Maxwell Libbrecht, Simon Fraser University

Research

Chromatin architecture Chromatin state Deep learning Epigenomics Functional genomics Gene regulation Genomics Interpretable machine learning

Latest papers

GAME: Genomic API for Model Evaluation.
bioRxiv : the preprint server for biology · 2025
Integrative chromatin domain annotation through graph embedding of Hi-C data.
Bioinformatics (Oxford, England) · 2023 · senior author
VSS: variance-stabilized signals for sequencing-based genomic signals.
Bioinformatics (Oxford, England) · 2021 · senior author

All 5 publications

Latest funding

Decoding the genotype-phenotype relationship through interpretable, robust and integrative machine learning
NSERC · 2023 · Principal investigator
$82,000
Unsupervised machine learning methods that discover the molecular programs underlying cellular biology
NSERC · 2018 · Principal investigator
$12,500
Unsupervised machine learning methods that discover the molecular programs underlying cellular biology
NSERC · 2018 · Principal investigator
$115,000

All 3 grants and awards

5 publications.

01

GAME: Genomic API for Model Evaluation.

Luthra I, Priyadarshi S, Guo R, Mahieu L, Kempynck N, Dooley D, Penzar D, Vorontsov I, Sheng Y, Tu X, Klie A, Drusinsky S, Floren A, Armand E, Alasoo K, Seelig G, Tewhey R, Koo P, Agarwal V, Gosai S, Pinello L, White MA, Lal A, Zeitlinger J, Pollard KS, Libbrecht M, Carter H, Mostafavi S, Kulakovskiy I, Hsiao W, Aerts S, Zhou J, de Boer CG

bioRxiv : the preprint server for biology2025

DOI: 10.1101/2025.07.04.663250 PMID: 40672207

02

Integrative chromatin domain annotation through graph embedding of Hi-C data.

Shokraneh N, Arab M, Libbrecht M

Bioinformatics (Oxford, England)2023Senior author

DOI: 10.1093/bioinformatics/btac813 PMID: 36534827

03

VSS: variance-stabilized signals for sequencing-based genomic signals.

Bayat F, Libbrecht M

Bioinformatics (Oxford, England)2021Senior author

DOI: 10.1093/bioinformatics/btab457 PMID: 34165492

04

INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis.

Zabeti H, Dexter N, Safari AH, Sedaghat N, Libbrecht M, Chindelevitch L

Algorithms for molecular biology : AMB2021

DOI: 10.1186/s13015-021-00198-1 PMID: 34376217

05

SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data.

Gabbassov E, Moreno-Molina M, Comas I, Libbrecht M, Chindelevitch L

Microbial genomics2021

DOI: 10.1099/mgen.0.000607 PMID: 34165419

Decoding the genotype-phenotype relationship through interpretable, robust and integrative machine learning

Principal investigatorNSERC2023Discovery Grants Program - Individual

Principal investigators: Libbrecht, Maxwell

Keywords: genomics; epigenomics; deep learning; interpretable machine learning; probabilistic graphical models; gene regulation; chromatin state; chromatin architecture; representation learning; functional genomics

$82,000

Unsupervised machine learning methods that discover the molecular programs underlying cellular biology

Principal investigatorNSERC2018Discovery Launch Supplement

Principal investigators: Libbrecht, Maxwell

$12,500

Unsupervised machine learning methods that discover the molecular programs underlying cellular biology

Principal investigatorNSERC2018Discovery Grants Program - Individual

Principal investigators: Libbrecht, Maxwell

$115,000

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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Paper to mentionMention their NSERC grant from 2023

Subject: Prospective PhD student: Chromatin architecture Dear Professor Libbrecht, 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 "GAME: Genomic API for Model Evaluation." (2025), 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 "Decoding the genotype-phenotype relationship through interpretable, robust and integrative machine learning" (2023), 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]