Career goal. Education. Employment. Awards and honors. Sébastien Boisvert Lemont, U.S.A. Software programmer for biology and science

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1 Sébastien Boisvert Lemont, U.S.A. Career goal Software programmer for biology and science Education Ph.D., Physiology-endocrinology, Université Laval, Québec, Québec, Canada, 2010/ /04 M.Sc., Physiology-endocrinology, Université Laval, Québec, Québec, Canada, 2008/ /12 B.Sc., Biotechnology, concentration in bioinformatics, Sherbrooke, Québec, Canada, 2005/ /04 D.E.C., Laboratory techniques in biotechnologies, Cégep de Lévis-Lauzon, Lévis, Québec, Canada, 2002/ /04 Employment Argonne Scholar Director s Fellow, Argonne National Laboratory, 2014/10 Postdoctoral Appointee, Argonne National Laboratory, 2014/ /09 High-performance computing specialist (part time), Calcul Québec, 2012/ /12 Summer Intern in Genome Technologies, Ontario Institute for Cancer Research, 2011/ /08 Summer Intern in sequencing bioinformatics, McGill University and Génome Québec Innovation Center, 2008/ /07 Intern in Artificial Intelligence, Department of Computer Science and Engineering, Université Laval, 2007/ /12 Intern in Bioinformatics, CHUQ-Centre hospitalier Université Laval, 2007/ /04 Intern in Bioinformatics, CHUQ-Centre hospitalier Université Laval, 2006/ /08 Consultant (bioinformatics, part time), Department of Biology, Université de Sherbrooke, 2006/ /04 Summer Laboratory Intern, CHUQ-Centre hospitalier Université Laval, 2005/ /07 Awards and honors Argonne Director s Fellowship, Office of the Director, Argonne National Laboratory, USD$78,000 per year, 2014/10 Michel G. Bergeron Prize, $500 (Canadian dollars), 2013 Award winner of the Fonds Santé Étudiants-chercheurs étoiles, Fonds de recherche du Québec - Santé (FRQS), $1,000 (Canadian dollars), 2013 Frederick Banting and Charles Best Canada Graduate Scholarship - Doctoral Award, Canadian Institutes of Health Research (CIHR), $105,000 (Canadian dollars), Frederick Banting and Charles Best Canada Graduate Scholarship - Master s Award, Canadian Institutes of Health Research (CIHR), $17,500 (Canadian dollars), Mention of academic excellence from the Dean, University of Sherbrooke, $0, 2006 Scholarship for academic achievement in college, University of Sherbrooke, $1,000 (Canadian dollars),

2 Scholarship for a pedagogical project, $500 (Canadian dollars), Fondation du Cégep de Lévis- Lauzon, 2005 Teaching Publications Refereed Journal Articles 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): 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 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 , April 2013 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 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. 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 , October 2011 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. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Research (Oxford University Press). (2012) 40 (3): Sébastien Boisvert, François Laviolette, and Jacques Corbeil. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of Computational Biology (Mary Ann Liebert, Inc. publishers). November 2010, 17(11):

3 Frédéric Raymond, Julie Carbonneau, Nancy Boucher, Lynda Robitaille, Sébastien Boisvert, Whei-Kuo Wu, Gaston De Serres, Guy Boivin, and Jacques Corbeil. Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. Journal of Clinical Microbiology (American Society for Microbiology) Mar;47(3): Sébastien Boisvert, Mario Marchand, François Laviolette, and Jacques Corbeil. HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology (BioMed Central Ltd) Dec 4;5:110. 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. Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biology (BioMed Central Ltd) ;9(7):R115. Epub 2008 Jul 18. Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Martin Smith, Nadine Messier, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Marc Ouellette, and Barbara Papadopoulou. Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics (BioMed Central Ltd) May 29;9:255. doi: / Refereed Conference Publications Mikhail Kandel, Steve Behling, Bill Long, Carlos P. Sosa, Sébastien Boisvert, Jacques Corbeil, Lorenzo Pesce. Early Experience on Crays with Genomic Applications Used as Part of Next Generation Sequencing Workflow. Cray User Group Conference 2013, May 6-9, 2013 pap104s1 Refereed Workshop Publications 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 , Vancouver, BC, Canada. Refereed Posters / abstracts 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. 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 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). 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). 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 Soumission #

4 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. Unrefereed posters 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 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. 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. Unrefereed invited presentations Ray and Ray Cloud Browser for Metagenomics Sébastien Boisvert Beatles and Bioinformatics The Chapel, The Foresight Centre, University of Liverpool :00 GMT Messages, keys and values in genomics Sébastien Boisvert BlueGene Active Storage (BGAS) Workshop for Medical Sciences SciNet Consortium, University of Toronto :00 Métagénomique adaptative à grande vitesse. Sébastien Boisvert Département de biologie, Université de Sherbrooke :00-12:00 Massively parallel assemblers for massively parallel DNA sequencers. Sébastien Boisvert, Élénie Godzaridis SciNet Developer Seminar, SciNet Consortium, University of Toronto :00-14:00 Granularities and messages: from design to abstraction to implementation to virtualization. Élénie Godzaridis, Sébastien Boisvert SciNet Developer Seminar, SciNet Consortium, University of Toronto :00-16:00 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 Meeting participation 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 Thesis Sébastien Boisvert Assemblage adaptatif de génomes et de méta-génomes par passage de messages Doctorat, Philosophiæ doctor (Ph. D.), Physiologie-endocrinologie, Faculté de Médecine, Université Laval 4

5 Activities Technical Referee for International Journals and Magazines Supervision Professional Memberships and Other Affiliations Citizenship Canadian Skills Software engineering Native languages: C, C++ Libraries: MPI, pthreads Build tools: Make SCM: git, mercurial, subversion, github Continuous integration: jenkins Interpreted languages: Python, Ruby, Java Web servers: Apache, lighttpd Frameworks: rails OS: Linux, Minix, CNK Platforms: IBM Blue Gene/Q, Cray XC30, Cray XE6, IBM idataplex Compilers: IBM XL, Cray CC, GNU gcc, clang, Intel icc Biotechnology Sequencers: 454, Illumina Project management SCRUM meetings Personal Languages English (fluent), French (native) Interests Cycling, winter, software design, LWN.net, reading, open source 5

6 Web profiles References Available on request 6

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