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Dominique Lavenier

Researcher identifiers


CNRS Research Director GenScale team leader IRISA / INRIA Campus de Beaulieu 35042 Rennes cedex – France tel: (33) 2 99 84 72 17 – mail: – office: A114 #### Research Area - Bioinformatics, Genomic, NGS Processing - Data Structures, Optimisation - Parallelism, Computer Design


Stocker les données : la piste prometteuse de l’ADN

Dominique Lavenier , Marc Antonini , Yannick Rondelez , A.J. Genot
Interstices, 2023
Journal articles 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⟩
Journal articles hal-03790140v1
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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
Microbiology Resource Announcements, 2020, 9 (11), pp.e00129-20. ⟨10.1128/MRA.00129-20⟩
Journal articles hal-02532959v1
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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⟩
Journal articles hal-03032737v1
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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, inPress, pp.1-28. ⟨10.1142/S0219720019500148⟩
Journal articles hal-02151798v1
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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
Journal articles hal-03697534v1

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
Scientific Reports, 2018, 8 (1), pp.1-5. ⟨10.1038/s41598-018-26623-x⟩
Journal articles hal-01919836v1
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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
Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩
Journal articles hal-01588181v1
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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
Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩
Journal articles hal-01500475v1

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⟩
Journal articles 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
Nature Methods, 2017, 14 (11), pp.1063 - 1071. ⟨10.1038/nmeth.4458⟩
Journal articles 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
Genome Announcements, 2017, 5 (39), pp.e00957. ⟨10.1128/genomeA.00957-17⟩
Journal articles hal-01617890v1

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
Genome Announcements, 2016, 4 (4), pp.e00689-16. ⟨10.1128/genomeA.00689-16⟩
Journal articles hal-01385659v1
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Multiple comparative metagenomics using multiset k -mer counting

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath
PeerJ Computer Science, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩
Journal articles hal-01397150v1
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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
BMC Bioinformatics, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩
Journal articles hal-01214682v1

Combining execution pipelines to improve parallel implementation of HMMER on FPGA

Naeem Abbas , Steven Derrien , Sanjay Rajopadhye , Patrice Quinton , Alexandre Cornu
Microprocessors and Microsystems: Embedded Hardware Design , 2015, 39, pp.457-470. ⟨10.1016/j.micpro.2015.06.006⟩
Journal articles hal-01235328v1
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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⟩
Journal articles hal-01235331v1
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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⟩
Journal articles hal-01235348v1

Assembler un génome sur un pico-ordinateur

Dominique Lavenier
Biofutur, 2015, 34 (363)
Journal articles hal-01235355v1
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GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre
Bioinformatics, 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩
Journal articles hal-01088571v1
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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
Genome Announcements, 2014, 2 (1), pp.1. ⟨10.1128/genomeA.01176-13⟩
Journal articles hal-01019560v1
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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⟩
Journal articles 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⟩
Journal articles hal-00903794v1
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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
GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩
Journal articles hal-00868822v1
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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⟩
Journal articles 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
Journal articles 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
Genome Research, 2011, ⟨10.1101/gr.126599.111⟩
Journal articles inria-00637571v1
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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
BMC Genomics, 2010, 11 (1), pp.281. ⟨10.1186/1471-2164-11-281⟩
Journal articles inserm-00482283v1

GASSST: Global Alignment Short Sequence Search Tool

Guillaume Rizk , Dominique Lavenier
Bioinformatics, 2010, 26 (20), pp 2534-2540
Journal articles hal-00531499v1
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PLAST: parallel local alignment search tool for database comparison

van Hoa Nguyen , Dominique Lavenier
BMC Bioinformatics, 2009, 10, pp.24
Journal articles 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⟩
Journal articles inria-00426856v1

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⟩
Journal articles inria-00347594v1

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

Dominique Lavenier
Techniques de l'Ingénieur, 2008, November (IN89)
Journal articles inria-00347596v1
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Optimal neighborhood indexing for protein similarity search

Pierre Peterlongo , Laurent Noé , Dominique Lavenier , van Hoa Nguyen , Gregory Kucherov
BMC Bioinformatics, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩
Journal articles inria-00340510v1

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⟩
Journal articles inria-00178314v1
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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⟩
Journal articles inria-00271646v1

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
Bioinformatics, 2006, 22(16), pp.1948-1954
Journal articles hal-00090517v1

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

Dominique Lavenier
Interstices, 2005
Journal articles 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
Nucleic Acids Research, 2004, 32 (1), pp.17-24. ⟨10.1093/nar/gkg928⟩
Journal articles 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
Journal articles hal-02013412v1
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Dynamic sliding window encoding for data storage on DNA under biological and indexing constraints

Dominique Lavenier , Chloé Berton , Gouenou Coatrieux , Haddad S.
EUSIPCO, Sep 2023, Helsiinki, Finland
Conference papers hal-04246615v1
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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
Conference papers 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
Conference papers hal-03817374v1
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Optimal Scaffolding for Chloroplasts' Inverted Repeats

Victor Epain , Rumen Andonov , Dominique Lavenier
JOBIM2022, Jul 2022, Rennes, France
Conference papers hal-03625229v1

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
Conference papers hal-03864075v1

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
Conference papers hal-03817385v1
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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
Conference papers hal-03817360v1
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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
Conference papers 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
WABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩
Conference papers 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
Conference papers hal-03006764v1
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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
Conference papers hal-02289484v1
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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
Conference papers hal-02288091v1
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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⟩
Conference papers 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⟩
Conference papers 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
Conference papers hal-01499859v1
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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
Conference papers hal-01567134v1
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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
Conference papers 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
Conference papers hal-01385665v1
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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⟩
Conference papers hal-01385614v1
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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
World Congress in Computer Science, Computer Engineering, and Applied Computing, Jul 2015, Las Vegas,, United States
Conference papers hal-01235339v1
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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
Conference papers hal-01080050v1
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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
Conference papers hal-00905738v1
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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
Conference papers hal-01088595v1
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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
Conference papers hal-00829055v1
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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
Conference papers hal-00881507v1
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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
Conference papers hal-00720951v1

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
Conference papers hal-01363562v1 a repository of interoperable open-source code for many-core bioinformatics

Jean-Frédéric Berthelot , Charles Deltel , Mathieu Giraud , Stéphane Janot , Laetitia Jourdan
JOBIM 2011, Jul 2011, Paris, France
Conference papers hal-00637847v1
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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
Conference papers hal-00637830v1
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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
Conference papers inria-00638694v1

GPU Accelerted QTLMap

Guillaume Chapuis , Olivier Filangi , Pascale Le Roy , Jean-Michel Elsen , Dominique Lavenier
The 15th QTL-MAS workshop, May 2011, -, France
Conference papers hal-00637840v1
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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
Conference papers 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⟩
Conference papers inria-00637535v1
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Biomanycores, open-source parallel code for many-core bioinformatics

Mathieu Giraud , Stéphane Janot , Jean-Frédéric Berthelot , Charles Deltel , Laetitia Jourdan
Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria
Conference papers inria-00623390v1
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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⟩
Conference papers inria-00425373v1
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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
Conference papers 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
Conference papers hal-00425543v1
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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
Conference papers inria-00321456v1

GPU Accelerated RNA-RNA Interaction Algorithm

Guillaume Rizk , Dominique Lavenier
EMBnet, Sep 2008, Martina Franca, Italy
Conference papers inria-00323566v1
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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
Conference papers 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:
Conference papers hal-00322703v1
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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
Conference papers inria-00321457v1
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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 :
Conference papers hal-00322696v1
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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:
Conference papers hal-00322732v1
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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
Parallel Bio-Computing, Sep 2007, Gdansk,, Poland
Conference papers inria-00178325v1
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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
Conference papers hal-00186471v1

Fine-Grained Parallelism for Genomic Computation

Dominique Lavenier
Conference on Parallel Processing for Scientific Computing, Feb 2006, United States
Conference papers hal-00179996v1
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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
Symposium en archichecture de machines (Sympa) 2006, Oct 2006, Perpignan, France. pp.142-153
Conference papers 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.
Conference papers hal-00179994v1
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Recherche dans les banques d'ADN par indexation parallèle

van Hoa Nguyen , Dominique Lavenier
RVIF, Feb 2006, HCM, Vietnam
Conference papers inria-00180372v1

Path-Equivalent Removal of Epsilon-Transitions

Dominique Lavenier , Philippe Veber , Mathieu Giraud
2006, pp.23--33, ⟨10.1007/11812128_4⟩
Conference papers hal-00107094v1
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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
Conference papers inria-00001036v1

Le projet GénoGRID : une grille expérimentale pour la génomique

Dominique Lavenier , Hugues Leroy , Michel Hurfin , Rumen Andonov , L. Mouchard
Journées Ouvertes Biologie Informatique et Mathématiques, 2002, Saint Malo, France. pp.27-32
Conference papers hal-00465092v1

Genome Assembly

Dominique Lavenier
From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics - SCIENCES - Bioinformatics - ISTE Wiley, 2022, 9781789450668
Book sections 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⟩
Book sections 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
Book sections hal-01385634v1

GPU accelerated RNA folding algorithm

Dominique Lavenier , Guillaume Rizk , Sanjay Rajopadhye
Wen-mei W. Hwu. GPU Computing Gems, ELSEVIER, pp.560, 2011, ⟨10.0123849888⟩
Book sections hal-00637827v1

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
Book sections hal-00531507v1

Parallel Genomic Sequence Comparison

Dominique Lavenier
Parallel and Distributed Computing, INTECH, pp.273-290, 2010
Book sections hal-00531505v1

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
Book sections inria-00000501v1
Image document

Conception d'architectures systoliques integrées

Dominique Lavenier
Architectures Matérielles [cs.AR]. Université de Rennes 1 [UR1], 1997
Habilitation à diriger des recherches tel-01567436v1