Mathieu Blanchette

Mathieu Blanchette: Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinformatics 13(S-19): S2 (2012)

Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk: A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics 13(S-19): S4 (2012)

Mathieu Blanchette, Ethan Kim, Adrian Vetta: Clique Cover on Sparse Networks. ALENEX 2012: 93-102

Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette: Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics [ISMB/ECCB] 27(13): 266-274 (2011)

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 Bioinformatics 12: 414 (2011)

Emmanuel Mongin, Ken Dewar, Mathieu Blanchette: Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny. Journal of Computational Biology 18(9): 1115-1130 (2011)

Glenn Hickey, Mathieu Blanchette: A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. Journal of Computational Biology 18(11): 1449-1464 (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. Biology Bioinform. 8(2): 551-556 (2011)

Glenn Hickey, Mathieu Blanchette: A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. RECOMB 2011: 85-103

Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette: Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms for Molecular Biology 5: 34 (2010)

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette: Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics 26(1): 130-131 (2010)

Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette: Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. Journal of Computational Biology 17(3): 443-457 (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 Computational Biology 6(7) (2010)

Glenn Hickey, Mathieu Blanchette: A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. Pacific Symposium on Biocomputing 2010: 31-42

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

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

Abdoulaye Baniré Diallo, Dunarel Badescu, Mathieu Blanchette, Vladimir Makarenkov: A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. Journal of Computational Biology 16(10): 1461-1473 (2009)

Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk: Genetic Map Refinement Using a Comparative Genomic Approach. Journal of Computational Biology 16(10): 1475-1486 (2009)

Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette: Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. RECOMB 2009: 302-320

François Fauteux, Mathieu Blanchette, Martina V. Stromvik: Seeder: discriminative seeding DNA motif discovery. Bioinformatics 24(20): 2303-2307 (2008)

Martin Smith, Mathieu Blanchette, Barbara Papadopoulou: Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics 9 (2008)

Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov: An Evolutionary Study of the Human Papillomavirus Genomes. RECOMB-CG 2008: 128-142

Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk: A Phylogenetic Approach to Genetic Map Refinement. RECOMB-CG 2008: 198-210

Mathieu Blanchette: Substring Parsimony. Encyclopedia of Algorithms 2008

Xiaoyu Chen, Mathieu Blanchette: Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics 8(S-10) (2007)

Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk: Gene Maps Linearization Using Genomic Rearrangement Distances. Journal of Computational Biology 14(4): 394-407 (2007)

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette: Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. Journal of Computational Biology 14(4): 446-461 (2007)

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 Research 35(Database-Issue): 122-126 (2007)

Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette: On the Inference of Parsimonious Indel Evolutionary Scenarios. J. Bioinformatics and Computational Biology 4(3): 721-744 (2006)

Fei Fang, Mathieu Blanchette: FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Research 34(Web-Server-Issue): 617-620 (2006)

Eric Blais, Mathieu Blanchette: Common Substrings in Random Strings. CPM 2006: 129-140

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

Éric Gaul, Mathieu Blanchette: Ordering Partially Assembled Genomes Using Gene Arrangements. Comparative Genomics 2006: 113-128

Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette: Finding Maximum Likelihood Indel Scenarios. Comparative Genomics 2006: 171-185

Saurabh Sinha, Mathieu Blanchette, Martin Tompa: PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5: 170 (2004)

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

Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa: Motif Discovery in Heterogeneous Sequence Data. Pacific Symposium on Biocomputing 2004: 348-359

Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cedric Chauve: Reconstructing Ancestral Gene Orders Using Conserved Intervals. WABI 2004: 14-25

Mathieu Blanchette, Martin Tompa: FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Research 31(13): 3840-3842 (2003)

Mathieu Blanchette, Samson Kwong, Martin Tompa: An Empirical Comparison of Tools for Phylogenetic Footprinting. BIBE 2003: 69-78

Mathieu Blanchette: A comparative analysis method for detecting binding sites in coding regions. RECOMB 2003: 57-66

Mathieu Blanchette, Benno Schwikowski, Martin Tompa: Algorithms for Phylogenetic Footprinting. Journal of Computational Biology 9(2): 211-223 (2002)

Mathieu Blanchette: Evolutionary Puzzles: An Introduction to Genome Rearrangement. International Conference on Computational Science (2) 2001: 1003-1011

Mathieu Blanchette, Saurabh Sinha: Separating real motifs from their artifacts. ISMB (Supplement of Bioinformatics) 2001: 30-38

Mathieu Blanchette: Algorithms for phylogenetic footprinting. RECOMB 2001: 49-58

Mathieu Blanchette, Benno Schwikowski, Martin Tompa: An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. ISMB 2000: 37-45

David Sankoff, Mathieu Blanchette: Phylogenetic Invariants for Genome Rearrangements. Journal of Computational Biology 6(3/4): 431-445 (1999)

David Sankoff, Mathieu Blanchette: Probability models for genome rearrangement and linear invariants for phylogenetic inference. RECOMB 1999: 302-309

David Sankoff, Mathieu Blanchette: Multiple Genome Rearrangement and Breakpoint Phylogeny. Journal of Computational Biology 5(3): 555-570 (1998)

David Sankoff, Mathieu Blanchette: Multiple genome rearrangements. RECOMB 1998: 243-247

David Sankoff, Mathieu Blanchette: The Median Problem for Breakpoints in Comparative Genomics. COCOON 1997: 251-264