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JOURNALS
CHAPTERS
CONFERENCES
REPORTS
LIVRES
REVUES
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VULGARISATION
BREVETS
Last Publications
2011
A. Cornu, S. Derrien, D. Lavenier, How to accelerate genomic sequence alignment 4X using half an FPGA, EE Times Design, vol 7, no 5, 2011 [link]
R. Chikhi, D. Lavenier, Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph, LNCS, Algorithms in Bioinformatics , vol 6833, 2011 [link]
D. A. Earl et al., Assemblathon 1: A competitive assessment of de novo short read assembly methods, Genome Research, 2011 [link]
G. Rizk, D. Lavenier, S. Rajopadhye, GPU accelerated RNA folding algorithm, GPU Computing Gems Vol. 1, chapter 14, editor: NVIDIA, publisher: Addison-Wesley, 2011 [link]
R. Chikhi, G. Chapuis, D. Lavenier, Parallel and memory-efficient reads indexing for genome assembly, Workshop on Parallel Computational Biology , Torun, Poland, 2011 [pdf] [link]
N. Maillet, D. Lavenier, P. Peterlongo, Comparison of large scale metagenomic data in Tara Oceans project, Conférences Jacques-Monod, Integrative ecological genomics, Roscoff, France, 2011 [pdf] [link]
JF. Berthelot, C. Deltel, M. Giraud, S. Janot,L. Jourdan, D. Lavenier, H. Touzet, JF. Viarré, biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics, Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Paris, France, 2011 [pdf] [link]
M. Giraud, S. Janot, JF. Berthelot, C. Deltel, L. Jourdan, D. Lavenier, H. Touzet, JF. Viarré, Biomanycores, open-source parallel code for many-core bioinformatics, 12th Annual Bioinformatics Open Source Conference (BOSC 2011), Vienna, Austria, 2011 [pdf] [link]
J. Piat, F. Moreews, O. Collin, A. Cornu, D. Lavenier, SLICEE: A Service oriented middleware for intensive scientific computation, 7th IEEE 2011 World Congress on Services (SERVICES 2011), Washington DC, USA, 2011 [pdf] [link]
G. Chapuis, O. Filangi, P. Leroy, JM. Elsen, D. Lavenier, GPU Accelerted QTLMap, 15Th QTL-MAS Workshop, Rennes, France, 2011 [pdf] [link]
A. Cornu, S. Derrien, D. Lavenier, HLS Tools for FPGA : faster development with better performances, The 7th International Symposium on Applied Reconfigurable Computing, Queen's University of Belfast, 2011 [pdf] [link]
2010
G. Risk, D. Lavenier, GASSST: Global Alignment Short Sequence Search Tool, Bioinformatics, vol 26, no 20, 2010 [link]
F. Legeai, G. Risk, T. Walsh, O. Edwards, K. Gordon, D. Lavenier, N. Leterme, A. Mereau, J. Nicolas, D. Tagu, S. Jaubert-Possamai, Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum, BMC Genomics, vol 11, no 281, 2010 [link]
The International Aphid Genomic Consortium, Genome Sequence of the Pea Aphid Acyrthosiphon pisum, PLOS Biology, vol 8, no 2, 2010 [link]
D. Lavenier, V-H. Hnguyen, Seed-Based Parallel Protein SequenceComparison Combining Multithreading, GPU, and FPGA technologies, Bioinformatics: High Performance Parallel Computer Architectures, chapter 9, editor: B. Schmidt, publisher: Taylor & Francis/CRC Press, 2010 [link]
D. Lavenier, Parallel Genomic Sequence Comparison, Parallel and Distributed Computing, chapter 14, editor: Alberto Ros Bardisa, publisher: IN-TECH, 2010 [link]
M. Darouich1, S. Guyetant, D. Lavenier, A Reconfigurable Disparity Engine for Stereovision in Advanced Driver Assistance Systems, The 6th International Symposium on Applied Reconfigurable Computing (ARC), Bangkok, Thailand , 2010 [pdf] [link]
2009
V.H. Nguyen, D. Lavenier, PLAST: parallel local alignment search tool for database comparison, BMC Bioinformatics, vol 10, no 329, 2009 [link]
R. Chikhi, D. Lavenier, Paired-end read length lower bounds for genome re-sequensing, ISMB / ECCB, Stockholm, 2009 [link]
P. Perterlongo, J. Nicolas, D. Lavenier, R. Vorc h, J. Querellou, c-GAMMA: comparative genome analysis of molecular markers, 4th IAPR International Conference on Pattern Recognition in Bioinformatics, LNCS 5780 , Sheffield, UK, 2009 [pdf]
V.H. Nguyen, A. Cornu, D. Lavenier, Implementing protein seed-based comparison algorithm on the SGI RASC-100 platform, IPDPS, 16th Reconfigurable Architectures Workshop , Rome, Italy, 2009 [pdf]
G. Rizk, D. Lavenier, GPU accelerated Rna folding algorithm, International Conference on Computational Science, LNCS 5544, Baton Rouge, Louisiana, U.S.A., 2009 [pdf]
2008
P. Peterlongo, L. Noe, D. Lavenier, V.H. Nguyen, G. Kucherov, M. Giraud, Optimal neighborhood indexing for protein similarity search, BMC Bioinformatics, vol 9, no 534, 2008 [link]
X. Jiang, D. Lavenier, S. Yau, Coding Region Prediction Based on a Universal DNA Sequence Representation Method, Journal of Computational Biology, vol 15, no 10, 2008 [link]
G. Rizk, D. Lavenier, GPU accelerated Rna-Rna interaction algorithm, EMB Conference 2008: Leading Applications and Technologies in bioinformatics, Martina Franka (Taranto), Italy, 2008 [link]
Y. Xiaochun, V-H. Nguyen, D. Lavenier, F. Dongruy, Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture, Ninth International Conference on Parallel and Distributed Computing, Applications and Technologies, Dunedin, New Zealand, 2008 [pdf]
D. Lavenier, J. Jacques, Parallelizing the ACGT OncoSimulator, 3rd International Advanced Research Workshop on In Silico Oncology: Advances and Challenges, Istanbul, Turkey, 2008 [pdf]
V-H. Nguyen, D. Lavenier, Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison, 6th International Conference on research, innovation & vision for the future, Ho Chi Minh Ville, Vietnam, 2008 [pdf]
D. Lavenier, Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison, HiComb 2008: IEEE International Workshop on High Performance Computational Biology, Miami, Florida, 2008 [pdf]
A. Cornu, F. Dussaugey, D. Lavenier, Parallel Reconfigurable Operator for Genomic Sequence Comparison: Architecture and Performance analyses, INRIA report RR-6776, 2008 [link]
V.H. Nguyen, D. Lavenier, Fine-grained parallelization of similarity search between protein sequences, INRIA report RR-6513, 2008 [link]
2007
M. Giraud, P. Veber, D. Lavenier, Path-equivalent developments in acyclic weighted automata, Internatinonal Journal of Foundations of Computer Science, vol 18, no 4, 2007 [link]
D. Lavenier, G. Georges, X. Liu, A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms, The Journal of VLSI signal processing systems. Special issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, vol 48, no 3, 2007 [link]
M. Giraud, G. Kucherov, D. Lavenier, L. Noé, P. Peterlongo, Utilization of Subset Seeds on a Reconfigurable Architecture, LAW 2007 (Lonfon Algorithm Workshop), King's London College, London, UK, 2007 [pdf]
P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, M. Giraud, Protein similarity search with subset seeds on a dedicated reconfigurable hardware, Parallel Bio-Computing, Gdansk, Poland, 2007 [pdf]