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Claire Lemaitre

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MTG-Link: leveraging barcode information from linked-reads to assemble specific loci

Anne Guichard , Fabrice Legeai , Denis Tagu , Claire Lemaitre
BMC Bioinformatics, 2023, 24 (1), pp.284. ⟨10.1186/s12859-023-05395-w⟩
Journal articles hal-04166273v1
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SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph

Sandra Romain , Claire Lemaitre
Bioinformatics, 2023, 39 (Supplement_1), pp.270 - 278. ⟨10.1093/bioinformatics/btad237⟩
Journal articles hal-04155714v1
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Critical Assessment of Metagenome Interpretation: the second round of challenges

Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Journal articles hal-03832903v1
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Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2

Hélène Touzet , Mikaël Salson , Claire Lemaitre
Interstices, 2022
Journal articles hal-03750389v1
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Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont
eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩
Journal articles hal-02399723v2
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SVJedi: genotyping structural variations with long reads

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre
Bioinformatics, 2020, 36 (17), pp.4568-4575. ⟨10.1093/bioinformatics/btaa527⟩
Journal articles hal-03032737v1
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Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Fabrice F. Legeai , Bernardo F Santos , Stéphanie Robin , Anthony Bretaudeau , Rebecca B Dikow
BMC Biology, 2020, 18 (1), pp.1-23. ⟨10.1186/s12915-020-00822-3⟩
Journal articles hal-02918230v1
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Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Jérémy Gauthier , Donna Lisa De‐silva , Zachariah Gompert , Annabel Whibley , Céline Houssin
Molecular Ecology, 2020, 29 (7), pp.1328-1343. ⟨10.1111/mec.15403⟩
Journal articles hal-02800429v1
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DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

Jérémy Gauthier , Charlotte Mouden , Tomasz Suchan , Nadir Alvarez , Nils Arrigo
PeerJ, 2020, pp.1-20. ⟨10.7717/peerj.9291⟩
Journal articles hal-01634232v4
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MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Cervin Guyomar , Wesley Delage , Fabrice Legeai , Christophe Mougel , Jean-Christophe Simon
NAR Genomics and Bioinformatics, 2020, 2 (3), pp.1-11. ⟨10.1093/nargab/lqaa047⟩
Journal articles hal-02891885v1
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Towards a better understanding of the low recall of insertion variants with short-read based variant callers

Wesley J Delage , Julien Thevenon , Claire Lemaitre
BMC Genomics, 2020, 21 (762), ⟨10.1186/s12864-020-07125-5⟩
Journal articles hal-03032763v2
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SimkaMin: fast and resource frugal de novo comparative metagenomics

Gaëtan Benoit , Mahendra Mariadassou , Stéphane Robin , Sophie Schbath , Pierre Peterlongo
Bioinformatics, 2020, 36 (4), pp.1-2. ⟨10.1093/bioinformatics/btz685⟩
Journal articles hal-02308101v1
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Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Cervin Guyomar , Fabrice Legeai , Emmanuelle Jousselin , Christophe Mougel , Claire Lemaitre
Microbiome, 2018, 6 (1), pp.1-21. ⟨10.1186/s40168-018-0562-9⟩
Journal articles hal-01926402v1

Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Pierre Nouhaud , Mathieu Gautier , Anaïs Gouin , Julie Jaquiéry , Jean Peccoud
Molecular Ecology, 2018, 27 (16), pp.3287 - 3300. ⟨10.1111/mec.14799⟩
Journal articles hal-01892027v1
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Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Journal articles hal-01633879v1
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Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Alexander Sczyrba , Peter Hofmann , Peter Belmann , David Koslicki , Stefan Janssen
Nature Methods, 2017, 14 (11), pp.1063 - 1071. ⟨10.1038/nmeth.4458⟩
Journal articles hal-01633525v1
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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras , Olivier Collin , Cyril Monjeaud , Vincent Lacroix , Eric Rivals
GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩
Journal articles hal-01280238v1
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Multiple comparative metagenomics using multiset k -mer counting

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath
PeerJ Computer Science, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩
Journal articles hal-01397150v1
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Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Gaëtan Benoit , Claire Lemaitre , Dominique Lavenier , Erwan Drezen , Thibault Dayris
BMC Bioinformatics, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩
Journal articles hal-01214682v1
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Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

Pascaline Dumas , Fabrice Legeai , Claire Lemaitre , Erwan Scaon , Marion Orsucci
Genetica, 2015, 143 (3), pp.305-316. ⟨10.1007/s10709-015-9829-2⟩
Journal articles hal-01208780v2
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Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

Anaïs Gouin , Fabrice Legeai , Pierre Nouhaud , Annabel Whibley , Jean-Christophe Simon
Heredity, 2015, 114, pp.494-501. ⟨10.1038/hdy.2014.85⟩
Journal articles hal-01081094v1
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Reference-free detection of isolated SNPs

Raluca Uricaru , Guillaume Rizk , Vincent Lacroix , Elsa Quillery , Olivier Plantard
Nucleic Acids Research, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩
Journal articles hal-01083715v1
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MindTheGap: integrated detection and assembly of short and long insertions

Guillaume Rizk , Anaïs Gouin , Rayan Chikhi , Claire Lemaitre
Bioinformatics, 2014, 30 (24), pp.3451 - 3457. ⟨10.1093/bioinformatics/btu545⟩
Journal articles hal-01081089v1
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Genetic control of contagious asexuality in the pea aphid

Julie Jaquiéry , Jean Peccoud , Tiphaine Ouisse , Fabrice Legeai , Nathalie Prunier-Leterme
PLoS Genetics, 2014, 10 (12), pp.e1004838. ⟨10.1371/journal.pgen.1004838⟩
Journal articles hal-01701165v1
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GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre
Bioinformatics, 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩
Journal articles hal-01088571v1
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Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

Virginie Dupuy , Pascal Sirand-Pugnet , Eric Baranowski , Aurélien Barré , Marc Breton
Genome Announcements, 2013, 1 (3), pp.e00354-13. ⟨10.1128/genomeA.00354-13⟩
Journal articles hal-00907450v1
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Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle

Lucía Manso-Silván , Florence Tardy , Eric Baranowski , Aurélien Barré , Alain Blanchard
Genome Announcements, 2013, 1 (3), pp.e00348-13. ⟨10.1128/genomeA.00348-13⟩
Journal articles hal-00907454v1
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Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae

Emilie Dordet-Frisoni , Eric Baranowski , Aurélien Barré , Alain Blanchard , Marc Breton
Genome Announcements, 2013, 1 (3), pp.e00280-13. ⟨10.1128/genomeA.00280-13⟩
Journal articles hal-00907449v1
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Compareads: comparing huge metagenomic experiments

Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo
BMC Bioinformatics, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩
Journal articles hal-00784394v1
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Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Amélie Véron , Claire Lemaitre , Christian Gautier , Vincent Lacroix , Marie-France Sagot
BMC Genomics, 2011, 12 (1), pp.303. ⟨10.1186/1471-2164-12-303⟩
Journal articles hal-00784423v1
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A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

Claire Lemaitre , Aurélien Barré , Christine Citti , Florence Tardy , François Thiaucourt
BMC Bioinformatics, 2011, 12 (1), pp.457. ⟨10.1186/1471-2105-12-457⟩
Journal articles hal-00784414v1

Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet , Claire Lemaitre , Zanoni Dias , Christian Gautier , Eric Tannier
Bioinformatics, 2010, 26 (15), pp.1897-8. ⟨10.1093/bioinformatics/btq301⟩
Journal articles hal-00681095v1

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre , Marília D.V. Braga , Christian Gautier , M.-F. Sagot , Eric Tannier
Genome Biology and Evolution, 2009, 1(1), pp.56-66
Journal articles hal-00428362v1
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Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre , Lamia Zaghloul , Marie-France Sagot , Christian Gautier , Alain Arneodo
BMC Genomics, 2009, 10 (1), pp.335. ⟨10.1186/1471-2164-10-335⟩
Journal articles hal-00784451v1
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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre , Eric Tannier , Christian Gautier , Marie-France Sagot
BMC Bioinformatics, 2008, 9 (1), pp.286. ⟨10.1186/1471-2105-9-286⟩
Journal articles hal-00784460v1

A small trip in the untranquil world of genomes a survey on the detection and analysis of genome rearrangement breakpoints

Claire Lemaitre , M.-F. Sagot
Theoretical Computer Science, 2008, 395, pp.171-192
Journal articles hal-00428176v1
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Towards an edit distance between pangenome graphs

Siegfried Dubois , Benjamin Linard , Matthias Zytnicki , Claire Lemaitre , Thomas Faraut
SeqBIM 2023 - Journées sur les Séquences en Bioinformatique, Informatique et Mathématiques, Nov 2023, Lille, France. pp.1-2
Conference papers hal-04320771v1
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Towards a better understanding of the low discovery rate of short-read based insertion variant callers

Wesley Delage , Julien Thevenon , Claire Lemaitre
JOBIM 2020 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier, France
Conference papers hal-03120668v1
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Genotyping Structural Variations using Long Read Data

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre
HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3
Conference papers hal-02289484v1
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Reference-guided genome assembly in metagenomic samples

Cervin Guyomar , Wesley Delage , Fabrice Legeai , Christophe Mougel , Jean-Christophe Simon
JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8
Conference papers hal-02308257v1
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Genotyping Structural Variations using Long Read data

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre
JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8
Conference papers hal-02288091v1

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Cervin Guyomar , Fabrice Legeai , Christophe Mougel , Claire Lemaitre , Jean-Christophe Simon
International Conference on Holobionts, Apr 2017, Paris, France
Conference papers hal-01638839v1
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Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads

Claire Lemaitre , Liviu Ciortuz , Pierre Peterlongo
Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.119-130, ⟨10.1007/978-3-319-07953-0_10⟩
Conference papers hal-01063157v3

Analyse de transcriptomes de foies de canards par séquençage d’ARN (RNA-Seq)

Christian Diot , Magalie Houee , Olivier Demeure , Elisabeth Baéza , Alain Vignal
10. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, La Rochelle., Mar 2013, La Rochelle, France
Conference papers hal-01210404v1
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Whole genome re-sequencing : lessons from unmapped reads

Anaïs Gouin , Pierre Nouhaud , Fabrice Legeai , Guillaume Rizk , Jean-Christophe Simon
Journées Ouvertes Biologie Informatique Mathématiques, Jul 2013, Toulouse, France
Conference papers hal-00907446v1
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Compareads: comparing huge metagenomic experiments

Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo
RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil
Conference papers hal-00720951v1

Molligen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes

Aurélien Barré , Claire Lemaitre , Patricia Thébault , Antoine de Daruvar , Alain A. Blanchard
18. Congress of the International Organization for Mycoplasmology, Jul 2010, Chianciano Terme, Italy
Conference papers hal-02756212v1

MolliGen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes

Aurélien Barré , Claire Lemaitre , Patricia Thebault , Antoine de Daruvar , Alain Blanchard
Congress of the International Organization for Mycoplasmology ; 2010/07/11-16 ; Chianciano Terme (ITA). IOM congress 2010., 2010, Italy
Conference papers hal-00649151v1
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Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing

Carole Belliardo , Samuel Mondy , Arthur Pere , Claire Lemaitre , Riccardo Vicedomini
Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France.
Conference poster hal-04423917v1
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Metagenomic assembly of complex ecosystems with highly accurate long-reads

Nicolas Maurice , Claire Lemaitre , Clémence Frioux , Riccardo Vicedomini
Journées 2024 du PEPR Agroécologie et Numérique, Jan 2024, Rennes, France. pp.1-1, 2024
Conference poster hal-04425626v1
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SVJedi-graph: genotyping close and overlapping structural variants with a variation graph and long-reads

Sandra Romain , Claire Lemaitre
JOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France
Conference poster hal-03885541v1
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SVJedi-graph: Structural Variant genotyping with long-reads using a variation graph

Sandra Romain , Claire Lemaitre
JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. pp.1
Conference poster hal-03441915v1

MTG-Link: filling gaps in draft genome assemblies with linked read data

Anne Guichard , Fabrice Legeai , Arthur Le Bars , Paul Yann Jay , Mathieu Joron
Biodiversity Genomics 2020, Oct 2020, Virtual, France
Conference poster hal-03074227v1

MTG-Link: filling gaps in draft genome assemblies with linked read data

Anne Guichard , Fabrice Legeai , Arthur Le Bars , Paul Yann Jay , Mathieu Joron
JOBIM 2020 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier, France
Conference poster hal-03073966v1
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SVJedi : Structural variation genotyping using long reads

Lolita Lecompte , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre
HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland
Conference poster hal-02290884v1
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Reference guided genome assembly in metagenomic samples

Cervin Guyomar , Wesley Delage , Fabrice Legeai , Christophe Mougel , Jean-Christophe Simon
RECOMB 2018 - 22nd International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France. pp.1
Conference poster hal-01934823v1

Simka: large scale de novo comparative metagenomics

Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath
JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. , pp.234, 2017, JOBIM 2017 LILLE
Conference poster hal-01595071v1
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Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Cervin Guyomar , Fabrice Legeai , Christophe Mougel , Claire Lemaitre , Jean-Christophe Simon
JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France
Conference poster hal-01638884v1
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Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains

Anaïs Gouin , Anthony Bretaudeau , K Labadie , Jean-Marc Aury , Emmanuelle d'Alençon
Arthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015
Conference poster hal-01240443v1
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Improvement of the assembly of heterozygous genomes of non-model organisms

Anaïs Gouin , Anthony Bretaudeau , Emmanuelle d'Alençon , Claire Lemaitre , Fabrice Legeai
Genome Informatics, Oct 2015, Cold Spring Harbor Laboratory, United States. 2015
Conference poster hal-01231793v1
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Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets

Gaëtan Benoit , Pierre Peterlongo , Dominique Lavenier , Claire Lemaitre
JOBIM 2015, Jul 2015, Clermont-Ferrand, France. , ⟨10.1093/Bioinforma-cs/btu406⟩
Conference poster hal-01180603v1
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VCF$\_$creator: Mapping and VCF Creation features in DiscoSnp++

Chloé Riou , Claire Lemaitre , Pierre Peterlongo
JOBIM 2015, Jul 2015, Clermont-Ferrand, France
Conference poster hal-01176492v1
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Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

Susete Alves Carvalho , Raluca Uricaru , Jorge Duarte , Claire Lemaitre , Nathalie Rivière
ECCB 2014, Sep 2014, Strasbourg, France
Conference poster hal-01091184v1
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GATB: a software toolbox for genome assembly and analysis

Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre
Bio-IT World Conference, Apr 2014, Boston, United States
Conference poster hal-01088641v1
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Bloocoo, a memory efficient read corrector

Gaëtan Benoit , Dominique Lavenier , Claire Lemaitre , Guillaume Rizk
European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. ECCB 2014, 2014
Conference poster hal-01092960v1
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Identification and correction of genome mis-assemblies due to heterozygosity

Anaïs Gouin , Anthony Bretaudeau , Claire Lemaitre , Fabrice Legeai
European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , ECCB 2014, 2014
Conference poster hal-01092959v1
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Speeding up NGS software development

Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre
Sequencing, Finishing and Analysis in the Future Meeting, May 2014, Santa Fé, United States
Conference poster hal-01088683v1
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MindTheGap: integrated detection and assembly of short and long insertions

Guillaume Rizk , Anaïs Gouin , Rayan Chikhi , Claire Lemaitre
European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , ECCB 2014, 2014
Conference poster hal-01087832v1
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Compareads: comparing huge metagenomic experiments

Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo
13e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 2012
Conference poster hal-00760332v1
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Métagénomique et métatranscriptomique

Cervin Guyomar , Claire Lemaitre
Des séquences aux graphes. Méthodes et structures discrètes pour la bioinformatique, ISTE, pp.1-36, 2023, 9781789480665
Book sections hal-04338891v1

Metagenomics and Metatranscriptomics

Cervin Guyomar , Claire Lemaitre
From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, ISTE, 2022, 9781789450668
Book sections hal-03844316v1
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De Novo NGS Data Compression

Gaëtan Benoit , Claire Lemaitre , Guillaume Rizk , Erwan Drezen , Dominique Lavenier
Mourad Elloumi. Algorithms for Next-Generation Sequencing Data, Springer, pp.91-115, 2017, 978-3-319-59826-0. ⟨10.1007/978-3-319-59826-0_4⟩
Book sections hal-01633718v1