Mathieu Blanchette

According to our database, Mathieu Blanchette authored at least 75 papers between 1997 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

PERFUMES: pipeline to extract RNA functional motifs and exposed structures.

Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl

Bioinform., February, 2024

2023

PhyloGFN: Phylogenetic inference with generative flow networks.

Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio

CoRR, 2023

Reference panel-guided super-resolution inference of Hi-C data.

Yanlin Zhang, Mathieu Blanchette

Bioinform., 2023

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

Proceedings of The ACM Collective Intelligence Conference, 2023

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

Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems, 2023

2021

Neural representation and generation for RNA secondary structures.

Zichao Yan, William L. Hamilton, Mathieu Blanchette

Proceedings of the 9th International Conference on Learning Representations, 2021

2020

oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species.

Louis Philip Benoit Bouvrette, Samantha Bovaird, Mathieu Blanchette, Eric Lécuyer

Nucleic Acids Res., 2020

Mycorrhiza: Genotype Assignment usingPhylogenetic Networks.

Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette

CoRR, 2020

Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions.

Zichao Yan, William L. Hamilton, Mathieu Blanchette

Bioinform., 2020

EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM.

Dongjoon Lim, Mathieu Blanchette

Bioinform., 2020

Mycorrhiza: genotype assignment using phylogenetic networks.

Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette

Bioinform., 2020

Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites.

Faizy Ahsan, Alexandre Drouin, François Laviolette, Doina Precup, Mathieu Blanchette

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019

Prediction of mRNA subcellular localization using deep recurrent neural networks.

Zichao Yan, Eric Lécuyer, Mathieu Blanchette

Bioinform., 2019

Large-scale mammalian genome rearrangements coincide with chromatin interactions.

Krister M. Swenson, Mathieu Blanchette

Bioinform., 2019

2018

Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches.

Jaspal Singh, Ramchalam Kinattinkara Ramakrishnan, Mathieu Blanchette

Proceedings of the 18th IEEE International Conference on Bioinformatics and Bioengineering, 2018

RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment.

Ramchalam Kinattinkara Ramakrishnan, Jaspal Singh, Mathieu Blanchette

Proceedings of the 18th IEEE International Conference on Bioinformatics and Bioengineering, 2018

2017

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.

Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, B. Franz Lang, Nadia El-Mabrouk

Bioinform., 2017

Lessons from an Online Massive Genomics Computer Game.

Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl

Proceedings of the Fifth AAAI Conference on Human Computation and Crowdsourcing, 2017

2016

Substring Parsimony.

Mathieu Blanchette

Encyclopedia of Algorithms, 2016

Models and algorithms for genome rearrangement with positional constraints.

Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette

Algorithms Mol. Biol., 2016

Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy.

Faizy Ahsan, Doina Precup, Mathieu Blanchette

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

BigDataScript: a scripting language for data pipelines.

Pablo Cingolani, Rob Sladek, Mathieu Blanchette

Bioinform., 2015

Models and Algorithms for Genome Rearrangement with Positional Constraints.

Krister M. Swenson, Mathieu Blanchette

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014

Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics.

Jérôme Waldispühl, Mathieu Blanchette

Proceedings of the Seconf AAAI Conference on Human Computation and Crowdsourcing, 2014

2013

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.

Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl

Nucleic Acids Res., 2013

2012

A flexible ancestral genome reconstruction method based on gapped adjacencies.

Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk

BMC Bioinform., 2012

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.

Mathieu Blanchette

BMC Bioinform., 2012

Clique Cover on Sparse Networks.

Mathieu Blanchette, Ethan Kim, Adrian Vetta

Proceedings of the 14th Meeting on Algorithm Engineering & Experiments, 2012

2011

An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss.

Glenn Hickey, Mathieu Blanchette, Paz Carmi, Anil Maheshwari, Norbert Zeh

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Mapping Association between Long-Range <i>cis</i>-Regulatory Regions and Their Target Genes Using Synteny.

Emmanuel Mongin, Ken Dewar, Mathieu Blanchette

J. Comput. Biol., 2011

A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels.

Glenn Hickey, Mathieu Blanchette

J. Comput. Biol., 2011

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

Mathieu Rousseau, James Fraser, Maria A. Ferraiuolo, Josee Dostie, Mathieu Blanchette

BMC Bioinform., 2011

Predicting site-specific human selective pressure using evolutionary signatures.

Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette

Bioinform., 2011

2010

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human.

James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette

PLoS Comput. Biol., 2010

Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks.

Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette

J. Comput. Biol., 2010

Ancestors 1.0: a web server for ancestral sequence reconstruction.

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette

Bioinform., 2010

Predicting direct protein interactions from affinity purification mass spectrometry data.

Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette

Algorithms Mol. Biol., 2010

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss.

Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk

Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Mapping Association between Long-Range <i>Cis</i>-Regulatory Regions and Their Target Genes Using Comparative Genomics.

Emmanuel Mongin, Ken Dewar, Mathieu Blanchette

Proceedings of the Comparative Genomics - International Workshop, 2010

A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error.

Glenn Hickey, Mathieu Blanchette

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses.

Abdoulaye Baniré Diallo, Dunarel Badescu, Mathieu Blanchette, Vladimir Makarenkov

J. Comput. Biol., 2009

Genetic Map Refinement Using a Comparative Genomic Approach.

Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk

J. Comput. Biol., 2009

2008

Substring Parsimony.

Mathieu Blanchette

Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Improving the prediction of mRNA extremities in the parasitic protozoan <i>Leishmania</i>.

Martin A. Smith, Mathieu Blanchette, Barbara Papadopoulou

BMC Bioinform., 2008

Seeder: discriminative seeding DNA motif discovery.

François Fauteux, Mathieu Blanchette, Martina V. Stromvik

Bioinform., 2008

A Phylogenetic Approach to Genetic Map Refinement.

Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk

Proceedings of the Comparative Genomics, International Workshop, 2008

An Evolutionary Study of the Human Papillomavirus Genomes.

Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov

Proceedings of the Comparative Genomics, International Workshop, 2008

2007

PReMod: a database of genome-wide mammalian <i>cis</i>-regulatory module predictions.

Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette

Nucleic Acids Res., 2007

Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem.

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette

J. Comput. Biol., 2007

Gene Maps Linearization Using Genomic Rearrangement Distances.

Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk

J. Comput. Biol., 2007

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees.

Xiaoyu Chen, Mathieu Blanchette

BMC Bioinform., 2007

2006

A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model.

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette, François-Joseph Lapointe

Proceedings of the Data Science and Classification, 2006

FootPrinter3: phylogenetic footprinting in partially alignable sequences.

Fei Fang, Mathieu Blanchette

Nucleic Acids Res., 2006

On the Inference of Parsimonious Indel Evolutionary Scenarios.

Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette

J. Bioinform. Comput. Biol., 2006

Ordering Partially Assembled Genomes Using Gene Arrangements.

Éric Gaul, Mathieu Blanchette

Proceedings of the Comparative Genomics, 2006

Finding Maximum Likelihood Indel Scenarios.

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette

Proceedings of the Comparative Genomics, 2006

Inferring Gene Orders from Gene Maps Using the Breakpoint Distance.

Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk

Proceedings of the Comparative Genomics, 2006

Common Substrings in Random Strings.

Eric Blais, Mathieu Blanchette

Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2004

PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences.

Saurabh Sinha, Mathieu Blanchette, Martin Tompa

BMC Bioinform., 2004

Reconstructing Ancestral Gene Orders Using Conserved Intervals.

Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Motif Discovery in Heterogeneous Sequence Data.

Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa

Proceedings of the Biocomputing 2004, 2004

Into the heart of darkness: large-scale clustering of human non-coding DNA.

Gill Bejerano, David Haussler, Mathieu Blanchette

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

FootPrinter: a program designed for phylogenetic footprinting.

Mathieu Blanchette, Martin Tompa

Nucleic Acids Res., 2003

A comparative analysis method for detecting binding sites in coding regions.

Mathieu Blanchette

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

An Empirical Comparison of Tools for Phylogenetic Footprinting.

Mathieu Blanchette, Samson Kwong, Martin Tompa

Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

2002

Algorithms for Phylogenetic Footprinting.

Mathieu Blanchette, Benno Schwikowski, Martin Tompa

J. Comput. Biol., 2002

2001

Algorithms for phylogenetic footprinting.

Mathieu Blanchette

Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

Separating real motifs from their artifacts.

Mathieu Blanchette, Saurabh Sinha

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Evolutionary Puzzles: An Introduction to Genome Rearrangement.

Mathieu Blanchette

Proceedings of the Computational Science - ICCS 2001, 2001

2000

An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species.

Mathieu Blanchette, Benno Schwikowski, Martin Tompa

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999

Phylogenetic Invariants for Genome Rearrangements.

David Sankoff, Mathieu Blanchette

J. Comput. Biol., 1999

Probability models for genome rearrangement and linear invariants for phylogenetic inference.

David Sankoff, Mathieu Blanchette

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998

Multiple Genome Rearrangement and Breakpoint Phylogeny.

David Sankoff, Mathieu Blanchette

J. Comput. Biol., 1998

Multiple genome rearrangements.

David Sankoff, Mathieu Blanchette

Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997

The Median Problem for Breakpoints in Comparative Genomics.

David Sankoff, Mathieu Blanchette

Proceedings of the Computing and Combinatorics, Third Annual International Conference, 1997