Journals

  1. SVJedi: genotyping structural variations with long reads
    L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre
    Bioinformatics, Volume 36, Issue 17, 1 September 2020

  2. Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm89 in Brittany, France
    M Devaere, S Boukthir, S Moullec, E Roux, D Lavenier, A Faili, S Kayal
    Microbiology Resource Announcements 9 (11), 2020

  3. Complete assembly of circular and chloroplast genomes based on global optimization
    R. Andonov, H. Djidjev, S. François, D. Lavenier
    J. Bioinformatics and Computational Biology 17(3), 2019

  4. Global Optimization for Scaffolding and Completing Genome Assemblies
    S. François, R. Andonov, D. Lavenier, H. Djidjev
    Electronic Notes in Discrete Mathematics 64: 185-194 (2018)

  5. A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes : Bryconadae) an endangered migratory Neotropical fish
    G. Yazbeck, R. Oliveira, J. Ribeiro, R. Graciano, R. Santos, F. Carmo, D. Lavenier
    Scientific reports 8 (1) 8511, 2018

  6. Critical Assessment of Metagenome Interpretation− a benchmark of computational metagenomics software
    A. Sczyrba et al.
    Nature Methods, 14, p. 1063–1071, doi:10.1038/nmeth.4458, 2017

  7. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
    TC Mathers et al.
    Genome biology, 18:27, 2017

  8. Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany
    A Rochefort, S Boukthir, S Moullec, A Meygret, Y Adnani, D Lavenier, A. Faili, S. Kayal
    Genome Announcements 5 (39), e00957-17, 2017

  9. 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

  10. 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 Announcements 4(4):e00689-16, 2016

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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

  19. 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

  20. 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

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

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

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

  24. 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

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

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

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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

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

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

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

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

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

  43. 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

  44. 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

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

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