Mathieu Blanchette

94 papers A* 5A 2B 9C 7Misc 4Journal 52Unranked 11

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Inference-Time Compute Scaling For Flow Matching. CoRR Adam Stecklov, Noah El Rimawi-Fine, Mathieu Blanchette
2025	A*	`conf`	Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold. ICLR Lazar Atanackovic, Xi Zhang, Brandon Amos, Mathieu Blanchette, Leo J. Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov
2025	J	`jnl`	R3Design: deep tertiary structure-based RNA sequence design and beyond. Briefings Bioinform. Cheng Tan, Yijie Zhang, Zhangyang Gao, Hanqun Cao, Siyuan Li, Siqi Ma, Mathieu Blanchette, Stan Z. Li
2025	J	`jnl`	Simulation-free Structure Learning for Stochastic Dynamics. CoRR Noah El Rimawi-Fine, Adam Stecklov, Lucas Nelson, Mathieu Blanchette, Alexander Tong, Stephen Y. Zhang, Lazar Atanackovic
2025	J	`jnl`	Sparsity regularization via tree-structured environments for disentangled representations. Trans. Mach. Learn. Res. Elliot Layne, Jason S. Hartford, Sébastien Lachapelle, Mathieu Blanchette, Dhanya Sridhar
2025	A*	`conf`	dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. AAAI Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li
2025	J	`jnl`	dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. CoRR Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li
2024	J	`jnl`	ARGV: 3D genome structure exploration using augmented reality. BMC Bioinform. Chrisostomos Drogaris, Yanlin Zhang, Eric Zhang, Elena Nazarova, Roman Sarrazin-Gendron, Sélik Wilhelm-Landry, Yan Cyr, Jacek Majewski, Mathieu Blanchette, Jérôme Waldispühl
2024	C	`conf`	Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. FDG 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	J	`jnl`	Leveraging Structure Between Environments: Phylogenetic Regularization Incentivizes Disentangled Representations. CoRR Elliot Layne, Jason S. Hartford, Sébastien Lachapelle, Mathieu Blanchette, Dhanya Sridhar
2024	J	`jnl`	Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold. CoRR Lazar Atanackovic, Xi Zhang, Brandon Amos, Mathieu Blanchette, Leo J. Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov
2024	J	`jnl`	PERFUMES: pipeline to extract RNA functional motifs and exposed structures. Bioinform. Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl
2024	A*	`conf`	PhyloGFN: Phylogenetic inference with generative flow networks. ICLR Ming-Yang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio
2023	J	`jnl`	PhyloGFN: Phylogenetic inference with generative flow networks. CoRR Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio
2023	—	`conf`	Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. CI Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2023	A*	`conf`	Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? CHI Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2023	J	`jnl`	Posterior inference of Hi-C contact frequency through sampling. Frontiers Bioinform. Yanlin Zhang, Christopher J. F. Cameron, Mathieu Blanchette
2023	J	`jnl`	Reference panel-guided super-resolution inference of Hi-C data. Bioinform. Yanlin Zhang, Mathieu Blanchette
2022	J	`jnl`	PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information. Bioinform. Faizy Ahsan, Zichao Yan, Doina Precup, Mathieu Blanchette
2021	A*	`conf`	Neural representation and generation for RNA secondary structures. ICLR Zichao Yan, William L. Hamilton, Mathieu Blanchette
2021	J	`jnl`	Neural representation and generation for RNA secondary structures. CoRR Zichao Yan, William L. Hamilton, Mathieu Blanchette
2020	J	`jnl`	EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM. Bioinform. Dongjoon Lim, Mathieu Blanchette
2020	J	`jnl`	Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions. Bioinform. Zichao Yan, William L. Hamilton, Mathieu Blanchette
2020	J	`jnl`	Mycorrhiza: Genotype Assignment usingPhylogenetic Networks. CoRR Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette
2020	J	`jnl`	Mycorrhiza: genotype assignment using phylogenetic networks. Bioinform. Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette
2020	—	`conf`	Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites. BIBM Faizy Ahsan, Alexandre Drouin, François Laviolette, Doina Precup, Mathieu Blanchette
2020	J	`jnl`	Supervised learning on phylogenetically distributed data. Bioinform. Elliot Layne, Erika N. Dort, Richard C. Hamelin, Yue Li, Mathieu Blanchette
2020	J	`jnl`	oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. Nucleic Acids Res. Louis Philip Benoit Bouvrette, Samantha Bovaird, Mathieu Blanchette, Eric Lécuyer
2019	J	`jnl`	Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinform. Krister M. Swenson, Mathieu Blanchette
2019	J	`jnl`	Prediction of mRNA subcellular localization using deep recurrent neural networks. Bioinform. Zichao Yan, Eric Lécuyer, Mathieu Blanchette
2018	—	`ed.`	Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings RECOMB-CG Mathieu Blanchette, Aïda Ouangraoua
2018	C	`conf`	Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches. BIBE Jaspal Singh, Ramchalam Kinattinkara Ramakrishnan, Mathieu Blanchette
2018	C	`conf`	RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment. BIBE Ramchalam Kinattinkara Ramakrishnan, Jaspal Singh, Mathieu Blanchette
2017	J	`jnl`	CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinform. Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, B. Franz Lang, Nadia El-Mabrouk
2017	B	`conf`	Lessons from an Online Massive Genomics Computer Game. HCOMP Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl
2016	J	`jnl`	Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette
2016	—	`conf`	Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy. BCB Faizy Ahsan, Doina Precup, Mathieu Blanchette
2016	—	`ch.`	Substring Parsimony. Encyclopedia of Algorithms Mathieu Blanchette
2015	J	`jnl`	BigDataScript: a scripting language for data pipelines. Bioinform. Pablo Cingolani, Rob Sladek, Mathieu Blanchette
2015	C	`conf`	Models and Algorithms for Genome Rearrangement with Positional Constraints. WABI Krister M. Swenson, Mathieu Blanchette
2014	B	`conf`	Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP Jérôme Waldispühl, Mathieu Blanchette
2013	J	`jnl`	SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl
2012	J	`jnl`	A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinform. Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk
2012	A	`conf`	Clique Cover on Sparse Networks. ALENEX Mathieu Blanchette, Ethan Kim, Adrian Vetta
2012	J	`jnl`	Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinform. Mathieu Blanchette
2011	B	`conf`	A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. RECOMB Glenn Hickey, Mathieu Blanchette
2011	J	`jnl`	A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. J. Comput. Biol. Glenn Hickey, Mathieu Blanchette
2011	J	`jnl`	An Approximation Algorithm for the Noah's Ark Problem with Random Feature Loss. IEEE ACM Trans. Comput. Biol. Bioinform. Glenn Hickey, Mathieu Blanchette, Paz Carmi, Anil Maheshwari, Norbert Zeh
2011	J	`jnl`	Mapping Association between Long-Range J. Comput. Biol. Emmanuel Mongin, Ken Dewar, Mathieu Blanchette
2011	J	`jnl`	Predicting site-specific human selective pressure using evolutionary signatures. Bioinform. Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette
2011	J	`jnl`	Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinform. Mathieu Rousseau, James Fraser, Maria A. Ferraiuolo, Josee Dostie, Mathieu Blanchette
2010	Misc	`conf`	A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. Pacific Symposium on Biocomputing Glenn Hickey, Mathieu Blanchette
2010	J	`jnl`	Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinform. Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
2010	J	`jnl`	Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human. PLoS Comput. Biol. James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette
2010	J	`jnl`	Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. J. Comput. Biol. Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette
2010	—	`conf`	Mapping Association between Long-Range RECOMB-CG Emmanuel Mongin, Ken Dewar, Mathieu Blanchette
2010	J	`jnl`	Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol. Biol. Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette
2010	C	`conf`	Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. WABI Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk
2009	J	`jnl`	A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. J. Comput. Biol. Abdoulaye Baniré Diallo, Dunarel Badescu, Mathieu Blanchette, Vladimir Makarenkov
2009	B	`conf`	Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. RECOMB Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette
2009	J	`jnl`	Genetic Map Refinement Using a Comparative Genomic Approach. J. Comput. Biol. Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk
2008	—	`conf`	A Phylogenetic Approach to Genetic Map Refinement. RECOMB-CG Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk
2008	—	`conf`	An Evolutionary Study of the Human Papillomavirus Genomes. RECOMB-CG Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov
2008	J	`jnl`	Improving the prediction of mRNA extremities in the parasitic protozoan BMC Bioinform. Martin A. Smith, Mathieu Blanchette, Barbara Papadopoulou
2008	J	`jnl`	Seeder: discriminative seeding DNA motif discovery. Bioinform. François Fauteux, Mathieu Blanchette, Martina V. Stromvik
2008	—	`ch.`	Substring Parsimony. Encyclopedia of Algorithms Mathieu Blanchette
2007	J	`jnl`	Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. J. Comput. Biol. Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
2007	J	`jnl`	Gene Maps Linearization Using Genomic Rearrangement Distances. J. Comput. Biol. Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk
2007	J	`jnl`	PReMod: a database of genome-wide mammalian Nucleic Acids Res. Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette
2007	J	`jnl`	Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinform. Xiaoyu Chen, Mathieu Blanchette
2006	—	`ch.`	A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model. Data Science and Classification Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette, François-Joseph Lapointe
2006	B	`conf`	Common Substrings in Random Strings. CPM Eric Blais, Mathieu Blanchette
2006	—	`conf`	Finding Maximum Likelihood Indel Scenarios. Comparative Genomics Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette
2006	J	`jnl`	FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res. Fei Fang, Mathieu Blanchette
2006	—	`conf`	Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. Comparative Genomics Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk
2006	J	`jnl`	On the Inference of Parsimonious Indel Evolutionary Scenarios. J. Bioinform. Comput. Biol. Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette
2006	—	`conf`	Ordering Partially Assembled Genomes Using Gene Arrangements. Comparative Genomics Éric Gaul, Mathieu Blanchette
2004	—	`conf`	Into the heart of darkness: large-scale clustering of human non-coding DNA. ISMB/ECCB (Supplement of Bioinformatics) Gill Bejerano, David Haussler, Mathieu Blanchette
2004	Misc	`conf`	Motif Discovery in Heterogeneous Sequence Data. Pacific Symposium on Biocomputing Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa
2004	J	`jnl`	PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinform. Saurabh Sinha, Mathieu Blanchette, Martin Tompa
2004	C	`conf`	Reconstructing Ancestral Gene Orders Using Conserved Intervals. WABI Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve
2003	B	`conf`	A comparative analysis method for detecting binding sites in coding regions. RECOMB Mathieu Blanchette
2003	C	`conf`	An Empirical Comparison of Tools for Phylogenetic Footprinting. BIBE Mathieu Blanchette, Samson Kwong, Martin Tompa
2003	J	`jnl`	FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res. Mathieu Blanchette, Martin Tompa
2002	J	`jnl`	Algorithms for Phylogenetic Footprinting. J. Comput. Biol. Mathieu Blanchette, Benno Schwikowski, Martin Tompa
2001	B	`conf`	Algorithms for phylogenetic footprinting. RECOMB Mathieu Blanchette
2001	Misc	`conf`	Evolutionary Puzzles: An Introduction to Genome Rearrangement. International Conference on Computational Science (2) Mathieu Blanchette
2001	—	`conf`	Separating real motifs from their artifacts. ISMB (Supplement of Bioinformatics) Mathieu Blanchette, Saurabh Sinha
2000	A	`conf`	An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. ISMB Mathieu Blanchette, Benno Schwikowski, Martin Tompa
1999	J	`jnl`	Phylogenetic Invariants for Genome Rearrangements. J. Comput. Biol. David Sankoff, Mathieu Blanchette
1999	B	`conf`	Probability models for genome rearrangement and linear invariants for phylogenetic inference. RECOMB David Sankoff, Mathieu Blanchette
1998	J	`jnl`	Multiple Genome Rearrangement and Breakpoint Phylogeny. J. Comput. Biol. David Sankoff, Mathieu Blanchette
1998	B	`conf`	Multiple genome rearrangements. RECOMB David Sankoff, Mathieu Blanchette
1997	Misc	`conf`	The Median Problem for Breakpoints in Comparative Genomics. COCOON David Sankoff, Mathieu Blanchette