Mila > Team > Mathieu Blanchette

# Mathieu Blanchette

Associate Academic Member
blanchem@cs.mcgill.ca
https://www.cs.mcgill.ca/~blanchem/
514-398-5209
Computational Biology
Machine Learning (ML)
Associate Academic Member
Associate Professor, McGill University

Mathieu Blanchette is an Associate Professor and Director of the School of Computer Science at McGill University.

After completing his Ph.D. (U. of Washington, 2002) and postdoc (UC Santa Cruz, 2003), Mathieu joined the School of Computer Science at McGill and founded the Computational Genomics Lab. The research made by his awesome team has been published in more than 70 publications. Recently elected member of the College of Scholar of the Canadian Royal Society, he was a Sloan Fellow (2009), and received the Outstanding Young Computer Scientist Researcher Prize from the Canadian Association for Computer Science (2012), and the Chris Overton prize (2006). He loves teaching and supervising students, and received the Leo Yaffe prize for teaching (2008).

## Publications

### 2021-07

ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells.
Sharon Harel, Veronica Sanchez, Alaa Moamer, Javier E Sanchez-Galan, Mohammad N Abid Hussein, Dominique Mayaki, Mathieu Blanchette and Sabah N A Hussain
Frontiers in Physiology
(2021-07-26)
www.frontiersin.org

### 2021-05

Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.
Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher J F Cameron, Matthew Valentine, Yulia A Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M Luscombe... (9 more)
Nature Communications
(2021-05-19)
www.nature.com
Neural representation and generation for RNA secondary structures
Zichao Yan, William L. Hamilton and Mathieu Blanchette
ICLR 2021
(2021-05-03)
dblp.uni-trier.de PDF[Also on arXiv preprint arXiv:2102.00925 (2021-02-01)]

### 2021-01

Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP.
Xue Qing David Wang, Christopher J F Cameron, Dana Segal, Denis Paquette, Mathieu Blanchette and Josée Dostie
Methods of Molecular Biology
(2021-01-01)
europepmc.org

### 2020-12

Supervised learning on phylogenetically distributed data.
Elliot Layne, Erika N Dort, Richard Hamelin, Yue Li and Mathieu Blanchette
Bioinformatics
(2020-12-30)
academic.oup.com
Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites
Faizy Ahsan, Alexandre Drouin, Francois Laviolette, Doina Precup and Mathieu Blanchette
BIBM 2020
(2020-12-16)
dblp.uni-trier.de
Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis
Carol C.L. Chen, Shriya Deshmukh, Selin Jessa, Djihad Hadjadj, Véronique Lisi, Augusto Faria Andrade, Damien Faury, Wajih Jawhar, Rola Dali, Hiromichi Suzuki, Manav Pathania, Deli A, Frank Dubois, Eleanor Woodward, Steven Hébert, Marie Coutelier, Jason Karamchandani, Steffen Albrecht, Sebastian Brandner, Nicolas De Jay... (44 more)
Cell
(2020-12-10)
www.ncbi.nlm.nih.gov

### 2020-10

SACSANN: identifying sequence-based determinants of chromosomal compartments
Julie A Prost, Christopher Jf Cameron and Mathieu Blanchette
bioRxiv
(2020-10-07)
www.biorxiv.org PDF

### 2020-07

EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM.
Dongjoon Lim and Mathieu Blanchette
Bioinformatics
(2020-07-01)
academic.oup.com
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions.
Zichao Yan, William L Hamilton and Mathieu Blanchette
Bioinformatics
(2020-07-01)
academic.oup.com[Also on bioRxiv (2020-02-12)]

### 2020-06

LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads.
Christopher J. F. Cameron, Xue Q. D. Wang, Josée Dostie and Mathieu Blanchette
BMC Research Notes
(2020-06-03)
bmcresnotes.biomedcentral.com PDF

### 2020-03

Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila
Julie Bergalet, Dhara Patel, Félix Legendre, Catherine Lapointe, Louis Philip Benoit Bouvrette, Ashley Chin, Mathieu Blanchette, Eunjeong Kwon and Eric Lécuyer
Cell Reports
(2020-03-10)
www.sciencedirect.com

### 2020-02

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J. Nash, Marco Ghilotti, Christopher J. F. Cameron, Matthew Valentine, Yulia A. Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M. Luscombe... (9 more)
Nature Communications
(2020-02-24)
doaj.org PDF[Also on bioRxiv (2019-06-27)]

### 2020-01

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
Christopher Jf Cameron, Josée Dostie and Mathieu Blanchette
Genome Biology
(2020-01-14)
genomebiology.biomedcentral.com PDF
Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome.
Philippe Cloutier, Christian Poitras, Denis Faubert, Annie Bouchard, Mathieu Blanchette, Marie-Soleil Gauthier and Benoit Coulombe
Journal of Proteome Research
(2020-01-03)
pubag.nal.usda.gov
Mycorrhiza: Genotype Assignment using Phylogenetic Networks.
Jeremy Georges-Filteau, Richard C Hamelin and Mathieu Blanchette
Bioinformatics
(2020-01-01)
academic.oup.com PDF

### 2019-11

oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species
Louis Philip Benoit Bouvrette, Samantha Bovaird, Mathieu Blanchette and Eric Lécuyer
Nucleic Acids Research
(2019-11-14)
academic.oup.com

### 2019-07

Prediction of mRNA subcellular localization using deep recurrent neural networks.
Zichao Yan, Eric Lécuyer and Mathieu Blanchette
Bioinformatics
(2019-07-15)
academic.oup.com
Large-scale mammalian genome rearrangements coincide with chromatin interactions.
Krister M Swenson and Mathieu Blanchette
Bioinformatics
(2019-07-15)
academic.oup.com PDF

### 2019-04

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes
Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, Nadia El-Mabrouk and Bernd Franz Lang
Molecular Biology and Evolution
(2019-04-01)
academic.oup.com

### 2019-02

2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing
Xue Qing David Wang, Christopher J. F. Cameron, Denis Paquette, Dana Segal, Reid Warsaba, Mathieu Blanchette and Josée Dostie
BMC Genomics
(2019-02-28)
bmcgenomics.biomedcentral.com PDF

### 2019-01

Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization.
Louis Philip Benoit Bouvrette, Mathieu Blanchette and Eric Lécuyer
Advances in Experimental Medicine and Biology
(2019-01-01)
europepmc.org

### 2018-12

Double-Stranded Biotinylated Donor Enhances Homology-Directed Repair in Combination with Cas9 Monoavidin in Mammalian Cells.
Philip J R Roche, Heidi Gytz, Faiz Hussain, Christopher J F Cameron, Denis Paquette, Mathieu Blanchette, Josée Dostie, Bhushan Nagar and Uri David Akavia
The CRISPR journal
(2018-12-20)
pubmed.ncbi.nlm.nih.gov

Publications collected and formatted using Paperoni