Lincoln Stein

Lincoln Stein

Faculty Affiliate

Head Adaptive Oncology, Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto

Lincoln Stein is an MD/PhD who works on biological data integration and visualization. Following his training at Harvard Medical School, he worked at the Whitehead Institute/MIT Center for Genome Research developing databases used for the mouse and human genome maps. From 1998-2008 he was a professor at Cold Spring Harbor Laboratory, working on a variety of genome-scale databases including WormBase, the database of the C. elegans genome, Gramene, a comparative genome mapping database for rice and other monocots, the International HapMap Project Database, and a human biological pathways database called Reactome. He is now Head, Adaptive Oncology, at the Ontario Institute for Cancer Research in Toronto, where he works on on large-scale genomic data integration projects, including the Reactome knowledgebase of biological pathways and processes, the Pan-Canadian Genome Library, and the International Cancer Genome Consortium.

In the area of machine learning, Lincoln is currently applying deep learning techniques to the tasks of identifying cancer subtypes from passenger mutation patterns, predicting the effects of biological pathway perturbations, and creating conversational interfaces to biological knowledgebases.

Research Interests

  • Computational Biology
  • Deep Learning
  • Generative Modelling


  • Clarivate list of highly-cited researchers (2019, 2020, 2021, 2022)
  • Canadian Cancer Research Society Award for Outstanding Achievements in Cancer Research (2019)
  • Fellow, International Society of Computation Biology (2016)
  • Benjamin Franklin Award for Free and Open Access in the Field of Bioinformatics