
Dominique Lavenier
107
Documents
Identifiants chercheurs
Présentation
Publications
Publications
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Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence AlignmentICPP 2024 - International Conference on Parallel Processing, Aug 2024, Gotland, Sweden. pp.1-10
Communication dans un congrès
hal-04739328
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MiMyCS: A Processing-in-Memory Read Mapper for Compressing Next-Gen Sequencing DatasetsBIBM 2024 - IEEE International Conference on Bioinformatics and Biomedicine, Dec 2024, Lisbonne, Portugal. pp.7176
Communication dans un congrès
hal-04821180
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Primer design for DNA storage random accessCORESA 2024 - 23ème conférence sur COmpression et REprésentation des Signaux Audiovisuels, Nov 2024, Rennes, France. pp.1-3
Communication dans un congrès
hal-04739300
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Dynamic sliding window encoding for data storageon DNA under biological and indexing constraintsEUSIPCO 2023: 31st European Signal Processing Conference, Sep 2023, Helsiinki, Finland. pp.1-5, ⟨10.23919/EUSIPCO58844.2023.10289957⟩
Communication dans un congrès
hal-04246615
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HairSplitter: separating strains in metagenome assemblies with long readsJOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané, France. pp.1-8
Communication dans un congrès
hal-04272455
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A first proposal for secure data storage into DNA molecules compliant with biological constraintsDSMM 2022 - 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France
Communication dans un congrès
hal-03817385
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Processing-in-Memory to speed up NGS analysisSFA²F 2022 - Sequencing to Function: Analysis and Application for the Future, Jun 2022, Santa Fe, United States
Communication dans un congrès
hal-03817360
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HairSplitter: assembling long reads in an unknown number of haplotypesSeqBIM 2022 - Journées sur les Séquences en Bioinformatique, Informatique et Mathématiques, Nov 2022, Bordeaux, France
Communication dans un congrès
hal-03864075
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Optimal Scaffolding for Chloroplasts' Inverted RepeatsJOBIM2022, Jul 2022, Rennes, France
Communication dans un congrès
hal-03625229
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DNA Storage: Synthesis and Sequencing Semiconductor TechnologiesIEDM 2022 - 68th Annual IEEE International Electron Devices Meeting, Dec 2022, San Francisco, United States. pp.1-4
Communication dans un congrès
hal-03902786
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Experimental DNA storage platformDSMM 2022 - 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France. pp.1-1
Communication dans un congrès
hal-03817374
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Optimal de novo assemblies for chloroplast genomes based on inverted repeats patternsBiATA 2021 - 4th International conference Bioinformatics: from Algorithms to Applications, Jul 2021, St. Petersbourg, Russia. pp.1-2
Communication dans un congrès
hal-03534195
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Variant Calling Parallelization on Processor-in-Memory ArchitectureBIBM 2020 - IEEE International Conference on Bioinformatics and Biomedicine, Dec 2020, Virtual, South Korea. pp.1-4
Communication dans un congrès
hal-03006764
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A Graph-Theoretic Barcode Ordering Model for Linked-ReadsWABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩
Communication dans un congrès
hal-03008334
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Genotyping Structural Variations using Long Read DataHiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3
Communication dans un congrès
hal-02289484
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Genotyping Structural Variations using Long Read dataJOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8
Communication dans un congrès
hal-02288091
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Statistically Significant Discriminative Patterns SearchingDaWaK 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⟩
Communication dans un congrès
hal-02190793
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Global optimization approach for circular and chloroplast genome assemblyBICoB 2018 - 10th International Conference on Bioinformatics and Computational Biology, Mar 2018, Las Vegas, United States. pp.1-11, ⟨10.1101/231324⟩
Communication dans un congrès
hal-01666830
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Global Optimization for Scaffolding and Completing Genome AssembliesInternational Network Optimization Conference , European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15
Communication dans un congrès
hal-01499859
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DNA Mapping using Processor-in-Memory ArchitectureWorkshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics, Dec 2016, Shenzhen, China
Communication dans un congrès
hal-01399997
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Global Optimization Methods for Genome Scaffolding12th International Workshop on Constraint-Based Methods for Bioinformatics , Sep 2016, Toulouse, France
Communication dans un congrès
hal-01385665
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Identifying Genetic Variant Combinations using Skypatterns7th International Workshop on Biological Knowledge Discovery and Data Mining (Workshop BIOKDD '16 ), DEXA, Sep 2016, Porto, Portugal. ⟨10.1109/DEXA.2016.13⟩
Communication dans un congrès
hal-01385614
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Global Optimization for Scafolding and Completing Genome Assemblies12th International Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France
Communication dans un congrès
hal-01567134
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KLAST: fast and sensitive software to compare large genomic databanks on cloudWorld Congress in Computer Science, Computer Engineering, and Applied Computing, Jul 2015, Las Vegas,, United States
Communication dans un congrès
hal-01235339
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Quality metrics for benchmarking sequences comparison tools9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Honrizonte, Brazil. pp.144-153
Communication dans un congrès
hal-01088595
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Efficient Multi-GPU Algorithm for All-Pairs Shortest PathsIPDPS 2014, Manish Parashar, May 2014, Phoenix, United States
Communication dans un congrès
hal-00905738
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COMMET: comparing and combining multiple metagenomic datasetsIEEE BIBM 2014, Nov 2014, Belfast, United Kingdom
Communication dans un congrès
hal-01080050
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Parallel seed-based approach to protein structure similarity detectionPPAM 2013, Roman Wyrzykowski, Sep 2013, Varsovie, Poland
Communication dans un congrès
hal-00881507
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FAssem : FPGA based Acceleration of De Novo Genome AssemblyProceeding of The 21st Annual International IEEE Symposium on Field Programmable Custom Computing Machines, Apr 2013, Seattle, United States. pp.FCCM'2013
Communication dans un congrès
hal-00829055
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Accelerating QTL mapping with graphics cardsJournées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 516 p
Communication dans un congrès
hal-01363562
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Compareads: comparing huge metagenomic experimentsRECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil
Communication dans un congrès
hal-00720951
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Biomanycores, open-source parallel code for many-core bioinformaticsBioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria
Communication dans un congrès
inria-00623390
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Parallel and memory-efficient reads indexing for genome assemblyParallel Bio-Computing 2011, Sep 2011, torun, Poland
Communication dans un congrès
inria-00637536
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Localized genome assembly from reads to scaffolds: practical traversal of the paired string graphWABI 2011, Sep 2011, Sarrebruck, Germany. ⟨10.1007/978-3-642-23038-7_4⟩
Communication dans un congrès
inria-00637535
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HLS Tools for FPGA : faster development with better performancesProceeding of the 7th International Symposium on Applied Reconfigurable Computing, Feb 2011, Belfast, United Kingdom. pp.67-78
Communication dans un congrès
hal-00637830
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biomanycores.org: a repository of interoperable open-source code for many-core bioinformaticsJOBIM 2011, Jul 2011, Paris, France
Communication dans un congrès
hal-00637847
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GPU Accelerted QTLMapThe 15th QTL-MAS workshop, May 2011, -, France
Communication dans un congrès
hal-00637840
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SLICEE: A Service oriented middleware for intensive scientific computationSERVICES 2011, Jul 2011, WASHINGTON DC, United States
Communication dans un congrès
inria-00638694
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Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 PlatformReconfigurable Architectures Workshop - IPDPS, May 2009, Rome, Italy
Communication dans un congrès
inria-00425237
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GPU accelerated Rna folding algorithm9th International Conference on Computational Science, May 2009, Baton Rouge, United States. pp.1031
Communication dans un congrès
hal-00425543
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c-GAMMA: Comparative Genome Analysis of Molecular MarkersPattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩
Communication dans un congrès
inria-00425373
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Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore ArchitectureNinth International Conference on Parallel and Distributed Computing, Applications and Technologies, Dec 2008, France. online proceedings: http://www.cs.otago.ac.nz/pdcat08/
Communication dans un congrès
hal-00322732
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Parallelizing the ACGT OncoSimulator3rd International Advanced Research Workshop on In Silico Oncology, Sep 2008, Istanbul, Turkey. online proceedings: http://www.3rd-iarwiso.iccs.ntua.gr/
Communication dans un congrès
hal-00322703
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Comparaison intensive des séquences protéiques : indexation des banques et usage des instructions SIMD des microprocesseursJournées Ouvertes Biologie Informatique Mathématiques - JOBIM, Jun 2008, Lille, France
Communication dans un congrès
inria-00325020
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Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison6th IEEE International Conference on research, innovation & vision for the future, Jul 2008, Ho Chi Minh Ville, Vietnam
Communication dans un congrès
inria-00321457
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Ordered Index Seed Algorithm for Intensive DNA Sequence ComparisonHiCOMB 2008 : Seventh IEEE International Workshop on High Performance Computational Biology, Apr 2008, Miami, United States. online proceeding : http://www.hicomb.org/HiCOMB2008/
Communication dans un congrès
hal-00322696
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GPU Accelerated RNA-RNA Interaction AlgorithmEMBnet, Sep 2008, Martina Franca, Italy
Communication dans un congrès
inria-00323566
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Parallélisation de la recherche de similarités entre séquences protéiques sur GPURenPar'18 : Rencontres francophones du Parallélisme, Feb 2008, Fribourg, Suisse
Communication dans un congrès
inria-00321456
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Détection de domaines dans des séquences génomiques : un problème de couverture optimaleFRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France
Communication dans un congrès
hal-00186471
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Protein similarity search with subset seeds on a dedicated reconfigurable hardwareParallel Bio-Computing, Sep 2007, Gdansk,, Poland
Communication dans un congrès
inria-00178325
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Recherche dans les banques d'ADN par indexation parallèleRVIF, Feb 2006, HCM, Vietnam
Communication dans un congrès
inria-00180372
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Path-Equivalent Removal of Epsilon-Transitions2006, pp.23--33, ⟨10.1007/11812128_4⟩
Communication dans un congrès
istex
hal-00107094
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Remix : une architecture pour la recherche dans les masses de données indexéesSymposium en archichecture de machines (Sympa) 2006, Oct 2006, Perpignan, France. pp.142-153
Communication dans un congrès
hal-00505589
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Seed-based Genomic Sequence Comparison using a FPGA/FLASH AcceleratorInternational IEEE Conference on Field Programmable Technology, Dec 2006, Thailand. http://fpt.selfip.org/fpt06/program.php
Communication dans un congrès
hal-00179994
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Fine-Grained Parallelism for Genomic ComputationConference on Parallel Processing for Scientific Computing, Feb 2006, United States
Communication dans un congrès
hal-00179996
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Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matériellesMajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC, IRISA – IETR – LTSI, Nov 2005, Rennes/France, pp.18--37
Communication dans un congrès
inria-00001036
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Le projet GénoGRID : une grille expérimentale pour la génomiqueJournées Ouvertes Biologie Informatique et Mathématiques, 2002, Saint Malo, France. pp.27-32
Communication dans un congrès
hal-00465092
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Genome AssemblyFrom Sequences to Graphs: Discrete Methods and Structures for Bioinformatics - SCIENCES - Bioinformatics - ISTE Wiley, 2022, 9781789450668
Chapitre d'ouvrage
hal-03817447
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De Novo NGS Data CompressionMourad 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⟩
Chapitre d'ouvrage
hal-01633718
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GPU-accelerated shortest paths computations for planar graphsHamid Azad Advances in GPU Research and Practice , Elsevier, pp.774, 2016, 9780128037386
Chapitre d'ouvrage
hal-01385634
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GPU accelerated RNA folding algorithmWen-mei W. Hwu. GPU Computing Gems, ELSEVIER, pp.560, 2011, ⟨10.1016/B978-0-12-384988-5.00014-0⟩
Chapitre d'ouvrage
hal-00637827
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Parallel Genomic Sequence ComparisonParallel and Distributed Computing, INTECH, pp.273-290, 2010
Chapitre d'ouvrage
hal-00531505
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Seed-Based Parallel Protein SequenceComparison Combining Multithreading, GPU, and FPGA technologiesBioinformatics: High Performance Parallel Computer Architectures, Taylor & Francis Group / CRC Press, pp.181-202, 2010
Chapitre d'ouvrage
hal-00531507
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Bioinformatics ApplicationsGokhale, Maya B., Graham, Paul S. Reconfigurable Computing. Accelerating Computation with Field-Programmable Gate Arrays, Springer, 2005, Foundation of computing, 0-387-26105-2
Chapitre d'ouvrage
inria-00000501
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Conception d'architectures systoliques integréesArchitectures Matérielles [cs.AR]. Université de Rennes 1 [UR1], 1997
HDR
tel-01567436
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