It is with deep sadness that we note the passing of Atul J. Butte on June 13, 2025, at age 55 in California. A visionary in bioinformatics, computational biology, and personalized medicine, Dr. Butte's work revolutionized genomic data analysis, disease risk assessment, and big data in biomedicine. With an h-index over 110 and 70,000+ citations, he championed open science and integrative biology—authoring Microarrays for an Integrative Genomics and delivering a 2012 TEDMED talk on outsourcing experiments.
His career spanned Brown University (BS/MS in computer science), Harvard Medical School (MD), and Harvard–MIT (PhD in 2004). He advanced from Stanford faculty to UCSF's Bakar Computational Health Sciences Institute director in 2015, founding Personalis and NuMedii to translate research into clinical tools.
A key contribution relevant to Biostars: His 2011 paper "The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders" exposed biases in hg19/GRCh37, where rare disease alleles inflate variant calls for conditions like thrombosis or celiac disease. This echoed a 2017 Biostars thread on exome sequencing allele frequencies (my response here), where I highlighted reference-driven inversions in minor allele expectations—later tied to Butte's findings in 2021. I referenced this in a 2022 tweet: https://x.com/KevinBiostar/status/1537550923991502850.
Honored as a National Academy of Medicine member (2015), ISCB Fellow (2021), and Morris F. Collen Awardee (2024), Butte's legacy in open data and precision medicine endures.
Condolences to his family and mentees. Share your reflections below.
Rest in peace, Dr. Butte.
The Bioinformatics Community
