Dominique Lavenier

According to our database1, Dominique Lavenier
  • authored at least 74 papers between 1988 and 2017.
  • has a "Dijkstra number"2 of three.

Timeline

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Bibliography

2017
Hardware acceleration of de novo genome assembly.
IJES, 2017

2016
Multiple comparative metagenomics using multiset k-mer counting.
PeerJ Computer Science, 2016

Identifying Genetic Variant Combinations Using Skypatterns.
Proceedings of the 27th International Workshop on Database and Expert Systems Applications, 2016

DNA mapping using Processor-in-Memory architecture.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection.
Scientific Programming, 2015

Combining execution pipelines to improve parallel implementation of HMMER on FPGA.
Microprocessors and Microsystems - Embedded Hardware Design, 2015

All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters.
J. Parallel Distrib. Comput., 2015

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.
BMC Bioinformatics, 2015

2014
Compression of high throughput sequencing data with probabilistic de Bruijn graph.
CoRR, 2014

GATB: Genome Assembly & Analysis Tool Box.
Bioinformatics, 2014

Quality Metrics for Benchmarking Sequences Comparison Tools.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014

Efficient Multi-GPU Computation of All-Pairs Shortest Paths.
Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014

Commet: Comparing and combining multiple metagenomic datasets.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013
Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection.
Journal of Computational Biology, 2013

DSK: k-mer counting with very low memory usage.
Bioinformatics, 2013

Seamless coarse grained parallelism integration in intensive bioinformatics workflows.
Proceedings of the 20th European MPI Users's Group Meeting, 2013

Parallel Seed-Based Approach to Protein Structure Similarity Detection.
Proceedings of the Parallel Processing and Applied Mathematics, 2013

FAssem: FPGA Based Acceleration of De Novo Genome Assembly.
Proceedings of the 21st IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2013

2012
Compareads: comparing huge metagenomic experiments.
BMC Bioinformatics, 2012

2011
Étude quantitative d'algorithmes de stéréovision pour les systèmes embarqués d'aide à la conduite.
Technique et Science Informatiques, 2011

Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Parallel and Memory-Efficient Reads Indexing for Genome Assembly.
Proceedings of the Parallel Processing and Applied Mathematics, 2011

HLS Tools for FPGA: Faster Development with Better Performance.
Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011

2010
GASSST: global alignment short sequence search tool.
Bioinformatics, 2010

A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems.
Proceedings of the Reconfigurable Computing: Architectures, 2010

2009
PLAST: parallel local alignment search tool for database comparison.
BMC Bioinformatics, 2009

Paired-end read length lower bounds for genome re-sequencing.
BMC Bioinformatics, 2009

c-GAMMA: Comparative Genome Analysis of Molecular Markers.
Proceedings of the Pattern Recognition in Bioinformatics, 2009

Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

GPU Accelerated RNA Folding Algorithm.
Proceedings of the Computational Science, 2009

2008
Coding Region Prediction Based on a Universal DNA Sequence Representation Method.
Journal of Computational Biology, 2008

Optimal neighborhood indexing for protein similarity search.
BMC Bioinformatics, 2008

Speeding up subset seed algorithm for intensive protein sequence comparison.
Proceedings of the 2008 IEEE International Conference on Research, 2008

Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture.
Proceedings of the Ninth International Conference on Parallel and Distributed Computing, 2008

Ordered index seed algorithm for intensive DNA sequence comparison.
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.
VLSI Signal Processing, 2007

Path-Equivalent Developments in Acyclic Weighted Automata.
Int. J. Found. Comput. Sci., 2007

Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware.
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.
Bioinformatics, 2006

Path-Equivalent Removals of epsilon-transitions in a Genomic Weighted Finite Automaton.
Proceedings of the Implementation and Application of Automata, 2006

Seed-based genomic sequence comparison using a FPGA/FLASH accelerator.
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.
Technique et Science Informatiques, 2005

Du microprocesseur au circuit FPGA. Une analyse sous l'angle de la reconfiguration.
Technique et Science Informatiques, 2005

Cluster of re-configurable nodes for scanning large genomic banks.
Parallel Computing, 2005

Dealing with Hardware Space Limits when Removing Epsilon-Transitions in a Genomic Weighted Finite Automaton.
Journal of Automata, Languages and Combinatorics, 2005

Dynamic programming for LR-PCR segmentation of bacterium genomes.
Concurrency and Computation: Practice and Experience, 2005

A Low Complex Scheduling Algorithm for Multi-processor System-on-Chip.
Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Networks, 2005

2004
Linear Encoding Scheme for Weighted Finite Automata.
Proceedings of the Implementation and Application of Automata, 2004

Dynamic Programming for LR-PCR Segmention of Bacterium Genomes.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

2003
ROOM. Des machines reconfigurables orientées objet pour les applications spécifiques.
Technique et Science Informatiques, 2003

Experience with a Hybrid Processor: K-Means Clustering.
The Journal of Supercomputing, 2003

A Reconfigurable Parallel Disk System for Filtering Genomic Banks.
Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms, June 23, 2003

2001
Mutable Functional Units and Their Applications on Microprocessors.
Proceedings of the 19th International Conference on Computer Design (ICCD 2001), 2001

Placing, Routing, and Editing Virtual FPGAs.
Proceedings of the Field-Programmable Logic and Applications, 2001

Evaluation of the streams-C C-to-FPGA compiler: an applications perspective.
Proceedings of the ACM/SIGDA International Symposium on Field Programmable Gate Arrays, 2001

Mutable Functional Units: Initial Results.
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.
Integration, 2000

Placement of Linear Arrays.
Proceedings of the Field-Programmable Logic and Applications, 2000

1998
Computing Goldbach Partitions Using Pseudo-random Bit Generator Operators on a FPFA Systolic Array.
Proceedings of the Field-Programmable Logic and Applications, 1998

1997
SAMBA: hardware accelerator for biological sequence comparison.
Computer Applications in the Biosciences, 1997

Parallel Processing for Scanning Genomic Data-Bases.
Proceedings of the Parallel Computing: Fundamentals, 1997

Conception d'architectures systoliques integrées.
, 1997

1996
Prototyping of VLSI components from a formal specification.
VLSI Signal Processing, 1996

Dedicated Hardware for Biological Sequence Comparison.
J. UCS, 1996

Design and Implementation of a Parallel Architecture for Biological Sequence Comparison.
Proceedings of the Euro-Par '96 Parallel Processing, 1996

1995
I/O and computation overlap on SIMD systolic arrays.
VLSI Signal Processing, 1995

Systolic Filter for Fast DNA Similarity Search.
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.
IJPRAI, 1994

From behavioral to RTL models: an approach.
Proceedings of IEEE 5th International Workshop on Rapid System Prototyping, 1994

1993
An integrated 2D systolic array for spelling correction.
Integration, 1993

1992
From Equations to Hardware: Towards Systematic Mapping of Algorithms onto Parallel Architectures.
Proceedings of the Parallel Image Analysis, Second International Conference, 1992

1991
A Fully Integrated Systolic Spelling Co-Processor.
VLSI, 1991

Experience in the design of paralle processor arrays.
Proceedings of the Algorithms and Parallel VLSI Architectures II, 1991

1988
Fast Machine for Prototyping String Correction Algorithms.
Proceedings of the Computer-Assisted Information Retrieval (Recherche d'Information et ses Applications), 1988


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