Dominique Lavenier

Publication Activity (10 Years)

Years Active: 1988-2024
Publications (10 Years): 19

Top Topics

Global Optimization

Top Venues

Publications

Meven Mognol, Dominique Lavenier, Julien Legriel
Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment. ICPP (2024)
Chloé Berton, Gouenou Coatrieux, Dominique Lavenier, Sahar Haddad
Dynamic Sliding Window Encoding for Data Storage on DNA Under Biological and Indexing Constraints. EUSIPCO (2023)
Dominique Lavenier
Constrained Consensus Sequence Algorithm for DNA Archiving. CoRR (2021)
Belaid Hamoum, Elsa Dupraz, Laura Conde-Canencia, Dominique Lavenier
Channel Model with Memory for DNA Data Storage with Nanopore Sequencing. ISTC (2021)
Dominique Lavenier, Remy Cimadomo, Romaric Jodin
Variant Calling Parallelization on Processor-in-Memory Architecture. BIBM (2020)
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi
A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI (2020)
Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre
SVJedi: genotyping structural variations with long reads. Bioinform. 36 (17) (2020)
Rumen Andonov, Hristo N. Djidjev, Sebastien François, Dominique Lavenier
Complete assembly of circular and chloroplast genomes based on global optimization. J. Bioinform. Comput. Biol. 17 (3) (2019)
Hoang-Son Pham, Gwendal Virlet, Dominique Lavenier, Alexandre Termier
Statistically Significant Discriminative Patterns Searching. CoRR (2019)
Hoang-Son Pham, Gwendal Virlet, Dominique Lavenier, Alexandre Termier
Statistically Significant Discriminative Patterns Searching. DaWaK (2019)
Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo N. Djidjev
Global Optimization for Scaffolding and Completing Genome Assemblies. Electron. Notes Discret. Math. 64 (2018)
B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan, Dominique Lavenier
Hardware acceleration of de novo genome assembly. Int. J. Embed. Syst. 9 (1) (2017)
Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre
-mer counting. PeerJ Comput. Sci. 2 (2016)
Dominique Lavenier, Jean-François Roy, David Furodet
DNA mapping using Processor-in-Memory architecture. BIBM (2016)
Hoang-Son Pham, Dominique Lavenier, Alexandre Termier
Identifying Genetic Variant Combinations Using Skypatterns. DEXA Workshops (2016)
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinform. 16 (2015)
Hristo N. Djidjev, Guillaume Chapuis, Rumen Andonov, Sunil Thulasidasan, Dominique Lavenier
All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters. J. Parallel Distributed Comput. 85 (2015)
Naeem Abbas, Steven Derrien, Sanjay V. Rajopadhye, Patrice Quinton, Alexandre Cornu, Dominique Lavenier
Combining execution pipelines to improve parallel implementation of HMMER on FPGA. Microprocess. Microsystems 39 (7) (2015)
Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier
Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Sci. Program. 2015 (2015)
Hristo N. Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier
Efficient Multi-GPU Computation of All-Pairs Shortest Paths. IPDPS (2014)
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Guillaume Rizk
Compression of high throughput sequencing data with probabilistic de Bruijn graph. CoRR (2014)
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
GATB: Genome Assembly & Analysis Tool Box. Bioinform. 30 (20) (2014)
Erwan Drezen, Dominique Lavenier
Quality Metrics for Benchmarking Sequences Comparison Tools. BSB (2014)
Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo
Commet: Comparing and combining multiple metagenomic datasets. BIBM (2014)
Guillaume Chapuis, Olivier Filangi, Jean-Michel Elsen, Dominique Lavenier, Pascale Le Roy
Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection. J. Comput. Biol. 20 (9) (2013)
B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan, Dominique Lavenier
FAssem: FPGA Based Acceleration of De Novo Genome Assembly. FCCM (2013)
François Moreews, Dominique Lavenier
Seamless coarse grained parallelism integration in intensive bioinformatics workflows. EuroMPI (2013)
Guillaume Rizk, Dominique Lavenier, Rayan Chikhi
-mer counting with very low memory usage. Bioinform. 29 (5) (2013)
Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier
Parallel Seed-Based Approach to Protein Structure Similarity Detection. PPAM (2) (2013)
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
Compareads: comparing huge metagenomic experiments. BMC Bioinform. 13 (S-19) (2012)
Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier
Étude quantitative d'algorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite. Tech. Sci. Informatiques 30 (5) (2011)
Rayan Chikhi, Dominique Lavenier
Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. WABI (2011)
Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier
Parallel and Memory-Efficient Reads Indexing for Genome Assembly. PPAM (2) (2011)
Alexandre Cornu, Steven Derrien, Dominique Lavenier
HLS Tools for FPGA: Faster Development with Better Performance. ARC (2011)
Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier
A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems. ARC (2010)
Guillaume Rizk, Dominique Lavenier
GASSST: global alignment short sequence search tool. Bioinform. 26 (20) (2010)
Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'h, Joël Querellou
c-GAMMA: Comparative Genome Analysis of Molecular Markers. PRIB (2009)
Van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier
Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform. IPDPS (2009)
Guillaume Rizk, Dominique Lavenier
GPU Accelerated RNA Folding Algorithm. ICCS (1) (2009)
Van Hoa Nguyen, Dominique Lavenier
PLAST: parallel local alignment search tool for database comparison. BMC Bioinform. 10 (2009)
Rayan Chikhi, Dominique Lavenier
Paired-end read length lower bounds for genome re-sequencing. BMC Bioinform. 10 (S-13) (2009)
Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau
Coding Region Prediction Based on a Universal DNA Sequence Representation Method. J. Comput. Biol. 15 (10) (2008)
Xiaochun Ye, Van Hoa Nguyen, Dominique Lavenier, Dongrui Fan
Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture. PDCAT (2008)
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud
Optimal neighborhood indexing for protein similarity search. BMC Bioinform. 9 (2008)
Van Hoa Nguyen, Dominique Lavenier
Speeding up subset seed algorithm for intensive protein sequence comparison. RIVF (2008)
Dominique Lavenier
Ordered index seed algorithm for intensive DNA sequence comparison. IPDPS (2008)
Dominique Lavenier, Gilles Georges, Xinchun Liu
A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms. J. VLSI Signal Process. 48 (3) (2007)
Mathieu Giraud, Philippe Veber, Dominique Lavenier
Path-Equivalent Developments in Acyclic Weighted Automata. Int. J. Found. Comput. Sci. 18 (4) (2007)
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, Mathieu Giraud
Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware. PPAM (2007)
Mathieu Giraud, Philippe Veber, Dominique Lavenier
-transitions in a Genomic Weighted Finite Automaton. CIAA (2006)
Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, Jacques Nicolas
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements. Bioinform. 22 (16) (2006)
Dominique Lavenier, Xinchun Liu, Gilles Georges
Seed-based genomic sequence comparison using a FPGA/FLASH accelerator. FPT (2006)
Mathieu Giraud, Dominique Lavenier
Dealing with Hardware Space Limits when Removing Epsilon-Transitions in a Genomic Weighted Finite Automaton. J. Autom. Lang. Comb. 10 (2/3) (2005)
Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev
Dynamic programming for LR-PCR segmentation of bacterium genomes. Concurr. Comput. Pract. Exp. 17 (14) (2005)
Mathieu Giraud, Stéphane Guyetant, Dominique Lavenier
Encodage linéaire d'automates pondérés. Filtrage de motifs génomiques et application sur l'architecture prototype R-disk. Tech. Sci. Informatiques 24 (6) (2005)
Nicolas Ventroux, Frédéric Blanc, Dominique Lavenier
A Low Complex Scheduling Algorithm for Multi-processor System-on-Chip. Parallel and Distributed Computing and Networks (2005)
Stéphane Guyetant, Mathieu Giraud, Ludovic L'Hours, Steven Derrien, Stéphane Rubini, Dominique Lavenier, Frédéric Raimbault
Cluster of re-configurable nodes for scanning large genomic banks. Parallel Comput. 31 (1) (2005)
Raphaël David, Dominique Lavenier, Sébastien Pillement
Du microprocesseur au circuit FPGA. Une analyse sous l'angle de la reconfiguration. Tech. Sci. Informatiques 24 (4) (2005)
Mathieu Giraud, Dominique Lavenier
Linear Encoding Scheme for Weighted Finite Automata. CIAA (2004)
Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev
Dynamic Programming for LR-PCR Segmention of Bacterium Genomes. IPDPS (2004)
Dominique Lavenier, Stéphane Guyetant, Steven Derrien, Stéphane Rubini
A Reconfigurable Parallel Disk System for Filtering Genomic Banks. Engineering of Reconfigurable Systems and Algorithms (2003)
Frédéric Raimbault, Dominique Lavenier
ROOM. Des machines reconfigurables orientées objet pour les applications spécifiques. Tech. Sci. Informatiques 22 (6) (2003)
Maya B. Gokhale, Janette Frigo, Kevin McCabe, James Theiler, Christophe Wolinski, Dominique Lavenier
Experience with a Hybrid Processor: K-Means Clustering. J. Supercomput. 26 (2) (2003)
Janette Frigo, Maya B. Gokhale, Dominique Lavenier
Evaluation of the streams-C C-to-FPGA compiler: an applications perspective. FPGA (2001)
Loïc Lagadec, Dominique Lavenier, Erwan Fabiani, Bernard Pottier
Placing, Routing, and Editing Virtual FPGAs. FPL (2001)
Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale
Mutable Functional Units and Their Applications on Microprocessors. ICCD (2001)
Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale
Mutable Functional Units: Initial Results. FCCM (2001)
Dominique Lavenier
An FPGA systolic array using pseudo-random bit generators for computing Goldbach partitions. Integr. 30 (1) (2000)
Erwan Fabiani, Dominique Lavenier
Placement of Linear Arrays. FPL (2000)
Dominique Lavenier, Yannick Saouter
Computing Goldbach Partitions Using Pseudo-random Bit Generator Operators on a FPFA Systolic Array. FPL (1998)
Pascale Guerdoux-Jamet, Dominique Lavenier
SAMBA: hardware accelerator for biological sequence comparison. Comput. Appl. Biosci. 13 (6) (1997)
Dominique Lavenier, Jean-Lin Pacherie
Parallel Processing for Scanning Genomic Data-Bases. PARCO (1997)
Roderick McConnell, Dominique Lavenier
Prototyping of VLSI components from a formal specification. J. VLSI Signal Process. 12 (2) (1996)
Dominique Lavenier
Dedicated Hardware for Biological Sequence Comparison. J. Univers. Comput. Sci. 2 (2) (1996)
Pascale Guerdoux-Jamet, Dominique Lavenier, Charles Wagner, Patrice Quinton
Design and Implementation of a Parallel Architecture for Biological Sequence Comparison. Euro-Par, Vol. I (1996)
Dominique Lavenier, Frédéric Raimbault, Patrice Frison
I/O and computation overlap on SIMD systolic arrays. J. VLSI Signal Process. 9 (3) (1995)
Pascale Guerdoux-Jamet, Dominique Lavenier
Systolic Filter for Fast DNA Similarity Search. ASAP (1995)
Dominique Lavenier, Roderick McConnell
From behavioral to RTL models: an approach. RSP (1994)
Patrice Frison, François Charot, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Frédéric Raimbault, Charles Wagner
From Equations to Hardware. Towards the Systematic Mapping of Algorithms onto Parallel Architectures. Int. J. Pattern Recognit. Artif. Intell. 8 (2) (1994)
Patrice Frison, Dominique Lavenier, Frédéric Raimbault
I/O data management on SIMD systolic arrays. ASAP (1993)
Dominique Lavenier
An integrated 2D systolic array for spelling correction. Integr. 15 (1) (1993)
Frédéric Raimbault, Dominique Lavenier
RELACS for systolic programming. ASAP (1993)
François Charot, Patrice Frison, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Charles Wagner
From Equations to Hardware: Towards Systematic Mapping of Algorithms onto Parallel Architectures. ICPIA (1992)
Patrice Frison, Dominique Lavenier
A Fully Integrated Systolic Spelling Co-Processor. VLSI (1991)
Patrice Frison, Dominique Lavenier
Experience in the design of paralle processor arrays. Algorithms and Parallel VLSI Architectures (1991)
Patrice Frison, Eric Gautrin, Dominique Lavenier, J. L. Scharbarg
Designing specific systolic arrays with the API15C chip. ASAP (1990)
Patrice Frison, Dominique Lavenier
Fast Machine for Prototyping String Correction Algorithms. RIAO (1988)