Dominique Lavenier

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Publications

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De-Bruijn graph partitioning for scalable and accurate DNA storage processing

Florestan de Moor , Olivier Boullé , Dominique Lavenier

Bioinformatics, 2025, 41 (11), pp.1-9. ⟨10.1093/bioinformatics/btaf618⟩

Article dans une revue hal-05375444v1
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Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

Sergio Gabriel Olvera-Vazquez , Xilong Chen , Aurélie Mesnil , Camille Meslin , Fabricio Almeida-Silva et al.

Molecular Biology and Evolution, 2025, 42 (12), pp.msaf238. ⟨10.1093/molbev/msaf238⟩

Article dans une revue anses-05299488v1
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A Dynamic Sliding Window Encoding for Secured DNA Data Storage Compliant With Biological and Indexing Constraints

Chloé Berton , Gouenou Coatrieux , Héléne Gasnier , Sahar Haddad , Reda Bellafqira et al.

IEEE Access, 2025, 13, pp.66009-66030. ⟨10.1109/ACCESS.2025.3560387⟩

Article dans une revue hal-05067257v1
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Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information

Julien Leblanc , Olivier Boulle , Emeline Roux , Jacques Nicolas , Dominique Lavenier et al.

Biotechniques, 2024, 76 (5), pp.203-215. ⟨10.2144/btn-2023-0109⟩

Article dans une revue hal-04567229v1
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HairSplitter: haplotype assembly from long, noisy reads

Roland Faure , Dominique Lavenier , Jean-François Flot

Peer Community In Mathematical and Computational Biology, 2024, 4 (96), pp.1-16. ⟨10.24072/pcjournal.481⟩

Article dans une revue hal-04739354v1

Stocker les données : la piste prometteuse de l’ADN

Dominique Lavenier , Marc Antonini , Yannick Rondelez , A.J. Genot

Interstices, 2023

Article dans une revue hal-04073357v1
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QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data

Roland Faure , Dominique Lavenier

Bioinformatics Advances, 2022, pp.1-8. ⟨10.1093/bioadv/vbac068/6717790⟩

Article dans une revue hal-03790140v1
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SVJedi: genotyping structural variations with long reads

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre

Bioinformatics, 2020, 36 (17), pp.4568-4575. ⟨10.1093/bioinformatics/btaa527⟩

Article dans une revue hal-03032737v1
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Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm89 in Brittany, France

Marie Devaere , Sarrah Boukthir , Séverine Moullec , Emeline Roux , Dominique Lavenier et al.

Microbiology Resource Announcements, 2020, 9 (11), pp.e00129-20. ⟨10.1128/MRA.00129-20⟩

Article dans une revue hal-02532959v1
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Complete Assembly of Circular and Chloroplast Genomes Based on Global Optimization

Rumen Andonov , Hristo Djidjev , Sébastien François , Dominique Lavenier

Journal of Bioinformatics and Computational Biology, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩

Article dans une revue hal-02151798v1

A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish

Gabriel Yazbeck , Rafael Sachetto Oliveira , José Mauro Ribeiro , Raíssa Graciano , Rosiane Santos et al.

Scientific Reports, 2018, 8 (1), pp.1-5. ⟨10.1038/s41598-018-26623-x⟩

Article dans une revue hal-01919836v1
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Global Optimization for Scaffolding and Completing Genome Assemblies

Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev

Electronic Notes in Discrete Mathematics, 2018

Article dans une revue hal-03697534v1

Hardware acceleration of de novo genome assembly

Sharat Chandra Varma , Paul Kolin , M. Balakrishnan , Dominique Lavenier

International Journal of Embedded Systems, 2017, 9 (1), pp.74-89. ⟨10.1504/IJES.2017.10002593⟩

Article dans une revue hal-01481800v1
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Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Alexander Sczyrba , Peter Hofmann , Peter Belmann , David Koslicki , Stefan Janssen et al.

Nature Methods, 2017, 14 (11), pp.1063 - 1071. ⟨10.1038/nmeth.4458⟩

Article dans une revue hal-01633525v1
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Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany

Aude Rochefort , Sarrah Boukthir , Séverine Moullec , Alexandra Meygret , Yahia Adnani et al.

Genome Announcements, 2017, 5 (39), pp.e00957. ⟨10.1128/genomeA.00957-17⟩

Article dans une revue hal-01617890v1
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Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.

Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩

Article dans une revue hal-01500475v1
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Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford et al.

Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩

Article dans une revue hal-01588181v1
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Multiple comparative metagenomics using multiset k -mer counting

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath et al.

PeerJ Computer Science, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩

Article dans une revue hal-01397150v1

Genome sequence of the uncommon Streptococcus pyogenes M/emm66 strain STAB13021, isolated from clonal clustered cases in French Brittany

Alexandra Meygret , Vincent Pascal , Séverine Moullec , Jessica Nacazume , Yahia Adnani et al.

Genome Announcements, 2016, 4 (4), pp.e00689-16. ⟨10.1128/genomeA.00689-16⟩

Article dans une revue hal-01385659v1
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All-Pairs Shortest Path Algorithms for Planar Graph for GPU-Accelerated Clusters

Hristo Djidjev , Guillaume Chapuis , Rumen Andonov , Sunil Thulasidasan , Dominique Lavenier

Journal of Parallel and Distributed Computing, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩

Article dans une revue hal-01235348v1
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Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Guillaume Chapuis , Mathilde Le Boudic-Jamin , Rumen Andonov , Hristo Djidjev , Dominique Lavenier

Scientific Programming, 2015, 2015, ⟨10.1155/2015/279715⟩

Article dans une revue hal-01235331v1

Assembler un génome sur un pico-ordinateur

Dominique Lavenier

Biofutur, 2015, 34 (363)

Article dans une revue hal-01235355v1
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Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Gaëtan Benoit , Claire Lemaitre , Dominique Lavenier , Erwan Drezen , Thibault Dayris et al.

BMC Bioinformatics, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩

Article dans une revue hal-01214682v1

Combining execution pipelines to improve parallel implementation of HMMER on FPGA

Naeem Abbas , Steven Derrien , Sanjay Rajopadhye , Patrice Quinton , Alexandre Cornu et al.

Microprocessors and Microsystems: Embedded Hardware Design , 2015, 39, pp.457-470. ⟨10.1016/j.micpro.2015.06.006⟩

Article dans une revue hal-01235328v1
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Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.

Hélène Falentin , Delphine Naquin , Valentin Loux , Frédérique Barloy-Hubler , Pascal Loubière et al.

Genome Announcements, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩

Article dans une revue hal-01019560v1
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GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre et al.

Bioinformatics, 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩

Article dans une revue hal-01088571v1
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Keith Bradnam , Joseph Fass , Anton Alexandrov , Paul Baranay , Michael Bechner et al.

GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩

Article dans une revue hal-00868822v1
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DSK: k-mer counting with very low memory usage

Guillaume Rizk , Dominique Lavenier , Rayan Chikhi

Bioinformatics, 2013, 29 (5), pp.652-653. ⟨10.1093/bioinformatics/btt020⟩

Article dans une revue hal-00778473v1
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Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Guillaume Chapuis , Olivier Filangi , Jean Michel J. M. Elsen , Dominique Lavenier , Pascale Le Roy

Journal of Computational Biology, 2013, 20 (9), pp.672-686. ⟨10.1089/cmb.2012.0136⟩

Article dans une revue hal-00903794v1
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Compareads: comparing huge metagenomic experiments

Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo

BMC Bioinformatics, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩

Article dans une revue hal-00784394v1

Etude quantitative dálgorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite

Mehdi Darouich , Stéphane Guyetant , Dominique Lavenier

Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2011, 30 (5), pp.539-569

Article dans une revue hal-00637835v1

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent A. Earl , Keith Bradnam , John St. John , Aaron Darling , Dawei Lin et al.

Genome Research, 2011, ⟨10.1101/gr.126599.111⟩

Article dans une revue inria-00637571v1

GASSST: Global Alignment Short Sequence Search Tool

Guillaume Rizk , Dominique Lavenier

Bioinformatics, 2010, 26 (20), pp 2534-2540

Article dans une revue hal-00531499v1
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Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.

Fabrice Legeai , Guillaume Rizk , Thomas Walsh , Owain Edwards , Karl Gordon et al.

BMC Genomics, 2010, 11 (1), pp.281. ⟨10.1186/1471-2164-11-281⟩

Article dans une revue inserm-00482283v1
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PLAST: parallel local alignment search tool for database comparison

van Hoa Nguyen , Dominique Lavenier

BMC Bioinformatics, 2009, 10, pp.24

Article dans une revue inria-00425301v1
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Paired-end read length lower bounds for genome re-sequencing

Rayan Chikhi , Dominique Lavenier

BMC Bioinformatics, 2009, ⟨10.1186/1471-2105-10-S13-O2⟩

Article dans une revue inria-00426856v1

RDISK : une architecture reconfigurable pour l'exploration des banques génomiques

Dominique Lavenier

Techniques de l'Ingénieur, 2008, November (IN89)

Article dans une revue inria-00347596v1
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Optimal neighborhood indexing for protein similarity search

Pierre Peterlongo , Laurent Noé , Dominique Lavenier , van Hoa Nguyen , Gregory Kucherov et al.

BMC Bioinformatics, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩

Article dans une revue inria-00340510v1

Coding Region Prediction Based on a Universal DNA Sequence Representation Method

Dominique Lavenier , Xianyang Jiang , Stephen Yau

Journal of Computational Biology, 2008, 15 (10), pp.1237-1256. ⟨10.1089/cmb.2008.0041⟩

Article dans une revue inria-00347594v1
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Path-equivalent developments in acyclic weighted automata

Mathieu Giraud , Philippe Veber , Dominique Lavenier

International Journal of Foundations of Computer Science, 2007, 18 (4), pp.799-812. ⟨10.1142/S012905410700498X⟩

Article dans une revue inria-00271646v1

A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms

Dominique Lavenier , Gilles Georges , Xinchun Liu

The Journal of VLSI Signal, 2007, 48 (3), pp.255-269. ⟨10.1007/s11265-007-0073-6⟩

Article dans une revue istex inria-00178314v1

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

Sébastien Tempel , Mathieu Giraud , Dominique Lavenier , Israël-César C. Lerman , Anne-Sophie Valin et al.

Bioinformatics, 2006, 22(16), pp.1948-1954

Article dans une revue hal-00090517v1

Accélérer l'exploration et l'analyse des textes des génomes

Dominique Lavenier

Interstices, 2005

Article dans une revue inria-00000526v1
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GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Nouri Ben Zakour , Michel Gautier , Rumen Andonov , Dominique Lavenier , Marie-Françoise Cochet et al.

Nucleic Acids Research, 2004, 32 (1), pp.17-24. ⟨10.1093/nar/gkg928⟩

Article dans une revue hal-01454461v1
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Placing, Routing, and Editing Virtual FPGAs

Loïc Lagadec , Dominique Lavenier , Erwan Fabiani , Bernard Pottier

Transactions on Computational Science, 2001

Article dans une revue hal-02013412v1

Optimized phylogenetic batching of million-genome collections for reduced storage requirements and faster data retrieval

Tam Khac Minh Truong , Dominique Lavenier , Pierre Peterlongo , Karel Břinda

SeqBIM 2025, Nov 2025, Nantes, France

Communication dans un congrès hal-05448733v1
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Evaluating Energy Efficiency of Genomics Algorithms on Processing-in-Memory Architectures

Meven Mognol , Florestan de Moor , Erwan Drezen , Yann Falevoz , Dominique Lavenier

PECS 2025 - International Workshop on Performance and Energy Efficiency in Concurrent and Distributed Systems, Biagio Cosenza, Aug 2025, Dresden, Germany. pp.1-12

Communication dans un congrès hal-05375465v1
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Protein database search using Processing-in-Memory architecture

Charly Airault , Charles Deltel , Florestan de Moor , Erwan Drezen , Meven Mognol et al.

IPDPS 2025 - IEEE International Parallel and Distributed Processing Symposium, IPDPS, Jun 2025, Milano, Italy. pp.939-948, ⟨10.1109/IPDPSW66978.2025.00146⟩

Communication dans un congrès hal-05375748v1
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Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment

Meven Mognol , Dominique Lavenier , Julien Legriel

ICPP 2024 - International Conference on Parallel Processing, Aug 2024, Gotland, Sweden. pp.1-10

Communication dans un congrès hal-04739328v1
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Primer design for DNA storage random access

Jeremy Mateos , Dominique Lavenier , Melpomeni Dimopoulou , Anthony Genot , Marc Antonini

CORESA 2024 - 23ème conférence sur COmpression et REprésentation des Signaux Audiovisuels, Nov 2024, Rennes, France. pp.1-3

Communication dans un congrès hal-04739300v1
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MiMyCS: A Processing-in-Memory Read Mapper for Compressing Next-Gen Sequencing Datasets

Florestan de Moor , Meven Mognol , Charles Deltel , Erwan Drezen , Julien Legriel et al.

BIBM 2024 - IEEE International Conference on Bioinformatics and Biomedicine, Dec 2024, Lisbonne, Portugal. pp.7176

Communication dans un congrès hal-04821180v1
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Dynamic sliding window encoding for data storageon DNA under biological and indexing constraints

Chloé Berton , Gouenou Coatrieux , Dominique Lavenier , Haddad S.

EUSIPCO 2023: 31st European Signal Processing Conference, Sep 2023, Helsiinki, Finland. pp.1-5, ⟨10.23919/EUSIPCO58844.2023.10289957⟩

Communication dans un congrès hal-04246615v1
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HairSplitter: separating strains in metagenome assemblies with long reads

Roland Faure , Jean-François Flot , Dominique Lavenier

JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané, France. pp.1-8

Communication dans un congrès hal-04272455v1

HairSplitter: assembling long reads in an unknown number of haplotypes

Roland Faure , Jean-François Flot , Dominique Lavenier

SeqBIM 2022 - Journées sur les Séquences en Bioinformatique, Informatique et Mathématiques, Nov 2022, Bordeaux, France

Communication dans un congrès hal-03864075v1
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Processing-in-Memory to speed up NGS analysis

Dominique Lavenier

SFA²F 2022 - Sequencing to Function: Analysis and Application for the Future, Jun 2022, Santa Fe, United States

Communication dans un congrès hal-03817360v1

A first proposal for secure data storage into DNA molecules compliant with biological constraints

Chloé Berton , Gouenou Coatrieux , Dominique Lavenier

DSMM 2022 - 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France

Communication dans un congrès hal-03817385v1
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Optimal Scaffolding for Chloroplasts' Inverted Repeats

Victor Epain , Rumen Andonov , Dominique Lavenier

JOBIM2022, Jul 2022, Rennes, France

Communication dans un congrès hal-03625229v1
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DNA Storage: Synthesis and Sequencing Semiconductor Technologies

Dominique Lavenier

IEDM 2022 - 68th Annual IEEE International Electron Devices Meeting, Dec 2022, San Francisco, United States. pp.1-4

Communication dans un congrès hal-03902786v1
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Experimental DNA storage platform

Olivier Boullé , Dominique Lavenier

DSMM 2022 - 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France. pp.1-1

Communication dans un congrès hal-03817374v1
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Optimal de novo assemblies for chloroplast genomes based on inverted repeats patterns

Rumen Andonov , Victor Epain , Dominique Lavenier

BiATA 2021 - 4th International conference Bioinformatics: from Algorithms to Applications, Jul 2021, St. Petersbourg, Russia. pp.1-2

Communication dans un congrès hal-03534195v1
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A Graph-Theoretic Barcode Ordering Model for Linked-Reads

Yoann Dufresne , Chen Sun , Pierre Marijon , Dominique Lavenier , Cedric Chauve et al.

WABI 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-03008334v1
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Variant Calling Parallelization on Processor-in-Memory Architecture

Dominique Lavenier , Remy Cimadomo , Romaric Jodin

BIBM 2020 - IEEE International Conference on Bioinformatics and Biomedicine, Dec 2020, Virtual, South Korea. pp.1-4

Communication dans un congrès hal-03006764v1
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Genotyping Structural Variations using Long Read data

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre

JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8

Communication dans un congrès hal-02288091v1
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Genotyping Structural Variations using Long Read Data

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre

HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3

Communication dans un congrès hal-02289484v1
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Statistically Significant Discriminative Patterns Searching

Hoang Son Pham , Gwendal Virlet , Dominique Lavenier , Alexandre Termier

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⟩

Communication dans un congrès hal-02190793v1
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Global optimization approach for circular and chloroplast genome assembly

Sébastien Francois , Rumen Andonov , Dominique Lavenier , Hristo Djidjev

BICoB 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-01666830v1
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Global Optimization for Scaffolding and Completing Genome Assemblies

Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev

International Network Optimization Conference , European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15

Communication dans un congrès hal-01499859v1
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Identifying Genetic Variant Combinations using Skypatterns

Hoang-Son Pham , Dominique Lavenier , Alexandre Termier

7th 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-01385614v1
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DNA Mapping using Processor-in-Memory Architecture

Dominique Lavenier , Jean-Francois Roy , David Furodet

Workshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics, Dec 2016, Shenzhen, China

Communication dans un congrès hal-01399997v1
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Global Optimization Methods for Genome Scaffolding

Sebastien François , Rumen Andonov , Hristo Djidjev , Dominique Lavenier

12th International Workshop on Constraint-Based Methods for Bioinformatics , Sep 2016, Toulouse, France

Communication dans un congrès hal-01385665v1
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Global Optimization for Scafolding and Completing Genome Assemblies

Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev

12th International Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France

Communication dans un congrès hal-01567134v1
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KLAST: fast and sensitive software to compare large genomic databanks on cloud

Ivaylo Petrov , Sébastien Brillet , Erwan Drezen , Sylvain Quiniou , L Antin et al.

World Congress in Computer Science, Computer Engineering, and Applied Computing, Jul 2015, Las Vegas,, United States

Communication dans un congrès hal-01235339v1
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Quality metrics for benchmarking sequences comparison tools

Erwan Drezen , Dominique Lavenier

9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Honrizonte, Brazil. pp.144-153

Communication dans un congrès hal-01088595v1
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Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths

Guillaume Chapuis , Hristo Djidjev , Rumen Andonov , Sunil Thulasidasan , Dominique Lavenier

IPDPS 2014, Manish Parashar, May 2014, Phoenix, United States

Communication dans un congrès hal-00905738v1
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COMMET: comparing and combining multiple metagenomic datasets

Nicolas Maillet , Guillaume Collet , Thomas Vannier , Dominique Lavenier , Pierre Peterlongo

IEEE BIBM 2014, Nov 2014, Belfast, United Kingdom

Communication dans un congrès hal-01080050v1
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Parallel seed-based approach to protein structure similarity detection

Guillaume Chapuis , Mathilde Le Boudic-Jamin , Rumen Andonov , Hristo Djidjev , Dominique Lavenier

PPAM 2013, Roman Wyrzykowski, Sep 2013, Varsovie, Poland

Communication dans un congrès hal-00881507v1
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FAssem : FPGA based Acceleration of De Novo Genome Assembly

Sharat Chandra Varma , Paul Kolin , M. Balakrishnan , Dominique Lavenier

Proceeding 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-00829055v1

Accelerating QTL mapping with graphics cards

Guillaume Chapuis , Olivier Filangi , Jean Michel Elsen , Dominique Lavenier , Pascale Le Roy

Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 516 p

Communication dans un congrès hal-01363562v1
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Compareads: comparing huge metagenomic experiments

Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo

RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil

Communication dans un congrès hal-00720951v1
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Biomanycores, open-source parallel code for many-core bioinformatics

Mathieu Giraud , Stéphane Janot , Jean-Frédéric Berthelot , Charles Deltel , Laetitia Jourdan et al.

Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria

Communication dans un congrès inria-00623390v1
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Parallel and memory-efficient reads indexing for genome assembly

Rayan Chikhi , Guillaume Chapuis , Dominique Lavenier

Parallel Bio-Computing 2011, Sep 2011, torun, Poland

Communication dans un congrès inria-00637536v1
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Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph

Rayan Chikhi , Dominique Lavenier

WABI 2011, Sep 2011, Sarrebruck, Germany. ⟨10.1007/978-3-642-23038-7_4⟩

Communication dans un congrès inria-00637535v1
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HLS Tools for FPGA : faster development with better performances

Alexandre Cornu , Steven Derrien , Dominique Lavenier

Proceeding of the 7th International Symposium on Applied Reconfigurable Computing, Feb 2011, Belfast, United Kingdom. pp.67-78

Communication dans un congrès hal-00637830v1

biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics

Jean-Frédéric Berthelot , Charles Deltel , Mathieu Giraud , Stéphane Janot , Laetitia Jourdan et al.

JOBIM 2011, Jul 2011, Paris, France

Communication dans un congrès hal-00637847v1

GPU Accelerted QTLMap

Guillaume Chapuis , Olivier Filangi , Pascale Le Roy , Jean-Michel Elsen , Dominique Lavenier

The 15th QTL-MAS workshop, May 2011, -, France

Communication dans un congrès hal-00637840v1
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SLICEE: A Service oriented middleware for intensive scientific computation

Jonathan Piat , François Moreews , Olivier Collin , Dominique Lavenier , Alexandre Cornu

SERVICES 2011, Jul 2011, WASHINGTON DC, United States

Communication dans un congrès inria-00638694v1
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Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform

van Hoa Nguyen , Alexandre Cornu , Dominique Lavenier

Reconfigurable Architectures Workshop - IPDPS, May 2009, Rome, Italy

Communication dans un congrès inria-00425237v1
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GPU accelerated Rna folding algorithm

Guillaume Rizk , Dominique Lavenier

9th International Conference on Computational Science, May 2009, Baton Rouge, United States. pp.1031

Communication dans un congrès hal-00425543v1
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c-GAMMA: Comparative Genome Analysis of Molecular Markers

Pierre Peterlongo , Jacques Nicolas , Dominique Lavenier , Raoul Vorc'H , Joël Querellou

Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩

Communication dans un congrès inria-00425373v1
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Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison

van Hoa Nguyen , Dominique Lavenier

6th IEEE International Conference on research, innovation & vision for the future, Jul 2008, Ho Chi Minh Ville, Vietnam

Communication dans un congrès inria-00321457v1
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Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture

Xioachun Ye , van Hoa Nguyen , Dominique Lavenier , Dongrui Fan

Ninth 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-00322732v1
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Comparaison intensive des séquences protéiques : indexation des banques et usage des instructions SIMD des microprocesseurs

van Hoa Nguyen , Dominique Lavenier

Journées Ouvertes Biologie Informatique Mathématiques - JOBIM, Jun 2008, Lille, France

Communication dans un congrès inria-00325020v1
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Parallelizing the ACGT OncoSimulator

Dominique Lavenier , Julien Jacques

3rd 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-00322703v1
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Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison

Dominique Lavenier

HiCOMB 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-00322696v1

GPU Accelerated RNA-RNA Interaction Algorithm

Guillaume Rizk , Dominique Lavenier

EMBnet, Sep 2008, Martina Franca, Italy

Communication dans un congrès inria-00323566v1
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Parallélisation de la recherche de similarités entre séquences protéiques sur GPU

van Hoa Nguyen , Dominique Lavenier

RenPar'18 : Rencontres francophones du Parallélisme, Feb 2008, Fribourg, Suisse

Communication dans un congrès inria-00321456v1
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Détection de domaines dans des séquences génomiques : un problème de couverture optimale

Philippe Veber , Sébastien Tempel , Rumen Andonov , Dominique Lavenier , Jacques Nicolas

FRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France

Communication dans un congrès hal-00186471v1
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Protein similarity search with subset seeds on a dedicated reconfigurable hardware

Pierre Peterlongo , Laurent Noé , Dominique Lavenier , Gilles Georges , Julien Jacques et al.

Parallel Bio-Computing, Sep 2007, Gdansk,, Poland

Communication dans un congrès inria-00178325v1
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Recherche dans les banques d'ADN par indexation parallèle

van Hoa Nguyen , Dominique Lavenier

RVIF, Feb 2006, HCM, Vietnam

Communication dans un congrès inria-00180372v1

Path-Equivalent Removal of Epsilon-Transitions

Dominique Lavenier , Philippe Veber , Mathieu Giraud

2006, pp.23--33, ⟨10.1007/11812128_4⟩

Communication dans un congrès istex hal-00107094v1
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Remix : une architecture pour la recherche dans les masses de données indexées

Gilles Georges , Steven Derrien , Stéphane Rubini , Frédéric Raimbault , Laurent Amsaleg et al.

Symposium en archichecture de machines (Sympa) 2006, Oct 2006, Perpignan, France. pp.142-153

Communication dans un congrès hal-00505589v1
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Seed-based Genomic Sequence Comparison using a FPGA/FLASH Accelerator

Dominique Lavenier , Liu Xinchun , Gilles Georges

International IEEE Conference on Field Programmable Technology, Dec 2006, Thailand. http://fpt.selfip.org/fpt06/program.php

Communication dans un congrès hal-00179994v1

Fine-Grained Parallelism for Genomic Computation

Dominique Lavenier

Conference on Parallel Processing for Scientific Computing, Feb 2006, United States

Communication dans un congrès hal-00179996v1
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Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles

Mathieu Giraud , Laurent Noé , Gregory Kucherov , Dominique Lavenier

MajecSTIC 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-00001036v1

Le projet GénoGRID : une grille expérimentale pour la génomique

Dominique Lavenier , Hugues Leroy , Michel Hurfin , Rumen Andonov , L. Mouchard et al.

Journées Ouvertes Biologie Informatique et Mathématiques, 2002, Saint Malo, France. pp.27-32

Communication dans un congrès hal-00465092v1
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Stockage d'information sur ADN

Dominique Lavenier , Marc Antonini

Le calcul à découvert, CNRS Editions, 2025, 978-2-271-15373-9

Chapitre d'ouvrage hal-05376118v1
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Délocaliser les calculs en mémoire : le concept « processing-in-memory »

Dominique Lavenier

CNRS Editions. Le calcul à découvert, pp.1-3, 2025, 978-2-271-15373-9

Chapitre d'ouvrage hal-05376135v1

Genome Assembly

Dominique Lavenier

From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics - SCIENCES - Bioinformatics - ISTE Wiley, 2022, 9781789450668

Chapitre d'ouvrage hal-03817447v1
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De Novo NGS Data Compression

Gaëtan Benoit , Claire Lemaitre , Guillaume Rizk , Erwan Drezen , Dominique Lavenier

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⟩

Chapitre d'ouvrage hal-01633718v1

GPU-accelerated shortest paths computations for planar graphs

Guillaume Chapuis , Hristo Djidjev , Dominique Lavenier , Rumen Andonov

Hamid Azad Advances in GPU Research and Practice , Elsevier, pp.774, 2016, 9780128037386

Chapitre d'ouvrage hal-01385634v1

GPU accelerated RNA folding algorithm

Dominique Lavenier , Guillaume Rizk , Sanjay Rajopadhye

Wen-mei W. Hwu. GPU Computing Gems, ELSEVIER, pp.560, 2011, ⟨10.1016/B978-0-12-384988-5.00014-0⟩

Chapitre d'ouvrage hal-00637827v1

Parallel Genomic Sequence Comparison

Dominique Lavenier

Parallel and Distributed Computing, INTECH, pp.273-290, 2010

Chapitre d'ouvrage hal-00531505v1

Seed-Based Parallel Protein SequenceComparison Combining Multithreading, GPU, and FPGA technologies

Dominique Lavenier , van Hoa Nguyen

Bioinformatics: High Performance Parallel Computer Architectures, Taylor & Francis Group / CRC Press, pp.181-202, 2010

Chapitre d'ouvrage hal-00531507v1

Bioinformatics Applications

Dominique Lavenier , Mathieu Giraud

Gokhale, 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-00000501v1
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Conception d'architectures systoliques integrées

Dominique Lavenier

Architectures Matérielles [cs.AR]. Université de Rennes 1 [UR1], 1997

HDR tel-01567436v1