Dominique Lavenier

Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. SVJedi: genotyping structural variations with long reads. Bioinformatics, Oxford University Press (OUP), 2020, 36 (17), pp.4568-4575. ⟨10.1093/bioinformatics/btaa527⟩. ⟨hal-03032737⟩

Marie Devaere, Sarrah Boukthir, Séverine Moullec, Emeline Roux, Dominique Lavenier, et al.. Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm89 in Brittany, France. Microbiology Resource Announcements, American Society for Microbiology, 2020, 9 (11), pp.e00129-20. ⟨10.1128/MRA.00129-20⟩. ⟨hal-02532959⟩

Rumen Andonov, Hristo Djidjev, Sébastien François, Dominique Lavenier. Complete Assembly of Circular and Chloroplast Genomes Based on Global Optimization. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩. ⟨hal-02151798⟩

Gabriel Yazbeck, Rafael Sachetto Oliveira, José Mauro Ribeiro, Raíssa Graciano, Rosiane Santos, et al.. A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish. Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.1-5. ⟨10.1038/s41598-018-26623-x⟩. ⟨hal-01919836⟩

Sharat Chandra Varma, Paul Kolin, M. Balakrishnan, Dominique Lavenier. Hardware acceleration of de novo genome assembly. International Journal of Embedded Systems, Inderscience, 2017, 9 (1), pp.74-89. ⟨10.1504/IJES.2017.10002593⟩. ⟨hal-01481800⟩

Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, et al.. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, BioMed Central, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩. ⟨hal-01500475⟩

Aude Rochefort, Sarrah Boukthir, Séverine Moullec, Alexandra Meygret, Yahia Adnani, et al.. Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany. Genome Announcements, American Society for Microbiology, 2017, 5 (39), pp.e00957. ⟨10.1128/genomeA.00957-17⟩. ⟨hal-01617890⟩

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, et al.. Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software. Nature Methods, Nature Publishing Group, 2017, 14 (11), pp.1063 - 1071. ⟨10.1038/nmeth.4458⟩. ⟨hal-01633525⟩

Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, et al.. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, BioMed Central, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩. ⟨hal-01588181⟩

Alexandra Meygret, Vincent Pascal, Séverine Moullec, Jessica Nacazume, Yahia Adnani, et al.. Genome sequence of the uncommon Streptococcus pyogenes M/emm66 strain STAB13021, isolated from clonal clustered cases in French Brittany. Genome Announcements, American Society for Microbiology, 2016, 4 (4), pp.e00689-16. ⟨10.1128/genomeA.00689-16⟩. ⟨hal-01385659⟩

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Multiple comparative metagenomics using multiset k -mer counting. PeerJ Computer Science, PeerJ, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩. ⟨hal-01397150⟩

Hristo Djidjev, Guillaume Chapuis, Rumen Andonov, Sunil Thulasidasan, Dominique Lavenier. All-Pairs Shortest Path Algorithms for Planar Graph for GPU-Accelerated Clusters. Journal of Parallel and Distributed Computing, Elsevier, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩. ⟨hal-01235348⟩

Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo Djidjev, Dominique Lavenier. Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Scientific Programming, IOS Press, 2015, 2015, ⟨10.1155/2015/279715⟩. ⟨hal-01235331⟩

Naeem Abbas, Steven Derrien, Sanjay Rajopadhye, Patrice Quinton, Alexandre Cornu, et al.. Combining execution pipelines to improve parallel implementation of HMMER on FPGA. Microprocessors and Microsystems: Embedded Hardware Design (MICPRO), Elsevier, 2015, 39, pp.457-470. ⟨10.1016/j.micpro.2015.06.006⟩. ⟨hal-01235328⟩

Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, et al.. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics, BioMed Central, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩. ⟨hal-01214682⟩

Dominique Lavenier. Assembler un génome sur un pico-ordinateur. Biofutur, Elsevier - Cachan : Lavoisier, 2015, 34 (363). ⟨hal-01235355⟩

Hélène Falentin, Delphine Naquin, Valentin Loux, Frédérique Barloy-Hubler, Pascal Loubière, et al.. Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.. Genome Announcements, American Society for Microbiology, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩. ⟨hal-01019560⟩

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, et al.. GATB: Genome Assembly & Analysis Tool Box. Bioinformatics, Oxford University Press (OUP), 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩. ⟨hal-01088571⟩

Guillaume Rizk, Dominique Lavenier, Rayan Chikhi. DSK: k-mer counting with very low memory usage. Bioinformatics, Oxford University Press (OUP), 2013, 29 (5), pp.652-653. ⟨10.1093/bioinformatics/btt020⟩. ⟨hal-00778473⟩

Keith Bradnam, Joseph Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, et al.. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, BioMed Central, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩. ⟨hal-00868822⟩

Guillaume Chapuis, Olivier Filangi, Dominique Lavenier, Jean Michel Elsen, Pascale Leroy. Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection. Journal of Computational Biology, Mary Ann Liebert, 2013, 20 (9), pp.672-686. ⟨10.1089/cmb.2012.0136⟩. ⟨hal-00903794⟩

Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. BMC Bioinformatics, BioMed Central, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩. ⟨hal-00784394⟩

Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier. Etude quantitative dálgorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite. Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, Lavoisier, 2011, 30 (5), pp.539-569. ⟨hal-00637835⟩

Dent A. Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, et al.. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, Cold Spring Harbor Laboratory Press, 2011, ⟨10.1101/gr.126599.111⟩. ⟨inria-00637571⟩

Guillaume Rizk, Dominique Lavenier. GASSST: Global Alignment Short Sequence Search Tool. Bioinformatics, Oxford University Press (OUP), 2010, 26 (20), pp 2534-2540. ⟨hal-00531499⟩

Pierre Peterlongo, Laurent Noé, Dominique Lavenier, van Hoa Nguyen, Gregory Kucherov, et al.. Optimal neighborhood indexing for protein similarity search. BMC Bioinformatics, BioMed Central, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩. ⟨inria-00340510⟩

Dominique Lavenier. RDISK : une architecture reconfigurable pour l'exploration des banques génomiques. Techniques de l'Ingenieur, Techniques de l'ingénieur, 2008, November (IN89). ⟨inria-00347596⟩

Dominique Lavenier, Xianyang Jiang, Stephen Yau. Coding Region Prediction Based on a Universal DNA Sequence Representation Method. Journal of Computational Biology, Mary Ann Liebert, 2008, 15 (10), pp.1237-1256. ⟨10.1089/cmb.2008.0041⟩. ⟨inria-00347594⟩

Mathieu Giraud, Philippe Veber, Dominique Lavenier. Path-equivalent developments in acyclic weighted automata. International Journal of Foundations of Computer Science, World Scientific Publishing, 2007, 18 (4), pp.799-812. ⟨10.1142/S012905410700498X⟩. ⟨inria-00271646⟩

Dominique Lavenier, Gilles Georges, Xinchun Liu. A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms. The Journal of VLSI Signal, Springer Verlag, 2007, 48 (3), pp.255-269. ⟨10.1007/s11265-007-0073-6⟩. ⟨inria-00178314⟩

Dominique Lavenier. Accélérer l'exploration et l'analyse des textes des génomes. Interstices, INRIA, 2005. ⟨inria-00000526⟩

Nouri Ben Zakour, Michel Gautier, Rumen Andonov, Dominique Lavenier, Marie-Françoise Cochet, et al.. GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.. Nucleic Acids Research, Oxford University Press, 2004, 32 (1), pp.17-24. ⟨10.1093/nar/gkg928⟩. ⟨hal-01454461⟩

Loïc Lagadec, Dominique Lavenier, Erwan Fabiani, Bernard Pottier. Placing, Routing, and Editing Virtual FPGAs. LNCS Transactions on Computational Science, Springer, 2001. ⟨hal-02013412⟩

Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, et al.. A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩. ⟨hal-03008334⟩

Dominique Lavenier, Remy Cimadomo, Romaric Jodin. Variant Calling Parallelization on Processor-in-Memory Architecture. BIBM 2020 - IEEE International Conference on Bioinformatics and Biomedicine, Dec 2020, Virtual, South Korea. pp.1-4. ⟨hal-03006764⟩

Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. Genotyping Structural Variations using Long Read data. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8. ⟨hal-02288091⟩

Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. Genotyping Structural Variations using Long Read Data. HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3. ⟨hal-02289484⟩

Hoang Pham, Gwendal Virlet, Dominique Lavenier, Alexandre Termier. Statistically Significant Discriminative Patterns Searching. DaWaK 2019 - 21st International Conference on Big Data Analytics and Knowledge Discovery, Aug 2019, Linz, Austria. pp.105-115, ⟨10.1007/978-3-030-27520-4_8⟩. ⟨hal-02190793⟩

Sébastien Francois, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global optimization approach for circular and chloroplast genome assembly. BICoB 2018 - 10th International Conference on Bioinformatics and Computational Biology, Mar 2018, Las Vegas, United States. pp.1-11, ⟨10.1101/231324⟩. ⟨hal-01666830⟩

Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global Optimization for Scaffolding and Completing Genome Assemblies. International Network Optimization Conference , European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15. ⟨hal-01499859⟩

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⟩

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 ), DEXA, Sep 2016, Porto, Portugal. ⟨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. ⟨hal-01385665⟩

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. ⟨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, Manish Parashar, May 2014, Phoenix, United States. ⟨hal-00905738⟩

Erwan Drezen, Dominique Lavenier. Quality metrics for benchmarking sequences comparison tools. 9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Honrizonte, Brazil. pp.144-153. ⟨hal-01088595⟩

Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo. COMMET: comparing and combining multiple metagenomic datasets. IEEE BIBM 2014, Nov 2014, Belfast, United Kingdom. ⟨hal-01080050⟩

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. ⟨hal-00829055⟩

Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo Djidjev, Dominique Lavenier. Parallel seed-based approach to protein structure similarity detection. PPAM 2013, Roman Wyrzykowski, Sep 2013, Varsovie, Poland. ⟨hal-00881507⟩

Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil. ⟨hal-00720951⟩

Guillaume Chapuis, Olivier Filangi, Jean Michel Elsen, Dominique Lavenier, Pascale Le Roy. Accelerating QTL mapping with graphics cards. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 516 p. ⟨hal-01363562⟩

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⟩

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. ⟨inria-00623390⟩

Rayan Chikhi, Dominique Lavenier. Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph. WABI 2011, Sep 2011, Sarrebruck, Germany. ⟨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. SERVICES 2011, Jul 2011, WASHINGTON DC, United States. ⟨inria-00638694⟩

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. pp.67-78. ⟨hal-00637830⟩

Guillaume Chapuis, Olivier Filangi, Pascale Le Roy, 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. ⟨inria-00425237⟩

Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩. ⟨inria-00425373⟩

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/. ⟨hal-00322696⟩

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/. ⟨hal-00322732⟩

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/. ⟨hal-00322703⟩

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. ⟨inria-00321457⟩

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. ⟨inria-00321456⟩

Guillaume Rizk, Dominique Lavenier. GPU Accelerated RNA-RNA Interaction Algorithm. EMBnet, Sep 2008, Martina Franca, Italy. ⟨inria-00323566⟩

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. ⟨inria-00178325⟩

van Hoa Nguyen, Dominique Lavenier. Recherche dans les banques d'ADN par indexation parallèle. RVIF, Feb 2006, HCM, Vietnam. ⟨inria-00180372⟩

Mathieu Giraud, Laurent Noé, Gregory Kucherov, Dominique Lavenier. Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles. MajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC, IRISA – IETR – LTSI, Nov 2005, Rennes/France, pp.18--37. ⟨inria-00001036⟩

Gaëtan Benoit, Claire Lemaitre, Guillaume Rizk, Erwan Drezen, Dominique Lavenier. De Novo NGS Data Compression. Mourad Elloumi. Algorithms for Next-Generation Sequencing Data, Springer, pp.91-115, 2017, 978-3-319-59826-0. ⟨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. ⟨hal-01385634⟩

Dominique Lavenier, Guillaume Rizk, Sanjay Rajopadhye. GPU accelerated RNA folding algorithm. Wen-mei W. Hwu. GPU Computing Gems, ELSEVIER, pp.560, 2011, ⟨10.0123849888⟩. ⟨hal-00637827⟩

Dominique Lavenier. Parallel Genomic Sequence Comparison. Parallel and Distributed Computing, INTECH, pp.273-290, 2010. ⟨hal-00531505⟩

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, 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⟩

Dominique Lavenier. Conception d'architectures systoliques integrées. Architectures Matérielles [cs.AR]. Université de Rennes 1 [UR1], 1997. ⟨tel-01567436⟩