Jiarui Ding, University of British Columbia

Research

Crc

Latest papers

Computational identification of antigen-specific T cell groups through generative epitope modeling.
iScience · 2026 · senior author
ProtoCloud: A prototypical self-explaining model for single-cell analysis.
Cell genomics · 2026 · senior author
TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects.
Nature biotechnology · 2026

All 26 publications

Latest funding

Uncovering the latent structure in single-cell multi-omics data to study human diseases
NSERC · 2022 · Principal investigator
$87,000
Uncovering the latent structure in single-cell multi-omics data to study human diseases
NSERC · 2022 · Principal investigator
$12,500
Canada Research Chair - Tier 2
CIHR · 2022 · Nominated PI
$600,000

All 3 grants and awards

26 publications.

01

Computational identification of antigen-specific T cell groups through generative epitope modeling.

Ma M, Tu W, Vasquez-Rios C, Ding J

iScience2026Senior author

DOI: 10.1016/j.isci.2026.116505 PMID: 42491743

02

ProtoCloud: A prototypical self-explaining model for single-cell analysis.

Guo K, Ding J

Cell genomics2026Senior author

DOI: 10.1016/j.xgen.2026.101217 PMID: 41997134

03

TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects.

Wenkel F, Tu W, Masschelein C, Shirzad H, Hodgson L, Bendidi I, Eastwood C, Whitfield ST, Russell C, El Mesbahi Y, Ding J, Fay MM, Earnshaw B, Noutahi E, Denton AK

Nature biotechnology2026

DOI: 10.1038/s41587-026-03113-4 PMID: 42067667

04

CellUntangler: Separating distinct biological signals in single-cell data with deep generative models.

Chen S, Regev A, Condon A, Ding J

Cell genomics2026Senior author

DOI: 10.1016/j.xgen.2025.101073 PMID: 41330382

05

Single-cell multiomics data integration and generation with scPairing.

Niu J, Vasquez-Rios C, Ding J

Cell reports methods2025Senior author

DOI: 10.1016/j.crmeth.2025.101211 PMID: 41151585

06

An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission.

Ding J, Garber JJ, Uchida A, Lefkovith A, Carter GT, Vimalathas P, Canha L, Dougan M, Staller K, Yarze J, Delorey TM, Rozenblatt-Rosen O, Ashenberg O, Graham DB, Deguine J, Regev A, Xavier RJ

Nature communications2024First author

DOI: 10.1038/s41467-024-47647-0 PMID: 38637492

07

Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury.

Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A

Nature immunology2023

DOI: 10.1038/s41590-023-01437-w PMID: 36807640

08

Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma.

Aoki T, Chong LC, Takata K, Milne K, Hav M, Colombo A, Chavez EA, Nissen M, Wang X, Miyata-Takata T, Lam V, Viganò E, Woolcock BW, Telenius A, Li MY, Healy S, Ghesquiere C, Kos D, Goodyear T, Veldman J, Zhang AW, Kim J, Saberi S, Ding J, Farinha P, Weng AP, Savage KJ, Scott DW, Krystal G, Nelson BH, Mottok A, Merchant A, Shah SP, Steidl C

Cancer discovery2020

DOI: 10.1158/2159-8290.cd-19-0680 PMID: 31857391

09

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

Ding J, Condon A, Shah SP

Nature communications2018First author

DOI: 10.1038/s41467-018-04368-5 PMID: 29784946

10

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Ding J, Shah S, Condon A

Bioinformatics (Oxford, England)2016First author

DOI: 10.1093/bioinformatics/btw227 PMID: 27153661

Uncovering the latent structure in single-cell multi-omics data to study human diseases

Principal investigatorNSERC2022Discovery Grants Program - Individual

Principal investigators: Ding, Jiarui

$87,000

Uncovering the latent structure in single-cell multi-omics data to study human diseases

Principal investigatorNSERC2022Discovery Launch Supplement

Principal investigators: Ding, Jiarui

$12,500

Canada Research Chair - Tier 2

Nominated PICIHR2022Canada Research Chairs - CIHR Funded - Tier 2

Principal investigators: Ding, Jiarui

Keywords: Crc

$600,000

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

Molecular Oncology
Pathology and Laboratory Medicine
Microbiology and Immunology
Experimental Therapeutics
Genome Sciences Centre
Genetics
Medicine/Obstetrics & Gynecology
Other

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

Ali Bashashati

Pathology and Laboratory Medicine

7 shared papers, latest 2015

Sohrab Shah

Faculty

5 shared papers, latest 2016

Samuel Aparicio

Molecular Oncology

5 shared papers, latest 2015

Martin Hirst

Microbiology and Immunology

5 shared papers, latest 2012

David Huntsman

Molecular Oncology

3 shared papers, latest 2015

Christian Steidl

Experimental Therapeutics

3 shared papers, latest 2020

Steven Jones

Genetics

2 shared papers, latest 2013

Inanc Birol

Genome Sciences Centre

2 shared papers, latest 2013

Michael Anglesio

Medicine/Obstetrics & Gynecology

1 shared papers, latest 2013

Peter Watson

Faculty

1 shared papers, latest 2012

Yuzhuo Wang

Urologic Sciences

1 shared papers, latest 2016

Nathalie Johnson

Medicine

1 shared papers, latest 2015

Write to this professor

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Applying for

Paper to mentionMention their NSERC grant from 2022

Subject: Prospective PhD student: Crc Dear Professor Ding, 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 "Computational identification of antigen-specific T cell groups through generative epitope modeling." (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 NSERC-funded project "Uncovering the latent structure in single-cell multi-omics data to study human diseases" (2022), 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]