Publications

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
JR Wagner, S Busche, B Ge, T Kwan, T Pastinen, M Blanchette
Genome biology 15 (2), R37
2014
¬ Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora
R Williamson, EB Josephs, AE Platts, KM Hazzouri, A Haudry, …
bioRxiv
2014
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
M Blanchette
Plant and Animal Genome XXII Conference
2014
Hox in motion: tracking HoxA cluster conformation during differentiation
M Rousseau, JL Crutchley, H Miura, M Suderman, M Blanchette, J Dostie
Nucleic acids research, gkt998
2013
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment
D Kwak, A Kam, D Becerra, Q Zhou, A Hops, E Zarour, A Kam, …
Genome biology 14 (10), R116
2013
Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin
P Cloutier, M Lavallée-Adam, D Faubert, M Blanchette, B Coulombe
Journal of proteomics
2013
Genome-Wide Mouse Mutagenesis Reveals CD45-Mediated T Cell Function as Critical in Protective Immunity to HSV-1
G Caignard, GA Leiva-Torres, M Leney-Greene, B Charbonneau, …
PLoS pathogens 9 (9), e1003637
  2013
Computational prediction of the localization of microRNAs within their pre-miRNA
M Leclercq, AB Diallo, M Blanchette
Nucleic acids research 41 (15), 7200-7211
  2013
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2
D Forget, AA Lacombe, P Cloutier, M Lavallée-Adam, M Blanchette, …
Nucleic acids research 41 (14), 6881-6891
  2013
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
A Haudry, AE Platts, E Vello, DR Hoen, M Leclercq, RJ Williamson, …
Nature genetics 45 (8), 891-898
  2013
SPARCS: a web server to analyze (un) structured regions in coding RNA sequences
Y Zhang, Y Ponty, M Blanchette, E Lécuyer, J Waldispühl
Nucleic acids research 41 (W1), W480-W485
  2013
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
T Slotte, KM Hazzouri, JA Ågren, D Koenig, F Maumus, YL Guo, K Steige, …
Nature genetics 45 (7), 831-835
  2013
Positional Mapping and Candidate Gene Analysis of the Mouse Ccs3 Locus That Regulates Differential Susceptibility to Carcinogen-Induced Colorectal Cancer
C Meunier, L Van Der Kraak, C Turbide, N Groulx, I Labouba, P Cingolani, …
PloS one 8 (3), e58733
2013
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity
P Cloutier, M Lavallée-Adam, D Faubert, M Blanchette, B Coulombe
PLoS genetics 9 (1), e1003210
  2013
A flexible ancestral genome reconstruction method based on gapped adjacencies
Y Gagnon, M Blanchette, N El-Mabrouk
BMC bioinformatics 13 (Suppl 19), S4
  2012
Discovery of Cell Compartment Specific Protein–Protein Interactions using Affinity Purification Combined with Tandem Mass Spectrometry
M Lavalle´e-Adam, J Rousseau, C Domecq, A Bouchard, D Forget, …
Journal of proteome research 12 (1), 272-281
  2012
Protein-protein binding site identification by enumerating the configurations
F Guo, SC Li, L Wang, D Zhu
BMC bioinformatics 13 (1), 158
  2012
Phylo: a citizen science approach for improving multiple sequence alignment
A Kawrykow, G Roumanis, A Kam, D Kwak, C Leung, C Wu, E Zarour, …
PloS one 7 (3), e31362
  2012
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria
SE Bongfen, IG Rodrigue-Gervais, J Berghout, S Torre, P Cingolani, …
PloS one 7 (2), e31012
  2012
Clique Cover on Sparse Networks.
M Blanchette, E Kim, A Vetta
ALENEX, 93-102
  2012
2011 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 8
C Abdul-Wahid, S Abdul-Wahid, A Aberer, L Acharya, A Agrawal, …
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (6), 1
2011
A probabilistic model for sequence alignment with context-sensitive indels
G Hickey, M Blanchette
Journal of Computational Biology 18 (11), 1449-1464
  2011
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
M Rousseau, J Fraser, MA Ferraiuolo, J Dostie, M Blanchette
BMC bioinformatics 12 (1), 414
  2011
Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny
E Mongin, K Dewar, M Blanchette
Journal of Computational Biology 18 (9), 1115-1130
2011
Predicting site-specific human selective pressure using evolutionary signatures
J Sadri, AB Diallo, M Blanchette
Bioinformatics 27 (13), i266-i274
  2011
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish
E Mongin, TO Auer, F Bourrat, F Gruhl, K Dewar, M Blanchette, J Wittbrodt, …
PloS one 6 (5), e19747
  2011
An Approximation Algorithm for the Noah’s Ark Problem with Random Feature Loss
G Hickey, M Blanchette, P Carmi, A Maheshwari, N Zeh
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 8 …
  2011
Classification of the Human Papilloma Viruses
AB Diallo, D Badescu, M Blanchette, V Makarenkov
Classification and Multivariate Analysis for Complex Data Structures, 457-464
2011
Mapping association between long-range cis-regulatory regions and their target genes using comparative genomics
E Mongin, K Dewar, M Blanchette
Comparative Genomics, 216-227
  2011
Modeling contaminants in AP-MS/MS experiments
M Lavallée-Adam, P Cloutier, B Coulombe, M Blanchette
Journal of proteome research 10 (2), 886-895
  2010
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II
D Forget, AA Lacombe, P Cloutier, R Al-Khoury, A Bouchard, …
Molecular & Cellular Proteomics 9 (12), 2827-2839
  2010
The three-dimensional architecture of Hox cluster silencing
MA Ferraiuolo, M Rousseau, C Miyamoto, S Shenker, XQD Wang, …
Nucleic acids research 38 (21), 7472-7484
  2010
Predicting direct protein interactions from affinity purification mass spectrometry data.
E Kim, A Sabharwal, A Vetta, M Blanchette
Algorithms for Molecular Biology 5, 34
  2010
Computational analysis of whole-genome differential allelic expression data in human
JR Wagner, B Ge, D Pokholok, KL Gunderson, T Pastinen, M Blanchette
PLoS computational biology 6 (7), e1000849
  2010
Nuclear import of RNA polymerase II requires the conserved GPN-loop GTPase XAB1/GPN1
D Forget, AA Lacombe, P Cloutier, R Al-Khoury, A Bouchard, …
FEBS JOURNAL 277, 191-191
2010
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of novel RNA polymerase II-associated chaperone
P Cloutier, R Al-Khoury, M Lavallee-Adam, D Faubert, H Jiang, C Poitras, …
BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE 88 (2), 416-416
2010
Nuclear import of RNA polymerase II requires the conserved GPN-loop GTPase XAB1/GPN1
AA Lacombe, D Forget, P Cloutier, R Al-Khoury, A Bouchard, …
The FASEB Journal
2010
Detection of locally over-represented GO terms in protein-protein interaction networks
M Lavallée-Adam, B Coulombe, M Blanchette
Journal of Computational Biology 17 (3), 443-457
  2010
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error.
G Hickey, M Blanchette
Pacific Symposium on Biocomputing 15, 31-42
2010
ISMB 2010 ORGANIZATION
Y Moreau, E Eskin, E Halperin, R Sharan, B Berger, N Ben-Tal, M Brudno, …
2010
Computing chromosome conformation
J Fraser, M Rousseau, M Blanchette, J Dostie
Computational Biology of Transcription Factor Binding, 251-268
  2010
Ancestors 1.0: a web server for ancestral sequence reconstruction
AB Diallo, V Makarenkov, M Blanchette
Bioinformatics 26 (1), 130-131
  2010
Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss
D Bertrand, Y Gagnon, M Blanchette, N El-Mabrouk
Algorithms in Bioinformatics, 78-89
  2010
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis
B Ge, DK Pokholok, T Kwan, E Grundberg, L Morcos, DJ Verlaan, J Le, …
Nature genetics 41 (11), 1216-1222
  2009
Genetic map refinement using a comparative genomic approach
D Bertrand, M Blanchette, N El-Mabrouk
Journal of Computational Biology 16 (10), 1475-1486
  2009
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses
AB Diallo, D Badescu, M Blanchette, V Makarenkov
Journal of Computational Biology 16 (10), 1461-1473
  2009
A probabilistic approach for SNP discovery in high-throughput human resequencing data
R Hoberman, J Dias, B Ge, E Harmsen, M Mayhew, DJ Verlaan, T Kwan, …
Genome research 19 (9), 1542-1552
  2009
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes
P Cloutier, R Al-Khoury, M Lavallée-Adam, D Faubert, H Jiang, C Poitras, …
Methods 48 (4), 381-386
  2009
Long-range regulation is a major driving force in maintaining genome integrity
E Mongin, K Dewar, M Blanchette
BMC Evolutionary Biology 9 (1), 203
  2009
Chromatin conformation signatures of cellular differentiation
J Fraser, M Rousseau, S Shenker, MA Ferraiuolo, Y Hayashizaki, …
Genome Biol 10 (4), R37
  2009
Computational prediction of functional elements through comparative genomics
X Ling
2009
Detection of locally over-represented GO terms in protein-protein interaction networks
M Lavallée-Adam, B Coulombe, M Blanchette
Research in Computational Molecular Biology, 302-320
  2009
Seeder: discriminative seeding DNA motif discovery
F Fauteux, M Blanchette, MV Strömvik
Bioinformatics 24 (20), 2303-2307
  2008
High-precision mapping of the protein interaction network for the human transcription machinery reveals a novel class of cellular regulatory factors
B Coulombe, P Cloutier, C Jeronimo, R Al-Khoury, M Lavallée-Adam, …
The FASEB Journal 22, 795.1
2008
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI) This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB-Systems and Chemical Biology, and has undergone the Journal’s usual peer review process.
B Coulombe, M Blanchette, C Jeronimo
Biochemistry and Cell Biology 86 (2), 149-156
  2008
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania
M Smith, M Blanchette, B Papadopoulou
BMC bioinformatics 9 (1), 158
  2008
Substring Parsimony
M Blanchette
Encyclopedia of Algorithms, 910-912
2008
A phylogenetic approach to genetic map refinement
D Bertrand, M Blanchette, N El-Mabrouk
Comparative Genomics, 198-210
  2008
An Evolutionary Study of the Human Papillomavirus Genomes
D Badescu, AB Diallo, M Blanchette, V Makarenkov
Comparative Genomics, 128-142
  2008
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees
X Chen, M Blanchette
BMC bioinformatics 8 (Suppl 10), S2
  2007
Computation and analysis of genomic multi-sequence alignments
M Blanchette
Annu. Rev. Genomics Hum. Genet. 8, 193-213
  2007
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme
C Jeronimo, D Forget, A Bouchard, Q Li, G Chua, C Poitras, C Thérien, …
Molecular cell 27 (2), 262-274
  2007
Systematic characterization of the protein interaction network for the human transcription machinery
B Coulombe, C Jeronimo, D Forget, A Bouchard, Q Li, G Chua, …
FEBS JOURNAL 274, 56-56
2007
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRa and ?
CR Dufour, BJ Wilson, JM Huss, DP Kelly, WA Alaynick, M Downes, …
Cell metabolism 5 (5), 345-356
  2007
Gene maps linearization using genomic rearrangement distances
G Blin, E Blais, D Hermelin, P Guillon, M Blanchette, N El-Mabrouk
Journal of Computational Biology 14 (4), 394-407
  2007
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem
AB Diallo, V Makarenkov, M Blanchette
Journal of Computational Biology 14 (4), 446-461
  2007
Overview of the first phylogenomics conference
H Philippe, M Blanchette
BMC Evolutionary Biology 7 (Suppl 1), S1
  2007
Detecting non-coding selective pressure in coding regions
H Chen, M Blanchette
BMC evolutionary biology 7 (Suppl 1), S9
  2007
PReMod: a database of genome-wide mammalian cis-regulatory module predictions
V Ferretti, C Poitras, D Bergeron, B Coulombe, F Robert, M Blanchette
Nucleic acids research 35 (suppl 1), D122-D126
  2007
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.
H Philippe, M Blanchette
BMC evolutionary biology 7 (Suppl 1), S1-16
2006
Reconstructing contiguous regions of an ancestral genome
J Ma, L Zhang, BB Suh, BJ Raney, RC Burhans, WJ Kent, M Blanchette, …
Genome Research 16 (12), 1557-1565
  2006
FootPrinter3: phylogenetic footprinting in partially alignable sequences
F Fang, M Blanchette
Nucleic acids research 34 (suppl 2), W617-W620
  2006
On the inference of parsimonious indel evolutionary scenarios
L Chindelevitch, Z Li, E Blais, M Blanchette
Journal of bioinformatics and computational biology 4 (03), 721-744
  2006
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
M Blanchette, AR Bataille, X Chen, C Poitras, J Laganière, C Lefèbvre, …
Genome research 16 (5), 656-668
  2006
A new efficient method for assessing missing nucleotides in DNA sequences in the framework of a generic evolutionary model
AB Diallo, V Makarenkov, M Blanchette, FJ Lapointe
Data Science and Classification, 333-340
2006
Common substrings in random strings
E Blais, M Blanchette
Combinatorial Pattern Matching, 129-140
  2006
Inferring gene orders from gene maps using the breakpoint distance
G Blin, E Blais, P Guillon, M Blanchette, N El-Mabrouk
Comparative Genomics, 99-112
  2006
Finding maximum likelihood indel scenarios
AB Diallo, V Makarenkov, M Blanchette
Comparative Genomics, 171-185
  2006
Ordering partially assembled genomes using gene arrangements
É Gaul, M Blanchette
Comparative Genomics, 113-128
  2006
Variant histone H2A. Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning
B Guillemette, AR Bataille, N Gévry, M Adam, M Blanchette, F Robert, …
PLoS biology 3 (12), e384
  2005
BH3-ligand regulates access of MCL-1 to its E3 ligase
MR Warr, S Acoca, Z Liu, M Germain, M Watson, M Blanchette, SS Wing, …
FEBS letters 579 (25), 5603-5608
  2005
Figures and Tables
M Blanchette, ED Green, W Miller, D Haussler
Genome Res 15 (3), 451
2005
Operations on sets of conserved intervals
A Bergeron, M Blanchette, A Chateau, C Chauve
Report, CGL, UQAM, Montreal, Canada
  2005
PUBLICATIONS> 2005© 2007-IRCM–Institut de recherches cliniques de Montréal, affilié à l’Université de Montréal
B Guillemette, AR Bataille, N Gevry, M Adam, M Blanchette, F Robert, …
PLos Biology 3 (12), 2100-2110
  2005
Reconstructing large regions of an ancestral mammalian genome in silico
M Blanchette, ED Green, W Miller, D Haussler
Genome Research 14 (12), 2412-2423
  2004
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences
S Sinha, M Blanchette, M Tompa
BMC bioinformatics 5 (1), 170
  2004
Evolutionarily conserved sequence elements that positively regulate IFN-? expression in T cells
M Shnyreva, WM Weaver, M Blanchette, SL Taylor, M Tompa, …
Proceedings of the National Academy of Sciences of the United States of …
  2004
Into the heart of darkness: large-scale clustering of human non-coding DNA
G Bejerano, D Haussler, M Blanchette
Bioinformatics 20 (suppl 1), i40-i48
  2004
Aligning multiple genomic sequences with the threaded blockset aligner
M Blanchette, WJ Kent, C Riemer, L Elnitski, AFA Smit, KM Roskin, …
Genome research 14 (4), 708-715
  2004
Intervalles conservés et Neighbor-Joining
A Bergeron, M Blanchette, C Chauve
Proceedings of the Rencontres de la Société Francophone de Classification …
2004
STRUCTMINER: a tool for alignment and detection of conserved secondary structure
Q Yang, M Blanchette
GENOME INFORMATICS SERIES 15 (2), 102
  2004
Reconstructing ancestral gene orders using conserved intervals
A Bergeron, M Blanchette, A Chateau, C Chauve
Algorithms in Bioinformatics, 14-25
  2004
Motif discovery in heterogeneous sequence data.
A Prakash, M Blanchette, S Sinha, M Tompa
Pacific Symposium on Biocomputing 9, 348-359
  2004
Identification and characterization of multi-species conserved sequences
EH Margulies, M Blanchette, D Haussler, ED Green
Genome research 13 (12), 2507-2518
  2003
Comparative analyses of multi-species sequences from targeted genomic regions
JW Thomas, JW Touchman, RW Blakesley, GG Bouffard, …
Nature 424 (6950), 788-793
  2003
FootPrinter: a program designed for phylogenetic footprinting
M Blanchette, M Tompa
Nucleic acids research 31 (13), 3840-3842
  2003
A comparative analysis method for detecting binding sites in coding regions
M Blanchette
Proceedings of the seventh annual international conference on Research in …
  2003
An empirical comparison of tools for phylogenetic footprinting
M Blanchette, S Kwong, M Tompa
Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium …
  2003
Comparative genome analysis and genome evolution
B Snel
2003
Discovery of regulatory elements by a computational method for phylogenetic footprinting
M Blanchette, M Tompa
Genome research 12 (5), 739-748
  2002
Algorithms for phylogenetic footprinting
M Blanchette, B Schwikowski, M Tompa
Journal of Computational Biology 9 (2), 211-223
  2002
Discovery of Regulatory Elements by a Computational Method for
P Footprinting, M Blanchette, M Tompa
2002
Separating real motifs from their artifacts
M Blanchette, S Sinha
Bioinformatics 17 (suppl 1), S30-S38
  2001
Evolutionary puzzles: An introduction to genome rearrangement
M Blanchette
Computational Science-ICCS 2001, 1003-1011
  2001
An exact algorithm to identify motifs in orthologous sequences from multiple species.
M Blanchette, B Schwikowski, M Tompa
ISMB, 37-45
  2000
Phylogenetic invariants for genome rearrangements
D Sankoff, M Blanchette
Journal of Computational Biology 6 (3-4), 431-445
  1999
Gene order breakpoint evidence in animal mitochondrial phylogeny
M Blanchette, T Kunisawa, D Sankoff
Journal of Molecular Evolution 49 (2), 193-203
  1999
Probability models for genome rearrangement and linear invariants for phylogenetic inference
D Sankoff, M Blanchette
Proceedings of the third annual international conference on Computational …
  1999
Comparative genomics via phylogenetic invariants for Jukes-Cantor semigroups
D Sankoff, M Blanchette
Stochastic models (Ottawa, ON, 1998) 26, 399-418
  1999
Multiple genome rearrangements
D Sankoff, M Blanchette
Proceedings of the second annual international conference on Computational …
  1998
Phylogenetic invariants for metazoan mitochondrial genome evolution
D Sankoff, M Blanchette
GENOME INFORMATICS SERIES, 22-31
  1998
Multiple genome rearrangement and breakpoint phylogeny
D Sankoff, M Blanchette
Journal of Computational Biology 5 (3), 555-570
  1998
Gene Order Comparison for the Phylogenetic Inference of Plastid Genomes
T Kunisawa, M Blanchette, D Sankoff
RESEARCH COMMUNICATIONS IN BIOCHEMISTRY AND CELL AND MOLECULAR BIOLOGY 1 …
  1997
The median problem for breakpoints in comparative genomics
D Sankoff, M Blanchette
Computing and combinatorics, 251-263
  1997
Breakpoint phylogenies
M Blanchette, G Bourque, D Sankoff
Genome Informatics 1997, 25-34
  1997
Parametric genome rearrangement
M Blanchette, T Kunisawa, D Sankoff
Gene 172 (1), GC11-GC17
  1996