Faculty profile

Mathieu Lupien

ResearcherMedical BiophysicsUniversity 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 may be missing. Find their university profile.

Mathieu Lupien

Researcher

Medical Biophysics

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.
38 publications in the last five years, latest in 2026.
Senior (last) author on 11 recent papers, a sign of leading a research group.
Principal investigator on 11 research grants (11 CIHR), most recently in 2025.
Supervised 9 trainees who won CIHR awards, most recently in 2019.

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

116

Publications

1,389

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 Chromatin Epigenetic Epigenetics Plasticity Regulatory Elements Repetitive Dna Transcription Factor

Latest papers

Transposable elements shape stemness in normal and leukemic hematopoiesis.
Nature genetics · 2026 · senior author
Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.
Genome biology · 2026
Preclinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma: An Applied Case Report.
Cancer research communications · 2026

All 116 publications

Latest funding

Finding vulnerabilities in advanced breast cancer from the chromatin state of repeat DNA
CIHR · 2025 · Nominated PI
$1,147,500
Discovery of sex-dimorphic leukemia-protective programs embedded in human hematopoietic stem cells
CIHR · 2025 · Co-investigator
$1,591,200
The ELDER Study: Timing cancer by tracking how tissue-specific aging shapes malignancy
CIHR · 2025 · Principal investigator
$2,000,000

All 29 grants and awards

116 publications.

Transposable elements shape stemness in normal and leukemic hematopoiesis.

Grillo G, Nadorp B, Qamra A, Drylie B, Mitchell A, Arlidge C, Nand A, Takayama N, Murison A, Madani Tonekaboni SA, Kang KK, Arruda A, Wang JCY, Minden MD, Deniz Ö, Boutzen H, Dick JE, Lupien M

Nature genetics2026Senior author

DOI: 10.1038/s41588-026-02585-z PMID: 42082719

Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.

Moreno-Rodriguez T, Zhang M, Lundberg A, Shrestha R, Sjöström M, Pasam A, Chan J, Devereux L, Foye A, Zhu X, Weinstein AS, Trigos AS, Wyatt AW, Alumkal JJ, Small EJ, Aggarwal R, Dehm SM, Bootsma ML, Zhao SG, Lupien M, Feng FY, Sandhu S, Quigley DA

Genome biology2026

DOI: 10.1186/s13059-026-04074-2 PMID: 41987223

Preclinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma: An Applied Case Report.

Radulovich N, Pina PS, Udaskin ML, Li Q, Nixon KCJ, Xie IY, Nand A, Rosen JC, Li M, Hodgson A, Pham NA, Oza AM, Lupien M, Rottapel R, Tsao MS, Lheureux S

Cancer research communications2026

DOI: 10.1158/2767-9764.crc-25-0634 PMID: 41886729

A chromatin-informed transcriptional regulatory framework to stratify patients and guide therapy selection in triple-negative breast cancer.

Bahl S, Dogan-Artun N, Nguyen J, Mahmoud H, Ba-Alawi W, Madani Tonekaboni SA, Kang KK, McGuire M, Tobin C, Silvester J, Savage P, Cressot L, Nand A, Feng G, Guilhamon P, Mer AS, Arlidge C, Elliott MJ, Park M, Cescon DW, Haibe-Kains B, Lupien M

Nature communications2026Senior author

DOI: 10.1038/s41467-026-76385-8 PMID: 42749733

METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers.

Xu X, Wang Y, Zhu H, Lam M, Luo W, Teng M, Liu Y, Guo WY, Aastha A, Xu X, Chen S, Ci X, Wang S, Zeng Y, Zhu G, Kislinger T, Lupien M, Tsao MS, He HH

Nature cancer2026

DOI: 10.1038/s43018-026-01117-2 PMID: 41652220

Circulating Cell-Free DNA Methylation Profiling Enables Detection, Distinction, and Estrogen Receptor Status Classification of Advanced Breast Cancer.

Main SC, Elliott MJ, Singhawansa A, Zou J, Zeng Y, Cheng N, Yu C, Hilton JF, Awadalla P, He HH, Bedard PL, Lupien M, Bratman SV, Cescon DW

Cancer research2026

DOI: 10.1158/0008-5472.can-26-0076 PMID: 42268298

A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.

Zeng Y, Abelman DD, Singhawansa A, Cheng N, Fang Y, Main SC, Bell E, Ye W, Luo P, Wilson SL, Stutheit-Zhao EY, Wong D, Znassi N, Chen K, Mohanraj S, Sanz-Garcia E, Notta F, Ghanekar A, Awadalla P, Lok BH, Hoffman MM, Kim RH, Zadeh G, De Carvalho DD, Bratman SV, Lupien M, Pugh TJ, He HH

Nature cancer2026

DOI: 10.1038/s43018-026-01116-3 PMID: 41714824

Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution.

Furlano K, Keshavarzian T, Biernath N, Fendler A, de Santis M, Weischenfeldt J, Lupien M

International journal of cancer2026Senior author

DOI: 10.1002/ijc.35327 PMID: 39853587

Meeting report: 10th Annual Canadian Conference on Epigenetics.

Nouruzi S, Grégoire S, Lupien M, Hirst M

Biochemistry and cell biology = Biochimie et biologie cellulaire2026

DOI: 10.1139/bcb-2026-0013 PMID: 41734369

Numbat-multiome: inferring copy number variations by combining RNA and chromatin accessibility information from single-cell data.

Li R, Alberge JB, Keshavarzian T, Tsuji J, Gustafsson J, Rahmat M, Lightbody ED, Deng SL, Riviero S, Miller M, Naz Cemre Kalayci F, Wiestner A, Sun C, Lupien M, Ghobrial I, Parry E, Gao T, Getz G

Briefings in bioinformatics2025

DOI: 10.1093/bib/bbaf516 PMID: 41104806

Finding vulnerabilities in advanced breast cancer from the chromatin state of repeat DNA

Nominated PICIHR2025Project Grant

Principal investigators: Lupien, Mathieu

Keywords: Breast Cancer; Chromatin; Epigenetic; Plasticity; Regulatory Elements; Repetitive Dna; Single-Cell Multiome; Transcription Factor; Transposable Elements

$1,147,500

Discovery of sex-dimorphic leukemia-protective programs embedded in human hematopoietic stem cells

Co-investigatorCIHR2025Project Grant

Principal investigators: Dick, John E; Kaufmann, Kerstin B

Keywords: Acute Myeloid Leukemia Biology,; Early Leukemogenesis; Human Hematopoietic Stem Cells; Human Leukemia Stem Cell Biology; Myeloproliferative Neoplasm Biology; Preleukemia; Sccut&Tag; Sex Dimorphisms; Single Cell Atac/Rna-Sequencing; Target-Seq,

$1,591,200

The ELDER Study: Timing cancer by tracking how tissue-specific aging shapes malignancy

Principal investigatorCIHR2025Team Grant: Bringing Bio to Cancer Prev- Int Japan-Canada Geroscience

Principal investigators: Notta, Faiyaz; Gallinger, Steven; Grant, Robert; Lupien, Mathieu; Yachida, Shinichi

Keywords: Aging; Clonal Evolution; Colorectal Cancer; Early-Onset; Endogenous Retroviral Elements; Epigenetic; Metabolic Reprogramming; Microbiome; Pancreatic Ductal Adenocarcinoma; Patient-Derived Organoid

$2,000,000

Discovery of epigenetic determinants regulating stemness to target the eradication of human pre-leukemic and leukemic stem cells

Principal investigatorCIHR2024Project Grant

Principal investigators: Dick, John E; Lupien, Mathieu

Keywords: Aml Biology; Crispr-Editing Of Human Hsc; Epigenetics; Human Hematopoietic Stem Cells; Human Leukemia Stem Cells; Non-Coding Regulatory Elements; Pre-Leukemic Human Hsc; Single Cell Atac/Rna-Sequencing; Single Cell Multiomics; Xenografting

$1,419,942

Finding vulnerabilities in breast cancer from the state of chromatin accessibility at transposable elements

Nominated PICIHR2024Pr. Gr.- PA: Sex/Gender in Health Res.- Understanding sex/gender mech./processes

Principal investigators: Lupien, Mathieu

Keywords: Breast Cancer; Chromatin; Epigenetic; Plasticity; Regulatory Elements; Repetitive Dna; Single-Cell Multiome; Transcription Factor; Transposable Elements

$100,000

AR locus amplification awakens transposable elements to promote metastatic castration-resistant prostate cancer

Nominated PICIHR2023Project Grant

Principal investigators: Lupien, Mathieu

Keywords: Androgen Receptor; Chromatin; Epigenetic; Metastasis; Plasticity; Prostate Cancer; Regulatory Elements; Repetitive Dna; Transcription Factor; Transposable Elements

$872,100

Organoids to guide Post-resistance Therapy In driver MutAted Lung cancers (OPTIMAL)

Co-investigatorCIHR2020Project Grant

Principal investigators: Liu, Geoffrey

Keywords: Anaplastic Lymphoma Kinase Rearrangements; Drug Resistance Mechanisms; Drug Sensitivity Screening; Epidermal Growth Factor Receptor; Epigenetics; Genomics; Non-Small Cell Lung Cancer; Patient-Derived Organoids; Ros1 Rearrangements; Trascriptomics

$1,147,500

Tackling Childhood Brain Cancer at the root to improve survival and quality of life

Co-investigatorCIHR2020Genomics and Precision Health Top-up

Principal investigators: Taylor, Michael D

Keywords: Data Portal; Human Brain Development; Pediatric Brain Tumours

$100,000

Chromatin context of somatic mutations delineate oncogenic drivers in triple-negative breast cancer

Nominated PICIHR2019Project Grant

Principal investigators: Lupien, Mathieu

Keywords: Breast Cancer; Chromatin; Endocrine; Epigenetic; Gene Expression; Genetic; Genome; Mutations; Noncoding; Transcriptional Regulation

$841,500

Targeting protein arginine methyltransferases as a therapy for triple negative breast cancer

SupervisorCIHR2019CIHR Fellowship

Principal investigators: WU, QIN

Keywords: Chemical Probes; Epigenetic Therapy; Molecular Predictors; Triple Negative Breast Cancer

$90,000

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

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Mathieu Lupien

Research

Latest papers

Latest funding

Transposable elements shape stemness in normal and leukemic hematopoiesis.

Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.

Preclinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma: An Applied Case Report.

A chromatin-informed transcriptional regulatory framework to stratify patients and guide therapy selection in triple-negative breast cancer.

METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers.

Circulating Cell-Free DNA Methylation Profiling Enables Detection, Distinction, and Estrogen Receptor Status Classification of Advanced Breast Cancer.

A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.

Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution.

Meeting report: 10th Annual Canadian Conference on Epigenetics.

Numbat-multiome: inferring copy number variations by combining RNA and chromatin accessibility information from single-cell data.

Frequent collaborators

Benjamin Haibe-Kains

Dalia Barsyte-Lovejoy

Nada Jabado

Mark Bernstein

Marco Gallo

Thomas Kislinger

Stephane Angers

Sunit Das

Ming-Sound Tsao

Samuel Weiss

Vijay Ramaswamy

Sheila Singh

Daniel Schramek

David Cescon

Annie Huang

Morag Park

Sorana Morrissy

Alejandro Berlin

Katie Houlahan

Rama Khokha

Gelareh Zadeh

Faiyaz Notta

Chiara Gorrini

Amina Zoubeidi

Guillaume Bourque

Eric Bouffet

Morag Park

Cheryl Arrowsmith

Martin Hirst

Uri Tabori

Stefan Hofer

Robert Rottapel

Tak Mak

Ian Scott

Jack Greenblatt

Jacques Simard

Georgia Perona-Wright

Nizar Bahlis

John Lee

Jean Gariepy