See also my
Google scholar citation profile.
Preprints
Publications
- Chromosome-level assembly and annotation of the pearly heath Coenonympha arcania butterfly genome
Legeai F, Romain S, Capblancq T, Doniol-Valcroze P, Joron M, Lemaitre C, Desprès L.
Genome Biology and Evolution 2024, evae055 doi:10.1093/gbe/evae055
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci
Guichard A, Legeai F, Tagu D, Lemaitre C.
BMC Bioinformatics 2023, 24:284 doi:10.1186/s12859-023-05395-w
- SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph
Romain S and Lemaitre C
ISMB/ECCB 2023, COSI HiTSeq, Lyon, July 2023.
Bioinformatics 2023, 39(suppl_1):i270–i278 doi:10.1093/bioinformatics/btad237
- First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies
Gauthier J, Meier J, Legeai F, McClure M, Whibley A, ..., Lemaitre C, Elias M.
Molecular Ecology Resources 2022, doi:10.1111/1755-0998.13749.
- Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems
Richetr DJ, Watteaux R, Vannier T, ..., Lemaitre C, ..., Iudicone D, Jaillon O
eLife 2022, 11:e78129. doi:10.7554/eLife.78129.
- Critical Assessment of Metagenome Interpretation - the second round of challenges
Meyer F, Fritz A, ..., Lemaitre C, ..., Sczyrba A, McHardy AC.
Nature Methods 2022, 19:429–440. doi:10.1038/s41592-022-01431-4
- LRez: C ++ API and toolkit for analyzing and managing Linked-Reads data.
Morisse P, Lemaitre C, Legeai F
Bioinformatics Advances 2021. doi:10.1093/bioadv/vbab022
- Towards a better understanding of the low recall of insertion variants with short-read based variant callers.
Delage W, Thevenon J, Lemaitre C
BMC Genomics 2020, 21(1):762. doi:10.1186/s12864-020-07125-5
- Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps
Legeai F, Santos BF, Robin S, Bretaudeau B, ..., Lemaitre C, ... , Volkoff AN
BMC Biology, 2020, 18(1):89 doi:10.1186/s12915-020-00822-3
- MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities
Guyomar C, Delage W, Legeai F, Mougel C, Simon JC, Lemaitre C
NAR Genomics and Bioinformatics, 2020, 2(3):lqaa047 doi:10.1093/nargab/lqaa047
- DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
Gauthier J, Mouden C, Suchan T, Alvarez N, Arrigo N, Riou C, Lemaitre C, Peterlongo P
PeerJ, 2020, 8:e9291, doi:10.7717/peerj.9291
- SVJedi: Genotyping structural variations with long reads
Lecompte L, Peterlongo P, Lavenier D, Lemaitre C
Bioinformatics 2020 36(17):4568–4575 doi:10.1093/bioinformatics/btaa527
- Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone.
Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J and Elias M.
Molecular Ecology, 2020, 29(7):1328-1343, doi:10.1111/mec.15403.
- SimkaMin: fast and resource frugal de novo comparative metagenomics.
Benoit G, Mariadassou M, Robin S, Schbath S, Peterlongo P, Lemaitre C.
Bioinformatics 2020 36(4):1275–1276 doi:10.1093/bioinformatics/btz685.
- Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.
Guyomar C, Legeai F, Jousselin E, Mougel C, Lemaitre C, Simon JC.
Microbiome 2018 6(1):181.
- Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races.
Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja C, Lemaitre C, Vitalis R, Simon JC.
Molecular Ecology 2018 27(16):3287-3300.
- Disentangling the causes for faster-X evolution in aphids.
Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A,..., Lemaitre C, ..., Simon JC, Rispe C.
Genome Biology and Evolution 2018 10(2):507-520.
- Critical Assessment of Metagenome Interpretation -- a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, ..., Lemaitre C, ..., Mc Hardy AC.
Nature Methods 2017 14:1063–1071.
- Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.
Gouin A, Bretaudeau A, ..., Lemaitre C, Legeai F, d’Alençon E, Fournier P.
Scientific Reports 2017 7:11816.
- Multiple comparative metagenomics using multiset k-mer counting.
Benoit G, Peterlongo P, Mariadassou M, Drezen E, Schbath S, Lavenier D, Lemaitre C.
PeerJ Computer Science 2016 2:e94.
- Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals E, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P.
Gigascience 2016 5:9.
- Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?
Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d'Alençon E.
Genetica 2015 143(3):305-16.
- 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 2015 16:288.
- Reference-free detection of isolated SNPs
R. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard, R. Chikhi, C. Lemaitre, P. Peterlongo.
Nucleic Acids Research 2015 43(2):e11.
- Whole genome re-sequencing of non-model organisms: lessons from unmapped reads
A. Gouin, F. Legeai, P. Nouhaud, A. Whibley, J.-C. Simon, C. Lemaitre.
Heredity 2015 114:494-501.
- MindTheGap : integrated detection and assembly of short and long insertions
G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
Bioinformatics 2014 30(24):3451-3457.
- GATB: Genome Assembly & Analysis Tool Box
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier.
Bioinformatics 2014 30(20):2959-2961.
- Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads
C. Lemaitre, L. Ciortuz, P. Peterlongo.
AlCoB 2014, July 2014, Tarragona, Spain. (slides) (hal pdf)
in Algorithms for Computational Biology, LNCS vol. 8542, pp. 119--130.
- Compareads: comparing huge metagenomic experiments.
N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo.
RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil
BMC Bioinformatics 2012 13 (Suppl 19):S10. (pdf)
- A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships.
C. Lemaitre, A. Barré, C. Citti, F. Tardy, F. Thiaucourt, P. Sirand-Pugnet, P. Thébault.
BMC Bioinformatics, 2011 12:457. (pdf)
- Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.
A. Véron, C. Lemaitre, C. Gautier, V. Lacroix, M.-F. Sagot.
BMC Genomics, 2011 12:303. (pdf)
- Cassis: Detection of genomic rearrangement breakpoints.
C. Baudet, C. Lemaitre, Z. Dias, C. Gautier, E. Tannier, M.-F. Sagot.
Bioinformatics, 2010 26(15):1897-1898. (pdf)
- Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relations to genome organisation and open chromatin.
C. Lemaitre, L. Zaghloul, M.-F. Sagot, C. Gautier, A. Arnéodo, E. Tannier, B. Audit.
BMC Genomics, 2009 10:335. (pdf, commented on by David Sankoff)
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Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes.
C. Lemaitre, M. Braga Dias Vieira, C. Gautier, M.-F. Sagot, E. Tannier, G.A.B. Marais.
Genome Biology and Evolution, 2009 1(1):56-66. (pdf)
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Precise detection of rearrangement breakpoints in mammalian genomes.
C. Lemaitre, E. Tannier, C. Gautier, M.-F. Sagot.
BMC Bioinformatics, 2008 9(1):286. (pdf)
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A Small Trip in the Untranquil World of Genomes : A survey on the detection and analysis of genome rearrangement breakpoints.
C. Lemaitre, M.-F. Sagot.
Theoretical Computer Science, 2008 395(2-3):171-192. (pdf)
Book chapters
- Métagénomique et métatranscriptomique.
C. Guyomar, C. Lemaitre.
In: Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, Annie Chateau and Mikaël Salson (editors), ISTE Science Publishing, to appear 2022.
- Metagenomics and Metatranscriptomics.
C. Guyomar, C. Lemaitre.
In: From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, Annie Chateau and Mikaël Salson (editors), ISTE (isbn 9781789450668), Oct. 2022.
- de novo NGS Data Compression.
G. Benoit, C. Lemaitre, G. rizk, E. Drezen, D. Lavenier.
In: Algorithms for Next-Generation Sequencing Data: Techniques, Approaches, and Applications, M. Eloumi (editor), Springer, July 2017.
PhD and HDR manuscripts
Communications
- P. Morisse, F. Legeai, C. Lemaitre.
LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data.
JOBIM 2021, Paris, juillet 2021.
- A. Guichard, F. Legeai, D. Tagu, C. Lemaitre.
MTG-Link: filling gaps in draft genome assemblies with linked read data.
JOBIM 2021, Paris, juillet 2021.
- W. Delage, J. Thevenon, C. Lemaitre.
Towards a better understanding of the low discovery rate of short-read based insertion variant callers.
JOBIM 2020, Montpellier, juillet 2021.
- L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.
SVJedi : Structural variation genotyping using long reads. HiTSeq 2019, Basel, Switzerland, July 2019.
- L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.
Genotyping Structural Variations using Long Read Data. JOBIM 2019, Nantes, France, July 2019. (pdf)
- C. Guyomar, W. Delage, F. Legeai, C. Mougel, Jean-Christophe Simon, C. Lemaitre. Reference guided genome assembly in metagenomic samples. JOBIM 2019, Nantes, France, July 2019. (pdf)
- C. Guyomar, F. Legeai, C. Mougel, C. Lemaitre, Jean-Christophe Simon.
Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.
International Conference on Holobionts, Paris, France, April 19-21 2017.
- G. Benoit, P. Peterlongo, M. Mariadassou,E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.
Multiple comparative metagenomics using multiset k-mer counting.
JOBIM 2017, Lille, 3-6 juillet 2017.
- G. Benoit, P. Peterlongo, M. Mariadassou,E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.
Simka: fast kmer-based method for estimating the similarity between numerous metage- nomic datasets
RCAM 2015 (Recent Computational Advances in Metagenomics), Paris, France, October 2015.
- A. Gouin, F. Legeai, P. Nouhaud, G. Rizk, J.-C. Simon C. Lemaitre. Whole genome re-sequencing : lessons from unmapped reads. JOBIM 2013 , Toulouse , 1-4 juillet 2013 (pdf).
- P. Sirand-Pugnet, M. Breton, E. Dorset-Frisoni, E. Baranowski, A. Barré, C. Couture, V. Dupuy, P. Gaurivaud, D. Jacob, C. Lemaitre, L. Manso-Silvan, M. Nikolski, LX. Nouvel, F. Poumarat, F. Tardy, P. Thébault, S. Theil, C. Citti, F. Thiaucourt, A. Blanchard. Evaluation of the relative importance between gene loss and gene gain during mollicute evolution. 19th Congress of the International Organization for Mycoplasmology (IOM), Toulouse , 15-20 juillet 2012.
- A. Barré, P. Thébault, C. Lemaitre, M. Nikolski, A. Blanchard, P. Sirand-Pugnet. MolliGen 3.0, a database dedicated to the comparative genomics of mollicutes. 19th Congress of the International Organization for Mycoplasmology (IOM), Toulouse , 15-20 juillet 2012.
- A. Barré, C. Lemaitre, P. Thébault, A. de Daruvar, A. Blanchard, P. Sirand-Pugnet. Molligen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes. 18th Congress of the International Organization for Mycoplasmology (IOM), Chianciano Terme (ITA), 11-16 juillet 2010.
- A. Veron, C. Lemaitre, C. Gautier, V. Lacroix and M.-F. Sagot, Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, IPG 2010, Lyon, 25-26th of november 2010.
- C. Lemaitre, E. Tannier, C. Gautier, M.-F. Sagot, Precise detection and analysis of rearrangement breakpoints in mammalian genomes, 13th Evolutionary Biology Meeting at Marseilles, Marseille, September 2009.
- C. Lemaitre, M. Braga Dias Vieira, C. Gautier, M.-F. Sagot, E. Tannier, G.A.B. Marais, Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes, IPG 2008, Lyon, 19-20th of november 2008.
- L. Zaghloul, C. Lemaitre, M.-F. Sagot, C. Gautier, A. Arnéodo, E. Tannier, B. Audit, Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relations to genome organisation and open chromatin, IPG 2008, Lyon, 19-20th of november 2008.
- E. Billoir, C. Lemaitre, S. Charles, La modélisation des réseaux de gènes : une situation-problème pour l'apprentissage de méthodes mathématiques avancées, Poster at the 25ème Congrès de l'Association Internationale de Pédagogie Universitaire (AIPU), Montpellier, May 2008. (poster,proceedings)
- C. Lemaitre, E. Tannier, C. Gautier, M.-F. Sagot, A method to detect precisely rearrangement breakpoints in mammalian genomes. Dynamics of genomes, workshop à Valparaiso, Chili, march 2008.
- C. Lemaitre, E. Tannier, C. Gautier, M.-F. Sagot, Precise detection of rearrangement breakpoints in mammalian chromosomes, Rencontres Alphy, Lyon, January 2008.
Invited talks
- Methodological challenges
of Structural Variation characterization
and the particular case of insertions. (slides: 1.4 Mo pdf)
Keynote speaker at the meeting "
reads2genpop : From sequence reads to genomes and populations", Paris, Sept. 2022.
- Finding structural variants with sequencing data: the difficult case of insertions. (slides: 2.8 Mo pdf)
Keynote speaker at the annual meeting of GDR AIEM and Alphy working group (GDR BIM), Rennes, March 2022.
- Local assembly approaches for variant calling and genome assembly.
Invited talk at the INRA DGIMI seminar, Montpellier, France, 2021.
- Looking for genomic variants in the De Bruijn Graph.
Invited talk at the Institute for Advanced Bio-
sciences, University of Grenoble Alpes, Grenoble, France, Dec. 2017.
- Comparaison (massive) de (nombreux) metagénomes. Passons par les kmers pour passer à l'échelle.
Invited speaker at Journée scientifique sur le Microbiome", organized by Biogenouest, Rennes, France Dec. 2016.
- Comparing numerous metagenomics datasets.
Invited talk at Laboratoire de Biométrie et Biologie Evolutive, Lyon, France, Nov. 2016.
- Reference-free detection of genomic variants: from SNPs to inversions.
Restitution workshop of the ANR project Colib'read, Institut Curie, Paris, Nov 2016.
Workshop ABS4NGS, Institut Curie, Paris, Jun 2015.
- Chromosomal evolution and genome organisation : a complex relationship.
Invited talk au Center for Genome Regulation, Santiago, Chile, Apr 2012.
Invited talk au LINA, Nantes, Dec 2012.
- Réarrangements chromosomiques dans les génomes de mammifères : caractérisation des points de cassure.
Invited talk Inria Lille, Bonsai team, Lille, Feb 2012.
Invited talk at IRISA, Symbiose team, Rennes, Nov 2009.
Invited talk at Laboratoire Bordelais de Recherche en Informatique (LABRI), Bordeaux, Jan 2009.
- Détection et analyse des points de cassure de réarrangements dans les génomes de mammifères.
Invited talk at Centre de BioInformatique de Bordeaux, Bordeaux, Apr 2008.