Dominique Lavenier

According to our database, Dominique Lavenier authored at least 87 papers between 1988 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Dynamic Sliding Window Encoding for Data Storage on DNA Under Biological and Indexing Constraints.

Chloé Berton, Gouenou Coatrieux, Dominique Lavenier, Sahar Haddad

Proceedings of the 31st European Signal Processing Conference, 2023

2021

Constrained Consensus Sequence Algorithm for DNA Archiving.

Dominique Lavenier

CoRR, 2021

Channel Model with Memory for DNA Data Storage with Nanopore Sequencing.

Belaid Hamoum, Elsa Dupraz, Laura Conde-Canencia, Dominique Lavenier

Proceedings of the 11th International Symposium on Topics in Coding, 2021

2020

SVJedi: genotyping structural variations with long reads.

Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre

Bioinform., 2020

A Graph-Theoretic Barcode Ordering Model for Linked-Reads.

Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

Variant Calling Parallelization on Processor-in-Memory Architecture.

Dominique Lavenier, Remy Cimadomo, Romaric Jodin

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019

Complete assembly of circular and chloroplast genomes based on global optimization.

Rumen Andonov, Hristo N. Djidjev, Sebastien François, Dominique Lavenier

J. Bioinform. Comput. Biol., 2019

Statistically Significant Discriminative Patterns Searching.

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

Proceedings of the Big Data Analytics and Knowledge Discovery, 2019

2018

Global Optimization for Scaffolding and Completing Genome Assemblies.

Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo N. Djidjev

Electron. Notes Discret. Math., 2018

2017

Hardware acceleration of de novo genome assembly.

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

Int. J. Embed. Syst., 2017

De Novo NGS Data Compression.

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

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

Multiple comparative metagenomics using multiset <i>k</i>-mer counting.

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre

PeerJ Comput. Sci., 2016

Identifying Genetic Variant Combinations Using Skypatterns.

Hoang-Son Pham, Dominique Lavenier, Alexandre Termier

Proceedings of the 27th International Workshop on Database and Expert Systems Applications, 2016

DNA mapping using Processor-in-Memory architecture.

Dominique Lavenier, Jean-François Roy, David Furodet

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection.

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

Sci. Program., 2015

Combining execution pipelines to improve parallel implementation of HMMER on FPGA.

Naeem Abbas, Steven Derrien, Sanjay V. Rajopadhye, Patrice Quinton, Alexandre Cornu, Dominique Lavenier

Microprocess. Microsystems, 2015

All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters.

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

J. Parallel Distributed Comput., 2015

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.

Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk

BMC Bioinform., 2015

2014

Compression of high throughput sequencing data with probabilistic de Bruijn graph.

Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Guillaume Rizk

CoRR, 2014

GATB: Genome Assembly & Analysis Tool Box.

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier

Bioinform., 2014

Quality Metrics for Benchmarking Sequences Comparison Tools.

Erwan Drezen, Dominique Lavenier

Proceedings of the Advances in Bioinformatics and Computational Biology, 2014

Efficient Multi-GPU Computation of All-Pairs Shortest Paths.

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

Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014

Commet: Comparing and combining multiple metagenomic datasets.

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

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection.

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

J. Comput. Biol., 2013

DSK: <i>k</i>-mer counting with very low memory usage.

Guillaume Rizk, Dominique Lavenier, Rayan Chikhi

Bioinform., 2013

Seamless coarse grained parallelism integration in intensive bioinformatics workflows.

François Moreews, Dominique Lavenier

Proceedings of the 20th European MPI Users's Group Meeting, 2013

Parallel Seed-Based Approach to Protein Structure Similarity Detection.

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

Proceedings of the Parallel Processing and Applied Mathematics, 2013

FAssem: FPGA Based Acceleration of De Novo Genome Assembly.

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

Proceedings of the 21st IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2013

2012

Compareads: comparing huge metagenomic experiments.

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

BMC Bioinform., 2012

2011

Étude quantitative d'algorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite.

Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier

Tech. Sci. Informatiques, 2011

Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph.

Rayan Chikhi, Dominique Lavenier

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Parallel and Memory-Efficient Reads Indexing for Genome Assembly.

Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier

Proceedings of the Parallel Processing and Applied Mathematics, 2011

HLS Tools for FPGA: Faster Development with Better Performance.

Alexandre Cornu, Steven Derrien, Dominique Lavenier

Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011

2010

GASSST: global alignment short sequence search tool.

Guillaume Rizk, Dominique Lavenier

Bioinform., 2010

A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems.

Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier

Proceedings of the Reconfigurable Computing: Architectures, 2010

2009

PLAST: parallel local alignment search tool for database comparison.

Van Hoa Nguyen, Dominique Lavenier

BMC Bioinform., 2009

Paired-end read length lower bounds for genome re-sequencing.

Rayan Chikhi, Dominique Lavenier

BMC Bioinform., 2009

c-GAMMA: Comparative Genome Analysis of Molecular Markers.

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

Proceedings of the Pattern Recognition in Bioinformatics, 2009

Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform.

Van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

GPU Accelerated RNA Folding Algorithm.

Guillaume Rizk, Dominique Lavenier

Proceedings of the Computational Science, 2009

2008

Coding Region Prediction Based on a Universal DNA Sequence Representation Method.

Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau

J. Comput. Biol., 2008

Optimal neighborhood indexing for protein similarity search.

Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud

BMC Bioinform., 2008

Speeding up subset seed algorithm for intensive protein sequence comparison.

Van Hoa Nguyen, Dominique Lavenier

Proceedings of the 2008 IEEE International Conference on Research, 2008

Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture.

Xiaochun Ye, Van Hoa Nguyen, Dominique Lavenier, Dongrui Fan

Proceedings of the Ninth International Conference on Parallel and Distributed Computing, 2008

Ordered index seed algorithm for intensive DNA sequence comparison.

Dominique Lavenier

Proceedings of the 22nd IEEE International Symposium on Parallel and Distributed Processing, 2008

2007

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

Dominique Lavenier, Gilles Georges, Xinchun Liu

J. VLSI Signal Process., 2007

Path-Equivalent Developments in Acyclic Weighted Automata.

Mathieu Giraud, Philippe Veber, Dominique Lavenier

Int. J. Found. Comput. Sci., 2007

Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware.

Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, Mathieu Giraud

Proceedings of the Parallel Processing and Applied Mathematics, 2007

2006

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

Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, Jacques Nicolas

Bioinform., 2006

Path-Equivalent Removals of <i>epsilon</i>-transitions in a Genomic Weighted Finite Automaton.

Mathieu Giraud, Philippe Veber, Dominique Lavenier

Proceedings of the Implementation and Application of Automata, 2006

Seed-based genomic sequence comparison using a FPGA/FLASH accelerator.

Dominique Lavenier, Xinchun Liu, Gilles Georges

Proceedings of the 2006 IEEE International Conference on Field Programmable Technology, 2006

2005

Encodage linéaire d'automates pondérés. Filtrage de motifs génomiques et application sur l'architecture prototype R-disk.

Mathieu Giraud, Stéphane Guyetant, Dominique Lavenier

Tech. Sci. Informatiques, 2005

Du microprocesseur au circuit FPGA. Une analyse sous l'angle de la reconfiguration.

Raphaël David, Dominique Lavenier, Sébastien Pillement

Tech. Sci. Informatiques, 2005

Cluster of re-configurable nodes for scanning large genomic banks.

Stéphane Guyetant, Mathieu Giraud, Ludovic L'Hours, Steven Derrien, Stéphane Rubini, Dominique Lavenier, Frédéric Raimbault

Parallel Comput., 2005

Dealing with Hardware Space Limits when Removing Epsilon-Transitions in a Genomic Weighted Finite Automaton.

Mathieu Giraud, Dominique Lavenier

J. Autom. Lang. Comb., 2005

Dynamic programming for LR-PCR segmentation of bacterium genomes.

Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev

Concurr. Comput. Pract. Exp., 2005

A Low Complex Scheduling Algorithm for Multi-processor System-on-Chip.

Nicolas Ventroux, Frédéric Blanc, Dominique Lavenier

Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Networks, 2005

2004

Linear Encoding Scheme for Weighted Finite Automata.

Mathieu Giraud, Dominique Lavenier

Proceedings of the Implementation and Application of Automata, 2004

Dynamic Programming for LR-PCR Segmention of Bacterium Genomes.

Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev

Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

2003

ROOM. Des machines reconfigurables orientées objet pour les applications spécifiques.

Frédéric Raimbault, Dominique Lavenier

Tech. Sci. Informatiques, 2003

Experience with a Hybrid Processor: K-Means Clustering.

Maya B. Gokhale, Janette Frigo, Kevin McCabe, James Theiler, Christophe Wolinski, Dominique Lavenier

J. Supercomput., 2003

A Reconfigurable Parallel Disk System for Filtering Genomic Banks.

Dominique Lavenier, Stéphane Guyetant, Steven Derrien, Stéphane Rubini

Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms, June 23, 2003

2001

Mutable Functional Units and Their Applications on Microprocessors.

Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale

Proceedings of the 19th International Conference on Computer Design (ICCD 2001), 2001

Placing, Routing, and Editing Virtual FPGAs.

Loïc Lagadec, Dominique Lavenier, Erwan Fabiani, Bernard Pottier

Proceedings of the Field-Programmable Logic and Applications, 2001

Evaluation of the streams-C C-to-FPGA compiler: an applications perspective.

Janette Frigo, Maya B. Gokhale, Dominique Lavenier

Proceedings of the ACM/SIGDA International Symposium on Field Programmable Gate Arrays, 2001

Mutable Functional Units: Initial Results.

Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale

Proceedings of the 9th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, 2001

2000

An FPGA systolic array using pseudo-random bit generators for computing Goldbach partitions.

Dominique Lavenier

Integr., 2000

Placement of Linear Arrays.

Erwan Fabiani, Dominique Lavenier

Proceedings of the Field-Programmable Logic and Applications, 2000

1998

Computing Goldbach Partitions Using Pseudo-random Bit Generator Operators on a FPFA Systolic Array.

Dominique Lavenier, Yannick Saouter

Proceedings of the Field-Programmable Logic and Applications, 1998

1997

SAMBA: hardware accelerator for biological sequence comparison.

Pascale Guerdoux-Jamet, Dominique Lavenier

Comput. Appl. Biosci., 1997

Parallel Processing for Scanning Genomic Data-Bases.

Dominique Lavenier, Jean-Lin Pacherie

Proceedings of the Parallel Computing: Fundamentals, 1997

Conception d'architectures systoliques integrées.

Dominique Lavenier

, 1997

1996

Prototyping of VLSI components from a formal specification.

Roderick McConnell, Dominique Lavenier

J. VLSI Signal Process., 1996

Dedicated Hardware for Biological Sequence Comparison.

Dominique Lavenier

J. Univers. Comput. Sci., 1996

Design and Implementation of a Parallel Architecture for Biological Sequence Comparison.

Pascale Guerdoux-Jamet, Dominique Lavenier, Charles Wagner, Patrice Quinton

Proceedings of the Euro-Par '96 Parallel Processing, 1996

1995

I/O and computation overlap on SIMD systolic arrays.

Dominique Lavenier, Frédéric Raimbault, Patrice Frison

J. VLSI Signal Process., 1995

Systolic Filter for Fast DNA Similarity Search.

Pascale Guerdoux-Jamet, Dominique Lavenier

Proceedings of the International Conference on Application Specific Array Processors (ASAP'95), 1995

1994

From Equations to Hardware. Towards the Systematic Mapping of Algorithms onto Parallel Architectures.

Patrice Frison, François Charot, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Frédéric Raimbault, Charles Wagner

Int. J. Pattern Recognit. Artif. Intell., 1994

From behavioral to RTL models: an approach.

Dominique Lavenier, Roderick McConnell

Proceedings of IEEE 5th International Workshop on Rapid System Prototyping, 1994

1993

An integrated 2D systolic array for spelling correction.

Dominique Lavenier

Integr., 1993

RELACS for systolic programming.

Frédéric Raimbault, Dominique Lavenier

Proceedings of the International Conference on Application-Specific Array Processors, 1993

I/O data management on SIMD systolic arrays.

Patrice Frison, Dominique Lavenier, Frédéric Raimbault

Proceedings of the International Conference on Application-Specific Array Processors, 1993

1992

From Equations to Hardware: Towards Systematic Mapping of Algorithms onto Parallel Architectures.

François Charot, Patrice Frison, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Charles Wagner

Proceedings of the Parallel Image Analysis, Second International Conference, 1992

1991

A Fully Integrated Systolic Spelling Co-Processor.

Patrice Frison, Dominique Lavenier

Proceedings of the VLSI 91, 1991

Experience in the design of paralle processor arrays.

Patrice Frison, Dominique Lavenier

Proceedings of the Algorithms and Parallel VLSI Architectures II, 1991

1990

Designing specific systolic arrays with the API15C chip.

Patrice Frison, Eric Gautrin, Dominique Lavenier, J. L. Scharbarg

Proceedings of the Application Specific Array Processors, 1990

1988

Fast Machine for Prototyping String Correction Algorithms.

Patrice Frison, Dominique Lavenier

Proceedings of the Computer-Assisted Information Retrieval (Recherche d'Information et ses Applications), 1988