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We are the

Lemieux's Lab.

Bioinformatics & Cancer Reasearch

Lemieux's Lab

The Lab


The Lemieux's lab’s main focus of research is the analysis of -omics data, coming from high-throughput sequencing and screening experimentents. We aim to utilise this data to gain insight on human cancer by developing machine-learning approaches as well as using state-of-the-art tools. We work on creating and developing pipelines that can challenge old and sometimes outdated bioinformatics methods. We perform both fundamental and translational research, in that we try to contribute to the scientific advancements in bioinformatics as well as using them to the benefit of improving cancer treatment. Our team is truly multidisciplinary, uniting students of various backgrounds; biologists, bioinformaticians and computer scientists alike, all find a place here. The type of data we analyse is equally diverse; transcriptomics, chemo-genomics, proteomics, all are rich and contribute to our work.
Keywords: Transcriptomics, Chemogenomics, Proteomics, Bioinformatics, Machine-Learning, Development Anlaysis Pipelines , Computer Sciences

Members


Sébastien Lemieux, PhD

Principal investigator

Trained as a microbiologist, Sébastien Lemieux turned to bioinformatics in 1997 and completed his Master’s and Ph.D. studies at the Université de Montréal under the direction of François Major. After obtaining his Ph.D. in 2002, the young Investigator headed to the private sector to carry out postdoctoral training at Elitra Canada (now Merck & Co) under the supervision of Bo Jiang. There he acquired skills in sequence analysis and the analysis of DNA microarray data, as well as in computer integration of experimental data.

He finally joined the IRIC’s ranks in 2005. In 2018, he was appointed Associate Professor in the Department of Biochemistry and Molecular Medicine of the Faculty of Medicine of the Université de Montréal.

Lemieux's Lab

Assya Trofimov, MSc

PhD Student - Computer Science

Building an entirely data-driven, representation learning-based cell atlas

assya.trofimov _AT_ umontreal.ca
Assya Trofimov

Caroline Labelle, MSc

PhD Student - Bioinformatics

Using Bayesian inference to analyze dose-response experiment in the contexte of drug discovery (AML)

caroline.labelle _AT_ umontreal.ca
Caroline Labelle

Jeremie Zumer, MSc

PhD Student - Computer Science

Deep learning tools for MHC-I associated peptide identification from mass spectrometry and rna-seq data

jeremie.zumer _AT_ umontreal.ca
Jeremie Zumer

Leonard Sauve, Bsc

PhD Student - Bioinformatics

Identification of Cancer Subtypes using Batch-Effect Robust Supervised Learning Approaches from Acute Myeloid Leukemia Transcriptomes

leonard.sauve _AT_ umontreal.ca
Leonard Sauve

Marjolaine David, BSc

MSc Student - Computer Science

Investigate breast cancer heterogeneity using scRNA-seq data

marjolaine.david _AT_ umontreal.ca
Marjolaine David

Maria Virginia Ruiz Cuevas, MSc

PhD Student - Bioinformatics

Detection of Cryptic protein source of MHC-I associated peptides

maria.virginia.ruiz.cuevas _AT_ umontreal.ca
Maria Virginia Ruiz Cuevas

Tom MacDougall, BSc

MSc Student - Computer Science

Improving The Prediction of Chemical Compound Efficacy Using New Molecular Representations and Machine Learning

tom.macdougall _AT_ umontreal.ca
Tom MacDougall

PUBLICATIONS


Lab's Articles

[ 2019 ] Genetic characterization of ABT-199 sensitivity in human AML

Richard Bisaillon, Celine Moison, Clarisse Thiollier, Jana Krosl, Marie-Eve Bordeleau, Bernhard Lehnertz, Vincent-Philippe Lavallee, Tara MacRae, Nadine Mayotte, Caroline Labelle*, Genevieve Boucher, Jean-François Spinella, Isabel Boivin, Giovanni D’Angelo, Sylvie Lavallee, Anne Marinier, Sebastien Lemieux*, Josee Hebert, Guy Sauvageau
Leukemia

[ 2019 ] Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose–response experiments

Caroline Labelle*, Anne Marinier, Sebastien Lemieux*
Bioinformatics

[ 2018 ] Towards the Latent Transcriptome

Assya Trofimov*, Francis Dutil, Claude Perreault, Sebastien Lemieux*, Yoshua Bengio, Joseph Paul Cohen
arXiv preprint

[ 2017 ] Warp: a method for neural network interpretability applied to gene expression profiles

Trofimov Assya*, Lemieux Sebastien*, Perreault Claude
arXiv preprint

[ 2016 ] myCircos: Facilitating the Creation and Use of Circos Plots Online

Caroline Labelle*, Genevieve Boucher, Sebastien Lemieux*
bioRxiv

[ 2016 ] Expression of immunoproteasome genes is regulated by cell-intrinsic and–extrinsic factors in human cancers

Alexandre Rouette, Assya Trofimov*, David Haberl, Genevieve Boucher, Vincent-Philippe Lavallee, Giovanni D’Angelo, Josee Hebert, Guy Sauvageau, Sebastien Lemieux*, Claude Perreault
Scientific reports

[ 2015 ] Differential features of AIRE-induced and AIRE-independent promiscuous gene expression in thymic epithelial cells

Charles St-Pierre, Assya Trofimov*, Sylvie Brochu, Sebastien Lemieux*, Claude Perreault
The Journal of Immunology

Master & PhD Thesis

Contact Sébastien Lemieux


Lemieux's Lab

IRIC, Pavillon Marcelle-Coutu, 3306-9 , Montréal, Qc, Can

Phone: (514) 343-6111, p. 0635

Email: s.lemieux_at_umontreal.ca