| 2025 | AAAI | dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. | Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li |
| 2025 | ICLR | Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold. | Lazar Atanackovic, Xi Zhang, Brandon Amos, Mathieu Blanchette, Leo J. Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov |
| 2024 | FDG | 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, Sbastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jrme Waldisphl |
| 2024 | ICLR | PhyloGFN: Phylogenetic inference with generative flow networks. | Ming-Yang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio |
| 2023 | CHI | 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, Sbastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jrme Waldisphl |
| 2021 | ICLR | Neural representation and generation for RNA secondary structures. | Zichao Yan, William L. Hamilton, Mathieu Blanchette |
| 2018 | BIBE | RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment. | Ramchalam Kinattinkara Ramakrishnan, Jaspal Singh, Mathieu Blanchette |
| 2018 | BIBE | Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches. | Jaspal Singh, Ramchalam Kinattinkara Ramakrishnan, Mathieu Blanchette |
| 2017 | HCOMP | Lessons from an Online Massive Genomics Computer Game. | Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jrme Waldisphl |
| 2015 | WABI | Models and Algorithms for Genome Rearrangement with Positional Constraints. | Krister M. Swenson, Mathieu Blanchette |
| 2014 | HCOMP | Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. | Jrme Waldisphl, Mathieu Blanchette |
| 2012 | ALENEX | Clique Cover on Sparse Networks. | Mathieu Blanchette, Ethan Kim, Adrian Vetta |
| 2011 | RECOMB | A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. | Glenn Hickey, Mathieu Blanchette |
| 2010 | PSB | A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. | Glenn Hickey, Mathieu Blanchette |
| 2010 | RECOMB | Mapping Association between Long-Range | Emmanuel Mongin, Ken Dewar, Mathieu Blanchette |
| 2010 | WABI | Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. | Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk |
| 2009 | RECOMB | Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. | Mathieu Lavalle-Adam, Benoit Coulombe, Mathieu Blanchette |
| 2008 | RECOMB | An Evolutionary Study of the Human Papillomavirus Genomes. | Dunarel Badescu, Abdoulaye Banir Diallo, Mathieu Blanchette, Vladimir Makarenkov |
| 2008 | RECOMB | A Phylogenetic Approach to Genetic Map Refinement. | Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk |
| 2006 | CPM | Common Substrings in Random Strings. | Eric Blais, Mathieu Blanchette |
| 2006 | RECOMB | Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. | Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk |
| 2006 | RECOMB | Finding Maximum Likelihood Indel Scenarios. | Abdoulaye Banir Diallo, Vladimir Makarenkov, Mathieu Blanchette |
| 2006 | RECOMB | Ordering Partially Assembled Genomes Using Gene Arrangements. | ric Gaul, Mathieu Blanchette |
| 2004 | ISMB | Into the heart of darkness: large-scale clustering of human non-coding DNA. | Gill Bejerano, David Haussler, Mathieu Blanchette |
| 2004 | PSB | Motif Discovery in Heterogeneous Sequence Data. | Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa |
| 2004 | WABI | Reconstructing Ancestral Gene Orders Using Conserved Intervals. | Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cdric Chauve |
| 2003 | BIBE | An Empirical Comparison of Tools for Phylogenetic Footprinting. | Mathieu Blanchette, Samson Kwong, Martin Tompa |
| 2003 | RECOMB | A comparative analysis method for detecting binding sites in coding regions. | Mathieu Blanchette |
| 2001 | ICCS | Evolutionary Puzzles: An Introduction to Genome Rearrangement. | Mathieu Blanchette |
| 2001 | ISMB | Separating real motifs from their artifacts. | Mathieu Blanchette, Saurabh Sinha |
| 2001 | RECOMB | Algorithms for phylogenetic footprinting. | Mathieu Blanchette |
| 2000 | ISMB | An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. | Mathieu Blanchette, Benno Schwikowski, Martin Tompa |
| 1999 | RECOMB | Probability models for genome rearrangement and linear invariants for phylogenetic inference. | David Sankoff, Mathieu Blanchette |
| 1998 | RECOMB | Multiple genome rearrangements. | David Sankoff, Mathieu Blanchette |
| 1997 | COCOON | The Median Problem for Breakpoints in Comparative Genomics. | David Sankoff, Mathieu Blanchette |