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Dominique Lavenier


CNRS Research Director
GenScale team leader
 
IRISA / INRIA
Campus de Beaulieu
35042 Rennes cedex – France
tel: (33) 2 99 84 72 17 – mail: lavenier@irisa.fr – office: A114

Research Area

  • Bioinformatics, Genomic, NGS Processing
  • Data Structures, Optimisation
  • Parallelism, Computer Design


Article dans une revue21 documents

Communication dans un congrès27 documents

  • Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global Optimization for Scaffolding and Completing Genome Assemblies. International Network Optimization Conference , Feb 2017, Lisboa, Portugal. pp.15, 2017, 〈http://inoc2017.fc.ul.pt/〉. 〈hal-01499859〉
  • Hoang-Son Pham, Dominique Lavenier, Alexandre Termier. Identifying Genetic Variant Combinations using Skypatterns. 7th International Workshop on Biological Knowledge Discovery and Data Mining (Workshop BIOKDD '16 ), Sep 2016, Porto, Portugal. 2016, 〈http://www.dexa.org/biokdd2016〉. 〈10.1109/DEXA.2016.13〉. 〈hal-01385614〉
  • Sebastien François, Rumen Andonov, Hristo Djidjev, Dominique Lavenier. Global Optimization Methods for Genome Scaffolding. 12th International Workshop on Constraint-Based Methods for Bioinformatics , Sep 2016, Toulouse, France. 2016, 〈http://cp2016.a4cp.org/program/workshops/ws-wcb16.html〉. 〈hal-01385665〉
  • Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global Optimization for Scafolding and Completing Genome Assemblies . 12th International Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. 〈hal-01567134〉
  • Dominique Lavenier, Jean-Francois Roy, David Furodet. DNA Mapping using Processor-in-Memory Architecture. Workshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics, Dec 2016, Shenzhen, China. 2016. 〈hal-01399997〉
  • Ivaylo Petrov, Sébastien Brillet, Erwan Drezen, Sylvain Quiniou, L Antin, et al.. KLAST: fast and sensitive software to compare large genomic databanks on cloud. World Congress in Computer Science, Computer Engineering, and Applied Computing, Jul 2015, Las Vegas,, United States. 〈hal-01235339〉
  • Guillaume Chapuis, Hristo Djidjev, Rumen Andonov, Sunil Thulasidasan, Dominique Lavenier. Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths. IPDPS 2014, May 2014, Phoenix, United States. 2014. 〈hal-00905738〉
  • Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo Djidjev, Dominique Lavenier. Parallel seed-based approach to protein structure similarity detection. Roman Wyrzykowski. PPAM 2013, Sep 2013, Varsovie, Poland. Springer, 2013. 〈hal-00881507〉
  • Sharat Chandra Varma, Paul Kolin, M. Balakrishnan, Dominique Lavenier. FAssem : FPGA based Acceleration of De Novo Genome Assembly. Proceeding of The 21st Annual International IEEE Symposium on Field Programmable Custom Computing Machines, Apr 2013, Seattle, United States. pp.FCCM'2013, 2013. 〈hal-00829055〉
  • Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil. 2012. 〈hal-00720951〉
  • Alexandre Cornu, Steven Derrien, Dominique Lavenier. HLS Tools for FPGA : faster development with better performances. Proceeding of the 7th International Symposium on Applied Reconfigurable Computing, Feb 2011, Belfast, United Kingdom. 6578, pp.67-78, 2011. 〈hal-00637830〉
  • Jean-Frédéric Berthelot, Charles Deltel, Mathieu Giraud, Stéphane Janot, Laetitia Jourdan, et al.. biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics. JOBIM 2011, Jul 2011, Paris, France. 〈hal-00637847〉
  • Rayan Chikhi, Dominique Lavenier. Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph. Springer. WABI 2011, Sep 2011, Sarrebruck, Germany. 2011, Algorithms in Bioinformatics 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings. 〈10.1007/978-3-642-23038-7_4〉. 〈inria-00637535〉
  • Jonathan Piat, Francois Moreews, Olivier Collin, Dominique Lavenier, Alexandre Cornu. SLICEE: A Service oriented middleware for intensive scientific computation. IEEE. SERVICES 2011, Jul 2011, WASHINGTON DC, United States. 2011. 〈inria-00638694〉
  • Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, et al.. Biomanycores, open-source parallel code for many-core bioinformatics. Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria. 2011. 〈inria-00623390〉
  • Guillaume Chapuis, Olivier Filangi, Pascale Leroy, Jean-Michel Elsen, Dominique Lavenier. GPU Accelerted QTLMap. The 15th QTL-MAS workshop, May 2011, France. 〈hal-00637840〉
  • Van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier. Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform. Reconfigurable Architectures Workshop - IPDPS, May 2009, Rome, Italy. 2009. 〈inria-00425237〉
  • Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. LNCS. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. SpringerLink, 5780/2009, pp.255-269, 2009, Pattern Recognition in Bioinformatics. 〈10.1007/978-3-642-04031-3_23〉. 〈inria-00425373〉
  • Guillaume Rizk, Dominique Lavenier. GPU Accelerated RNA-RNA Interaction Algorithm. EMBnet, Sep 2008, Martina Franca, Italy. 2008. 〈inria-00323566〉
  • Xioachun Ye, Van Hoa Nguyen, Dominique Lavenier, Dongrui Fan. Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture. Ninth International Conference on Parallel and Distributed Computing, Applications and Technologies, Dec 2008, France. online proceedings: http://www.cs.otago.ac.nz/pdcat08/, 2008. 〈hal-00322732〉
  • Van Hoa Nguyen, Dominique Lavenier. Parallélisation de la recherche de similarités entre séquences protéiques sur GPU. RenPar'18 : Rencontres francophones du Parallélisme, Feb 2008, Fribourg, Suisse. 2008. 〈inria-00321456〉
  • Van Hoa Nguyen, Dominique Lavenier. Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison. 6th IEEE International Conference on research, innovation & vision for the future, Jul 2008, Ho Chi Minh Ville, Vietnam. 2008. 〈inria-00321457〉
  • Dominique Lavenier, Julien Jacques. Parallelizing the ACGT OncoSimulator. 3rd International Advanced Research Workshop on In Silico Oncology, Sep 2008, Istanbul, Turkey. online proceedings: http://www.3rd-iarwiso.iccs.ntua.gr/, 2008. 〈hal-00322703〉
  • Dominique Lavenier. Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison. HiCOMB 2008 : Seventh IEEE International Workshop on High Performance Computational Biology, Apr 2008, Miami, United States. online proceeding : http://www.hicomb.org/HiCOMB2008/, 2008. 〈hal-00322696〉
  • Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, et al.. Protein similarity search with subset seeds on a dedicated reconfigurable hardware. Parallel Bio-Computing, Sep 2007, Gdansk,, Poland. 2007. 〈inria-00178325〉
  • Van Hoa Nguyen, Dominique Lavenier. Recherche dans les banques d'ADN par indexation parallèle. RVIF, Feb 2006, HCM, Viêt Nam. 2006. 〈inria-00180372〉
  • Mathieu Giraud, Laurent Noé, Gregory Kucherov, Dominique Lavenier. Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles. Alexandre Vautier, Sylvie Saget. MajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC, Nov 2005, Rennes/France, pp.18--37, 2005. 〈inria-00001036〉

Chapitre d'ouvrage5 documents

  • Gaëtan Benoit, Claire Lemaitre, Guillaume Rizk, Dominique Lavenier, Erwan Drezen. De Novo NGS Data Compression. Springer. Algorithms for Next-Generation Sequencing Data, pp.91-115, 2017, 978-3-319-59826-0. 〈https://link.springer.com/chapter/10.1007/978-3-319-59826-0_4〉. 〈hal-01633718〉
  • Guillaume Chapuis, Hristo Djidjev, Dominique Lavenier, Rumen Andonov. GPU-accelerated shortest paths computations for planar graphs. Hamid Azad Advances in GPU Research and Practice , Elsevier, pp.774, 2016, 9780128037386 〈https://www.elsevier.com/books/advances-in-gpu-research-and-practice/azad/978-0-12-803738-6〉. 〈hal-01385634〉
  • Dominique Lavenier, Van Hoa Nguyen. Seed-Based Parallel Protein SequenceComparison Combining Multithreading, GPU, and FPGA technologies. Bioinformatics: High Performance Parallel Computer Architectures, Taylor & Francis Group / CRC Press, pp.181-202, 2010. 〈hal-00531507〉
  • Dominique Lavenier. Parallel Genomic Sequence Comparison. Parallel and Distributed Computing, INTECH, pp.273-290, 2010. 〈hal-00531505〉
  • Dominique Lavenier, Mathieu Giraud. Bioinformatics Applications. Gokhale, Maya B., Graham, Paul S. Reconfigurable Computing. Accelerating Computation with Field-Programmable Gate Arrays, Springer, 2005, Foundation of computing, 0-387-26105-2. 〈inria-00000501〉