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Mathieu Blanchette


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Email: blanchem AT cs DOT mcgill DOT ca
Home Page: http://www.mcb.mcgill.ca/~blanchem
Office: Trottier 3107
Phone: +1-514-398-5209
Fax: +1-514-398-3883
Address:

Research Description

Our lab focuses on the development of algorithmic and machine learning approaches to biological sequence analysis. We are particularly interested in the analysis of transcriptional regulation, in particular the prediction of transcription factor binding sites and regulatory modules, as well as in splicing regulation. Our approaches often rely on comparative genomics.

Research Interests

Research Labs

Teaching

Selected Publications (click link in front of each publication to see bibtex in ASCII format)

[1] Lavallée-Adam, M., Cloutier, P., Coulombe, B., and Blanchette, M. Modeling contaminants in ap-ms/ms experiments. J Proteome Research, 2011, v. 10, n. 2, pp. 886-895.
[2] Hickey, G., and Blanchette, M. A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. In Proceedings of the Pacific Symposium on Biocomputing, 2010, pp. 31-42.
[ http ]
[3] Diallo, A., Makarenkov, V., and Blanchette, M. Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics, 2010, v. 26(1), pp. 130-1.
[ http ]
[4] Ferraiuolo, M., Rousseau, M., Miyamoto, C., Shenker, S., Wang, X., Nadler, M., Blanchette, M., and Dostie, J. The three-dimensional architecture of hox cluster silencing. Nucleic Acids Research., 2010, v. 38, n. (21), pp. 7472-84.
[ http ]
[5] Forget, D., Lacombe, A., Cloutier, P., Al-Khoury, R., Bouchard, A., Lavallée-Adam, M., Faubert, D., Jeronimo, C., Blanchette, M., and Coulombe, B. 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. Molecular Cell Proteomics., 2010, v. 9, n. 12, pp. 2827-39.
[ http ]
[6] Wagner, J., Ge, B., Pokholok, D., Gunderson, K., Pastinen, T., and Blanchette, M. Computational analysis of whole-genome differential allelic expression data in human. PLoS Computational Biology, 2010, v. 6(7), p. e1000849.
[ http ]
[7] Lavallée-Adam, M., Coulombe, B., and Blanchette, M. Detection of locally over-represented go terms in protein-protein interaction networks. Journal of computational biology., 2010, v. 17(3), pp. 443-57.
[8] Hickey, G., Blanchette, M., Carmi, P., Maheshwari, A., and N., Z. An approximation algorithm for the noah’s ark problem with random feature loss. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, v. 8, n. 2, pp. 551-6.
[ http ]
[9] Mongin, E., Dewar, K., and Blanchette, M. Mapping association between long-range cis-regulatory regions and their target genes using comparative genomics. In Eighth Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2010, pp. 216-227.
[10] Bertrand, D., Gagnon, Y., Blanchette, M., and El-Mabrouk, N. Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss. In 10th Workshop on Algorithms in Bioinformatics (WABI), 2010, pp. 78-89.
[ http ]
[11] Dostie, J., Rousseau, M., Blanchette, M., and Fraser, J. Computing chromosome conformation, v. 674, pp. 251-68. 2010.
[12] Kim, E., Sabharwal, A., Vetta, A., and Blanchette, M. Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms in Molecular Biology, 2010, v. 5, n. 34, pp. 1-17.
[13] Cloutier, P., Al-Khoury, R., Lavallée-Adam, M., Faubert, D., Jiang, H., Poitras, C., Bouchard, A., Forget, D., Blanchette, M., and Coulombe, B. High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of rna polymerase ii-associated complexes. Methods., 2009.
[ http ]
[14] Fraser, J., Rousseau, M., Shenker, S., Ferraiuolo, M., Hayashizaki, Y., Blanchette, M., and Dostie, J. Chromatin conformation signatures of cellular differentiation. Genome Biology, 2009, v. 10, n. 4, p. R37.
[ http ]
[15] Diallo, A. B., Badescu, D., Blanchette, M., and Makarenkov, V. A whole genome study and identication of specific carcinogenic regions of the human papilloma viruses. Journal of Computational Biology, 2009, v. 16(10), pp. 1461-73.
[16] Bertrand, D., Blanchette, M., and El-Mabrouk, N. Genetic map refinement using a comparative genomic approach. Journal of Computational Biology, 2009, v. 16(10), pp. 1475-86.
[17] Lavallee-Adam, M., Coulombe, B., and Blanchette, M. Detection of locally over-represented go terms in protein-protein interaction networks. In RECOMB 2009, 2009.
[ .pdf ]
[18] Ge, B., Pokholok, D., Kwan, T., Grundberg, E., Morcos, L., Verlaan, D., Le, J., Koka, V., Lam, K., Gagné, V., Dias, J., Hoberman, R., Montpetit, A., Joly, M., Harvey, E., Sinnett, D., Beaulieu, P., Hamon, R., Graziani, A., Dewar, K., Harmsen, E., Majewski, J., Goring, H., Naumova, A., Blanchette, M., Gunderson, K., and Pastinen, T. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nature Genetics, 2009, v. 41(11), pp. 1216-22.
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[19] Mongin, E., Dewar, K., and Blanchette, M. Long-range regulation is a major driving force in maintaining genome integrity. BMC Evolution Biology, 2009, v. 9:203.
[20] Hoberman, R., Dias, J., Ge, B., Harmsen, E., Mayhew, M., Verlaan, D., Kwan, T., Dewar, K., Blanchette, M., and Pastinen, T. A probabilistic approach for snp discovery in high-throughput human resequencing data. Genome Research, 2009, n. 19(9), pp. 1542-52.
[ http ]
[21] Fauteux, F., Blanchette, M., and Strömvik, M. Seeder: Discriminative seeding dna motif discovery. Bioinformatics, 2008, v. 24, n. 20, pp. 2303-7.
[ http ]
[22] Smith, M., Blanchette, M., and Papadopoulou, B. Improving the prediction of mrna extremities in the parasitic protozoan leishmania. BMC Bioinformatics, 2008, v. 9, p. 158.
[ http ]
[23] Badescu, D., Diallo, A., Blanchette, M., and Makarenkov, V. An evolution study of the human papillomavirus genomes. Proceedings of RECOMB Comparative Genomics 2008, 2008, pp. 128-140.
[ http ]
[24] Bertrand, D., Blanchette, M., and El-Mabrouk, N. A phylogenetic approach for gene mapping refinement. In Proceedings of RECOMB Comparative Genomics Satellite Conference. Springer, Lecture Notes in Bioinformatics Series, 2008, pp. 198-210.
[ http ]
[25] Diallo, A., Badescu, D., Makarenkov, V., and Blanchette, M. Phylogeny of the human papilloma viruses and carcinoma classification. In Proceedings of the First joint meeting SFC-CLADAG, 2008, pp. 285-288.
[26] Coulombe, B., Blanchette, M., and Jeronimo, C. Steps towards a repertoire of comprehensive maps of human protein interaction networks: the human proteotheque initiative (hupi). Biochem Cell Biol, 2008, v. 86, n. 2, pp. 149-56.
[ http ]
[27] Blanchette, M., Diallo, A., Green, E., Miller, W., and Haussler, D. Computational reconstruction of ancestral dna sequences. 2008, v. 422, pp. 171-84.
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[28] Chen, H., and Blanchette, M. Detecting non-coding selective pressure in coding regions. BMC Evolutionary Biology, 2007, v. 8, n. 7 Supplemental 1, pp. S9:1-13.
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[29] Chen, X., and Blanchette, M. Prediction of tissue-specific cis-regulatory modules using bayesian networks and regression trees. BMC Bioinformatics, 2007, v. 8 Suppl 10, p. S2.
[30] Jeronimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Thérien, C., Bergeron, D., Bourassa, S., Greenblatt, J., Chabot, B., Poirier, G. G., Hughes, T. R., Blanchette, M., Price, D. H., and Coulombe, B. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7sk capping enzyme. Molecular Cell, July 2007, 20:27(2), pp. 262-74.
[31] Diallo, A. B., Makarenkov, V., and Blanchette, M. Exact and heuristic algorithms for the indel maximum likelihood problem. Journal of Computational Biology, May 2007, 14(4), pp. 446-61.
[32] Blin, G., Blais, E., Hermelin, D., Guillon, P., Blanchette, M., and El-Mabrouk, N. Gene maps linearization using genomic rearrangement distances. Journal of Computational Biology, May 2007, 14(4), pp. 394-407.
[33] Blanchette, M. Computation and analysis of genomic multi-sequence alignments. Annual Reviews on Genomics Human Genetics, 2007, 8, pp. 193-213.
[34] Dufour, C. R., Wilson, B. J., Huss, J. M., Kelly, D. P., Alaynick, W. A., Downes, M., Evans, R. M., Blanchette, M., and Giguère, V. Genome-wide orchestration of cardiac functions by the orphan nuclear receptors erralpha and gamma. Cell Metabolism, May 2007, 5(5), pp. 345-56.
[35] Ferretti, V., Poitras, C., Bergeron, D., Coulombe, B., Robert, F., and Blanchette, M. Premod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res, January 2007, 5(Database issue), pp. D122-D126. Epub 2006 Dec 5.
[36] Philippe, H., and Blanchette, M. Overview of the first phylogenomics conference. BMC Evol Biol, 2007, 7(Suppl 1), p. S1.
[37] Blanchette, M., Bataille, A., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D., Coulombe, B., and Robert, F. Genome-wide computation prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Research, 2006, v. 16, n. 5, pp. 656-68.
[ http ]
[38] Chindelevitch, L., Li, Z., Blais, E., and Blanchette, M. On the inference of parsimonious indel scenarios. Journal of Bioinformatics and Computational Biology, 2006, v. 4, n. 3, pp. 721-44.
[ http ]
[39] Blanchette, M., Diallo, A., Green, E., Miller, W., and Haussler, D. Computational Reconstruction of Ancestral DNA Sequences. Humana Press, 2006.
[40] Blais, E., and Blanchette, M. On the inference of parsimonious indel scenarios. In Proceeding of Combinatorial Pattern Matching, 2006, pp. 129-140.
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[41] Fang, F., and Blanchette, M. Footprinter3: Phylogenetic footprinting in partially alignable sequences. Nucleic Acids Research, 2006, v. 34, pp. W617-W620.
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[42] Diallo, A., Makarenkov, V., and Blanchette, M. Finding maximum likelihood indel scenarios. In Proceeding of the fourth Recomb satellite conference on Comparative Genomics, 2006, pp. 171-185.
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[43] Ma, J., Zhang, L., Suh, B., Raney, B., Burhans, R., Kent, W., Blanchette, M., Haussler, D., and Miller, W. Reconstructing contiguous regions of an ancestral genome. Genome Research, 2006, v. 16, n. 12, pp. 1557-65.
[ http ]
[44] Gaul, E., and Blanchette, M. Ordering partially assembled genomes using gene arrangements. In Proceedings of the Fourth RECOMB Satelite conference on Comparative Genomics, 2006, pp. 113-128.
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[45] Blin, G., Blais, E., Guillon, P., Blanchette, M., and El-Mabrouk, N. Inferring gene orders from gene maps using the breakpoint distance. In Proceedings of the Fourth RECOMB Satelite conference on Comparative Genomics, 2006, pp. 99-112.
[ .pdf ]
[46] Chen, X., and Blanchette, M. Prediction of tissue-specific cis-regulatory modules using bayesian networks and probability trees,. In Proceedings of the NIPS workshop on new problems and methods in computational biology, 2006.

Last Update:   2012/08/29 11:57:06.147 GMT-4