Publications of Sébastien Boisvert

2007

  1. 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

2008

  1. 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
  2. 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 | Self-archiving ]
  3. 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 | Self-archiving ]
  4. 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 | Self-archiving ]

2009

  1. 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
  2. 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 | Self-archiving ]

2010

  1. 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 | Self-archiving ]
  2. 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
  3. 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

2011

  1. 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.
  2. 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 ]
  3. 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
  4. 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

2012

  1. 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. February 14, 2012
    [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central | Self-archiving ]
  2. 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 | Self-archiving ]
  3. 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 | Self-archiving ]

2013

  1. 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).
    Volume 88, Issue 1, pages 189–202, April 2013
    [ Publisher | DOI | PubMed | PubMed Central | PubMed Central Canada | Europe PubMed Central | Self-archiving ]
  2. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
    Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis E, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
    GigaScience (BioMed Central Ltd).
    2013, 2:10
    [ Publisher | DOI | PubMed | arXiv | Twitter | Self-archiving ]
  3. 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
  4. 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.
    Cray User Group Conference 2013, May 6-9, 2013
    pap104s1
    [ abstract | Self-archiving ]
  5. 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, 2013-01-18, University of Minnesota Rochester.
    poster

2014

  1. Human analysts at superhuman scales: what has friendly software to do?
    Élénie Godzaridis, Sébastien Boisvert, Fangfang Xia, Mikhail Kandel, Steve Behling, Bill Long, Carlos P. Sosa, François Laviolette, Jacques Corbeil
    Big Data (Mary Ann Liebert, Inc. publishers).
    January 7, 2014, 1(4): 227-236.
    [ Publisher | DOI | Self-archiving ]
  2. Assemblage adaptatif de génomes et de méta-génomes par passage de messages
    Sébastien Boisvert
    Thèse de doctorat, Université Laval.
    Lien

2015

  1. Gene identification and strain classification using Random Forests.
    John Santerre, Sebastien Boisvert, Jim Davis, Fangfang Xia, and Rick Stevens.
    Great Lakes Bioinformatics Conference 2015, Poster 108, Session B, May 18-20, 2015, Purdue University.
    Poster
  2. Exploring the Protein Universe with Big Data Methods
    New York Scientific Data Summit (NYSDS)
    New York University, August 2-5, 2015
    Poster


Invitations

  1. Ray and Ray Cloud Browser for Metagenomics
    Sébastien Boisvert
    Beatles and Bioinformatics
    The Chapel, The Foresight Centre, University of Liverpool
    2013-11-27 13:00 GMT
    Video slides agenda
  2. Messages, keys and values in genomics
    Sébastien Boisvert
    BlueGene Active Storage (BGAS) Workshop for Medical Sciences
    SciNet Consortium, University of Toronto
    2013-08-07 9:00
    PDF OpenDocument
  3. Métagénomique adaptative à grande vitesse.
    Sébastien Boisvert
    Département de biologie, Université de Sherbrooke
    2012-02-07 11:00-12:00
    [ | abstract | PDF | OpenDocument ]
  4. 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
  5. 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
  6. 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)
  7. 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