JOURNALS

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. 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]

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

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]

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]

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

M. Giraud, D. Lavenier, Dealing with Hardware Space Limits when Removing Epsilon-Transitions in a Genomic Weighted Finite Automaton., Journal of Automata, Languages and Combinatorics, vol 10, no 2/3, 2005 [link]

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

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

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

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

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

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

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

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

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

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

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

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

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