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Zhaolei Zhang

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ProfessorTerrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto

Zhaolei Zhang

Professor

Terrence Donnelly Centre for Cellular and Biomolecular Research

Temerty Faculty of Medicine

University of Toronto

Toronto, Ontario, Canada

Scholar

Supervision signals

Professors usually supervise graduate students in their department's programs.
32 publications in the last five years, latest in 2026.
Senior (last) author on 7 recent papers, a sign of leading a research group.
Principal investigator on 5 research grants (3 CIHR, 2 NSERC), most recently in 2017.

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

122

Publications

Collaborators

Grants

Publications by year

Counts cover the publications linked to this profile. Citations and the h-index appear when the source records them.

Education

Graduate Student
MBB

Profiles and links

University Profile Google Scholar

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Signals and details

Research

Read how they describe their research on their University of Toronto profile.

Latest papers

Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma.
Nature · 2026
LLOT: application of Laplacian Linear Optimal Transport in spatial transcriptome reconstruction.
Biometrics · 2026 · senior author
MULGONET: An interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery.
Fundamental research · 2026

All 122 publications

Latest funding

Computational Modeling of Gene Regulation
NSERC · 2017 · Principal investigator
$156,000
Epigenomics of major depressive disorder: dissecting environmental, heritable, and stochastic contributions
CIHR · 2013 · Co-investigator
$1,191,865
Evolution and genetic variation of microRNA regulatory network in humans
CIHR · 2011 · Nominated PI
$688,745

All 8 grants and awards

122 publications.

Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma.

Zhang J, Ong W, Rasnitsyn A, Gonzalez RD, Lopez Gutierrez R, Balin P, Saadeldin A, Wu X, Vladoiu MC, Santa-Maria Lopez V, Gonzalez-Salinas F, Yadav N, Mohanakrishnan D, Boosi Narayana Rao K, Mooli RGR, Najem H, Pacheco S, Kharas K, Richman C, Przelicki D, Wang EY, Su H, Curry RN, Yang R, Kameda-Smith MM, Livingston B, Scott D, Luo Z, Xia M, Abeysundara N, Erickson AW, Mankahla N, Hu LZ, Pan C, Suarez R, Huang N, Wu Y, Wang H, Douglas T, Pallota J, Hébert S, Ng K, Mantione K, Whetstone H, Maan H, Lakkis H, Lee J, Ramakrishnan SK, Pei Y, Tang Y, Lin FY, Aldave G, Gallo M, Friedlander RM, Notta F, Donovan LK, Chintagumpala M, Wang B, Li Y, De Carvalho DD, Zhang Z, Mao Y, Hua W, Eberhart C, Lucas CG, Venneti S, Sorensen PH, Delaidelli A, Li H, Zhou W, Kirk J, Tang DG, Jiang T, Liu H, Lathia JD, Suzuki H, Rich JN, Stein LD, Jabado N, Ramaswamy V, Lu QR, Heimberger AB, Daniels C, Michealraj KA, Kleinman CL, Taylor MD

Nature2026

DOI: 10.1038/s41586-026-10264-6 PMID: 41882358

LLOT: application of Laplacian Linear Optimal Transport in spatial transcriptome reconstruction.

Zhu J, Zhang K, Kong D, Zhang Z

Biometrics2026Senior author

DOI: 10.1093/biomtc/ujag046 PMID: 41885893

MULGONET: An interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery.

Lan W, Tang Z, Liao H, Chen Q, Chen YP, Zhang Z, Wang J

Fundamental research2026

DOI: 10.1016/j.fmre.2025.01.004 PMID: 41647565

scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data.

Zou Z, Liu Y, Bai Y, Luo J, Zhang Z

PLoS computational biology2025Senior author

DOI: 10.1371/journal.pcbi.1012904 PMID: 40184563

Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning.

Yu Z, Yang Y, Chen X, Wong KC, Zhang Z, Zhao Y, Li X

Advanced science (Weinheim, Baden-Wurttemberg, Germany)2025

DOI: 10.1002/advs.202410081 PMID: 39605202

C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes.

Nabeel-Shah S, Pu S, Burns JD, Braunschweig U, Ahmed N, Burke GL, Lee H, Radovani E, Zhong G, Tang H, Marcon E, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF

Molecular cell2024

DOI: 10.1016/j.molcel.2024.08.037 PMID: 39303720

Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.

Yang Y, Li G, Pang K, Cao W, Zhang Z, Li X

Advanced science (Weinheim, Baden-Wurttemberg, Germany)2024

DOI: 10.1002/advs.202407013 PMID: 39159140

Recruitment of the m6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

Nabeel-Shah S, Pu S, Burke GL, Ahmed N, Braunschweig U, Farhangmehr S, Lee H, Wu M, Ni Z, Tang H, Zhong G, Marcon E, Zhang Z, Blencowe BJ, Greenblatt JF

Genome biology2024

DOI: 10.1186/s13059-024-03392-7 PMID: 39300486

Mutations in myeloid transcription factors and activated signaling genes predict chronic myeloid leukemia outcomes.

Perusini MA, Žáčková D, Kim T, Pagnano K, Pavlovsky C, Ježíšková I, Kvetková A, Jurček T, Kim J, Yoo Y, Yi S, Lee H, Kim KH, Chang M, Capo-Chichi JM, Medeiros JJF, Arruda A, Minden M, Zhang Z, Abelson S, Mayer J, Hwan Kim DD

Blood advances2024

DOI: 10.1182/bloodadvances.2023012127 PMID: 38447114

scGREAT: Transformer-based deep-language model for gene regulatory network inference from single-cell transcriptomics.

Wang Y, Chen X, Zheng Z, Huang L, Xie W, Wang F, Zhang Z, Wong KC

iScience2024

DOI: 10.1016/j.isci.2024.109352 PMID: 38510148

Computational Modeling of Gene Regulation

Principal investigatorNSERC2017Discovery Grants Program - Individual

Principal investigators: ZHANG, ZHAOLEI

$156,000

Epigenomics of major depressive disorder: dissecting environmental, heritable, and stochastic contributions

Co-investigatorCIHR2013Operating Grant

Principal investigators: Petronis, Arturas

Keywords: Animal Models; Computational Biology; Dna Modification; Environment; Epigenetic Heritability; Epigenomics; Epimutations; Major Depressive Disorder; Monozygotic Twins; Post-Mortem Brain

$1,191,865

Evolution and genetic variation of microRNA regulatory network in humans

Nominated PICIHR2011Operating Grant

Principal investigators: Zhang, Zhaolei

Keywords: Comparative Genomics; Evolution; Foxp2; Human Genetics; Microrna; Pigmentation; Population Genetics; Single Nucleotide Polymorphism

$688,745

A collaborative research program to integrate genomic and proteomic data for the identification of predictive biomarkers in bladder cancer

Nominated PICIHR2009Catalyst Grant: Bioinformatics Approaches to Cancer Research

Principal investigators: Zhang, Zhaolei; Evans, Kenneth R; Feilotter, Harriet E; Squire, Jeremy A; Van Der Kwast, Theodorus H

Keywords: Biomarkers; Bionformatics; Bladder Cancer; Cancer Diagnostics; Genomics; Proteomics

$100,000

Mapping the reference genetic network of a eukaryotic cell with automated yeast genetic analysis

Co-investigatorCIHR2009Operating Grant

Principal investigators: Boone, Charles M

Keywords: Complex Genetics; Functional Genomics; Genetic Conservation; Genetic Networks; Synthetic Genetic Array; Yeast Genetics

$2,099,007

Computational modeling of gene regulation

Principal investigatorNSERC2009Discovery Grants Program - Individual

Principal investigators: Zhang, Zhaolei

$125,000

Global Exploration of Cellular Networks and Pathways using Yeast Phenomics

Co-investigatorCIHR2009Operating Grant

Principal investigators: Boone, Charles M

Keywords: Cell Biology; Functional Genomics; Genetic Networks; Phenomics; Synthetic Genetic Array; Yeast Genetics

$737,737

Canadian Urogenital Microbiome Program: establishing the microbiota with immunity, sexual transmitted diseases and cancer

Nominated PICIHR2009Canadian Microbiome Initiative - LOI

Principal investigators: Zhang, Zhaolei; Evans, Kenneth R; Fleshner, Neil E; Gray-Owen, Scott D; Kaul, Rupert

Keywords: Infection; Metagenomics; Microbiome; Sexual Transmitted Disease; Urologica Cancer

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

Profile data last refreshed on September 25, 2026 from the university directory, publication records and CIHR, NSERC and SSHRC funding.

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Zhaolei Zhang

Research

Latest papers

Latest funding

Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma.

LLOT: application of Laplacian Linear Optimal Transport in spatial transcriptome reconstruction.

MULGONET: An interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery.

scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data.

Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning.

C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes.

Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.

Recruitment of the m6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

Mutations in myeloid transcription factors and activated signaling genes predict chronic myeloid leukemia outcomes.

scGREAT: Transformer-based deep-language model for gene regulatory network inference from single-cell transcriptomics.

Computational Modeling of Gene Regulation

Epigenomics of major depressive disorder: dissecting environmental, heritable, and stochastic contributions

Evolution and genetic variation of microRNA regulatory network in humans

A collaborative research program to integrate genomic and proteomic data for the identification of predictive biomarkers in bladder cancer

Mapping the reference genetic network of a eukaryotic cell with automated yeast genetic analysis

Computational modeling of gene regulation

Global Exploration of Cellular Networks and Pathways using Yeast Phenomics

Canadian Urogenital Microbiome Program: establishing the microbiota with immunity, sexual transmitted diseases and cancer

Frequent collaborators

Andrew Emili

Charles Boone

Jack Greenblatt

John Parkinson

Hyewon Lee

BO WANG

Mark Minden

Brenda Andrews

Rajat Kumar

Mohan Babu

Igor Stagljar

Anna Goldenberg

Andrew Freywald

Janice Robertson

Jean-Philippe Lambert

Anne-Claude Gingras

Michael Gollob

Darrell Mousseau

Jonas Mattsson

Vincent Tropepe