Acfas profil public - Sébastien Boisvert

Parce que j'aime

les algorithmes, la biologie, le passage de messages, la programmation.

Sébastien Boisvert

Étudiant·e au troisième cycle universitaire | Université Laval

Je fais de la biologie, des algorithmes et de la programmation. Je fais la promotion des logiciels libres, comme GNU, Linux, libreoffice, et Firefox.

Mes liens avec l'Acfas

Auteur

81e Congrès de l'Acfas : La génomique, les super ordinateurs et le logiciel d'assemblage Ray

Mes intérêts de recherche

Assemblage de novo Génomique Algorithmie Passage de messages

Formation

2010-2013, Université Laval, Doctorat en physiologie-endocrinologie (Ph.D.)
2008-2009, Université Laval, Maîtrise en physiologie-endocrinologie (M.Sc.)
2005-2008, Université de Sherbrooke, Baccalauréat en biotechnologie, incluant une concentration en bioinformatique (B.Sc.)
2002-2005, Cégep de Lévis-auzon, Techniques de laboratoire, spécialisation en biotechnologies

Mes contributions « Science et société »

Les logiciels Ray, RayPlatform et Ray Cloud Browser sont libres et disponibles gratuitement.

Mes publications

http://boisvert.info/publications.html

Publications of Sébastien Boisvert Back

Peer-reviewed journal articles (9)

Telomeric gene deletion and intrachromosomal amplification in antimony resistant Leishmania Angana Mukherjee, Sébastien Boisvert, Rubens Lima do Monte-Neto, Adriano C. Coelho, Frederic Raymond, Rita Mukhopadhyay, Jacques Corbeil and Marc Ouellette. Molecular Microbiology (Blackwell Publishing Ltd). [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central | Self-archiving ]

Ray Meta: scalable de novo metagenome assembly and profiling. Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. Genome Biology (BioMed Central Ltd). 13:R122, Published: 22 December 2012 [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing. Adriano C. Coelho, Sébastien Boisvert, Angana Mukherjee, Philippe Leprohon, Jacques Corbeil, Marc Ouellette. PLoS Neglected Tropical Diseases (Public Library of Science). 6(2): e1512. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Endonucleases: tools to correct the dystrophin gene. Joel Rousseau, Pierre Chapdelaine, Sébastien Boisvert, Luciana P. Almeida, Jacques Corbeil, Alexandre Montpetit and Jacques P. Tremblay. The Journal of Gene Medicine (John Wiley & Sons, Ltd). Volume 13, Issue 10, pages 522–537, October 2011 [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central | Self-archiving ]

Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Frédéric Raymond, Sébastien Boisvert, Gaétan Roy, Jean-François Ritt, Danielle Légaré, Amandine Isnard, Mario Stanke, Martin Olivier, Michel Tremblay, Barbara Papadopoulou, Marc Ouellette and Jacques Corbeil. Nucleic Acids Research (Oxford University Press). (2012) 40 (3): 1131-1147. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Sébastien Boisvert, François Laviolette, and Jacques Corbeil. Journal of Computational Biology (Mary Ann Liebert, Inc. publishers). November 2010, 17(11): 1519-1533. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. Frédéric Raymond , Julie Carbonneau, Nancy Boucher, Lynda Robitaille, Sébastien Boisvert, Whei-Kuo Wu, Gaston De Serres, Guy Boivin, and Jacques Corbeil. Journal of Clinical Microbiology (American Society for Microbiology). 2009 Mar;47(3):743-50. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Sébastien Boisvert, Mario Marchand, François Laviolette, and Jacques Corbeil. Retrovirology (BioMed Central Ltd). 2008 Dec 4;5:110. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Jean-Michel Ubeda, Danielle Légaré, Frédéric Raymond, Amin A Ouameur, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Michel J Tremblay, Martin Olivier, Barbara Papadopoulou, and Marc Ouellette. Genome Biology (BioMed Central Ltd). 2008 ;9(7):R115. Epub 2008 Jul 18. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Martin Smith, Nadine Messier, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Marc Ouellette, and Barbara Papadopoulou. BMC Genomics (BioMed Central Ltd). 2008 May 29;9:255. [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central ]

Peer-reviewed conference publications (0)Peer-reviewed congress publications (0)

La génomique, les super ordinateurs et le logiciel d'assemblage Ray. Sébastien Boisvert, François Laviolette, Jacques Corbeil. 81ème congrès de l'Association francophone pour le savoir (ACFAS), 6-10 mai 2013. Soumission # 2074 [ abstract PDF OpenDocument

Peer-reviewed workshop publications (1)

Constrained traversal of repeats with paired sequences. Sébastien Boisvert, Élénie Godzaridis, François Laviolette & Jacques Corbeil. First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27 2011, Vancouver, BC, Canada. abstract; presentation

Peer-reviewed symposium publications (1)

High Performance Genome Assembly on a Cray Supercomputer. Mikhail Kandel, Steve Behling, Bill Long, Carlos P. Sosa, Sébastien Boisvert, Lorenzo Pesce, Jacques Corbeil BICB January Symposium: Keeping Our Curriculum Current (University of Minnesota Rochester). poster

Peer-reviewed colloquium publications (2)

OpenAssembler: assembly of reads from a mix of high-throughput sequencing technologies. Sébastien Boisvert, François Laviolette, and Jacques Corbeil. Robert Cedergren Bioinformatics Colloquium 2009 (Université de Montréal). abstract; presentation

The distant segments kernel and the support vector machine: an alignment-free method for HIV type 1 coreceptor usage prediction. Sébastien Boisvert, Mario Marchand, François Laviolette, and Jacques Corbeil. Robert Cedergren Bioinformatics Colloquium 2008 (Université de Montréal). abstract; presentation; poster

Peer-reviewed meeting publications (2)

Whole Genome Sequencing and Comparative Genomic Hybridization of Leishmania and their Application to Antimony Resistance. Angana Mukherjee, Sébastien Boisvert, Rita Mukhopadhyay, Jacques Corbeil, Marc Ouellette. Kinetoplastid Molecular Cell Biology Meeting, Woods Hole, MA, USA, 8-12 April 2011.

Genome-wide analysis of stage and species-specific gene expression in Leishmania. Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Sébastien Boisvert, Jacques Corbeil, Marc Ouellette, and Barbara Papadopoulou. Kinetoplastid Molecular Cell Biology Meeting, 2007, Woods Hole Massachusetts. abstract

Other publications (3)

Assemblage de novo de génomes humains en quelques heures. Sébastien Boisvert, François Laviolette & Jacques Corbeil. Journée annuelle de la recherche, Faculté de médecine, Université Laval, 7 juin 2011 abstract poster

Assemblage parallèle de génomes à partir de séquences Illumina très courtes en paires. Sébastien Boisvert, François Laviolette, Mario Marchand, et Jacques Corbeil. 12ème journée annuelle de la recherche, 27 mai 2010, Université Laval. abstract; presentation

Assemblage parallèle de génomes avec des séquences très courtes en paires. Sébastien Boisvert, François Laviolette, Mario Marchand, et Jacques Corbeil. Journée de la science du 5 mai 2010 Institut des maladies infectieuses et immunitaires (III/IMII) des Instituts de recherche en santé du Canada (CIHR/IRSC) Fairmont le Château Frontenac. abstract; poster

Invitations (5)

Métagénomique adaptative à grande vitesse. Sébastien Boisvert Département de biologie, Université de Sherbrooke 2012-02-07 11:00-12:00 [ | abstract | PDF | OpenDocument ]

Massively parallel assemblers for massively parallel DNA sequencers. Sébastien Boisvert, Élénie Godzaridis SciNet Developer Seminar, SciNet Consortium, University of Toronto 2012-11-27 12:00-14:00 SciNet Developer Seminar #94 PDF OpenDocument

Granularities and messages: from design to abstraction to implementation to virtualization. Élénie Godzaridis, Sébastien Boisvert SciNet Developer Seminar, SciNet Consortium, University of Toronto 2012-11-26 14:00-16:00 SciNet Developer Seminar #95 PDF OpenDocument

Scalable Microbiome Metagenome Assembly and Profiling Sébastien Boisvert Seminars & Events, Mathematics and Computer Science Division (Argonne National Laboratory) October 16, 2012, 1:30 PM - 2:30 PM abstract link presentation presentation (OpenDocument)

Summer 2012 Week 3: Next Generation Sequence Analysis Sébastien Boisvert Workshops & Programs (Institute for Computing in Science) July 28, 2012 to August 4, 2012 Canyons Resort, 4000 Canyons Resort Drive, Park City, Utah link presentation

Thesis (0)In progress (6)

Le passage de messages pour les assembler tous, et dans la granularité les lier. Sébastien Boisvert en rédaction (51 pages so far, no embedded articles) Thèse de doctorat, Université Laval. [ Éditeur ]

The Ray Cloud Browser manuscript (title to be determined) authors here [ Amazon ]

Early Experience on Crays with Genomic Applications Used as Part of Next Generation Sequencing Workflow. Mikhail Kandel, Steve Behling, Bill Long, Carlos P. Sosa, Sébastien Boisvert, Jacques Corbeil, Lorenzo Pesce. Abstract submitted to Cray User Group Conference 2013 pap104s1 [ abstract ]

Human analysts at superhuman scales: what’s friendly software to do? Élénie Godzaridis, Sébastien Boisvert, Fangfang Xia, Keith Robison, Carlos P. Sosa, François Laviolette, Rick Stevens, Jacques Corbeil 2666 / 3000 words, will be submitted to Big Data (Mary Ann Liebert, Inc. publishers).

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species Bradman et al. (91 co-authors) submitted to GigaScience (BioMed Central Ltd). [ arXiv | Twitter ]

Mes prix et distinctions

2013, Lauréat du Fonds Santé — avril 2013 (étudiants-chercheurs étoiles), 1000 $ http://www.frq.gouv.qc.ca/laureats/sebastien-boisvert/
2012, Université Laval, Support du doyen de la Faculté de médecine dans le cadre du programme des distinctions honorifiques pour la Médaille du lieutenant-
gouverneur du Québec
2010-2013, Instituts de recherche en santé du Canada, Bourse d'études supérieures du Canada Frederick Banting et Charles Best - Bourse au doctorat, 105 000 $
2009-2010, Instituts de recherche en santé du Canada, Bourse d'études supérieures du Canada Frederick Banting et Charles Best - Bourse à la maîtrise, 17 500 $
2006, Université de Sherbrooke, Mention de l'excellence académique par le doyen de la Faculté des sciences, 0 $
2005, Université de Sherbrooke, Bourse d'admission pour la performance au cégep, 1000 $
2005, Fondation du Cégep de Lévis-Lauzon, Bourse pour un projet d'ordre pédagogique, 500 $

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