Mathieu Blanchette

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 25

Top Topics

Machine Learning Approaches

Manifold Regularization

Secondary Structure

Top Venues

Publications

Elliot Layne, Jason S. Hartford, Sébastien Lachapelle, Mathieu Blanchette, Dhanya Sridhar
Leveraging Structure Between Environments: Phylogenetic Regularization Incentivizes Disentangled Representations. CoRR (2024)
Ming-Yang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio
PhyloGFN: Phylogenetic inference with generative flow networks. ICLR (2024)
Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl
PERFUMES: pipeline to extract RNA functional motifs and exposed structures. Bioinform. 40 (2) (2024)
Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. FDG (2024)
Yanlin Zhang, Mathieu Blanchette
Reference panel-guided super-resolution inference of Hi-C data. Bioinform. 39 (Supplement-1) (2023)
Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. CI (2023)
Yanlin Zhang, Christopher J. F. Cameron, Mathieu Blanchette
Posterior inference of Hi-C contact frequency through sampling. Frontiers Bioinform. 3 (2023)
Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio
PhyloGFN: Phylogenetic inference with generative flow networks. CoRR (2023)
Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? CHI (2023)
Zichao Yan, William L. Hamilton, Mathieu Blanchette
Neural representation and generation for RNA secondary structures. ICLR (2021)
Zichao Yan, William L. Hamilton, Mathieu Blanchette
Neural representation and generation for RNA secondary structures. CoRR (2021)
Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette
Mycorrhiza: genotype assignment using phylogenetic networks. Bioinform. 36 (1) (2020)
Dongjoon Lim, Mathieu Blanchette
EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM. Bioinform. 36 (Supplement-1) (2020)
Faizy Ahsan, Alexandre Drouin, François Laviolette, Doina Precup, Mathieu Blanchette
Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites. BIBM (2020)
Louis Philip Benoit Bouvrette, Samantha Bovaird, Mathieu Blanchette, Eric Lécuyer
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. Nucleic Acids Res. 48 (Database-Issue) (2020)
Zichao Yan, William L. Hamilton, Mathieu Blanchette
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions. Bioinform. 36 (Supplement-1) (2020)
Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette
Mycorrhiza: Genotype Assignment usingPhylogenetic Networks. CoRR (2020)
Zichao Yan, Eric Lécuyer, Mathieu Blanchette
Prediction of mRNA subcellular localization using deep recurrent neural networks. Bioinform. 35 (14) (2019)
Krister M. Swenson, Mathieu Blanchette
Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinform. 35 (14) (2019)
Ramchalam Kinattinkara Ramakrishnan, Jaspal Singh, Mathieu Blanchette
RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment. BIBE (2018)
Jaspal Singh, Ramchalam Kinattinkara Ramakrishnan, Mathieu Blanchette
Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches. BIBE (2018)
Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, B. Franz Lang, Nadia El-Mabrouk
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinform. 33 (21) (2017)
Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl
Lessons from an Online Massive Genomics Computer Game. HCOMP (2017)
Faizy Ahsan, Doina Precup, Mathieu Blanchette
Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy. BCB (2016)
Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette
Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. 11 (2016)
Krister M. Swenson, Mathieu Blanchette
Models and Algorithms for Genome Rearrangement with Positional Constraints. WABI (2015)
Pablo Cingolani, Rob Sladek, Mathieu Blanchette
BigDataScript: a scripting language for data pipelines. Bioinform. 31 (1) (2015)
Jérôme Waldispühl, Mathieu Blanchette
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP (2014)
Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Mathieu Blanchette
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinform. 13 (S-19) (2012)
Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinform. 13 (S-19) (2012)
Mathieu Blanchette, Ethan Kim, Adrian Vetta
Clique Cover on Sparse Networks. ALENEX (2012)
Mathieu Rousseau, James Fraser, Maria A. Ferraiuolo, Josee Dostie, Mathieu Blanchette
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinform. 12 (2011)
Glenn Hickey, Mathieu Blanchette
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. RECOMB (2011)
Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette
Predicting site-specific human selective pressure using evolutionary signatures. Bioinform. 27 (13) (2011)
Glenn Hickey, Mathieu Blanchette
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. J. Comput. Biol. 18 (11) (2011)
Emmanuel Mongin, Ken Dewar, Mathieu Blanchette
-Regulatory Regions and Their Target Genes Using Synteny. J. Comput. Biol. 18 (9) (2011)
Glenn Hickey, Mathieu Blanchette, Paz Carmi, Anil Maheshwari, Norbert Zeh
An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (2) (2011)
Glenn Hickey, Mathieu Blanchette
A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. Pacific Symposium on Biocomputing (2010)
Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinform. 26 (1) (2010)
Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk
Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. WABI (2010)
Emmanuel Mongin, Ken Dewar, Mathieu Blanchette
-Regulatory Regions and Their Target Genes Using Comparative Genomics. RECOMB-CG (2010)
Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. J. Comput. Biol. 17 (3) (2010)
James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette
Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human. PLoS Comput. Biol. 6 (7) (2010)
Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol. Biol. 5 (2010)
Abdoulaye Baniré Diallo, Dunarel Badescu, Mathieu Blanchette, Vladimir Makarenkov
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. J. Comput. Biol. 16 (10) (2009)
Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk
Genetic Map Refinement Using a Comparative Genomic Approach. J. Comput. Biol. 16 (10) (2009)
Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. RECOMB (2009)
Martin A. Smith, Mathieu Blanchette, Barbara Papadopoulou
. BMC Bioinform. 9 (2008)
François Fauteux, Mathieu Blanchette, Martina V. Stromvik
Seeder: discriminative seeding DNA motif discovery. Bioinform. 24 (20) (2008)
Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov
An Evolutionary Study of the Human Papillomavirus Genomes. RECOMB-CG (2008)
Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk
A Phylogenetic Approach to Genetic Map Refinement. RECOMB-CG (2008)
Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette
-regulatory module predictions. Nucleic Acids Res. 35 (Database-Issue) (2007)
Xiaoyu Chen, Mathieu Blanchette
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinform. 8 (S-10) (2007)
Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. J. Comput. Biol. 14 (4) (2007)
Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk
Gene Maps Linearization Using Genomic Rearrangement Distances. J. Comput. Biol. 14 (4) (2007)
Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk
Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. Comparative Genomics (2006)
Éric Gaul, Mathieu Blanchette
Ordering Partially Assembled Genomes Using Gene Arrangements. Comparative Genomics (2006)
Eric Blais, Mathieu Blanchette
Common Substrings in Random Strings. CPM (2006)
Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette
On the Inference of Parsimonious Indel Evolutionary Scenarios. J. Bioinform. Comput. Biol. 4 (3) (2006)
Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
Finding Maximum Likelihood Indel Scenarios. Comparative Genomics (2006)
Fei Fang, Mathieu Blanchette
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Gill Bejerano, David Haussler, Mathieu Blanchette
Into the heart of darkness: large-scale clustering of human non-coding DNA. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve
Reconstructing Ancestral Gene Orders Using Conserved Intervals. WABI (2004)
Saurabh Sinha, Mathieu Blanchette, Martin Tompa
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinform. 5 (2004)
Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa
Motif Discovery in Heterogeneous Sequence Data. Pacific Symposium on Biocomputing (2004)
Mathieu Blanchette, Martin Tompa
FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res. 31 (13) (2003)
Mathieu Blanchette, Samson Kwong, Martin Tompa
An Empirical Comparison of Tools for Phylogenetic Footprinting. BIBE (2003)
Mathieu Blanchette
A comparative analysis method for detecting binding sites in coding regions. RECOMB (2003)
Mathieu Blanchette, Benno Schwikowski, Martin Tompa
Algorithms for Phylogenetic Footprinting. J. Comput. Biol. 9 (2) (2002)
Mathieu Blanchette
Algorithms for phylogenetic footprinting. RECOMB (2001)
Mathieu Blanchette
Evolutionary Puzzles: An Introduction to Genome Rearrangement. International Conference on Computational Science (2) (2001)
Mathieu Blanchette, Saurabh Sinha
Separating real motifs from their artifacts. ISMB (Supplement of Bioinformatics) (2001)
Mathieu Blanchette, Benno Schwikowski, Martin Tompa
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. ISMB (2000)
David Sankoff, Mathieu Blanchette
Phylogenetic Invariants for Genome Rearrangements. J. Comput. Biol. 6 (3/4) (1999)
David Sankoff, Mathieu Blanchette
Probability models for genome rearrangement and linear invariants for phylogenetic inference. RECOMB (1999)
David Sankoff, Mathieu Blanchette
Multiple Genome Rearrangement and Breakpoint Phylogeny. J. Comput. Biol. 5 (3) (1998)
David Sankoff, Mathieu Blanchette
Multiple genome rearrangements. RECOMB (1998)
David Sankoff, Mathieu Blanchette
The Median Problem for Breakpoints in Comparative Genomics. COCOON (1997)