Publications by authors named "Mathieu Blanchette"

99Publications

Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP.

Methods Mol Biol 2021 ;2157:127-157

Department of Biochemistry and Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-1-0716-0664-3_8DOI Listing
January 2021

Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions.

Bioinformatics 2020 Jul;36(Supplement_1):i276-i284

School of Computer Science, McGill University, Montreal, QC H3A 2B2, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btaa456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355240PMC
July 2020

EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM.

Bioinformatics 2020 Jul;36(Supplement_1):i353-i361

School of Computer Science, McGill University, Montreal, Quebec H3A 0G4, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btaa447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355264PMC
July 2020

LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads.

BMC Res Notes 2020 Jun 3;13(1):273. Epub 2020 Jun 3.

School of Computer Science, McGill University, Montréal, Canada.

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http://dx.doi.org/10.1186/s13104-020-05106-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271454PMC
June 2020

Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila.

Cell Rep 2020 03;30(10):3339-3352.e6

Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.02.047DOI Listing
March 2020

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.

Genome Biol 2020 01 14;21(1):11. Epub 2020 Jan 14.

School of Computer Science, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1186/s13059-019-1913-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961295PMC
January 2020

Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization.

Adv Exp Med Biol 2019 ;1203:165-194

Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-3-030-31434-7_7DOI Listing
December 2019

Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome.

J Proteome Res 2020 01 25;19(1):18-27. Epub 2019 Nov 25.

Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.

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http://dx.doi.org/10.1021/acs.jproteome.9b00599DOI Listing
January 2020

oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species.

Nucleic Acids Res 2020 01;48(D1):D166-D173

Institut de Recherches Cliniques de Montréal (IRCM) Montréal, Québec, Canada.

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http://dx.doi.org/10.1093/nar/gkz986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145663PMC
January 2020

Prediction of mRNA subcellular localization using deep recurrent neural networks.

Bioinformatics 2019 07;35(14):i333-i342

School of Computer Science, McGill University, Montreal, QC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612824PMC
July 2019

Large-scale mammalian genome rearrangements coincide with chromatin interactions.

Bioinformatics 2019 07;35(14):i117-i126

School of Computer Science, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612848PMC
July 2019

Mycorrhiza: genotype assignment using phylogenetic networks.

Bioinformatics 2020 01;36(1):212-220

School of Computer Science, McGill University, Montreal, QC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz476DOI Listing
January 2020

2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.

BMC Genomics 2019 Feb 28;20(1):162. Epub 2019 Feb 28.

Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.

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http://dx.doi.org/10.1186/s12864-019-5532-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394006PMC
February 2019

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.

Mol Biol Evol 2019 04;36(4):766-783

Département de Biochimie, Centre Robert Cedergren, Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.

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https://academic.oup.com/mbe/advance-article/doi/10.1093/mol
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http://dx.doi.org/10.1093/molbev/msz016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551751PMC
April 2019

3D genome mapping and analysis methods.

Methods 2018 06;142:1-2

Department of Biochemistry and Goodman Cancer Research Center McGill University Montréal, Québec, Canada; School of Computer Science McGill University Montréal, Québec, Canada.

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http://dx.doi.org/10.1016/j.ymeth.2018.05.017DOI Listing
June 2018

An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures.

Genet Epidemiol 2018 04 8;42(3):233-249. Epub 2018 Feb 8.

Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1002/gepi.22112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175336PMC
April 2018

Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks.

Nucleic Acids Res 2017 Oct;45(18):10415-10427

McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 0E9, Canada.

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http://dx.doi.org/10.1093/nar/gkx751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737372PMC
October 2017

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.

Bioinformatics 2017 Nov;33(21):3331-3339

Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btx421DOI Listing
November 2017

A critical assessment of topologically associating domain prediction tools.

Nucleic Acids Res 2017 04;45(6):2994-3005

School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1093/nar/gkx145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389712PMC
April 2017

Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.

Nucleic Acids Res 2017 01 29;45(2):556-566. Epub 2016 Nov 29.

School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, H3A0E9, Canada

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkw1085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314757PMC
January 2017

Models and algorithms for genome rearrangement with positional constraints.

Algorithms Mol Biol 2016 17;11:13. Epub 2016 May 17.

McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, H3C2B4 Canada.

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http://dx.doi.org/10.1186/s13015-016-0065-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869402PMC
May 2016

Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.

Mol Biol Evol 2016 08 28;33(8):1937-56. Epub 2016 Apr 28.

Department of Biology, McGill University, Montréal, QC, Canada

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http://dx.doi.org/10.1093/molbev/msw067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948706PMC
August 2016

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing.

Nat Commun 2015 Dec 8;6:10124. Epub 2015 Dec 8.

Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.

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http://www.nature.com/articles/ncomms10124
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http://dx.doi.org/10.1038/ncomms10124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4686818PMC
December 2015

A call for benchmarking transposable element annotation methods.

Mob DNA 2015 4;6:13. Epub 2015 Aug 4.

School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada.

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http://dx.doi.org/10.1186/s13100-015-0044-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524446PMC
August 2015

Specific dysregulation of IFNγ production by natural killer cells confers susceptibility to viral infection.

PLoS Pathog 2014 Dec 4;10(12):e1004511. Epub 2014 Dec 4.

Department of Human Genetics and Department of Microbiology and Immunology, McGill University, Life Sciences Complex, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1371/journal.ppat.1004511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256466PMC
December 2014

Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.

PLoS Genet 2014 Sep 25;10(9):e1004622. Epub 2014 Sep 25.

Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1004622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178662PMC
September 2014

BigDataScript: a scripting language for data pipelines.

Bioinformatics 2015 Jan 3;31(1):10-6. Epub 2014 Sep 3.

McGill University School of Computer Science, 3480 University Street, Montreal, Québec H3A 0E9 and McGill University and Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 0G1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271142PMC
January 2015

Hox in motion: tracking HoxA cluster conformation during differentiation.

Nucleic Acids Res 2014 Feb 29;42(3):1524-40. Epub 2013 Oct 29.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada.

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http://dx.doi.org/10.1093/nar/gkt998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919592PMC
February 2014

Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin.

J Proteomics 2014 Apr 16;100:115-24. Epub 2013 Oct 16.

Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Biochemistry, Université de Montréal, Montréal, Québec H3T 1J4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2013.10.008DOI Listing
April 2014

Computational prediction of the localization of microRNAs within their pre-miRNA.

Nucleic Acids Res 2013 Aug 8;41(15):7200-11. Epub 2013 Jun 8.

School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada H3A2B2 and Laboratoire de bioinformatique du département informatique, Université du Québec À Montréal, Montreal, Quebec, Canada H2X3Y7.

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https://academic.oup.com/nar/article/41/15/7200/2410969
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http://dx.doi.org/10.1093/nar/gkt466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753617PMC
August 2013

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.

Nucleic Acids Res 2013 Jul 8;41(Web Server issue):W480-5. Epub 2013 Jun 8.

School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montréal, H3A 0C6 QC, Canada.

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http://dx.doi.org/10.1093/nar/gkt461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692110PMC
July 2013

Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2.

Nucleic Acids Res 2013 Aug 30;41(14):6881-91. Epub 2013 May 30.

Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada H2W 1R7, McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada H3A 2B4.

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http://dx.doi.org/10.1093/nar/gkt455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737550PMC
August 2013

A flexible ancestral genome reconstruction method based on gapped adjacencies.

BMC Bioinformatics 2012 19;13 Suppl 19:S4. Epub 2012 Dec 19.

Département d'Informatique, DIRO, Université de Montréal, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-S19-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526437PMC
May 2013

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.

BMC Bioinformatics 2012 19;13 Suppl 19:S2. Epub 2012 Dec 19.

McGill Centre for Bioinformatics and School of Computer Science, McGill University, H3C 2B4 Québec, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-S19-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526440PMC
May 2013

Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry.

J Proteome Res 2013 Jan 4;12(1):272-81. Epub 2012 Dec 4.

McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada.

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http://dx.doi.org/10.1021/pr300778bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494838PMC
January 2013

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

BMC Bioinformatics 2011 Oct 25;12:414. Epub 2011 Oct 25.

McGill Centre for Bioinformatics, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montréal, Québec, H3G 0B1, Canada.

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http://dx.doi.org/10.1186/1471-2105-12-414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245522PMC
October 2011

A probabilistic model for sequence alignment with context-sensitive indels.

J Comput Biol 2011 Nov 27;18(11):1449-64. Epub 2011 Sep 27.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1089/cmb.2011.0157DOI Listing
November 2011

Mapping association between long-range cis-regulatory regions and their target genes using synteny.

J Comput Biol 2011 Sep;18(9):1115-30

McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1089/cmb.2011.0088DOI Listing
September 2011

Predicting site-specific human selective pressure using evolutionary signatures.

Bioinformatics 2011 Jul;27(13):i266-74

School of Computer Science, McGill University, 3630 University, Montreal, QC, Canada H3A 2B2.

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http://dx.doi.org/10.1093/bioinformatics/btr241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117352PMC
July 2011

Modeling contaminants in AP-MS/MS experiments.

J Proteome Res 2011 Feb 31;10(2):886-95. Epub 2010 Dec 31.

McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Canada.

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http://dx.doi.org/10.1021/pr100795zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494835PMC
February 2011

Predicting direct protein interactions from affinity purification mass spectrometry data.

Algorithms Mol Biol 2010 Oct 29;5:34. Epub 2010 Oct 29.

McGill Centre for Bioinformatics, McGill University, Quebec, Canada.

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http://dx.doi.org/10.1186/1748-7188-5-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991326PMC
October 2010

Computing chromosome conformation.

Methods Mol Biol 2010 ;674:251-68

Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-1-60761-854-6_16DOI Listing
December 2010

The three-dimensional architecture of Hox cluster silencing.

Nucleic Acids Res 2010 Nov 25;38(21):7472-84. Epub 2010 Jul 25.

Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, Canada.

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http://dx.doi.org/10.1093/nar/gkq644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995065PMC
November 2010

Computational analysis of whole-genome differential allelic expression data in human.

PLoS Comput Biol 2010 Jul 8;6(7):e1000849. Epub 2010 Jul 8.

School of Computer Science, McGill University, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1000849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900287PMC
July 2010

An approximation algorithm for the Noah's Ark problem with random feature loss.

IEEE/ACM Trans Comput Biol Bioinform 2011 Mar-Apr;8(2):551-6

School of Computer Science,McGill University, 3480 University Street, McConnell Engineering Building, Room 318, Montreal, QC H3A 2A7, Canada.

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https://www.computer.org/csdl/trans/tb/2011/02/ttb2011020551
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http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
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http://dx.doi.org/10.1109/TCBB.2010.37DOI Listing
June 2011

Detection of locally over-represented GO terms in protein-protein interaction networks.

J Comput Biol 2010 Mar;17(3):443-57

McGill Centre for Bioinformatics and School of Computer Science, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669221PMC
March 2010

A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error.

Pac Symp Biocomput 2010 :31-42

McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3480 University St., Montréal, Québec, H3A 2B4, Canada.

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http://dx.doi.org/10.1142/9789814295291_0005DOI Listing
November 2013

Ancestors 1.0: a web server for ancestral sequence reconstruction.

Bioinformatics 2010 Jan 22;26(1):130-1. Epub 2009 Oct 22.

Department of Computer Science, Université du Québec à Montréal, PO. Box 8888 Downtown Station, Montreal, QC H3C3P8, Canada.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp600DOI Listing
January 2010

A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses.

J Comput Biol 2009 Oct;16(10):1461-73

Département d'informatique, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Québec, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0091DOI Listing
October 2009

Genetic map refinement using a comparative genomic approach.

J Comput Biol 2009 Oct;16(10):1475-86

DIRO, Université de Montréal, Montréal, Quebec, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0094DOI Listing
October 2009

Long-range regulation is a major driving force in maintaining genome integrity.

BMC Evol Biol 2009 Aug 15;9:203. Epub 2009 Aug 15.

McGill Centre for Bioinformatics, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1186/1471-2148-9-203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741452PMC
August 2009

A probabilistic approach for SNP discovery in high-throughput human resequencing data.

Genome Res 2009 Sep 15;19(9):1542-52. Epub 2009 Jul 15.

McGill Centre for Bioinformatics, McGill University, Montréal H36 0B1, Canada;

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http://dx.doi.org/10.1101/gr.092072.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752119PMC
September 2009

Chromatin conformation signatures of cellular differentiation.

Genome Biol 2009 19;10(4):R37. Epub 2009 Apr 19.

Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, H3G1Y6, Canada.

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http://dx.doi.org/10.1186/gb-2009-10-4-r37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688928PMC
September 2009

Seeder: discriminative seeding DNA motif discovery.

Bioinformatics 2008 Oct 21;24(20):2303-7. Epub 2008 Aug 21.

Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btn444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562012PMC
October 2008

Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI).

Biochem Cell Biol 2008 Apr;86(2):149-56

Gene Transcription and Proteomics Laboratory and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.

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http://dx.doi.org/10.1139/O08-006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494828PMC
April 2008

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.

BMC Bioinformatics 2008 Mar 20;9:158. Epub 2008 Mar 20.

Research Centre in Infectious Diseases, CHUL Research Centre, 2705 Laurier Blvd,, Quebec, QC G1V 4G2, Canada.

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http://dx.doi.org/10.1186/1471-2105-9-158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335281PMC
March 2008

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees.

BMC Bioinformatics 2007 ;8 Suppl 10:S2

McGill Centre for Bioinformatics, 3775 University Street, room 332, Montreal, Quebec, Canada, H3A 2B4.

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http://dx.doi.org/10.1186/1471-2105-8-S10-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2230503PMC
April 2008

Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.

J Comput Biol 2007 May;14(4):446-61

McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.1089/cmb.2007.A006DOI Listing
May 2007

Gene maps linearization using genomic rearrangement distances.

J Comput Biol 2007 May;14(4):394-407

IGM-LabInfo, UMR CNRS 8049, Université Paris-Est, Marne-la-Vallée, France.

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http://dx.doi.org/10.1089/cmb.2007.A002DOI Listing
May 2007

Computation and analysis of genomic multi-sequence alignments.

Annu Rev Genomics Hum Genet 2007 ;8:193-213

McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada. email:

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http://dx.doi.org/10.1146/annurev.genom.8.080706.092300DOI Listing
December 2007

Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma.

Cell Metab 2007 May;5(5):345-56

Molecular Oncology Group, McGill University Health Centre, Montréal, Québec H3A 1A1, Canada.

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http://dx.doi.org/10.1016/j.cmet.2007.03.007DOI Listing
May 2007

Detecting non-coding selective pressure in coding regions.

BMC Evol Biol 2007 Feb 8;7 Suppl 1:S9. Epub 2007 Feb 8.

McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada H3A 2B4.

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http://dx.doi.org/10.1186/1471-2148-7-S1-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1796618PMC
February 2007

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Nucleic Acids Res 2007 Jan 5;35(Database issue):D122-6. Epub 2006 Dec 5.

McGill University and Genome Quebec Innovation Center, 740 Dr Penfield, Montreal, Qc, Canada H3A 1A4.

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http://dx.doi.org/10.1093/nar/gkl879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761432PMC
January 2007

Reconstructing contiguous regions of an ancestral genome.

Genome Res 2006 Dec 18;16(12):1557-65. Epub 2006 Sep 18.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5383506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665639PMC
December 2006

On the inference of parsimonious indel evolutionary scenarios.

J Bioinform Comput Biol 2006 Jun;4(3):721-44

School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada.

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http://dx.doi.org/10.1142/s0219720006002168DOI Listing
June 2006

FootPrinter3: phylogenetic footprinting in partially alignable sequences.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W617-20

McGill Centre for Bioinformatics, 3775 University St, Montréal, Québec, Canada, H3A 2B4.

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http://dx.doi.org/10.1093/nar/gkl123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538810PMC
July 2006

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.

PLoS Biol 2005 Dec 1;3(12):e384. Epub 2005 Nov 1.

Centre de Recherche sur les Mécanismes du Fonctionnement Cellulaire, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.

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http://dx.doi.org/10.1371/journal.pbio.0030384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1275524PMC
December 2005

BH3-ligand regulates access of MCL-1 to its E3 ligase.

FEBS Lett 2005 Oct 28;579(25):5603-8. Epub 2005 Sep 28.

Department of Biochemistry, McIntyre Medical Sciences Building, McGill University, Montréal, Que., Canada.

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http://dx.doi.org/10.1016/j.febslet.2005.09.028DOI Listing
October 2005

StructMiner: a tool for alignment and detection of conserved secondary structure.

Genome Inform 2004 ;15(2):102-11

Mcgill Center for Bioinformatics, McGill University, Montreal, Quebec, H3A 2B4, Canada.

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January 2006

Reconstructing large regions of an ancestral mammalian genome in silico.

Genome Res 2004 Dec;14(12):2412-23

Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.2800104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534665PMC
December 2004

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.

BMC Bioinformatics 2004 Oct 28;5:170. Epub 2004 Oct 28.

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA.

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http://dx.doi.org/10.1186/1471-2105-5-170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534098PMC
October 2004

Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells.

Proc Natl Acad Sci U S A 2004 Aug 10;101(34):12622-7. Epub 2004 Aug 10.

Department of Immunology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1073/pnas.0400849101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC515107PMC
August 2004

Into the heart of darkness: large-scale clustering of human non-coding DNA.

Bioinformatics 2004 Aug;20 Suppl 1:i40-8

Center for Biomolecular Science and Engineering, Baskin School of Engineering University of California in Santa Cruz, Santa Cruz, CA 95064, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bth946DOI Listing
August 2004

Identification and characterization of multi-species conserved sequences.

Genome Res 2003 Dec;13(12):2507-18

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1101/gr.1602203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403793PMC
December 2003

FootPrinter: A program designed for phylogenetic footprinting.

Nucleic Acids Res 2003 Jul;31(13):3840-2

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169012PMC
http://dx.doi.org/10.1093/nar/gkg606DOI Listing
July 2003

Algorithms for phylogenetic footprinting.

J Comput Biol 2002 ;9(2):211-23

Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195-2350, USA.

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http://dx.doi.org/10.1089/10665270252935421DOI Listing
October 2002

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Genome Res 2002 May;12(5):739-48

Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195-2350, USA.

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http://dx.doi.org/10.1101/gr.6902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186562PMC
May 2002