Paul Pavlidis, University of British Columbia

Research

Bioinformatics Cellular Neuroscience Genomics Molecular Neuroscience Cell Specification Cerebellar Development Chromatin Accessibility Developmental Genetics

Latest papers

Persistent hindrances to data re-use in single-cell genomics.
Scientific data · 2026 · senior author
Application of large language models to the annotation of cell lines and mouse strains in genomics data.
bioRxiv : the preprint server for biology · 2026 · senior author
Using semantic search to find publicly available gene-expression datasets.
Bioinformatics (Oxford, England) · 2026

All 94 publications

Latest funding

Large-scale multimodal genomics meta-analysis to gain insight into brain gene regulation
CIHR · 2025 · Nominated PI
$952,425
Pax6 regulation of glutamatergic lineages in cerebellar development
CIHR · 2022 · Principal investigator
$841,500
Neuroinformatics for genomics and anatomy
NSERC · 2022 · Principal investigator
$144,000

All 16 grants and awards

94 publications.

01

Persistent hindrances to data re-use in single-cell genomics.

Rogic S, Yu XX, Xu B, Millett A, Sherif S, Poirier-Morency G, Schwartz R, Pavlidis P

Scientific data2026Senior author

DOI: 10.1038/s41597-026-07582-9 PMID: 42342707

02

Application of large language models to the annotation of cell lines and mouse strains in genomics data.

Rogic S, Mancarci BO, Xu B, Xiao A, Yan C, Pavlidis P

bioRxiv : the preprint server for biology2026Senior author

DOI: 10.64898/2026.03.05.709906 PMID: 41867763

03

Using semantic search to find publicly available gene-expression datasets.

Brown GS, Wengler J, Fabelico AJS, Muir A, Tubbs A, Warren A, Millett AN, Xiang Yu X, Pavlidis P, Rogic S, Piccolo SR

Bioinformatics (Oxford, England)2026

DOI: 10.1093/bioinformatics/btag053 PMID: 41627879

04

Application of large language models to the annotation of cell lines and mouse strains in genomics data.

Rogic S, Mancarci BO, Xu B, Xiao A, Yan C, Pavlidis P

Database : the journal of biological databases and curation2026Senior author

DOI: 10.1093/database/baag041 PMID: 42483875

05

Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing.

Bhuiyan SA, Tyson JR, Belmadani M, Sicherman J, Snutch TP, Pavlidis P

BMC genomics2025Senior author

DOI: 10.1186/s12864-025-11887-1 PMID: 41013183

06

Revealing function-altering MECP2 mutations in individuals with autism spectrum disorder using yeast and Drosophila.

Chen E, Schmitt J, McIntosh G, Young BP, Lian T, Liu J, Chen KK, Liston JB, MacDonald L, Wang B, Medina Giro S, Boehme B, Das M, Indran S, Chao JT, Rogic S, Pavlidis P, Allan DW, Loewen CJR

Genetics2025

DOI: 10.1093/genetics/iyaf121 PMID: 40546018

07

Global partnerships in rare disease research.

Rogic S, Poirier-Morency G, Hieter P, Pavlidis P

Disease models & mechanisms2025Senior author

DOI: 10.1242/dmm.052401 PMID: 40719025

08

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.

Morin A, Chu CP, Pavlidis P

PLoS computational biology2025Senior author

DOI: 10.1371/journal.pcbi.1012962 PMID: 40257984

09

Using semantic search to find publicly available gene-expression datasets.

Brown GS, Wengler J, Fabelico AJS, Muir A, Tubbs A, Warren A, Millett AN, Yu XX, Pavlidis P, Rogic S, Piccolo SR

bioRxiv : the preprint server for biology2025

DOI: 10.1101/2025.03.13.643153 PMID: 40161731

10

Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics.

Morin A, Chu CP, Pavlidis P

bioRxiv : the preprint server for biology2025Senior author

DOI: 10.1101/2024.02.15.580581 PMID: 38559016

Large-scale multimodal genomics meta-analysis to gain insight into brain gene regulation

Nominated PICIHR2025Project Grant

Principal investigators: Pavlidis, Paul

Keywords: Bioinformatics; Cellular Neuroscience; Genomics; Molecular Neuroscience

$952,425

Pax6 regulation of glutamatergic lineages in cerebellar development

Principal investigatorCIHR2022Project Grant

Principal investigators: Goldowitz, Daniel; Pavlidis, Paul

Keywords: Cell Specification; Cerebellar Development; Chromatin Accessibility; Developmental Genetics; Gene Action; Genetic Determinants Of Survival; Mouse; Pax6; Single Cell Rnaseq; Transcriptional Regulation

$841,500

Neuroinformatics for genomics and anatomy

Principal investigatorNSERC2022Discovery Grants Program - Individual

Principal investigators: Pavlidis, Paul

$144,000

Canadian "Rare Diseases: Models and Mechanisms" (RDMM) Network

Co-investigatorCIHR2022Research Network: Rare Diseases

Principal investigators: Hieter, Philip A; Boycott, Kym M; Campeau, Philippe M

Keywords: Bioinformatics; Gene Functional Analysis; Genetics; Knowledge Translation; Model Organisms; Rare Diseases; Therapeutic Strategies

$2,500,000

Canadian "Rare Diseases: Models and Mechanisms" (RDMM) Network

Co-investigatorCIHR2018Research Network: Rare Diseases

Principal investigators: Hieter, Philip A; Boycott, Kym M; Campeau, Philippe M

Keywords: Bioinformatics; Gene Functional Analysis; Genetics; Knowledge Translation; Model Organisms; Rare Diseases; Therapeutic Strategies

$1,119,500

Neuroinformatics for genes, transcriptomes and cells

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Pavlidis, Paul

$264,000

Training Program in High-Dimensional Bioinformatics (HDB)

Principal investigatorNSERC2015Collaborative Research and Training Experience

Principal investigators: Pavlidis, Paul

$1,650,000

Canadian "Rare Diseases: Models & Mechanisms" Network (RDMM) Réseau Canadien "Maladies Rares: Modèles et Mécanismes" (MRMM)

Co-investigatorCIHR2014Research Network: Rare Diseases

Principal investigators: Hieter, Philip A; Boycott, Kym M; Rossant, Janet

Keywords: Bioinformatics; Collaborative Studies; Gene Functional Analysis; Genetics; Knowledge Translation; Model Organisms; Rare Disease Genes; Therapeutic Strategies

$2,100,000

Linking gene expression to neuronal behaviour in normal and disordered brains through large-scale meta-analysis

SupervisorCIHR2014CIHR Fellowship

Principal investigators: Tripathy, Shreejoy J

Keywords: Bioinformatics; Databases; Gene Expression; Meta-Analysis; Multi-Scale Models; Neuroinformatics; Neurological Disease; Neuron Physiology; Research Tools; Statistical Models

$135,000

Epigenetic effect of traumatic brain injury contributes to Alzheimer's Disease

Principal investigatorCIHR2013Catalyst Grant: Environments, Genes and Chronic Disease

Principal investigators: Song, Weihong; Pavlidis, Paul

Keywords: Alzheimer'S Disease; Epigenetic Modification; Gene Expression; Neurodegeneration; Transgenic Model Mice; Traumatic Brian Injury

$100,000

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

Faculty

1 shared papers, latest 2020

Catharine Rankin

Psychology

1 shared papers, latest 2020

Wyeth Wasserman

Medical Genetics

1 shared papers, latest 2011

Judy Illes

Medicine/Neurology

1 shared papers, latest 2023

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: Bioinformatics Dear Professor Pavlidis, 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 "Persistent hindrances to data re-use in single-cell genomics." (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 "Large-scale multimodal genomics meta-analysis to gain insight into brain gene regulation" (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]