Faculty profile

Lincoln Stein

ResearcherPhysical SciencesUniversity of Toronto

This profile is built from public research funding records (CIHR, NSERC and SSHRC) and PubMed. We have not imported them from a University of Toronto directory, so their courses and email address may be missing. Find their university profile.

Lincoln Stein

Researcher

Physical Sciences

Health Sciences

University of Toronto

Toronto, Ontario, Canada

Supervision signals

Has led research grants, which requires an independent research appointment. Ask their department whether they supervise graduate students.
27 publications in the last five years, latest in 2026.
Senior (last) author on 6 recent papers, a sign of leading a research group.
Principal investigator on 3 research grants (2 CIHR, 1 NSERC), most recently in 2018.

These signals come from public records, including CIHR, NSERC and SSHRC funding decisions. Ask the professor or the graduate program whether they are taking new students.

Academic metrics

Publications

459

Citations

h-index

Collaborators

Grants

Publications by year

Counts cover the works listed on the university profile; citation counts come from Dimensions.

Profiles and links

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Signals and details

Research

Breast Cancer Computational Pathology Deep Learning Digital Pathology Histopathology Risk Stratification Bioinformatics Cancer

Latest papers

Firefox, a protein encoded by circular PVT1, is essential for MYC-driven oncogenesis.
Genes & development · 2026
Honeybadger, a micropeptide encoded by an alternative PVT1 transcript, is a critical negative regulator of RAS-MAPK signaling in MYC-driven tumors.
Genes & development · 2026
Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2.
Journal of molecular biology · 2026

All 80 publications

Latest funding

Using deep learning to estimate breast cancer recurrence scores from histopathology images
CIHR · 2018 · Principal investigator
$780,300
DCIS-Precise: A Genomics-Driven Model for Predicting DCIS Response to Radiation
CIHR · 2017 · Co-investigator
$910,352
The Cancer Genome Collaboratory
CIHR · 2013 · Nominated PI
$900,000

All 4 grants and awards

80 publications.

Firefox, a protein encoded by circular PVT1, is essential for MYC-driven oncogenesis.

Tiwari A, Paithane U, Tashiro K, Hall B, Friedlein J, Saraswat M, Saulnier O, Barbosa K, Trinh Q, Saha S, Soni A, Nakashima T, Murad R, Maurya S, Chapman OS, James B, Erickson A, Lange JT, Leary R, Varshney J, Konety B, Dehm SM, Kawakami Y, Largaespada DA, Weiss WA, Stein L, Chavez L, Suzuki H, Wu S, Zhao J, Deshpande AJ, Taylor MD, Wechsler-Reya RJ, Bagchi A

Genes & development2026

DOI: 10.1101/gad.353355.125 PMID: 42618323

Honeybadger, a micropeptide encoded by an alternative PVT1 transcript, is a critical negative regulator of RAS-MAPK signaling in MYC-driven tumors.

Paithane U, Tiwari A, Hall B, Tashiro K, Saulnier O, Trinh Q, Soni A, Nakashima T, Bobkov AA, Fujimoto LM, Saraswat M, Sarmashghi S, Hendrikse LD, Masihi MB, Saha S, Ghosh S, James B, Erickson A, Eisemann T, Tzaridis T, Konety B, Dehm SM, Beroukhim R, Chavez L, Largaespada DA, Stein L, Suzuki H, Weiss WA, Yeh J, Zhao J, Wechsler-Reya RJ, Taylor MD, Bagchi A

Genes & development2026

DOI: 10.1101/gad.353356.125 PMID: 42618324

Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2.

Diesh C, Stevens G, Bridge C, Hogue G, Buels R, Cain S, Stein L, Holmes I

Journal of molecular biology2026

DOI: 10.1016/j.jmb.2026.169645 PMID: 41565000

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

Mohammadi H, Almodaresi F, Hogue GFJ, Wright A, Orlic-Milacic M, Li NT, Mawani A, Stein L

Research square2026Senior author

DOI: 10.21203/rs.3.rs-8865129/v1 PMID: 41756444

The Reactome Knowledgebase 2026.

Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, Griss J, Hogue GFJ, Li NT, Matthews L, May B, Milacic M, Mohammadi H, Petryszak R, Rothfels K, Shamovsky V, Stephan R, Tiwari K, Weiser J, Wright A, Gillespie M, Wu G, Stein L, Hermjakob H, D'Eustachio P

Nucleic acids research2026

DOI: 10.1093/nar/gkaf1223 PMID: 41251150

Application of Large Language Models for Annotating Genes into Reactome Pathways.

Wu G, Matthews L, Boyer N, Milacic M, Beavers D, Li NT, May B, Rothfels K, Shamovsky V, Stephan R, Gillespie M, Hermjakob H, D'Eustachio P, Stein L

bioRxiv : the preprint server for biology2025Senior author

DOI: 10.64898/2025.12.20.695723 PMID: 41497647

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

Mohammadi H, Almodaresi F, Hogue GFJ, Wright A, Orlic-Milacic M, Li NT, Mawani A, Stein L

bioRxiv : the preprint server for biology2025Senior author

DOI: 10.64898/2025.12.12.693752 PMID: 41427274

Setting up JBrowse 2 for Visualizing Genome Synteny.

Diesh C, Stevens G, Cain S, Stein L, Holmes I

Current protocols2025

DOI: 10.1002/cpz1.70236 PMID: 41347761

In silico generation of synthetic cancer genomes using generative AI.

Díaz-Navarro A, Zhang X, Jiao W, Wang B, Stein L

Cell genomics2025Senior author

DOI: 10.1016/j.xgen.2025.100969 PMID: 40803317

Intra-tumoral spatial heterogeneity in breast cancer quantified using high-dimensional protein multiplexing and single cell phenotyping.

Cheung AM, Wang D, Quintayo MA, Yerofeyeva Y, Spears M, Bartlett JMS, Stein L, Bayani J, Yaffe MJ

Breast cancer research : BCR2025

DOI: 10.1186/s13058-025-02038-1 PMID: 40399910

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Lincoln Stein

Research

Latest papers

Latest funding

Firefox, a protein encoded by circular PVT1, is essential for MYC-driven oncogenesis.

Honeybadger, a micropeptide encoded by an alternative PVT1 transcript, is a critical negative regulator of RAS-MAPK signaling in MYC-driven tumors.

Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2.

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

The Reactome Knowledgebase 2026.

Application of Large Language Models for Annotating Genes into Reactome Pathways.

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

Setting up JBrowse 2 for Visualizing Genome Synteny.

In silico generation of synthetic cancer genomes using generative AI.

Intra-tumoral spatial heterogeneity in breast cancer quantified using high-dimensional protein multiplexing and single cell phenotyping.

Using deep learning to estimate breast cancer recurrence scores from histopathology images

DCIS-Precise: A Genomics-Driven Model for Predicting DCIS Response to Radiation

The Cancer Genome Collaboratory

The cancer genome collaboratory

Frequent collaborators

David Malkin

Melanie Spears

Samira Mubareka

Guillaume Bourque

Vincent Ferretti

Vijay Ramaswamy

Livia Garzia

Natalie Prystajecky

Caroline Colijn

Yann Joly

Melanie Courtot

Nada Jabado

Trevor Pugh

Xi Huang

Faiyaz Notta

Steven Gallinger

BO WANG

Gary Bader

Rashmi Kothary

Quaid Morris

Jordan Lerner-Ellis

Anna Goldenberg

Sheila Singh

Benoit Chabot

Ana Duggan