Dominique Lavenier
Présentation
Publications
Publications
Optimized phylogenetic batching of million-genome collections for reduced storage requirements and faster data retrievalSeqBIM 2025, Nov 2025, Nantes, France |
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Evaluating Energy Efficiency of Genomics Algorithms on Processing-in-Memory ArchitecturesPECS 2025 - International Workshop on Performance and Energy Efficiency in Concurrent and Distributed Systems, Biagio Cosenza, Aug 2025, Dresden, Germany. pp.1-12 |
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Protein database search using Processing-in-Memory architectureIPDPS 2025 - IEEE International Parallel and Distributed Processing Symposium, IPDPS, Jun 2025, Milano, Italy. pp.939-948, ⟨10.1109/IPDPSW66978.2025.00146⟩ |
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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 |
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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 |
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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 |
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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⟩ |
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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 |
HairSplitter: assembling long reads in an unknown number of haplotypesSeqBIM 2022 - Journées sur les Séquences en Bioinformatique, Informatique et Mathématiques, Nov 2022, Bordeaux, France |
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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 |
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 |
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Optimal Scaffolding for Chloroplasts' Inverted RepeatsJOBIM2022, Jul 2022, Rennes, France |
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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 |
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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 |
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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 |
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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⟩ |
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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 |
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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 |
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Genotyping Structural Variations using Long Read DataHiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3 |
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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⟩ |
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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⟩ |
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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 |
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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⟩ |
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DNA Mapping using Processor-in-Memory ArchitectureWorkshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics, Dec 2016, Shenzhen, China |
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Global Optimization Methods for Genome Scaffolding12th International Workshop on Constraint-Based Methods for Bioinformatics , Sep 2016, Toulouse, France |
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Global Optimization for Scafolding and Completing Genome Assemblies12th International Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France |
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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 |
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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 |
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Efficient Multi-GPU Algorithm for All-Pairs Shortest PathsIPDPS 2014, Manish Parashar, May 2014, Phoenix, United States |
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COMMET: comparing and combining multiple metagenomic datasetsIEEE BIBM 2014, Nov 2014, Belfast, United Kingdom |
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Parallel seed-based approach to protein structure similarity detectionPPAM 2013, Roman Wyrzykowski, Sep 2013, Varsovie, Poland |
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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 |
Accelerating QTL mapping with graphics cardsJournées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 516 p |
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Compareads: comparing huge metagenomic experimentsRECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil |
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Biomanycores, open-source parallel code for many-core bioinformaticsBioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria |
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Parallel and memory-efficient reads indexing for genome assemblyParallel Bio-Computing 2011, Sep 2011, torun, Poland |
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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⟩ |
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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 |
biomanycores.org: a repository of interoperable open-source code for many-core bioinformaticsJOBIM 2011, Jul 2011, Paris, France |
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GPU Accelerted QTLMapThe 15th QTL-MAS workshop, May 2011, -, France |
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SLICEE: A Service oriented middleware for intensive scientific computationSERVICES 2011, Jul 2011, WASHINGTON DC, United States |
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Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 PlatformReconfigurable Architectures Workshop - IPDPS, May 2009, Rome, Italy |
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GPU accelerated Rna folding algorithm9th International Conference on Computational Science, May 2009, Baton Rouge, United States. pp.1031 |
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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⟩ |
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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 |
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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/ |
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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 |
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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/ |
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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/ |
GPU Accelerated RNA-RNA Interaction AlgorithmEMBnet, Sep 2008, Martina Franca, Italy |
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Parallélisation de la recherche de similarités entre séquences protéiques sur GPURenPar'18 : Rencontres francophones du Parallélisme, Feb 2008, Fribourg, Suisse |
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Détection de domaines dans des séquences génomiques : un problème de couverture optimaleFRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France |
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Protein similarity search with subset seeds on a dedicated reconfigurable hardwareParallel Bio-Computing, Sep 2007, Gdansk,, Poland |
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Recherche dans les banques d'ADN par indexation parallèleRVIF, Feb 2006, HCM, Vietnam |
Path-Equivalent Removal of Epsilon-Transitions2006, pp.23--33, ⟨10.1007/11812128_4⟩ |
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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 |
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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 |
Fine-Grained Parallelism for Genomic ComputationConference on Parallel Processing for Scientific Computing, Feb 2006, United States |
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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 |
Le projet GénoGRID : une grille expérimentale pour la génomiqueJournées Ouvertes Biologie Informatique et Mathématiques, 2002, Saint Malo, France. pp.27-32 |
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Stockage d'information sur ADNLe calcul à découvert, CNRS Editions, 2025, 978-2-271-15373-9 |
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Délocaliser les calculs en mémoire : le concept « processing-in-memory »CNRS Editions. Le calcul à découvert, pp.1-3, 2025, 978-2-271-15373-9 |
Genome AssemblyFrom Sequences to Graphs: Discrete Methods and Structures for Bioinformatics - SCIENCES - Bioinformatics - ISTE Wiley, 2022, 9781789450668 |
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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⟩ |
GPU-accelerated shortest paths computations for planar graphsHamid Azad Advances in GPU Research and Practice , Elsevier, pp.774, 2016, 9780128037386 |
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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⟩ |
Parallel Genomic Sequence ComparisonParallel and Distributed Computing, INTECH, pp.273-290, 2010 |
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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 |
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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 |
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Conception d'architectures systoliques integréesArchitectures Matérielles [cs.AR]. Université de Rennes 1 [UR1], 1997 |