Atul Butte

Atul Butte
All of Us Research Program (NIH) · Public domain · source
Name	Atul Butte
Birth date	1970s
Birth place	India
Nationality	United States
Fields	Biotechnology, Bioinformatics, Genomics, Biomedical informatics
Workplaces	Stanford University, University of California, San Francisco, University of California, Santa Cruz, Priscilla Chan and Mark Zuckerberg San Francisco General Hospital and Trauma Center, Sage Bionetworks, Oxford Nanopore Technologies
Alma mater	Brown University, Harvard University, University of Cambridge
Known for	Data-driven medicine, data mining, translational bioinformatics

Atul Butte is a physician-scientist and biomedical informatician known for pioneering efforts to repurpose public biomedical data for translational research and drug discovery. He has led academic, industry, and startup initiatives bridging genomics, electronic health records, and computational biology to accelerate therapeutics and diagnostics. His work has influenced institutions across biotechnology, pharma, and academic medical centers.

Early life and education

Born in India, Butte studied in the United States where he completed undergraduate training at Brown University and pursued medical training at Harvard University and research training at the University of Cambridge. During his early academic formation he engaged with faculty and centers associated with genomics projects and computational initiatives linked to institutions such as MIT, Stanford University Medical Center, and Massachusetts General Hospital. His formative mentors and collaborators included scientists affiliated with organizations like National Institutes of Health, Wellcome Trust, and European Bioinformatics Institute.

Career

Butte held faculty appointments at Stanford University School of Medicine and later served in leadership at University of California, San Francisco where he directed programs integrating electronic health records with molecular data. He founded and led startups and translational ventures connected with entities such as Sage Bionetworks, Eli Lilly and Company, Biogen, and venture-backed firms in the biotechnology sector. He has collaborated with research infrastructures including NIH Big Data to Knowledge (BD2K), All of Us Research Program, and commercial partners like Google Health, Amazon Web Services, and Microsoft Research. His career has spanned roles interacting with regulatory and funding bodies such as Food and Drug Administration, National Science Foundation, and philanthropic funders including Gates Foundation.

Research and contributions

Butte championed the concept of repurposing publicly available microarray and RNA sequencing datasets from repositories like Gene Expression Omnibus and Sequence Read Archive to identify therapeutic hypotheses. He developed methods combining data resources from consortia and projects such as Cancer Genome Atlas, ENCODE Project, 1000 Genomes Project, Human Microbiome Project, and International HapMap Project with clinical cohorts from institutions like Mayo Clinic, Cleveland Clinic, and Johns Hopkins Hospital. His teams produced integrative analyses leveraging tools and platforms related to Bioconductor, R Project, Python (programming language), and computational frameworks promoted by OpenAI-style research groups and academic centers including Harvard Medical School and Yale School of Medicine.

He published studies that connected differential expression signatures to drug perturbation datasets from resources such as Connectivity Map, LINCS Program, and compound libraries used by Pfizer, Novartis, and GlaxoSmithKline to prioritize repurposing candidates. His translational pipelines interfaced with clinical trials and translational units within organizations like National Cancer Institute, American Association for Cancer Research, and cooperative groups such as SWOG. Collaborations extended to diagnostic innovators including Illumina, Thermo Fisher Scientific, and single-cell technology developers like 10x Genomics and Fluidigm.

Butte's work also addressed integration of large-scale electronic health record data, working alongside informatics efforts tied to Observational Health Data Sciences and Informatics, PCORnet, and health systems like Kaiser Permanente. He has been involved in computational phenotyping, privacy-aware data sharing, and reproducible research practices promoted by groups such as The Carpentries and Center for Open Science.

Awards and honors

Butte's contributions have been recognized by awards and appointments from organizations including National Institutes of Health, American Medical Informatics Association, American Association for the Advancement of Science, and academic honors from institutions like Stanford University and University of California, San Francisco. He has delivered named lectures at venues such as Cold Spring Harbor Laboratory, Broad Institute, and international conferences including RECOMB, ISMB, and AAAI.

Personal life and public engagement

Outside his research he has participated in public forums, policy discussions, and media engagements with outlets and events linked to TED, The New York Times, Nature (journal), Science (journal), and The Wall Street Journal. He has engaged with entrepreneurship ecosystems including Y Combinator, Silicon Valley accelerators, and networks such as Biotech Investors Network and AngelList. He supports open data initiatives and has advised philanthropic and governmental programs spanning Wellcome Trust, Bill & Melinda Gates Foundation, and regional health authorities.

Category:Physician-scientists Category:Bioinformaticians Category:American physicians Category:Living people