Claire Lemaitre

Documents

Publications

	Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome Fabrice Legeai , Sandra Romain , Thibaut Capblancq , Paul Doniol-Valcroze , Mathieu Joron Genome Biology and Evolution, 2024, pp.1-7. ⟨10.1093/gbe/evae055⟩ Article dans une revue hal-04530573v1
	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⟩ Article dans une revue hal-04166273v1
	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⟩ Article dans une revue hal-04155714v1
	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⟩ Article dans une revue hal-02399723v2
	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⟩ Article dans une revue hal-03832903v1
	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⟩ Article dans une revue hal-03032763v2
	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⟩ Article dans une revue hal-02308101v1
	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⟩ Article dans une revue hal-02891885v1
	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⟩ Article dans une revue hal-02918230v1
	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⟩ Article dans une revue hal-02800429v1
	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⟩ Article dans une revue hal-01634232v4
	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⟩ Article dans une revue hal-03032737v1
	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⟩ Article dans une revue 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⟩ Article dans une revue hal-01892027v1
	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⟩ Article dans une revue hal-01633525v1
	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⟩ Article dans une revue hal-01633879v1
	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⟩ Article dans une revue hal-01280238v1
	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⟩ Article dans une revue hal-01397150v1
	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⟩ Article dans une revue hal-01081094v1
	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⟩ Article dans une revue hal-01214682v1
	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⟩ Article dans une revue hal-01208780v2
	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⟩ Article dans une revue hal-01701165v1
	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⟩ Article dans une revue hal-01081089v1
	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⟩ Article dans une revue hal-01088571v1
	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⟩ Article dans une revue hal-01083715v1
	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⟩ Article dans une revue hal-00907450v1
	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⟩ Article dans une revue hal-00907454v1
	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⟩ Article dans une revue hal-00907449v1
	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⟩ Article dans une revue hal-00784394v1
	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⟩ Article dans une revue hal-00784414v1
	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⟩ Article dans une revue hal-00784423v1
	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⟩ Article dans une revue 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 Article dans une revue hal-00428362v1
	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⟩ Article dans une revue hal-00784451v1
	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 Article dans une revue hal-00428176v1
	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⟩ Article dans une revue hal-00784460v1

	Métagénomique et métatranscriptomique Cervin Guyomar , Claire Lemaitre Des séquences aux graphes. Méthodes et structures discrètes pour la bioinformatique, ISTE, pp.1-36, 2023, 9781789480665 Chapitre d'ouvrage hal-04338891v1
	Metagenomics and Metatranscriptomics Cervin Guyomar , Claire Lemaitre From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, ISTE, 2022, 9781789450668 Chapitre d'ouvrage hal-03844316v1
	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⟩ Chapitre d'ouvrage hal-01633718v1

	Le SARS-CoV-2 : une expérience inédite de surveillance génomique mondiale Hélène Touzet , Mikaël Salson , Claire Lemaitre , Florence Débarre 2023 Article de blog scientifique hal-04155812v1
	Comment la bioinformatique a résolu le puzzle du génome du SARS-CoV-2 Claire Lemaitre , Mikaël Salson , Hélène Touzet 2022 Article de blog scientifique hal-03896532v1
	Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2 Hélène Touzet , Mikaël Salson , Claire Lemaitre 2022 Article de blog scientifique hal-03750389v1

	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 Poster de conférence hal-04425626v1
	Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics Carole Belliardo , Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024 Poster de conférence hal-04509213v1
	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. , pp.1-1, 2024 Poster de conférence hal-04423917v1
	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 Poster de conférence hal-03885541v1
	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 Poster de conférence 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, Online, France. Poster de conférence 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 Poster de conférence hal-03073966v1
	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 Poster de conférence hal-02290884v1
	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 Poster de conférence hal-01934823v1
	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 Poster de conférence hal-01638884v1
	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 Poster de conférence hal-01595071v1
	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⟩ Poster de conférence hal-01180603v1
	VCF$\_$creator: Mapping and VCF Creation features in DiscoSnp++ Chloé Riou , Claire Lemaitre , Pierre Peterlongo JOBIM 2015, Jul 2015, Clermont-Ferrand, France Poster de conférence hal-01176492v1
	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 Poster de conférence hal-01231793v1
	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 Poster de conférence hal-01240443v1
	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 Poster de conférence hal-01088683v1
	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 Poster de conférence hal-01087832v1
	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 Poster de conférence hal-01092959v1
	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 Poster de conférence hal-01091184v1
	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 Poster de conférence hal-01088641v1
	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 Poster de conférence hal-01092960v1
	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 Poster de conférence hal-00760332v1

	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 Communication dans un congrès hal-04320771v1
	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 Communication dans un congrès hal-03120668v1
	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 Communication dans un congrès hal-02288091v1
	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 Communication dans un congrès hal-02308257v1
	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 Communication dans un congrès hal-02289484v1
	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 Communication dans un congrès hal-01638839v1
	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⟩ Communication dans un congrès 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 Communication dans un congrès hal-01210404v1
	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 Communication dans un congrès hal-00907446v1
	Compareads: comparing huge metagenomic experiments Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil Communication dans un congrès hal-00720951v1
	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 Communication dans un congrès hal-00649151v1
	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 Communication dans un congrès hal-02756212v1

	Méthodes bioinformatiques pour l'étude des Variants de Structure avec des données de séquençages génomiques Claire Lemaitre Bio-informatique [q-bio.QM]. Université Rennes 1, 2021 HDR tel-03497793v1

	The Silene latifolia genome and its giant Y chromosome Carol Moraga , Catarina Branco , Quentin Rougemont , Paris Veltsos , Pavel Jedlička 2024 Pré-publication, Document de travail hal-04515245v1
	The Silene latifolia genome and its giant Y chromosome Carol Moraga , Catarina Branco , Quentin Rougemont , Paris Veltsos , Pavel Jedlička 2023 Pré-publication, Document de travail hal-04293712v1
	MTG-Link: leveraging barcode information from linked-reads to assemble specific loci Anne Guichard , Fabrice Legeai , Denis Tagu , Claire Lemaitre 2022 Pré-publication, Document de travail hal-03886951v1
	Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps Fabrice Legeai , Bernardo F. Santos , Stéphanie Robin , Anthony Bretaudeau , Rebecca B. Dikow 2019 Pré-publication, Document de travail hal-02788577v1
	Multiple Comparative Metagenomics using Multiset k-mer Counting Gaëtan Benoit , Pierre Peterlongo , Mahendra Mariadassou , Erwan Drezen , Sophie Schbath 2016 Pré-publication, Document de travail hal-01300485v1

	Comparaison et visualisation de graphes de pangénomes Siegfried Dubois , Claire Lemaitre , Thomas Faraut , Matthias Zytnicki Université de rennes. 2023, pp.1-38 Rapport hal-04213245v1
	SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins Samuel Alizon , Frédéric Cazals , Stéphane Guindon , Claire Lemaitre , Tristan Mary-Huard [Research Report] CNRS. 2021, pp.1-35 Rapport hal-03170023v1
	Precise detection of rearrangement breakpoints in mammalian chromosomes Claire Lemaitre , Eric Tannier , Christian Gautier , Marie-France Sagot [Research Report] RR-6533, INRIA. 2008, pp.26 Rapport inria-00278553v2

	Réarrangements chromosomiques dans les génomes de mammifères : caractérisation des points de cassure Claire Lemaitre Biochimie [q-bio.BM]. Université Claude Bernard - Lyon I, 2008. Français. ⟨NNT : ⟩ Thèse tel-00364265v1

Claire Lemaitre

Publications

Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome

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

SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Critical Assessment of Metagenome Interpretation: the second round of challenges

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

SimkaMin: fast and resource frugal de novo comparative metagenomics

MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

SVJedi: genotyping structural variations with long reads

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

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

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Multiple comparative metagenomics using multiset k -mer counting

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

Genetic control of contagious asexuality in the pea aphid

MindTheGap: integrated detection and assembly of short and long insertions

GATB: Genome Assembly & Analysis Tool Box

Reference-free detection of isolated SNPs

Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle

Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae

Compareads: comparing huge metagenomic experiments

A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Cassis: detection of genomic rearrangement breakpoints.

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

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

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

Precise detection of rearrangement breakpoints in mammalian chromosomes

Métagénomique et métatranscriptomique

Metagenomics and Metatranscriptomics

De Novo NGS Data Compression

Le SARS-CoV-2 : une expérience inédite de surveillance génomique mondiale

Comment la bioinformatique a résolu le puzzle du génome du SARS-CoV-2

Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2

Metagenomic assembly of complex ecosystems with highly accurate long-reads

Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics

Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing

SVJedi-graph: genotyping close and overlapping structural variants with a variation graph and long-reads

SVJedi-graph: Structural Variant genotyping with long-reads using a variation graph

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

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

SVJedi : Structural variation genotyping using long reads

Reference guided genome assembly in metagenomic samples

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

Simka: large scale de novo comparative metagenomics

Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets

VCF$\_$creator: Mapping and VCF Creation features in DiscoSnp++

Improvement of the assembly of heterozygous genomes of non-model organisms

Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains

Speeding up NGS software development

MindTheGap: integrated detection and assembly of short and long insertions

Identification and correction of genome mis-assemblies due to heterozygosity

Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

GATB: a software toolbox for genome assembly and analysis

Bloocoo, a memory efficient read corrector

Compareads: comparing huge metagenomic experiments

Towards an edit distance between pangenome graphs

Towards a better understanding of the low discovery rate of short-read based insertion variant callers

Genotyping Structural Variations using Long Read data

Reference-guided genome assembly in metagenomic samples

Genotyping Structural Variations using Long Read Data

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

Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads

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

Whole genome re-sequencing : lessons from unmapped reads

Compareads: comparing huge metagenomic experiments

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

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

Méthodes bioinformatiques pour l'étude des Variants de Structure avec des données de séquençages génomiques

The Silene latifolia genome and its giant Y chromosome