Dominique Lavenier

94 papers A 5B 5C 8Misc 3Journal 42Unranked 29

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Dynamic Sliding Window Encoding for Secured DNA Data Storage Compliant With Biological and Indexing Constraints. IEEE Access Chloé Berton, Gouenou Coatrieux, Héléne Gasnier, Sahar Haddad, Reda Bellafqira, Dominique Lavenier
2025	J	`jnl`	De-Bruijn graph partitioning for scalable and accurate DNA storage processing. Bioinform. Florestan De Moor, Olivier Boulle, Dominique Lavenier
2025	J	`jnl`	Processing-in-memory for genomics workloads. CoRR William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz, Yoshihiro Shibuya, Dominique Lavenier, Irem Boybat, Klea Zambaku, Berkan Sahin, Mohammad Sadrosadati, Onur Mutlu, Abu Sebastian, Rayan Chikhi, The BioPIM Consortium, Can Alkan
2025	—	`conf`	Protein database search using Processing-in-Memory architecture. IPDPS (Workshops) Charly Airault, Charles Deltel, Florestan De Moor, Erwan Drezen, Meven Mognol, Dominique Lavenier
2024	—	`conf`	MiMyCS: A Processing-in-Memory Read Mapper for Compressing Next-Gen Sequencing Datasets. BIBM Florestan De Moor, Meven Mognol, Charles Deltel, Erwan Drezen, Julien Legriel, Dominique Lavenier
2024	B	`conf`	Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment. ICPP Meven Mognol, Dominique Lavenier, Julien Legriel
2023	—	`conf`	Dynamic Sliding Window Encoding for Data Storage on DNA Under Biological and Indexing Constraints. EUSIPCO Chloé Berton, Gouenou Coatrieux, Dominique Lavenier, Sahar Haddad
2021	—	`conf`	Channel Model with Memory for DNA Data Storage with Nanopore Sequencing. ISTC Belaid Hamoum, Elsa Dupraz, Laura Conde-Canencia, Dominique Lavenier
2021	J	`jnl`	Constrained Consensus Sequence Algorithm for DNA Archiving. CoRR Dominique Lavenier
2020	C	`conf`	A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi
2020	J	`jnl`	SVJedi: genotyping structural variations with long reads. Bioinform. Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre
2020	—	`conf`	Variant Calling Parallelization on Processor-in-Memory Architecture. BIBM Dominique Lavenier, Remy Cimadomo, Romaric Jodin
2019	J	`jnl`	Complete assembly of circular and chloroplast genomes based on global optimization. J. Bioinform. Comput. Biol. Rumen Andonov, Hristo N. Djidjev, Sebastien François, Dominique Lavenier
2019	B	`conf`	Statistically Significant Discriminative Patterns Searching. DaWaK Hoang-Son Pham, Gwendal Virlet, Dominique Lavenier, Alexandre Termier
2019	J	`jnl`	Statistically Significant Discriminative Patterns Searching. CoRR Hoang-Son Pham, Gwendal Virlet, Dominique Lavenier, Alexandre Termier
2018	J	`jnl`	Global Optimization for Scaffolding and Completing Genome Assemblies. Electron. Notes Discret. Math. Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo N. Djidjev
2017	—	`ch.`	De Novo NGS Data Compression. Algorithms for Next-Generation Sequencing Data Gaëtan Benoit, Claire Lemaitre, Guillaume Rizk, Erwan Drezen, Dominique Lavenier
2017	J	`jnl`	Hardware acceleration of de novo genome assembly. Int. J. Embed. Syst. B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan, Dominique Lavenier
2016	—	`conf`	DNA mapping using Processor-in-Memory architecture. BIBM Dominique Lavenier, Jean-François Roy, David Furodet
2016	—	`conf`	Identifying Genetic Variant Combinations Using Skypatterns. DEXA Workshops Hoang-Son Pham, Dominique Lavenier, Alexandre Termier
2016	J	`jnl`	Multiple comparative metagenomics using multiset PeerJ Comput. Sci. Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre
2015	J	`jnl`	All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters. J. Parallel Distributed Comput. Hristo N. Djidjev, Guillaume Chapuis, Rumen Andonov, Sunil Thulasidasan, Dominique Lavenier
2015	J	`jnl`	Combining execution pipelines to improve parallel implementation of HMMER on FPGA. Microprocess. Microsystems Naeem Abbas, Steven Derrien, Sanjay V. Rajopadhye, Patrice Quinton, Alexandre Cornu, Dominique Lavenier
2015	J	`jnl`	Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Sci. Program. Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier
2015	J	`jnl`	Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinform. Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk
2014	—	`conf`	Commet: Comparing and combining multiple metagenomic datasets. BIBM Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo
2014	J	`jnl`	Compression of high throughput sequencing data with probabilistic de Bruijn graph. CoRR Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Guillaume Rizk
2014	A	`conf`	Efficient Multi-GPU Computation of All-Pairs Shortest Paths. IPDPS Hristo N. Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier
2014	J	`jnl`	GATB: Genome Assembly & Analysis Tool Box. Bioinform. Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
2014	—	`conf`	Quality Metrics for Benchmarking Sequences Comparison Tools. BSB Erwan Drezen, Dominique Lavenier
2013	J	`jnl`	DSK: Bioinform. Guillaume Rizk, Dominique Lavenier, Rayan Chikhi
2013	Misc	`conf`	FAssem: FPGA Based Acceleration of De Novo Genome Assembly. FCCM B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan, Dominique Lavenier
2013	J	`jnl`	Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection. J. Comput. Biol. Guillaume Chapuis, Olivier Filangi, Jean-Michel Elsen, Dominique Lavenier, Pascale Le Roy
2013	—	`conf`	Parallel Seed-Based Approach to Protein Structure Similarity Detection. PPAM (2) Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier
2013	C	`conf`	Seamless coarse grained parallelism integration in intensive bioinformatics workflows. EuroMPI François Moreews, Dominique Lavenier
2012	J	`jnl`	Compareads: comparing huge metagenomic experiments. BMC Bioinform. Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
2011	—	`conf`	HLS Tools for FPGA: Faster Development with Better Performance. ARC Alexandre Cornu, Steven Derrien, Dominique Lavenier
2011	C	`conf`	Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. WABI Rayan Chikhi, Dominique Lavenier
2011	—	`conf`	Parallel and Memory-Efficient Reads Indexing for Genome Assembly. PPAM (2) Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier
2011	J	`jnl`	Étude quantitative d'algorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite. Tech. Sci. Informatiques Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier
2010	—	`conf`	A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems. ARC Mehdi Darouich, Stéphane Guyetant, Dominique Lavenier
2010	J	`jnl`	GASSST: global alignment short sequence search tool. Bioinform. Guillaume Rizk, Dominique Lavenier
2009	—	`conf`	GPU Accelerated RNA Folding Algorithm. ICCS (1) Guillaume Rizk, Dominique Lavenier
2009	A	`conf`	Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform. IPDPS Van Hoa Nguyen, Alexandre Cornu, Dominique Lavenier
2009	J	`jnl`	PLAST: parallel local alignment search tool for database comparison. BMC Bioinform. Van Hoa Nguyen, Dominique Lavenier
2009	J	`jnl`	Paired-end read length lower bounds for genome re-sequencing. BMC Bioinform. Rayan Chikhi, Dominique Lavenier
2009	—	`conf`	c-GAMMA: Comparative Genome Analysis of Molecular Markers. PRIB Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'h, Joël Querellou
2008	J	`jnl`	Coding Region Prediction Based on a Universal DNA Sequence Representation Method. J. Comput. Biol. Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau
2008	C	`conf`	Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture. PDCAT Xiaochun Ye, Van Hoa Nguyen, Dominique Lavenier, Dongrui Fan
2008	J	`jnl`	Optimal neighborhood indexing for protein similarity search. BMC Bioinform. Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud
2008	A	`conf`	Ordered index seed algorithm for intensive DNA sequence comparison. IPDPS Dominique Lavenier
2008	—	`conf`	Speeding up subset seed algorithm for intensive protein sequence comparison. RIVF Van Hoa Nguyen, Dominique Lavenier
2007	J	`jnl`	A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms. J. VLSI Signal Process. Dominique Lavenier, Gilles Georges, Xinchun Liu
2007	J	`jnl`	Path-Equivalent Developments in Acyclic Weighted Automata. Int. J. Found. Comput. Sci. Mathieu Giraud, Philippe Veber, Dominique Lavenier
2007	Misc	`conf`	Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware. PPAM Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, Mathieu Giraud
2006	J	`jnl`	Domain organization within repeated DNA sequences: application to the study of a family of transposable elements. Bioinform. Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, Jacques Nicolas
2006	C	`conf`	Path-Equivalent Removals of CIAA Mathieu Giraud, Philippe Veber, Dominique Lavenier
2006	—	`conf`	Seed-based genomic sequence comparison using a FPGA/FLASH accelerator. FPT Dominique Lavenier, Xinchun Liu, Gilles Georges
2005	—	`conf`	A Low Complex Scheduling Algorithm for Multi-processor System-on-Chip. Parallel and Distributed Computing and Networks Nicolas Ventroux, Frédéric Blanc, Dominique Lavenier
2005	J	`jnl`	Cluster of re-configurable nodes for scanning large genomic banks. Parallel Comput. Stéphane Guyetant, Mathieu Giraud, Ludovic L'Hours, Steven Derrien, Stéphane Rubini, Dominique Lavenier, Frédéric Raimbault
2005	J	`jnl`	Dealing with Hardware Space Limits when Removing Epsilon-Transitions in a Genomic Weighted Finite Automaton. J. Autom. Lang. Comb. Mathieu Giraud, Dominique Lavenier
2005	J	`jnl`	Du microprocesseur au circuit FPGA. Une analyse sous l'angle de la reconfiguration. Tech. Sci. Informatiques Raphaël David, Dominique Lavenier, Sébastien Pillement
2005	J	`jnl`	Dynamic programming for LR-PCR segmentation of bacterium genomes. Concurr. Comput. Pract. Exp. Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev
2005	J	`jnl`	Encodage linéaire d'automates pondérés. Filtrage de motifs génomiques et application sur l'architecture prototype R-disk. Tech. Sci. Informatiques Mathieu Giraud, Stéphane Guyetant, Dominique Lavenier
2004	A	`conf`	Dynamic Programming for LR-PCR Segmention of Bacterium Genomes. IPDPS Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev
2004	C	`conf`	Linear Encoding Scheme for Weighted Finite Automata. CIAA Mathieu Giraud, Dominique Lavenier
2003	—	`conf`	A Reconfigurable Parallel Disk System for Filtering Genomic Banks. Engineering of Reconfigurable Systems and Algorithms Dominique Lavenier, Stéphane Guyetant, Steven Derrien, Stéphane Rubini
2003	J	`jnl`	Experience with a Hybrid Processor: K-Means Clustering. J. Supercomput. Maya B. Gokhale, Janette Frigo, Kevin McCabe, James Theiler, Christophe Wolinski, Dominique Lavenier
2003	J	`jnl`	ROOM. Des machines reconfigurables orientées objet pour les applications spécifiques. Tech. Sci. Informatiques Frédéric Raimbault, Dominique Lavenier
2001	A	`conf`	Evaluation of the streams-C C-to-FPGA compiler: an applications perspective. FPGA Janette Frigo, Maya B. Gokhale, Dominique Lavenier
2001	C	`conf`	Mutable Functional Units and Their Applications on Microprocessors. ICCD Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale
2001	Misc	`conf`	Mutable Functional Units: Initial Results. FCCM Yan Solihin, Kirk W. Cameron, Yong Luo, Dominique Lavenier, Maya B. Gokhale
2001	B	`conf`	Placing, Routing, and Editing Virtual FPGAs. FPL Loïc Lagadec, Dominique Lavenier, Erwan Fabiani, Bernard Pottier
2000	J	`jnl`	An FPGA systolic array using pseudo-random bit generators for computing Goldbach partitions. Integr. Dominique Lavenier
2000	B	`conf`	Placement of Linear Arrays. FPL Erwan Fabiani, Dominique Lavenier
1998	B	`conf`	Computing Goldbach Partitions Using Pseudo-random Bit Generator Operators on a FPFA Systolic Array. FPL Dominique Lavenier, Yannick Saouter
1997	—	`book`	Conception d'architectures systoliques integrées. Dominique Lavenier
1997	—	`conf`	Parallel Processing for Scanning Genomic Data-Bases. PARCO Dominique Lavenier, Jean-Lin Pacherie
1997	J	`jnl`	SAMBA: hardware accelerator for biological sequence comparison. Comput. Appl. Biosci. Pascale Guerdoux-Jamet, Dominique Lavenier
1996	J	`jnl`	Dedicated Hardware for Biological Sequence Comparison. J. Univers. Comput. Sci. Dominique Lavenier
1996	—	`conf`	Design and Implementation of a Parallel Architecture for Biological Sequence Comparison. Euro-Par, Vol. I Pascale Guerdoux-Jamet, Dominique Lavenier, Charles Wagner, Patrice Quinton
1996	J	`jnl`	Prototyping of VLSI components from a formal specification. J. VLSI Signal Process. Roderick McConnell, Dominique Lavenier
1995	J	`jnl`	I/O and computation overlap on SIMD systolic arrays. J. VLSI Signal Process. Dominique Lavenier, Frédéric Raimbault, Patrice Frison
1995	—	`conf`	Systolic Filter for Fast DNA Similarity Search. ASAP Pascale Guerdoux-Jamet, Dominique Lavenier
1994	J	`jnl`	From Equations to Hardware. Towards the Systematic Mapping of Algorithms onto Parallel Architectures. Int. J. Pattern Recognit. Artif. Intell. Patrice Frison, François Charot, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Frédéric Raimbault, Charles Wagner
1994	C	`conf`	From behavioral to RTL models: an approach. RSP Dominique Lavenier, Roderick McConnell
1993	J	`jnl`	An integrated 2D systolic array for spelling correction. Integr. Dominique Lavenier
1993	—	`conf`	I/O data management on SIMD systolic arrays. ASAP Patrice Frison, Dominique Lavenier, Frédéric Raimbault
1993	—	`conf`	RELACS for systolic programming. ASAP Frédéric Raimbault, Dominique Lavenier
1992	—	`conf`	From Equations to Hardware: Towards Systematic Mapping of Algorithms onto Parallel Architectures. ICPIA François Charot, Patrice Frison, Eric Gautrin, Dominique Lavenier, Patrice Quinton, Charles Wagner
1991	—	`conf`	A Fully Integrated Systolic Spelling Co-Processor. VLSI Patrice Frison, Dominique Lavenier
1991	—	`conf`	Experience in the design of paralle processor arrays. Algorithms and Parallel VLSI Architectures Patrice Frison, Dominique Lavenier
1990	—	`conf`	Designing specific systolic arrays with the API15C chip. ASAP Patrice Frison, Eric Gautrin, Dominique Lavenier, J. L. Scharbarg
1988	—	`conf`	Fast Machine for Prototyping String Correction Algorithms. RIAO Patrice Frison, Dominique Lavenier