Portrait de Mathieu Blanchette

Mathieu Blanchette

Membre académique associé
Directeur et professeur associé, McGill University, École d'informatique
Sujets de recherche
Apprentissage profond
Biologie computationnelle
Réseaux de neurones en graphes
Site web

Biographie

Mathieu Blanchette est professeur associé et directeur de l'École d'informatique de l'Université McGill.

Après avoir obtenu un doctorat (Université de Washington, 2002) et un postdoctorat (Université de Californie à Santa Cruz, 2003), il s'est joint à l'École d'informatique de l’Université McGill et a fondé le Laboratoire de génomique computationnelle. Les recherches effectuées par son équipe d’exception ont fait l'objet de plus de 70 publications. Récemment élu membre du Collège de nouveaux chercheurs et créateurs en art et science de la Société royale du Canada, il a été boursier Sloan (2009) et a reçu le prix Outstanding Young Computer Scientist Researcher de l'Association canadienne de l'informatique (2012) ainsi que le prix Chris Overton (2006). Il adore enseigner et superviser les étudiant·e·s, et a d’ailleurs reçu le prix Leo Yaffe pour l'enseignement (2008).

Étudiants actuels

Noah El Rimawi-Fine
Maîtrise recherche - McGill
Github
Lucas Nelson
Maîtrise recherche - McGill
Adam Stecklov
Maîtrise recherche - McGill
Github
César Miguel Valdez Cordova
Doctorat - McGill
Github
Google Scholar
Yijie Zhang
Doctorat - McGill
Site web
Google Scholar
Nicole Zhang
Doctorat - McGill
Site web
Github
Google Scholar

Publications

Multi-ancestry polygenic risk scores using phylogenetic regularization
Elliot Layne
Shadi Zabad
Yue Li
Mathieu Blanchette
2024-02-17
bioRxiv (prépublication)
doi.org
PERFUMES: pipeline to extract RNA functional motifs and exposed structures
Arnaud Chol
Roman Sarrazin-Gendron
Éric Lécuyer
Mathieu Blanchette
Jérôme Waldispühl
Abstract Motivation Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs relies on their ability to fold into 3D… (voir plus) structures. Specifically, nucleotides inside secondary structure loops form non-canonical base pairs that help stabilize complex local 3D structures. These RNA 3D motifs can promote specific interactions with other molecules or serve as catalytic sites. Results We introduce PERFUMES, a computational pipeline to identify 3D motifs that can be associated with observable features. Given a set of RNA sequences with associated binary experimental measurements, PERFUMES searches for RNA 3D motifs using BayesPairing2 and extracts those that are over-represented in the set of positive sequences. It also conducts a thermodynamics analysis of the structural context that can support the interpretation of the predictions. We illustrate PERFUMES’ usage on the SNRPA protein binding site, for which the tool retrieved both previously known binder motifs and new ones. Availability and implementation PERFUMES is an open-source Python package (https://jwgitlab.cs.mcgill.ca/arnaud_chol/perfumes).
2024-01-30
Bioinform. (publié)
doi.org
Graphylo: A deep learning approach for predicting regulatory DNA and RNA sites from whole-genome multiple alignments
Dongjoon Lim
Changhyun Baek
Mathieu Blanchette
2024-01-26
iScience (publié)
doi.org
PhyloGFN: Phylogenetic inference with generative flow networks
Ming Yang Zhou
Zichao Yan
Elliot Layne
Nikolay Malkin
Dinghuai Zhang
Moksh J. Jain
Mathieu Blanchette
Yoshua Bengio
2024-01-16
ICLR.cc/2024/Conference (poster)
doi.org
openreview.net
Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players
Eddie Cai
Roman Sarrazin-Gendron
Renata Mutalova
Parham Ghasemloo Gheidari
Alexander Butyaev
Gabriel Richard
Sébastien Caisse
Rob Knight
Mathieu Blanchette
Attila Szantner
Jérôme Waldispühl
2024-01-01
FDG (publié)
doi.org
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs
Brian Krug
Bo Hu
Haifen Chen
Adam Ptack
Xiao Chen
Kristjan H. Gretarsson
Shriya Deshmukh
Nisha Kabir
Augusto Faria Andrade
Elias Jabbour
Ashot S. Harutyunyan
John J. Y. Lee
Maud Hulswit
Damien Faury
Caterina Russo
Xinjing Xu
Michael Johnston
Audrey Baguette
Nathan A. Dahl
Alexander G. Weil … (voir 12 de plus)
Benjamin Ellezam
Rola Dali
Mathieu Blanchette
Khadija Wilson
Benjamin A. Garcia
Rajesh Kumar Soni
Marco Gallo
Michael D. Taylor
Claudia Kleinman
Jacek Majewski
Nada Jabado
Chao Lu
2023-11-28
bioRxiv (prépublication)
doi.org
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles
Renata Mutalova
Roman Sarrazin-Gendron
Parham Ghasemloo Gheidari
Eddie Cai
Gabriel Richard
Sébastien Caisse
Rob Knight
Mathieu Blanchette
Attila Szantner
Jérôme Waldispühl
2023-11-05
International Conference on Climate Informatics (publié)
doi.org
PhyloGFN: Phylogenetic inference with generative flow networks
Ming Yang Zhou
Zichao Yan
Elliot Layne
Nikolay Malkin
Dinghuai Zhang
Moksh J. Jain
Mathieu Blanchette
Yoshua Bengio
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history a… (voir plus)nd numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.
2023-10-12
ArXiv (prépublication)
doi.org
arxiv.org
Reference panel-guided super-resolution inference of Hi-C data
Yanlin Zhang
Mathieu Blanchette
Abstract Motivation Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding… (voir plus) the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types. Results Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains. Availability and implementation https://github.com/BlanchetteLab/RefHiC.
2023-06-30
Bioinformatics (publié)
doi.org
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?
Renata Mutalova
Roman Sarrazin-Gendron
Eddie Cai
Gabriel Richard
Parham Ghasemloo Gheidari
Sébastien Caisse
Rob Knight
Mathieu Blanchette
Attila Szantner
Jérôme Waldispühl
2023-04-19
International Conference on Human Factors in Computing Systems (publié)
doi.org
Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data
Melissa Zwaig
Audrey Baguette
Bo Hu
Michael Johnston
Hussein Lakkis
Emily M. Nakada
Damien Faury
Nikoleta Juretic
Benjamin Ellezam
Alexandre G. Weil
Jason Karamchandani
Jacek Majewski
Mathieu Blanchette
Michael D. Taylor
Marco Gallo
Claudia Kleinman
Nada Jabado
Jiannis Ragoussis
2022-12-12
BMC Cancer (publié)
doi.org
Reference panel guided topological structure annotation of Hi-C data
Yanlin Zhang
Mathieu Blanchette
2022-12-01
Nature Communications (publié)
doi.org