DL
Dominique Lavenier
SoftwarebioinformaticsAlgorithmsq-bio.GNq-bio.QMcs.DSDNAMetagenomicsadaptationaphid
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
42 papers in the corpus · 1997–2025SNooPy: a statistical framework for long-read metagenomic variant calling.42234577 · Faure, Roland, Faure, Ulysse, Truong, Tam et al.2026 · 0 citationsNucleic acids research. 2026;54(10)
Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.40986830 · Olvera-Vazquez, Sergio Gabriel, Chen, Xilong, Mesnil, Aurélie et al.2025 · 5 citationsMolecular biology and evolution. 2025;42(12)
De-Bruijn graph partitioning for scalable and accurate DNA storage processing.41206925 · De Moor, Florestan, Boullé, Olivier, Lavenier, Dominique2025 · 1 citationBioinformatics (Oxford, England). 2025;41(11)
Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler10.1101/2025.09.29.679204v2 · Faure, R., Hilaire, B., Flot, J.-F. et al.2025 · 0 citationsbioRxiv
Processing-in-memory for genomics workloads2506.00597v2 · William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi et al.2025 · 2 citationsIEEE Micro, 46 (2): 70-80, 2026
Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information.38573592 · Leblanc, Julien, Boulle, Olivier, Roux, Emeline et al.2024 · 1 citationBioTechniques. 2024;76(5):203-215
HairSplitter: haplotype assembly from long, noisy reads10.1101/2024.02.13.580067v4 · Faure, R., Lavenier, D., Flot, J.-F.2024 · 2 citationsbioRxiv
In vitro construction and long read sequencing analysis of a 24 kb long artificial DNA sequence encoding the Universal Declaration of the Rights of Man and of the Citizen.10.1101/2023.06.26.546242v1 · Leblanc, J., Boulle, O., Roux, E. et al.2023 · 1 citationbioRxiv
QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data.36699389 · Faure, Roland, Lavenier, Dominique2023 · 1 citationBioinformatics advances. 2022;2(1):vbac068
Constrained Consensus Sequence Algorithm for DNA Archiving2105.04993v1 · Dominique Lavenier2021 · 4 citationsarXiv
Variant Calling Parallelization on Processor-in-Memory Architecture10.1101/2020.11.03.366237v1 · LAVENIER, D., Jodin, R., Cimadomo, R.2020 · 34 citationsbioRxiv
SVJedi: genotyping structural variations with long reads.32437523 · Lecompte, Lolita, Peterlongo, Pierre, Lavenier, Dominique et al.2021 · 18 citationsBioinformatics (Oxford, England). 2020;36(17):4568-4575
Author Correction: A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish.32350396 · Yazbeck, Gabriel M, Oliveira, Rafael Sachetto, Ribeiro, José Mauro et al.2021 · 0 citationsScientific reports. 2020;10(1):7584
Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm89 in Brittany, France.32165385 · Devaere, Marie, Boukthir, Sarrah, Moullec, Séverine et al.2020 · 1 citationMicrobiology resource announcements. 2020;9(11)
Statistically Significant Discriminative Patterns Searching1906.01581v1 · Hoang Son Pham, Gwendal Virlet, Dominique Lavenier et al.2019 · 0 citationsarXiv
Complete assembly of circular and chloroplast genomes based on global optimization.31288643 · Andonov, Rumen, Djidjev, Hristo, François, Sebastien et al.2020 · 3 citationsJournal of bioinformatics and computational biology. 2019;17(3):1950014
A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish.29855493 · Yazbeck, Gabriel M, Oliveira, Rafael Sachetto, Ribeiro, José Mauro et al.2019 · 9 citationsScientific reports. 2018;8(1):8511
Global optimization approach for circular and chloroplast genome assembly10.1101/231324v1 · Francois, S., Andonov, R., Lavenier, D. et al.2017 · 1 citationbioRxiv
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.28967888 · Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter et al.2017 · 873 citationsNature methods. 2017;14(11):1063-1071
Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany.28963207 · Rochefort, Aude, Boukthir, Sarrah, Moullec, Séverine et al.2020 · 3 citationsGenome announcements. 2017;5(39)
Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.28376841 · Mathers, Thomas C, Chen, Yazhou, Kaithakottil, Gemy et al.2019 · 3 citationsGenome biology. 2017;18(1):63
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.28190401 · Mathers, Thomas C, Chen, Yazhou, Kaithakottil, Gemy et al.2018 · 824 citationsGenome biology. 2017;18(1):27
Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021, Isolated from Clonal Clustered Cases in French Brittany.27445380 · Meygret, Alexandra, Vincent, Pascal, Moullec, Séverine et al.2016 · 4 citationsGenome announcements. 2016;4(4)
Multiple Comparative Metagenomics using Multiset k-mer Counting1604.02412v3 · Gaetan Benoit, Pierre Peterlongo, Mahendra Mariadassou et al.2016 · 127 citationsarXiv
Commet: comparing and combining multiple metagenomic datasets1511.08317v1 · Maillet Nicolas, Collet Guillaume, Vanier Thomas et al.2015 · 0 citationsarXiv
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.26370285 · Benoit, Gaëtan, Lemaitre, Claire, Lavenier, Dominique et al.2016 · 99 citationsBMC bioinformatics. 2015;16:288
Compression of high throughput sequencing data with probabilistic de Bruijn graph1412.5932v1 · Gaetan Benoit, Claire Lemaitre, Dominique Lavenier et al.2014 · 8 citationsarXiv
GATB: Genome Assembly & Analysis Tool Box.24990603 · Drezen, Erwan, Rizk, Guillaume, Chikhi, Rayan et al.2014 · 79 citationsBioinformatics (Oxford, England). 2014;30(20):2959-61
Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.24435871 · Falentin, Hélène, Naquin, Delphine, Loux, Valentin et al.2014 · 14 citationsGenome announcements. 2014;2(1)
Graphics processing unit-accelerated quantitative trait Loci detection.24000926 · Chapuis, Guillaume, Filangi, Olivier, Elsen, Jean-Michel et al.2014 · 2 citationsJournal of computational biology : a journal of computational molecular cell biology. 2013;20(9):672-86
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
DSK: k-mer counting with very low memory usage.23325618 · Rizk, Guillaume, Lavenier, Dominique, Chikhi, Rayan2013 · 301 citationsBioinformatics (Oxford, England). 2013;29(5):652-3
Compareads: comparing huge metagenomic experiments.23282463 · Maillet, Nicolas, Lemaitre, Claire, Chikhi, Rayan et al.2013 · 56 citationsBMC bioinformatics. 2012;13 Suppl 19:S10
Assemblathon 1: a competitive assessment of de novo short read assembly methods.21926179 · Earl, Dent, Bradnam, Keith, St John, John et al.2012 · 507 citationsGenome research. 2011;21(12):2224-41
GASSST: global alignment short sequence search tool.20739310 · Rizk, Guillaume, Lavenier, Dominique2011 · 101 citationsBioinformatics (Oxford, England). 2010;26(20):2534-40
Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.20444247 · Legeai, Fabrice, Rizk, Guillaume, Walsh, Thomas et al.2010 · 109 citationsBMC genomics. 2010;11:281
PLAST: parallel local alignment search tool for database comparison.19821978 · Nguyen, Van Hoa, Lavenier, Dominique2010 · 84 citationsBMC bioinformatics. 2009;10:329
Optimal neighborhood indexing for protein similarity search.19087280 · Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique et al.2009 · 4 citationsBMC bioinformatics. 2008;9:534
Coding region prediction based on a universal DNA sequence representation method.19040362 · Jiang, Xianyang, Lavenier, Dominique, Yau, Stephen S-T2009 · 28 citationsJournal of computational biology : a journal of computational molecular cell biology. 2008;15(10):1237-56
Fine-grained parallelization of similarity search between protein sequences0804.3643v1 · Van Hoa Nguyen (IRISA), Dominique Lavenier (IRISA)2008 · 4 citationsarXiv
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.16809391 · Tempel, Sébastien, Giraud, Mathieu, Lavenier, Dominique et al.2006 · 10 citationsBioinformatics (Oxford, England). 2006;22(16):1948-54
SAMBA: hardware accelerator for biological sequence comparison.9475989 · Guerdoux-Jamet, P, Lavenier, D1998 · 66 citationsComputer applications in the biosciences : CABIOS. 1997;13(6):609-15
Career total: at least 361 works. 42 are in this corpus.
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