Publications

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Journals

Hardware Acceleration of De Novo Genome Assembly
S. Bogaraju, P. Kolin, M. Balakrishnan, D. Lavenier
International Journal of Embedded Systems, (IJES), Vol. 9, No. 1, 2017

Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021, Isolated from Clonal Clustered Cases in French Brittany
A. Meygret, P. Vincent, S. Moullec, J. Nacazume, Y. Adnani, D. Lavenier, S. Kayal, A. Faili.
Genome Announc 4(4):e00689-16, 2016

Multiple comparative metagenomics using multiset k-mer counting
G. Benoit​, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre,
PeerJ Computer Science, 2:e94, 2016

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk
BMC Bioinformatics, BMC Bioinformatics, 16:288, 2015

Parallel seed-based approach to multiple protein structure similarities detection
G Chapuis, M Le Boudic-Jamin, R Andonov, H Djidjev, D Lavenier
Scientific Programming, vol. 2015, Article ID 279715, 2015

All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters
H Djidjev, G Chapuis, R Andonov, S Thulasidasan, D Lavenier
Journal of Parallel and Distributed Computing, pp. 91-103, 2015

Combining execution pipelines to improve parallel implementation of HMMER on FPGA
N Abbas, S Derrien, S Rajopadhye, P Quinton, A Cornu, D Lavenier
Microprocessors and Microsystems 39 (7), 457-470, 2015

GATB: Genome Assembly & Analysis Tool Box
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P.Peterlongo, D. Lavenier
Bioinformatics, 0 (20): 2959-2961, 2014

Genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61
H Falentin, D Naquin, V Loux, F Barloy-Hubler, P Loubière, S Nouaille, D. Lavenier, P. Le Bourgeois, P. François, J. Schrenzel, D. Hernandez, S. Even, Y. Le Loir
Genome announcements 2 (1), e01176-13, 2014

DSK: k-mer counting with very low memory usage
G. Rizk, D. Lavenier, T. Chikhi
Bioinformatics, Volume 29, Issue 5, 2013

GPU accelerated QTL detection
G. Chapuis, O. Filangi, J.M. Elsen, D. Lavenier, P. Le Roy
Journal of Computational Biology, vol. 20, Issue 9, 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
K. R. Bradnam, J. N. Fass et al.
GigaScience, vol.2, 2013

Compareads: comparing huge metagenomic experiments
N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo
BMC Bioinformatics, 13 (Suppl 19):S10, 2012

Assemblathon 1: A competitive assessment of de novo short read assembly methods
D. A. Earl et al.
Genome Research, 21: 2224-2241, 2011

GASSST: Global Alignment Short Sequence Search Tool
G. Risk, D. Lavenier
Bioinformatics, vol 26, no 20, 2010

Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum
F. Legeai, G. Risk, T. Walsh, O. Edwards, K. Gordon, D. Lavenier, N. Leterme, A. Mereau, J. Nicolas, D. Tagu, S. Jaubert-Possamai
BMC Genomics, vol 11, no 281, 2010

Genome Sequence of the Pea Aphid Acyrthosiphon pisum
The International Aphid Genomic Consortium
PLOS Biology, vol 8, no 2, 2010

PLAST: parallel local alignment search tool for database comparison
V.H. Nguyen, D. Lavenier
BMC Bioinformatics, vol 10, no 329, 2009

Paired-end read length lower bounds for genome re-sequensing
R. Chikhi, D. Lavenier
BMC Bioinformatics, 10(Suppl 13):O2, 2009

Optimal neighborhood indexing for protein similarity search
P. Peterlongo, L. Noe, D. Lavenier, V.H. Nguyen, G. Kucherov, M. Giraud
BMC Bioinformatics, vol 9, no 534, 2008

Coding Region Prediction Based on a Universal DNA Sequence Representation Method
X. Jiang, D. Lavenier, S. Yau
Journal of Computational Biology, vol 15, no 10, 2008

Path-equivalent developments in acyclic weighted automata
M. Giraud, P. Veber, D. Lavenier
Internatinonal Journal of Foundations of Computer Science, vol 18, no 4, 2007

A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms
D. Lavenier, G. Georges, X. Liu
The Journal of VLSI signal processing systems. Special issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, vol 48, no 3, 2007

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements
S. Tempel, M. Giraud, D. Lavenier, IC. Lerman, AS. Valin, I. Couée, A. El Amrani, J. Nicolas
Bioinformatics, vol 22, no 16, 2006

Dynamic programming for LR-PCR segmentation of bacterium genomes
R. Andonov, D. Lavenier, P. Veber, N. Yanev
Concurrency and Computations: Practice and Experience, vol 17, no 14, 2005

Applying Complex Models on Genomic Data
P. Durand, D. Lavenier, M. Leborgne, A. Siegel, P. Veber, J. Nicolas
ERCIM News, vol , no 60, 2005

Cluster of re-configurable nodes for scanning large genomic bank
S. Guyetant, M. Giraud, L. L’Hours, S. Derrien, S. Rubini, D. Lavenier, F. Raimbault
Parallel Computing, vol 31, no 1, 2005

Dealing with hardware space limits when removing epsilon-transitions in a genomic weighted finite automaton
M. Giraud, D. Lavenier
Journal of Automata, Languages and Combinatorics (JALC), 10(2/3), 2005

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification
N. Ben Zakour, M. Gautier, R. Andonov, D. Lavenier, M-F. Cochet, P. Veber, A. Sorokin, Y. Le Loir
Nucleic Acids Research, vol 32, no 1, 2004

Early Experience with a Hybrid Processor: K-Means Clustering
M. Gokhale, J. Frigo, K. McKabe, J. Theiler, C. Wolinski, D. Lavenier
Journal of Supercomputing, vol 24, no 4, 2003

An FPGA Systolic Array Using Pseudo Random Bit Generator for Computing Goldbach Partitions
D. Lavenier
Integration, The VLSI Journal, vol 30, no 1, 2000

Speeding up genome computations with a systolic accelerator
D. Lavenier
SIAM news, vol 31, no 8, 1998

SAMBA: Hardware Accelerator for Biological Sequence Comparison
P. Guerdoux-Jamet, D. Lavenier
CABIOS, vol 13, no 6, 1997

Dedicated Hardware for Biological Sequence Comparison
D. Lavenier
Journal of Universal Computer Science, vol 2, no 2, 1996

Prototyping of VLSI Component from a Formal Verification
R. McConnell, D. Lavenier
Journal of VLSI Signal Processing, vol 12, no 1, 1996

I/O and Computation Overlap on SIMD Systolic Arrays
D. Lavenier, F. Raimbault, P. Frison
Journal of VLSI Signal Processing, vol 9, no 3, 1995

From equations to hardware. Towards the systematic mapping of algorithms onto parallel architectures
F. Charot, P. Frison, E. Gautrin, D. Lavenier, P. Quinton, C. Wagner
International Journal of Pattern Recognition and Artificial Intelligence, vol 8, no 2, 1994

An Integrated 2D Systolic Array for Spelling Correction
D. Lavenier
Integration, the VLSI Journal, vol 15, no 4, 1993

Book Chapters

G. Chapuis, H. Djidjev, D. Lavenier, R. Andonov
GPU-accelerated shortest paths computations for planar graphs
in Advances in GPU Research and Practice, chap 11, 2016

GPU accelerated RNA folding algorithm
G. Rizk, D. Lavenier, S. Rajopadhye
GPU Computing Gems Vol. 1, chapter 14, editor: NVIDIA, publisher: Addison-Wesley, 2011

Seed-Based Parallel Protein Sequence Comparison Combining Multithreading, GPU, and FPGA technologies
D. Lavenier, V-H. Hnguyen
Bioinformatics: High Performance Parallel Computer Architectures, chapter 9, editor: B. Schmidt, publisher: Taylor & Francis/CRC Press, 2010

Parallel Genomic Sequence Comparison
D. Lavenier
Parallel and Distributed Computing, chapter 14, IN-TECH, 2010

Conferences

KLAST: fast and sensitive software to compare large genomic databanks on cloud
I. Petrov, S. Brillet, E. Drezen, S. Quiniou, L. Antin, P. Durand, D. Lavenier
BIOCOMP’15, International Conference on Bioinformatics and
Computational Biology, 2015, Las Vegas

Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths
G. Chapuis, H. Djidjev, R. Andonov, S. Thulasidasan, D. Lavenier
28th IEEE International Parallel & Distributed Processing Symposium, May 19-23, PHOENIX (Arizona) USA, 2014

COMMET: comparing and combining multiple metagenomic datasets
N Maillet, G Collet, T Vannier, D Lavenier, P Peterlongo
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, 2-5 nov. 2014

FAssem: FPGA Based Acceleration of De Novo Genome Assembly
B. Sharat Chandra Varma, P. Kolin, M. Balakrishnan, D. Lavenier
Proceeding of The 21st Annual International IEEE Symposium on Field Programmable Custom Computing Machines, 2013

Parallel seed-based approach to protein structure similarity detection
G. Chapuis1, M. Le Boudic-Jamin, R. Andonov, H. Djidjev, D. Lavenier
10th International Conference on Parallel Processing and Applied Mathematics, Parallel Bio-Computing, 2013

Seamless coarse grained parallelism integration in intensive bioinformatics workflows
F. Moreews, D. Lavenier
International Workshop on Parallelism in Bioinformatics, 2013

Parallel and memory-efficient reads indexing for genome assembly
R. Chikhi, G. Chapuis, D. Lavenier
Parallel Processing and Applied Mathematics, LNCS Vol. 7204, 2012, pp 272-280

Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph
R. Chikhi, D. Lavenier
Algorithms in Bioinformatics, LNCS Vol. 6833, 2011, pp 39-48

HLS Tools for FPGA : faster development with better performances
A. Cornu, S. Derrien, D. Lavenier
Reconfigurable Computing: Architectures, Tools and Applications, LNCS Vol. 6578, 2011, pp 67-78

SLICEE: A Service oriented middleware for intensive scientific computation
J. Piat, F. Moreews, O. Collin, A. Cornu, D. Lavenier
World Congress on Services, 2011

A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems
M. Darouich1, S. Guyetant, D. Lavenier
International Symposium on Applied Reconfigurable Computing, 2010

c-GAMMA: comparative genome analysis of molecular markers, Pattern Recognition in Bioinformatics
P. Perterlongo, J. Nicolas, D. Lavenier, R. Vorc h, J. Querellou
Lecture Notes in Computer Science Volume 5780, 2009, pp 255-269

Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform
V.H. Nguyen, A. Cornu, D. Lavenier
IPDPS, Reconfigurable Architectures Workshop, 2009

GPU accelerated Rna folding algorithm
G. Rizk, D. Lavenier
Computational Science, ICCS 2009, Lecture Notes in Computer Science Volume 5544, 2009, pp 1004-1013

GPU accelerated Rna-Rna interaction algorithm
G. Rizk, D. Lavenier
EMB Conference 2008: Leading Applications and Technologies in bioinformatics, 2008

Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture
Y. Xiaochun, V-H. Nguyen, D. Lavenier, F. Dongruy
Ninth International Conference on Parallel and Distributed Computing, Applications and Technologies, 2008

Parallelizing the ACGT OncoSimulator
D. Lavenier, J. Jacques
International Advanced Research Workshop on In Silico Oncology: Advances and Challenges, 2008

Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison
V-H. Nguyen, D. Lavenier
International Conference on research, innovation & vision for the future, 2008

Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison
D. Lavenier
IEEE International Workshop on High Performance Computational Biology, 2008

Utilization of Subset Seeds on a Reconfigurable Architecture
M. Giraud, G. Kucherov, D. Lavenier, L. Noé, P. Peterlongo
London Algorithm Workshop, 2007

Protein similarity search with subset seeds on a dedicated reconfigurable hardware,
P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, M. Giraud
Parallel Bio-Computing Workshop, 2007

Seed-based Genomic Sequence Comparison using a FPGA/FLASH Accelerator
D. Lavenier, X. Xinchun, G. Georges
International IEEE Conference on Field Programmable Technology, 2006

Path-Equivalent Removals of Epsilon-Transitions in a Genomic Weighted Finite Automaton
M. Giraud, P. Veber, D. Lavenier
International Conference on implementation and application of Automata, 2006

A Low Complex Scheduling Algorithm for Multi-Processor System-on-Chip
N. Ventroux, D. Lavenier
International Conference on Parallel and Distributed Computing and Networks, 2005

Linear Encoding Scheme for Weighted Finite Automata
M. Giraud, D. Lavenier
Implementation and Application of Automata, Lecture Notes in Computer Science Volume 3317, 2005, pp 146-155

Dynamic programming for LR-PCR segmention of bacterium genomes
R. Andonov, D. Lavenier, P. Veber, N. Yanev
International Workshop on High Performance Computational Biology, 2004

Evaluation of anchoring scheme for fast DNA Sequence Alignment
S. Guyétant, D. Lavenier
European Conference on Computational Biology, 2003

GENOFRAG: a software to design primers optimized for whole genome scaning by long-range PCR amplification. Application to the study of Staphylococcus aureus genome plasticity
N. Ben Zacour, M. Gautier, R. Andonov, D. Lavenier, P. Veber, A. Sorokin, Y. Le Loir
European Conference on Computational Biology, 2003

A reconfigurable parallel disk system for filtering genomic banks
D. Lavenier, D. Guyétant, S. Derrien, S. Rubini
Engineering of Reconfigurable Systems and Algorithms, 2003

GénoGRID: an experimental grid for genomic applications
D. Lavenier, H. Leroy, M. Mac Wing, R. Andonov, M. Hurfin, P. Raipin-Parvedy, L. Mouchard, F. Guinand
HealthGrid Conference, 2003

Placing, Routing and Editing Virtual FPGAs
L. Lagadec, D. Lavenier, E. Fabiani, B. Pottier
Field-Programmable Logic and Applications, Lecture Notes in Computer Science Volume 2147, 2001, pp 357-366

Mutable Functional Units and their Applications on Microprocessors
Y. Solihin, K. Cameron, Y. Luo, D. Lavenier, M. Gokhale
International Conference on Computer Design, 2001

Systolic Array for computing the pixel purity index (PPI) algorithm on hyperspectral images
D. lavenier, E. Fabiani, S. Derrien, C. Wagner
SPIE Conference on Imaging Spectrometry, 2001

Experimental evaluation of place-and-route of regular arrays on Xilinx chips
E. Fabiani, D. Lavenier
International Conference on Engineering of Reconfigurable Systems and Algorithms, 2001

Early Experience with a Hybrid Processor: K-Means Clustering
M. Gokhale, J. Frigo, K. McCabe, J. Theiler, D. Lavenier
International Conference on Engineering of Reconfigurable Systems and Algorithms, 2001

Mutable Functional Units: Initial Results
Y. Solihin, K. Cameron, Y. Luo, D. Lavenier, M. Gokhale
IEEE Symposium on Field-Programmable Custom Computing Machines, 2001

Evaluation of the Streams-C C-to-FPGA Compiler: An Application Perspective
J. Frigo, M. Gokhale, D . Lavenier
ACM International Symposium on Field-Programmable Gate Arrays, 2001

FPGA Implementation of the Pixel Purity Index Algorithm
D. Lavenier, J. Theiler, J. Szymanski, M. Gokhale, J. Frigo
Workshop on Reconfigurable Architectures, 2000

Advanced processing for high-bandwith sensor systems
J. Szymanski, P. Blain, J. Bloch, C. Brislawn, S. Brumby, M. Caffrey, M. Dunham, J. Frigo, M. Gokhale, N. Harvey, G. Kenyon, W. Kim, J. Layne, D. Lavenier, K. McCabe, M. Mitchell, K. Moore, S. Perkins, R. Porter, S. Robinson, A. Salazar, J. Theiler, A. Young
SPIE International Conference on Optical Science and Technology, 2000

Using blocks of skewers for faster computation of pixel purity index
J. Theiler, D. Lavenier, N. Harvey, S. Perkins, J. Szymanski
SPIE International Conference on Optical Science and Technology, 2000

Placement of Linear Arrays
E. Fabiani, D. Lavenier,
International Conference on Field Programmable Logic and Applications, 2000

Reconfigurable Arithmetic and Logic Unit
D. Lavenier, Y. Solihin, K. Cameron
Symposium en Architecture de Machines, 2000

A systematic approach for investigating primary iron overloads : Generation of iron-related SNPs
J. Mosser, N. Soriano, F. Wojcik, V. Douabin, H. Ferran, S. Sachot, D. Lavenier, R. Moirand, Y. Deugnier, JY. Le Gall, V. David
Annual Meeting of the American Society of Human Genetics Applications, 1999

Loop Parallelization on a Reconfigurable Coprocessor
E. Fabiani, D. Lavenier, L. Perraudeau
Workshop on Design, Test and Applications, 1998

Computing Goldbach partitions using pseudo-random bit generator operators on a FPGA systolic array,
D. Lavenier, Y. Saouter
International Conference on Field Programmable Logic and Applications, 1998

Parallel Processing for Scanning Genomic Data-Bases
D. Lavenier, JL. Pacherie
International Conference on Parallel Computing, 1997

Design and Implementation of a Parallel Architecture for Biological Sequence Comparison
P. Guerdoux-Jamet, D. Lavenier, C. Wagner, P. Quinton
European Conference on Parallelism, 1996

Systolic Filter for fast DNA Similarity Search
P. Guerdoux-Jamet, D. Lavenier
International Conference on Application Specific Array Processors, 1995

From High Level Programming Model to FPGA Machines
JP. Banâtre, D. Lavenier, M. Viellot
IEEE Symposium on FPGAs for Custom Computing Machine, 1994

An Integrated 2-D Systolic Array for String Comparison

D. Lavenier
First South American Workshop on String Processing, 1993

Relacs for Systolic Programming
F. Raimbault, D. Lavenier
International Conference on Application Specific Array Processors, 1993

I/O Data Management on SIMD Systolic Arrays
P.Frison, D. Lavenier, F. Raimbault
International Conference on Application Specific Array Processors, 1993

Fine grain parallelism on a MIMD machine using FPGAs
D. Lavenier, B. Pottier, F. Raimbault, S. Rubini
IEEE Symposium on FPGAs for Custom Computing Machine, 1993

A High Performance Systolic Chip for Spelling Correction
D. Lavenier
Euro-Asic Conference 1992

Experience in the Design of Parallel Processor Arrays
P. Frison, D. Lavenier
Internationnal Workshop on Algorithms and Parallel VLSI Architectures, 1991

A Fully Integrated Systolic Spelling Co-processor
P. Frison, D. Lavenier
VLSI Conference, 1991

Designing Specific Systolic Array with the API15C chip
P. Frison, E. Gautrin, D. Lavenier, J-L. Scharbarg
Application Specifique Array Processor Conference, Princeton, NJ, USA, 1990

High Rate Sigma Filtering, Feasibility Studies on Processors Networks
D. Lavenier, B. Pottier
Workshop on Parallel Architectures on Silicon, Grenoble, France, 1989

A VLSI Programmable Systolic Architecture
P. Frison, D. Lavenier, H. Leverge, P. Quinton
International Conference on Systolic Array, Killarney, 1989

API15C A Programmable Chip for Systolic Architecture
P. Frison, E. Gautrin, D. Lavenier, J-L. Scharbarg
Workshop on Parallel Architectures on Silicon, 1989

A VLSI Systolic Machine for String Correction
P. Frison, D. Lavenier
International Conference on Supercomputing, 1988

A Fast Machine for Prototyping Correction Algorithms
P. Frison, D. Lavenier
User Oriented Contend-based text and Image Handling Conference, 1988

Communications

Reports

French corner

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