Cedric Chauve, Simon Fraser University

Research

Bioinformatics Algorithms Genomics Genotyping High-througput sequencing data Machine-learning Microbial diversity Mobile genomics elements

Latest papers

On using clustering statistics for assessing plasmid binning tools accuracy.
Briefings in bioinformatics · 2026 · senior author
Undesignable motifs in structural RNAs and combinatorial consequences.
Journal of mathematical biology · 2026
A vector representation for phylogenetic trees.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025 · first author

All 41 publications

Latest funding

Plasmids bioinformatics: detection and transmission
NSERC · 2024 · Principal investigator
$25,000
Genotyping bioinformatics tools for bacterial pathogens mobile genetic elements
NSERC · 2023 · Principal investigator
$90,000
Computational models, algorithms and methods for comparative genomics, applied to pathogens and anopheles mosquitoes genomes
NSERC · 2017 · Principal investigator
$156,000

All 10 grants and awards

41 publications.

01

On using clustering statistics for assessing plasmid binning tools accuracy.

Epain V, Mane A, Chauve C

Briefings in bioinformatics2026Senior author

DOI: 10.1093/bib/bbag240 PMID: 42153317

02

Undesignable motifs in structural RNAs and combinatorial consequences.

Yao HT, Chauve C, Regnier M, Ponty Y

Journal of mathematical biology2026

DOI: 10.1007/s00285-026-02358-6 PMID: 41817779

03

A vector representation for phylogenetic trees.

Chauve C, Colijn C, Zhang L

Philosophical transactions of the Royal Society of London. Series B, Biological sciences2025First author

DOI: 10.1098/rstb.2024.0226 PMID: 39976399

04

TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.

Karaoğlanoğlu F, Orabi B, Flannigan R, Chauve C, Hach F

Bioinformatics (Oxford, England)2024

DOI: 10.1093/bioinformatics/btae051 PMID: 38273664

05

AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.

Cribbie EP, Doerr D, Chauve C

Methods in molecular biology (Clifton, N.J.)2024Senior author

DOI: 10.1007/978-1-0716-3838-5_10 PMID: 38819563

06

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.

Sielemann J, Sielemann K, Brejová B, Vinař T, Chauve C

Frontiers in microbiology2023Senior author

DOI: 10.3389/fmicb.2023.1267695 PMID: 37869681

07

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.

Mane A, Faizrahnemoon M, Vinař T, Brejová B, Chauve C

Bioinformatics (Oxford, England)2023Senior author

DOI: 10.1093/bioinformatics/btad250 PMID: 37387134

08

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing.

Orabi B, Xie N, McConeghy B, Dong X, Chauve C, Hach F

Nucleic acids research2023

DOI: 10.1093/nar/gkac1112 PMID: 36478271

09

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments.

Ebrahimi G, Orabi B, Robinson M, Chauve C, Flannigan R, Hach F

iScience2022

DOI: 10.1016/j.isci.2022.104530 PMID: 35747387

10

Genion, an accurate tool to detect gene fusion from long transcriptomics reads.

Karaoglanoglu F, Chauve C, Hach F

BMC genomics2022

DOI: 10.1186/s12864-022-08339-5 PMID: 35164688

Plasmids bioinformatics: detection and transmission

Principal investigatorNSERC2024Alliance Grants

Principal investigators: Chauve, Cedric C

Keywords: antimicrobial resistance; bioinformatics; mathematical modelling; plasmids

$25,000

Genotyping bioinformatics tools for bacterial pathogens mobile genetic elements

Principal investigatorNSERC2023Discovery Grants Program - Individual

Principal investigators: Chauve, Cedric

Keywords: bioinformatics; high-througput sequencing data; mobile genomics elements; microbial diversity; genomics; genotyping; algorithms; machine-learning; software

$90,000

Computational models, algorithms and methods for comparative genomics, applied to pathogens and anopheles mosquitoes genomes

Principal investigatorNSERC2017Discovery Grants Program - Individual

Principal investigators: Chauve, Cedric

$156,000

PathOGiST: Calibrated multi-criterion genomic analysis for public health microbiology.

Co-investigatorCIHR2016Operating Grant: Bioinformatics and Computational Biology

Principal investigators: Chindelevitch, Leonid

Keywords: Bioinformatics

$133,332

PIMS: Pacific Institute for the Mathematical Sciences

Co-investigatorNSERC2014Thematic Resources Support in Mathematics and Statistics

Principal investigators: Colliander, James

$9,459,122

Create Program for Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (Create - CMADDG Training Program)

Co-investigatorNSERC2013Collaborative Research and Training Experience

Principal investigators: Ester, Martin

$750,000

Computational comparative genomics: inferring and analyzing ancestral genomes architectures

Principal investigatorNSERC2011Discovery Grants Program - Individual

Principal investigators: Chauve, Cedric

$180,000

RECOMB 2011, the 15th Annual International Conference on Research in Computational Molecular Biology

Nominated PICIHR2010Meetings, Planning & Dissemination Grant: Cancer Research

Principal investigators: Chauve, Cedric

Keywords: Cancer Genomics; Computational Biology; Next-Generation Sequencing

$10,000

RECOMB 2011: Research in Computational Molecular Biology

Principal investigatorNSERC2010Regional Office Discretionary Funds

Principal investigators: Chauve, Cedric

$5,000

Combinatorial models and algorithms for comparative genomics

Principal investigatorNSERC2006Discovery Grants Program - Individual

Principal investigators: Chauve, Cedric

$138,000

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

Mathematics
Urologic Sciences
Genome Sciences Centre
School of Computing Science
Pathology and Laboratory Medicine
School of Population and Public Health
Département d'informatique
Other

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

Faraz Hach

Urologic Sciences

7 shared papers, latest 2024

William Hsiao

Pathology and Laboratory Medicine

2 shared papers, latest 2018

Leonid Chindelevitch

School of Computing Science

2 shared papers, latest 2019

Adi Steif

Genome Sciences Centre

2 shared papers, latest 2017

Natalie Prystajecky

Laboratory Medicine and Pathology

1 shared papers, latest 2018

Xuesen Dong

Urologic Sciences

1 shared papers, latest 2023

Manuel Lafond

Département d'informatique

1 shared papers, latest 2020

Jennifer Gardy

School of Population and Public Health

1 shared papers, latest 2018

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 NSERC grant from 2024

Subject: Prospective PhD student: Bioinformatics Dear Professor Chauve, 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 "On using clustering statistics for assessing plasmid binning tools accuracy." (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 "Plasmids bioinformatics: detection and transmission" (2024), 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]

Cedric Chauve

Research

Latest papers

Latest funding

On using clustering statistics for assessing plasmid binning tools accuracy.

Undesignable motifs in structural RNAs and combinatorial consequences.

A vector representation for phylogenetic trees.

TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.

AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing.

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments.

Genion, an accurate tool to detect gene fusion from long transcriptomics reads.

Plasmids bioinformatics: detection and transmission

Genotyping bioinformatics tools for bacterial pathogens mobile genetic elements

Computational models, algorithms and methods for comparative genomics, applied to pathogens and anopheles mosquitoes genomes

PathOGiST: Calibrated multi-criterion genomic analysis for public health microbiology.

PIMS: Pacific Institute for the Mathematical Sciences

Create Program for Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (Create - CMADDG Training Program)

Computational comparative genomics: inferring and analyzing ancestral genomes architectures

RECOMB 2011, the 15th Annual International Conference on Research in Computational Molecular Biology

RECOMB 2011: Research in Computational Molecular Biology

Combinatorial models and algorithms for comparative genomics

Frequent collaborators

Faraz Hach

William Hsiao

Leonid Chindelevitch

Ryan Flannigan

Adi Steif

Tamon Stephen

Patrick Tang

Natalie Prystajecky

Xuesen Dong

Manuel Lafond

Jennifer Gardy