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ORCIDMathieu Blanchette
Person information
- affiliation: McGill University, Centre for Bioinformatics, Montreal, QC, Canada
- affiliation (former): University of California, Santa Cruz, Center for Biomolecular Science and Engineering, Santa Cruz, CA, USA
- affiliation (former, PhD 2002): University of Washington, Department of Computer Science, Seattle, WA, USA
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2020 – today
- 2025
[c37]Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li:
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. AAAI 2025: 782-790- [i6]Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li:
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. CoRR abs/2503.01910 (2025) - 2024
- [j42]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) - [j41]Chrisostomos Drogaris, Yanlin Zhang, Eric Zhang, Elena Nazarova, Roman Sarrazin-Gendron, Sélik Wilhelm-Landry, Yan Cyr, Jacek Majewski, Mathieu Blanchette, Jérôme Waldispühl:
ARGV: 3D genome structure exploration using augmented reality. BMC Bioinform. 25(1): 277 (2024) - [c36]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: 31 - [c35]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 - [i5]Elliot Layne, Jason S. Hartford, Sébastien Lachapelle, Mathieu Blanchette, Dhanya Sridhar:
Leveraging Structure Between Environments: Phylogenetic Regularization Incentivizes Disentangled Representations. CoRR abs/2405.20482 (2024) - [i4]Lazar Atanackovic, Xi Zhang, Brandon Amos, Mathieu Blanchette, Leo J. Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov:
Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold. CoRR abs/2408.14608 (2024) - 2023
- [j40]Yanlin Zhang, Mathieu Blanchette:
Reference panel-guided super-resolution inference of Hi-C data. Bioinform. 39(Supplement-1): 386-393 (2023) - [j39]Yanlin Zhang, Christopher J. F. Cameron, Mathieu Blanchette:
Posterior inference of Hi-C contact frequency through sampling. Frontiers Bioinform. 3 (2023) - [c34]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: 679:1-679:15 - [c33]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: 53-62 - [i3]Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio:
PhyloGFN: Phylogenetic inference with generative flow networks. CoRR abs/2310.08774 (2023) - 2022
- [j38]Faizy Ahsan, Zichao Yan, Doina Precup, Mathieu Blanchette:
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information. Bioinform. 38(Supplement_1): i299-i306 (2022) - 2021
- [c32]Zichao Yan, William L. Hamilton, Mathieu Blanchette:
Neural representation and generation for RNA secondary structures. ICLR 2021 - [i2]Zichao Yan, William L. Hamilton, Mathieu Blanchette:
Neural representation and generation for RNA secondary structures. CoRR abs/2102.00925 (2021) - 2020
- [j37]Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette:
Mycorrhiza: genotype assignment using phylogenetic networks. Bioinform. 36(1): 212-220 (2020) - [j36]Zichao Yan, William L. Hamilton, Mathieu Blanchette:
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions. Bioinform. 36(Supplement-1): i276-i284 (2020) - [j35]Dongjoon Lim, Mathieu Blanchette:
EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM. Bioinform. 36(Supplement-1): i353-i361 (2020) - [j34]Elliot Layne, Erika N. Dort, Richard C. Hamelin, Yue Li, Mathieu Blanchette:
Supervised learning on phylogenetically distributed data. Bioinform. 36(Supplement-2): i895-i902 (2020) - [j33]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): D166-D173 (2020) - [c31]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: 62-66 - [i1]Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette:
Mycorrhiza: Genotype Assignment usingPhylogenetic Networks. CoRR abs/2010.09483 (2020)
2010 – 2019
- 2019
- [j32]Krister M. Swenson, Mathieu Blanchette:
Large-scale mammalian genome rearrangements coincide with chromatin interactions. Bioinform. 35(14): i117-i126 (2019) - [j31]Zichao Yan, Eric Lécuyer, Mathieu Blanchette:
Prediction of mRNA subcellular localization using deep recurrent neural networks. Bioinform. 35(14): i333-i342 (2019) - 2018
- [c30]Jaspal Singh, Ramchalam Kinattinkara Ramakrishnan, Mathieu Blanchette:
Detection of Errors in Multi-genome Alignments Using Machine Learning Approaches. BIBE 2018: 47-53 - [c29]Ramchalam Kinattinkara Ramakrishnan, Jaspal Singh, Mathieu Blanchette:
RLALIGN: A Reinforcement Learning Approach for Multiple Sequence Alignment. BIBE 2018: 61-66 - [e1]Mathieu Blanchette, Aïda Ouangraoua:
Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings. Lecture Notes in Computer Science 11183, Springer 2018, ISBN 978-3-030-00833-8 [contents] - 2017
- [j30]Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, B. Franz Lang, Nadia El-Mabrouk:
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinform. 33(21): 3331-3339 (2017) - [c28]Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl:
Lessons from an Online Massive Genomics Computer Game. HCOMP 2017: 177-186 - 2016
- [j29]Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette:
Models and algorithms for genome rearrangement with positional constraints. Algorithms Mol. Biol. 11: 13 (2016) - [c27]Faizy Ahsan, Doina Precup, Mathieu Blanchette:
Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy. BCB 2016: 497-498 - [r2]Mathieu Blanchette:
Substring Parsimony. Encyclopedia of Algorithms 2016: 2129-2131 - 2015
- [j28]Pablo Cingolani, Rob Sladek, Mathieu Blanchette:
BigDataScript: a scripting language for data pipelines. Bioinform. 31(1): 10-16 (2015) - [c26]Krister M. Swenson, Mathieu Blanchette:
Models and Algorithms for Genome Rearrangement with Positional Constraints. WABI 2015: 243-256 - 2014
- [c25]Jérôme Waldispühl, Mathieu Blanchette:
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP 2014: 73-74 - 2013
- [j27]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): 480-485 (2013) - 2012
- [j26]Mathieu Blanchette:
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinform. 13(S-19): S2 (2012) - [j25]Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk:
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinform. 13(S-19): S4 (2012) - [c24]Mathieu Blanchette, Ethan Kim, Adrian Vetta:
Clique Cover on Sparse Networks. ALENEX 2012: 93-102 - 2011
- [j24]Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette:
Predicting site-specific human selective pressure using evolutionary signatures. Bioinform. 27(13): 266-274 (2011) - [j23]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: 414 (2011) - [j22]Emmanuel Mongin, Ken Dewar, Mathieu Blanchette:
Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny. J. Comput. Biol. 18(9): 1115-1130 (2011) - [j21]Glenn Hickey, Mathieu Blanchette:
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. J. Comput. Biol. 18(11): 1449-1464 (2011) - [j20]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): 551-556 (2011) - [c23]Glenn Hickey, Mathieu Blanchette:
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. RECOMB 2011: 85-103 - 2010
- [j19]Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette:
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol. Biol. 5: 34 (2010) - [j18]Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinform. 26(1): 130-131 (2010) - [j17]Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette:
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. J. Comput. Biol. 17(3): 443-457 (2010) - [j16]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) - [c22]Glenn Hickey, Mathieu Blanchette:
A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. Pacific Symposium on Biocomputing 2010: 31-42 - [c21]Emmanuel Mongin, Ken Dewar, Mathieu Blanchette:
Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics. RECOMB-CG 2010: 216-227 - [c20]Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk:
Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. WABI 2010: 78-89
2000 – 2009
- 2009
- [j15]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): 1461-1473 (2009) - [j14]Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk:
Genetic Map Refinement Using a Comparative Genomic Approach. J. Comput. Biol. 16(10): 1475-1486 (2009) - [c19]Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette:
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. RECOMB 2009: 302-320 - 2008
- [j13]François Fauteux, Mathieu Blanchette, Martina V. Stromvik:
Seeder: discriminative seeding DNA motif discovery. Bioinform. 24(20): 2303-2307 (2008) - [j12]Martin A. Smith, Mathieu Blanchette, Barbara Papadopoulou:
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinform. 9 (2008) - [c18]Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov:
An Evolutionary Study of the Human Papillomavirus Genomes. RECOMB-CG 2008: 128-142 - [c17]Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk:
A Phylogenetic Approach to Genetic Map Refinement. RECOMB-CG 2008: 198-210 - [r1]Mathieu Blanchette:
Substring Parsimony. Encyclopedia of Algorithms 2008 - 2007
- [j11]Xiaoyu Chen, Mathieu Blanchette:
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinform. 8(S-10) (2007) - [j10]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): 394-407 (2007) - [j9]Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. J. Comput. Biol. 14(4): 446-461 (2007) - [j8]Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette:
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res. 35(Database-Issue): 122-126 (2007) - 2006
- [j7]Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette:
On the Inference of Parsimonious Indel Evolutionary Scenarios. J. Bioinform. Comput. Biol. 4(3): 721-744 (2006) - [j6]Fei Fang, Mathieu Blanchette:
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res. 34(Web-Server-Issue): 617-620 (2006) - [c16]Eric Blais, Mathieu Blanchette:
Common Substrings in Random Strings. CPM 2006: 129-140 - [c15]Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk:
Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. Comparative Genomics 2006: 99-112 - [c14]Éric Gaul, Mathieu Blanchette:
Ordering Partially Assembled Genomes Using Gene Arrangements. Comparative Genomics 2006: 113-128 - [c13]Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Finding Maximum Likelihood Indel Scenarios. Comparative Genomics 2006: 171-185 - [p1]Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette, François-Joseph Lapointe:
A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model. Data Science and Classification 2006: 333-340 - 2004
- [j5]Saurabh Sinha, Mathieu Blanchette, Martin Tompa:
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinform. 5: 170 (2004) - [c12]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: 40-48 - [c11]Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa:
Motif Discovery in Heterogeneous Sequence Data. Pacific Symposium on Biocomputing 2004: 348-359 - [c10]Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve:
Reconstructing Ancestral Gene Orders Using Conserved Intervals. WABI 2004: 14-25 - 2003
- [j4]Mathieu Blanchette, Martin Tompa:
FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res. 31(13): 3840-3842 (2003) - [c9]Mathieu Blanchette, Samson Kwong, Martin Tompa:
An Empirical Comparison of Tools for Phylogenetic Footprinting. BIBE 2003: 69-78 - [c8]Mathieu Blanchette:
A comparative analysis method for detecting binding sites in coding regions. RECOMB 2003: 57-66 - 2002
- [j3]Mathieu Blanchette, Benno Schwikowski, Martin Tompa:
Algorithms for Phylogenetic Footprinting. J. Comput. Biol. 9(2): 211-223 (2002) - 2001
- [c7]Mathieu Blanchette:
Evolutionary Puzzles: An Introduction to Genome Rearrangement. International Conference on Computational Science (2) 2001: 1003-1011 - [c6]Mathieu Blanchette, Saurabh Sinha:
Separating real motifs from their artifacts. ISMB (Supplement of Bioinformatics) 2001: 30-38 - [c5]Mathieu Blanchette:
Algorithms for phylogenetic footprinting. RECOMB 2001: 49-58 - 2000
- [c4]Mathieu Blanchette, Benno Schwikowski, Martin Tompa:
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. ISMB 2000: 37-45
1990 – 1999
- 1999
- [j2]David Sankoff, Mathieu Blanchette:
Phylogenetic Invariants for Genome Rearrangements. J. Comput. Biol. 6(3/4): 431-445 (1999) - [c3]David Sankoff, Mathieu Blanchette:
Probability models for genome rearrangement and linear invariants for phylogenetic inference. RECOMB 1999: 302-309 - 1998
- [j1]David Sankoff, Mathieu Blanchette:
Multiple Genome Rearrangement and Breakpoint Phylogeny. J. Comput. Biol. 5(3): 555-570 (1998) - [c2]David Sankoff, Mathieu Blanchette:
Multiple genome rearrangements. RECOMB 1998: 243-247 - 1997
- [c1]David Sankoff, Mathieu Blanchette:
The Median Problem for Breakpoints in Comparative Genomics. COCOON 1997: 251-264
Coauthor Index
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