics training program

Director, Informatics Program, Harvard Catalyst (CTSA)




isaac_kohane at harvard dot edu


Looking to hire:

Senior programmer for i2b2.

Listening: kohane's Profile Page


Institute of Medicine

American College of Medical Informatics

American Society for Clinical Investigation

Society for Pediatric Research


CHIP Miscellany

Atul Butte at CHIP

Longwood mon amour


Selected Publications

Kohane IS, Taylor PL. Multidimensional results reporting to participants in genomic studies: getting it right. Sci Transl Med. 2010 Jun 23;2(37):37cm19.

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 diabetic medications using electronic medical records. Diabetes Care. 2009 Dec 15.

Murphy S, Churchill S, Bry L, Chueh H, Cai T, 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 Jul 14.

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 Jun 30.

Mandl KD, Kohane IS. No small change for the health information economy. N Engl J Med. 2009 Mar 26;360(13):1278-81.

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 Jul 8;9(7):R108.

Mandl KD, Kohane Isaac. Tectonic shifts in the health information economy. N Engl J Med. 2008 Apr 17;358(16):1732-7.

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.

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).

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

Kohane IS, Altman RB. Health-information altruists--a potentially critical resource. N Engl J Med 2005;353(19):2074-7.

Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, et al. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 2004;18(6):629-40.

Fukuoka Y, Inaoka H, Kohane IS. Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics 2004;5(1):4.

Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A 2002;99(14):9121-6.

Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002;18(3):405-12.

Mandl KD, Szolovits P, Kohane IS. Public standards and patients' control: how to keep electronic medical records accessible but private. Bmj 2001;322(7281):283-7.

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(22):12182-6.

Kohane IS, Kidwell JF. Effect of selection, mutation and linkage on the equilibrium structure of selfing systems. The Journal of Heredity 1983;75:175-180.

Full MEDLINE Bibliography (does not include computer science literature)


Miscellaneous Musings

Report of commercial activities

(disclosure in the interests of transparency and simplicity)


CurrentConflict status/role

Correlagen (founder)

None. Company Sold


Scientific Advisory Board (no equity)


Scientific Advisory Board (no equity)


Served on ad hoc internal scientific review committee. No equity.

Johnson & Johnson

Served on ad hoc internal scientific review committee. No equity.

An early (2002) view of the excitement and challenge and pragmatics of microarray applications to medicine: Microarrays for an Integrative Genomics


An earlier version of this page.