Atul Butte

Atul Butte, M.D., Ph.D. is Chief of the Division of Systems Medicine and Associate Professor of Pediatrics, Medicine, and by courtesy, Computer Science, at Stanford University and Lucile Packard Childrens Hospital. Dr. Butte trained in Computer Science at Brown University, worked as a software engineer at Apple and Microsoft, received his M.D. at Brown University, trained in Pediatrics and Pediatric Endocrinology at Children's Hospital Boston, and received his Ph.D. in Health Sciences and Technology from Harvard Medical School and MIT. The Butte Laboratory builds and applies tools that convert more than 300 billion points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade -- into diagnostics, therapeutics, and new insights into disease. Examples of this method include work on cancer drug discovery published in the Proceedings of the National Academy of Science (2000), on type 2 diabetes published in the Proceedings of the National Academy of Science (2003), on fat cell formation published in Nature Cell Biology (2005), on obesity in Bioinformatics (2007), and in transplantation published in Proceedings of the National Academy of Science (2009). To facilitate this, the Butte Lab has developed tools to automatically index and find genomic data sets based on the phenotypic and contextual details of each experiment, published in Nature Biotechnology (2006); to re-map microarray data, published in Nature Methods (2007); to deconvolve multi-cellular samples, published in Nature Methods (2010); and to perform these calculations on the internet “cloud”, as published in Nature Biotechnology (2010). The Butte Lab has used these tools on publicly-available molecular data to successfully find new uses for existing drugs, as published in back-to-back papers in Science Translational Medicine (2011). The Butte Lab has also been developing novel methods in comparing clinical data from electronic health record systems with gene expression data, as described in Science (2008), and was part of the team performing the first clinical annotation of a patient presenting with a whole genome, as described in The Lancet (2010). The Butte Laboratory currently has been funded by HHMI and under sixteen NIH grants. Dr. Butte has authored more than 100 publications and delivered more than 120 invited presentations in personalized and systems medicine, biomedical informatics, and molecular diabetes, including 20 at the National Institutes of Health or NIH-related meetings. Dr. Butte’s research has been featured in the New York Times Science Times and the International Herald Tribune (2008), Wall Street Journal (2010 and 2011), and San Jose Mercury News (2010). Dr. Butte's recent awards include the 2010 Society for Pediatric Research Young Investigator Award, induction into the American College of Medical Informatics in 2009, the 2008 AMIA New Investigator Award, the 2007 Genome Technology “Tomorrows Principal Investigator” Award, the 2007 Society for Medical Decision Making Award for Outstanding Short Course, the 2006 Howard Hughes Medical Institute Early Career Award, the 2006 PhRMA Foundation Research Starter Grant in Informatics, and the 2002 and 2003 American Association for Clinical Chemistry Outstanding Speaker Award. Dr. Butte also co-authored one of the first books on microarray analysis titled “Microarrays For An Integrative Genomics” published by MIT Press.

What if you outsource three double-blind mice? (Atul Butte)

Science Kit for Atul Butte 

Thanks for listening to my talk TEDMED on the data-driven revolution in biomedical research and how we can even use public data to reclassify diseases and find new uses for drugs!

I finally got a moment to get my science kit together, and figured it would be easier to send out links instead of large attachments.


Here are links to the web-sites I mentioned in my talk:

National Center for Biotechnology Information:

(part of the National Library of Medicine:

and their Gene Expression Omnibus (GEO):

European Bioinformatics Institute:

and their ArrayExpress:


Companies I mentioned:


Assay Depot:

and the company I co-founded to help find more uses for drugs and compounds



Here are links to some of the papers from my lab that I mentioned in my talk:

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets


Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease


and a story about that work from the Wall Street Journal



Here are the books I mentioned in my talk:

Linnaeus and his Genera Morborum


Manual of the International List of Causes of Death (Second revision)


Many other similar books are viewable at Google Books:


And here is some parallel thinking on the ideas I brought up:

Chris Anderson’s article in Wired: The End of Theory: The Data Deluge Makes the Scientific Method Obsolete


National Academy of Science report on Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease


Francis Collins’s article on drug repositioning in Nature Reviews Drug Discovery (paywall)


Recent news on NIH teaming up with pharmaceutical companies to find new uses for drugs



How to get started in bioinformatics:

National Institutes of General Medical Sciences: How you can be a bioinformatician


Stanford University: Make your own cancer diagnostic test


R, the free bioinformatics/biostatistics tool kit we use


And the course I teach on bioinformatics at Stanford, web accessible (but pay only access, for now…):


Thanks to

National Institute for General Medical Sciences:

National Library of Medicine:

Howard Hughes Medical Institute:

Lucile Packard Foundation for Children’s Health:

and Stanford for funding my lab’s research

and, of course, the incredible folks in my lab who do all the work!


My twitter handle is @atulbutte


Best wishes,


-- Atul