PeopleofSuperintelligence

Researcher

Lincoln Stein

Also known as Lincoln D. Stein, Lincoln David Stein

Lincoln Stein is a physician-scientist who builds genomics data resources and now applies deep learning to cancer data. After earning a Harvard MD-PhD in 1989, he directed informatics at the MIT Genome Center from 1992 to 1997 and joined Cold Spring Harbor Laboratory in 1998, where his work included WormBase and Reactome. He moved to the Ontario Institute for Cancer Research in 2007 and became a Fellow of the International Society for Computational Biology in 2016. In 2020, a Nature Communications paper that he jointly supervised described a deep learning classifier that predicts cancer type from passenger mutation patterns. As of October 2026, he is Head of Adaptive Oncology at OICR, having become its Acting Scientific Director in October 2024.

Now at
Ontario Institute for Cancer Research, University of Toronto and Vector Institute
Born
1960
Badges

Years link to their sources.

Timeline

  1. 1989–1997

    Harvard and the MIT Genome Center

    He completes the MD-PhD program at Harvard in 1989 with a doctoral thesis in cell biology, then a residency in anatomic pathology at Brigham and Women's Hospital. From 1992 to 1997 he is director of informatics at the MIT Genome Center at the Whitehead Institute, where he works under Eric Lander to develop the first physical clone map of the human genome.

  2. 1998

    Cold Spring Harbor and WormBase

    He joins Cold Spring Harbor Laboratory in 1998, where he works on genome-scale databases including WormBase, the C. elegans genome database, and the Reactome pathway database. His 1998 book Official Guide to Programming with CGI.pm covers the Perl module he originally developed.

  3. 2004

    A Benjamin Franklin Award

    He receives the Benjamin Franklin Award in Bioinformatics in 2004, an award for free and open access in the field.

  4. 2007

    Program director at OICR

    He joins the Ontario Institute for Cancer Research in 2007 as program director of informatics and bio-computing. At OICR he leads the data coordination centre for the International Cancer Genome Consortium and other international cancer data sharing initiatives.

  5. 2016

    Fellow of the ISCB

    The International Society for Computational Biology names him a Fellow in 2016 for his roles in the formative consortia of computational biology, including the Human Genome Project, HapMap, Reactome, BioPerl, WormBase and GMOD.

  6. 2020

    Deep learning on passenger mutations

    In 2020, he and Quaid Morris jointly supervise a Nature Communications paper from the PCAWG Consortium. Its deep learning classifier, trained on passenger mutation patterns from 2,606 tumours across 24 cancer types, reaches 91% accuracy on held-out samples.

  7. October 2024

    Interim scientific director at OICR

    In October 2024, he becomes OICR's Acting Scientific Director, co-leading the institute with Acting President Christine Williams while he continues as Head of Adaptive Oncology. In May 2026, OICR announces that Aaron Schimmer will become President and Scientific Director beginning in August 2026, and thanks Stein and Williams for their leadership through the transition.

  8. As of October 2026

    Head of Adaptive Oncology

    He is Head of Adaptive Oncology at OICR, a professor of molecular genetics at the University of Toronto and a faculty affiliate of the Vector Institute. His current deep learning work covers identifying cancer subtypes from passenger mutation patterns, predicting the effects of biological pathway perturbations and building conversational interfaces to biological knowledgebases.

Career

  1. Since 2007Ontario Institute for Cancer ResearchProgram Director of informatics and bio-computing, Acting Scientific Director
  2. NowUniversity of TorontoProfessor of molecular genetics
  3. NowVector InstituteFaculty Affiliate
  4. From 1998Cold Spring Harbor Laboratory
  5. 1992–1997Massachusetts Institute of TechnologyDirector of informatics
  6. Mass General BrighamResident in anatomic pathology

Education

  1. 1989Harvard UniversityMD-PhD

From the biography.

  1. 11% of AI doctorate holders from 2010 to 2016 founded or led a company or lab by 10 years after graduationIncludes Lincoln Stein. We estimate how often AI doctorate holders founded or led a company or lab by 10 years after graduation, how waiting times compare between founders and top jobs, and which universities trained the most.
  2. The median h-index is 48 at universities and 14 at frontier AI labsIncludes University of Toronto. The median h-index is 48 at universities and 14 at frontier AI labs. We compare publishing careers, recent citations, dual appointments and job moves across 2,420 university researchers and 308 frontier-lab researchers.
  3. Of 943 people shaping AI who worked at Google, 446 work there nowIncludes Vector Institute. Our estimates of where the 943 people shaping AI who worked at Google and Google DeepMind work now: 446 at Google and 452 across 278 other organizations.
  4. The Massachusetts Institute of Technology trained or employed 44 of the 187 AI major-prize winners, more than any other universityIncludes University of Toronto. The Massachusetts Institute of Technology trained or employed 44 of the 187 AI major-prize winners, more than any other university. We compare doctorate and 5+ year employment links, career timing and current workplaces for 187 major-prize and 1,111 best-paper winners.

Colleagues

People with dated positions at the same organization in the same years.

Sources and credits

Photo: We have no published photo of Lincoln Stein yet. Send us a free-licensed photo.

  1. MedGen Faculty Spotlight: Dr. Lincoln Stein | Molecular Genetics moleculargenetics.utoronto.ca. Checked 21 October 2026.
  2. Lincoln Stein - Wikipedia en.wikipedia.org. Checked 21 October 2026.
  3. Lincoln Stein - Vector Institute for Artificial Intelligence vectorinstitute.ai. Checked 21 October 2026.
  4. Dr. Lincoln Stein - Ontario Institute for Cancer Research oicr.on.ca. Checked 21 October 2026.
  5. Longtime OICR Executives to lead Institute through important new chapter - Ontario Institute for Cancer Research oicr.on.ca. Checked 21 October 2026.
  6. ISCB Congratulates & Introduces the 2016 Class of Fellows! iscb.org. Checked 21 October 2026.
  7. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns | Nature Communications nature.com. Checked 21 October 2026.
  8. Dr. Aaron Schimmer to join OICR as President and Scientific Director - Ontario Institute for Cancer Research oicr.on.ca. Checked 21 October 2026.