Lincoln Stein
Head Of Adaptive Oncology at Ontario Institute for Cancer Research
Old Toronto, Ontario, Canada
Summary
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RockstarLincoln Stein is a physician-scientist and computational biology leader with 28 years of experience directing large-scale cancer genomics and informatics programs, currently Head of Adaptive Oncology at the Ontario Institute for Cancer Research and faculty in Molecular Genetics at the University of Toronto. He has built and curated foundational biological knowledgebases (Reactome, WormBase, Gramene, HapMap) and steers international data standards and coordination efforts for projects like ICGC-ARGO’s plan to sequence 100,000 cancer genomes. His lab combines deep learning, pathway-aware models and LLM-driven conversational interfaces to predict drug effects, classify tumors by cell-of-origin, and probe non-coding mutation impact. A long-time open-source contributor, he has also applied practical software and DevOps skills to projects ranging from BioPerl core improvements to backend and UI fixes in high-profile AI tooling. Known for bridging bench biology, large consortia governance, and production-grade software, he brings rare fluency across clinical, computational and data-policy domains.
28 years of coding experience
9 years of employment as a software developer
Github Skills (11)
bioinformatics10
bioperl10
refactoring10
perl10
python10
refactor10
git9
algorithms8
algorithm8
implement8
front-end-development6
Programming languages (7)
Github contributions (5)
bioperl/bioperl-live
Oct 1999 - Jul 2014
Core BioPerl 1.x code
Role in this project:
Back-end Developer
Back-end DeveloperContributions:1019 commits in 14 years 11 months
Contributions summary:Lincoln primarily contributed to the BioPerl project's core code, focusing on enhancements to the glyph rendering engine. Their work involved refining existing glyphs like the "segments" glyph for displaying multiple alignments, correcting display issues, and introducing new features such as customizable display options (e.g. showing amino acid sequences). The user demonstrated proficiency in bioinformatics tools and the Perl programming language, working within a well-established open-source project for sequence analysis.
bioperlpdb-filesbiologytoolkitbioinformatics
invoke-ai/InvokeAI
Aug 2022 - Jan 2023
Invoke is a leading creative engine for Stable Diffusion models, empowering professionals, artists, and enthusiasts to generate and create visual media using the latest AI-driven technologies. The solution offers an industry leading WebUI, and serves as the foundation for multiple commercial products.
Role in this project:Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:40 releases, 1441 reviews, 1350 commits in 5 months
Contributions summary:Lincoln primarily contributed to the codebase by addressing ambiguous naming conventions and implementing fixes within the Python code. These commits show a focus on software correctness and improving code quality through refactoring. The user also implemented changes to the index.html file suggesting an awareness of and work with the project's user interface, including adding UI controls and functionality.
serveswebuioutpaintingdiffusionlatent-diffusion
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