Yue Li, McGill University

Research

Chromatin Accessibility Epigenetics Gene Regulatory Network Genome Foundation Model Machine Learning Major Depressive Disorder Single-Cell Genomics Single-Cell Transcriptomics

Latest papers

Epidermotropism of T-lymphocytes may provide insight into the pathogenesis of morphea.
JAAD international · 2026
Implementing a Domain-Adapted GPT Model to Support Genetic Counseling in a Genodermatology Clinic.
Journal of the American Academy of Dermatology · 2026
scE2TM improves single-cell embedding interpretability and reveals cellular perturbation signatures.
Nature communications · 2026 · senior author

All 61 publications

Latest funding

Mapping cellular diversity in the human dorsal raphe: Implications for depression and antidepressant mechanisms of action
CIHR · 2025 · Co-investigator
$1,147,500
Single-cell multi-omic integration and gene regulatory network inference towards personalized psychiatry for major depressive disorder
CIHR · 2025 · Nominated PI
$933,300
Extracellular vesicles (EVs) as a window into the depressed brain: an investigation of brain-cell derived EVs
CIHR · 2023 · Co-investigator
$1,296,676

All 14 grants and awards

61 publications.

01

Epidermotropism of T-lymphocytes may provide insight into the pathogenesis of morphea.

Khoury L, Osakwe A, Touma F, Martinez-Jaramillo E, Ghazal S, Rajaram A, Kaouache M, Alqahtani A, Kizilay O, Chergui M, Lefrançois P, Li Y, Litvinov IV, Netchiporouk E

JAAD international2026

DOI: 10.1016/j.jdin.2026.01.011 PMID: 42756642

02

Implementing a Domain-Adapted GPT Model to Support Genetic Counseling in a Genodermatology Clinic.

Udupa M, Mija LA, Bendayan E, Alamari A, Cutumisu M, Li Y, Joly-Chevrier M, Leblanc J, Tardif J, Martinez-Jaramillo E, Nedjar H, Rahme E, Foulkes WD, Marino TC, Netchiporouk E

Journal of the American Academy of Dermatology2026

DOI: 10.1016/j.jaad.2026.09.050 PMID: 42759719

03

scE2TM improves single-cell embedding interpretability and reveals cellular perturbation signatures.

Chen H, Lu Y, Zhao Y, Dai Z, Wang FL, Li Q, Rao Y, Li Y

Nature communications2026Senior author

DOI: 10.1038/s41467-026-76825-5 PMID: 42744811

04

Investigation of Epigenetic Age Acceleration in Juvenile Scleroderma.

Vu D, Jeremian R, Moustaqim-Barrette A, Osakwe A, Li Y, Torok K, Netchiporouk E

Journal of cutaneous medicine and surgery2026

DOI: 10.1177/12034754261470786 PMID: 42544405

05

scTimeBench: a streamlined benchmarking platform for single-cell time-series analysis.

Osakwe A, Huang EH, Li Y

Bioinformatics (Oxford, England)2026Senior author

DOI: 10.1093/bioinformatics/btag414 PMID: 42635195

06

MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences.

Gu J, Chen C, Li Y

Bioinformatics (Oxford, England)2026Senior author

DOI: 10.1093/bioinformatics/btag222 PMID: 42412822

07

DNA-aware evaluation and debiasing of sequence-to-function models.

Cakmakci D, Li Y

Bioinformatics (Oxford, England)2026Senior author

DOI: 10.1093/bioinformatics/btag266 PMID: 42412799

08

Immune-stromal dysregulation and senescence in chronic spontaneous urticaria.

Abboud A, Osakwe A, Martinez-Jaramillo E, Khoury L, Vu D, Chergui M, Lefrançois P, Xu L, Ben-Shoshan M, Osman M, Giménez-Arnau AM, Li Y, Netchiporouk E

The journal of allergy and clinical immunology. Global2026

DOI: 10.1016/j.jacig.2026.100712 PMID: 42436760

09

Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.

Raghavan V, Yoon B, Fonseca GJ, Li Y, Ding J

Molecular systems biology2026

DOI: 10.1038/s44320-026-00213-w PMID: 42092184

10

GFETM: Genome foundation-based embedded topic model for scATAC-seq modeling.

Fan Y, Osakwe A, Han S, Li Y, Ding J, Li Y

Cell systems2026Senior author

DOI: 10.1016/j.cels.2026.101563 PMID: 41932342

Mapping cellular diversity in the human dorsal raphe: Implications for depression and antidepressant mechanisms of action

Co-investigatorCIHR2025Project Grant

Principal investigators: Turecki, Gustavo X

Keywords: Antidepressants; Depression; Human Post-Mortem Brain Tissues; Machine Learning; Serotonin; Single-Cell Transcriptomics; Spatial Transcriptomics

$1,147,500

Single-cell multi-omic integration and gene regulatory network inference towards personalized psychiatry for major depressive disorder

Nominated PICIHR2025Project Grant

Principal investigators: Li, Yue

Keywords: Chromatin Accessibility; Epigenetics; Gene Regulatory Network; Genome Foundation Model; Machine Learning; Major Depressive Disorder; Single-Cell Genomics; Single-Cell Transcriptomics

$933,300

Extracellular vesicles (EVs) as a window into the depressed brain: an investigation of brain-cell derived EVs

Co-investigatorCIHR2023Project Grant

Principal investigators: Turecki, Gustavo X

Keywords: Antidepressant Response; Biomarkers; Depression; Extracellular Vesicles; Microrna

$1,296,676

An Integrative Single Cell Epigenetic Map for the study of Type-2 Diabetes.

SupervisorCIHR2023Doctoral Research Award: Canada Graduate Scholarships

Principal investigators: Osakwe, Adrien

Keywords: Bioinformatics; Genomics; Metabolism; Single Cell Genomics; Statistical Modeling; Type-2 Diabetes

$105,000

High resolution, single-cell characterization of molecular and cellular networks, within and across brain regions, related to sex-associated differences in major depressive disorder.

Co-investigatorCIHR2022Project Grant

Principal investigators: Nagy, Corina

Keywords: Depression; Functional Genomics; Human Research; Neurobiology; Postmortem Brain; Psychiatric Phenotype; Sex-Based Differences; Single-Cell

$872,100

Multi-omic single-cell, electronic health record, and biomedical knowledge graph data integration using interpretable deep learning approaches

Principal investigatorNSERC2022Alliance Grants

Principal investigators: Li, Yue Y

$25,000

Extracellular vesicles (EVs) as a window into the depressed brain: an investigation of brain-cell derived EVs

Co-investigatorCIHR2022Project Grant

Principal investigators: Turecki, Gustavo X

Keywords: Antidepressant Response; Biomarkers; Depression; Extracellular Vesicles; Microrna

$100,000

Canada Research Chair - Tier 2

Nominated PICIHR2022Canada Research Chairs - CIHR Funded - Tier 2

Principal investigators: Li, Yue

Keywords: Crc

$600,000

Cross-province federated machine learning of electronic health records in Canada

Principal investigatorNSERC2022Alliance Grants

Principal investigators: Li, Yue Y

$135,000

Single-cell, high-throughput characterization of the depressed brain

Co-investigatorCIHR2022Project Grant

Principal investigators: Turecki, Gustavo X

Keywords: Depression; Eqtls; Human Post-Mortem Brain Tissues; Machine Learning; Mood Regulation; Single-Cell Transcriptomics

$1,323,450

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

Frequent collaborators

Medicine
Psychiatry
Epidemiology and Biostatistics
Dermatology
Human Genetics
Meakins-Christie Laboratories
Physics
Other

Co-authors at McGill University, colored by department. Thicker lines mean more shared papers; select anyone to open their profile and their own map.

Simon Gravel

Human Genetics

4 shared papers, latest 2025

Jun Ding

Meakins-Christie Laboratories

3 shared papers, latest 2026

Hua Gu

Molecular Immunology

2 shared papers, latest 2021

David Buckeridge

Epidemiology, Biostatistics and Occupational Health

2 shared papers, latest 2025

Alain Dagher

Neurology and Neurosurgery

2 shared papers, latest 2021

Na Li

Community Health Sciences

1 shared papers, latest 2025

Moshe Ben-Shoshan

Allergy and Clinical Immunology

1 shared papers, latest 2026

Yasser Iturria Medina

Neurology and Neurosurgery

1 shared papers, latest 2024

Na Li

Computing and Software

1 shared papers, latest 2025

Elham Rahme

Medicine

1 shared papers, latest 2026

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their CIHR grant from 2025

Subject: Prospective PhD student: Chromatin Accessibility Dear Professor Li, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "Epidermotropism of T-lymphocytes may provide insight into the pathogenesis of morphea." (2026), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your CIHR-funded project "Single-cell multi-omic integration and gene regulatory network inference towards personalized psychiatry for major depressive disorder" (2025), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]

Yue Li

Research

Latest papers

Latest funding

Epidermotropism of T-lymphocytes may provide insight into the pathogenesis of morphea.

Implementing a Domain-Adapted GPT Model to Support Genetic Counseling in a Genodermatology Clinic.

scE2TM improves single-cell embedding interpretability and reveals cellular perturbation signatures.

Investigation of Epigenetic Age Acceleration in Juvenile Scleroderma.

scTimeBench: a streamlined benchmarking platform for single-cell time-series analysis.

MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences.

DNA-aware evaluation and debiasing of sequence-to-function models.

Immune-stromal dysregulation and senescence in chronic spontaneous urticaria.

Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.

GFETM: Genome foundation-based embedded topic model for scATAC-seq modeling.

Multi-omic single-cell, electronic health record, and biomedical knowledge graph data integration using interpretable deep learning approaches

Cross-province federated machine learning of electronic health records in Canada

Frequent collaborators

Ariane Marelli

Elena Netchiporouk

Simon Gravel

Danilo Bzdok

Jun Ding

Corina Nagy

Gustavo Turecki

Robert Sladek

David Buckeridge

Danilo Bzdok

Hua Gu

David Buckeridge

Alain Dagher

Luda Diatchenko

Xiangfei Meng

Jean Caron

Eva Kaufmann

Paul Khairy

Na Li

Yongjin Park

Qihuang Zhang

Naguib Mechawar

Moshe Ben-Shoshan

Michael Meaney

Stanley Nattel

Yasser Iturria Medina

Na Li

Maziar Divangahi

Mathieu Blanchette

Elham Rahme