Sébastien Lemieux, Université de Montréal

Research

Bioinformatics Computational biology Deep neural network k-mers Machine learning RNA-Seq Transcriptomics

Latest papers

Harnessing virtual machines to simplify next-generation DNA sequencing analysis.
Bioinformatics (Oxford, England) · 2013
Genome-wide fitness test and mechanism-of-action studies of inhibitory compounds in Candida albicans.
PLoS pathogens · 2007
Essential gene identification and drug target prioritization in Aspergillus fumigatus.
PLoS pathogens · 2007

All 3 publications

Latest funding

Exploiting Electrolytic Gating in Graphene Field-Effect Nanosensors to Achieve Multiplexed Breast Cancer Profiling for Personalized Medicine
SSHRC · 2024 · Co-investigator
$125,000
Development of reference-free algorithms for low coverage RNA-Seq characterization of cell states
NSERC · 2022 · Principal investigator
$102,000
Recruitment of SUMO E3 ligases as a new paradigm for transcription factor inactivation
SSHRC · 2020 · Co-investigator
$250,000

All 8 grants and awards

3 publications.

01

Harnessing virtual machines to simplify next-generation DNA sequencing analysis.

Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT

Bioinformatics (Oxford, England)2013

DOI: 10.1093/bioinformatics/btt352 PMID: 23786767

02

Genome-wide fitness test and mechanism-of-action studies of inhibitory compounds in Candida albicans.

Xu D, Jiang B, Ketela T, Lemieux S, Veillette K, Martel N, Davison J, Sillaots S, Trosok S, Bachewich C, Bussey H, Youngman P, Roemer T

PLoS pathogens2007

DOI: 10.1371/journal.ppat.0030092 PMID: 17604452

03

Essential gene identification and drug target prioritization in Aspergillus fumigatus.

Hu W, Sillaots S, Lemieux S, Davison J, Kauffman S, Breton A, Linteau A, Xin C, Bowman J, Becker J, Jiang B, Roemer T

PLoS pathogens2007

DOI: 10.1371/journal.ppat.0030024 PMID: 17352532

Exploiting Electrolytic Gating in Graphene Field-Effect Nanosensors to Achieve Multiplexed Breast Cancer Profiling for Personalized Medicine

Co-investigatorSSHRC2024New Frontiers in Research Fund - Exploration

Principal investigators: Bouilly, Delphine

$125,000

Development of reference-free algorithms for low coverage RNA-Seq characterization of cell states

Principal investigatorNSERC2022Discovery Grants Program - Individual

Principal investigators: Lemieux, Sébastien

Keywords: bioinformatics; computational biology; machine learning; transcriptomics; rna-seq; k-mers; deep neural network

$102,000

Recruitment of SUMO E3 ligases as a new paradigm for transcription factor inactivation

Co-investigatorSSHRC2020New Frontiers in Research Fund - Exploration

Principal investigators: Mader, Sylvie

Keywords: transcription factors Sumoylation hybrid drugs chromatin in silico screens

$250,000

Deep learning-based study of the endogenous retroviral-derived immunopeptidome in ovarian cancer.

SupervisorCIHR2017Doctoral Award - Frederick Banting and Charles Best Canada Graduate Scholarships

Principal investigators: Trofimov, Assya

Keywords: Genomics, Proteomics, And Bioinformatics; Molecular Biology; Ovarian Cancer

$105,000

Mechanisms controlling estrogen receptor alpha expression and activity in breast tumorigenesis

Co-investigatorCIHR2016Project Grant

Principal investigators: Mader, Sylvie N

Keywords: Breast Cancer; Cell Models; Chip-Seq; Crispr-Cas9; Estrogen Receptor Alpha; Functional Genomics; High Throughput Screens; Shrnas; Transcriptomes; Xenografts

$910,350

Clinical application of a novel molecule that expands human cord blood stem cells

Co-investigatorCIHR2014Operating Grant

Principal investigators: Roy, Jean; Cohen, Sandra; Sauvageau, Guy

Keywords: Cord Blood Transplantation; Fed Batch Culture System; Hematopoietic Stem Cell Expansion; Novel Agonist Of Stem Cell Renewal; Phase I Clinical Study

$1,013,167

Gene interdependence in microarray data analysis

Principal investigatorNSERC2008Discovery Grants Program - Individual

Principal investigators: Lemieux, Sebastien

$32,000

Automated analysis of DNA microarray images

Principal investigatorNSERC2005Discovery Grants Program - Individual

Principal investigators: Lemieux, Sebastien

$48,000

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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Applying for

Paper to mentionMention their NSERC grant from 2022

Subject: Prospective PhD student: Bioinformatics Dear Professor Lemieux, 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 "Harnessing virtual machines to simplify next-generation DNA sequencing analysis." (2013), 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 "Development of reference-free algorithms for low coverage RNA-Seq characterization of cell states" (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]