Camille Marchet
Chargée de recherche epst
Laboratoire / équipe
Publications
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"title_s":["A survey of mapping algorithms in the long-reads era"],
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"citationFull_s":"Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. <i>23rd International Workshop on Algorithms in Bioinformatics (WABI 2023</i>, Sep 2023, Houston, United States. <a target=\"_blank\" href=\"https://dx.doi.org/10.4230/LIPIcs.WABI.2023.15\">⟨10.4230/LIPIcs.WABI.2023.15⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04279798\">⟨hal-04279798⟩</a>",
"title_s":["Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching"],
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"title_s":["supersampler Fractionnal hitting set implementation for lightweight genomic data sketching"],
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"title_s":["A survey of mapping algorithms in the long-reads era"],
"authFullName_s":["Kristoffer Sahlin",
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"Bastien Cazaux",
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"citationFull_s":"Camille Marchet, Antoine Limasset. Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees. 2022. <a target=\"_blank\" href=\"https://hal.science/hal-03871213\">⟨hal-03871213⟩</a>",
"title_s":["Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees"],
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"citationFull_s":"Camille Marchet. Sneak peek at the -tig sequences: useful sequences built from nucleic acid data. 2022. <a target=\"_blank\" href=\"https://hal.science/hal-03768446v2\">⟨hal-03768446v2⟩</a>",
"title_s":["Sneak peek at the -tig sequences: useful sequences built from nucleic acid data"],
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"title_s":["Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees"],
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"Antoine Limasset"],
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"citationFull_s":"Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. Scalable long read self-correction and assembly polishing with multiple sequence alignment. <i>Scientific Reports</i>, 2021, 11 (1), pp.1-13. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41598-020-80757-5\">⟨10.1038/s41598-020-80757-5⟩</a>. <a target=\"_blank\" href=\"https://cnrs.hal.science/hal-03210290\">⟨hal-03210290⟩</a>",
"title_s":["Scalable long read self-correction and assembly polishing with multiple sequence alignment"],
"authFullName_s":["Pierre Morisse",
"Camille Marchet",
"Antoine Limasset",
"Thierry Lecroq",
"Arnaud Lefebvre"],
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"citationFull_s":"Camille Marchet, Yoann Dufresne, Antoine Limasset. Read correction for non-uniform coverages. 2021. <a target=\"_blank\" href=\"https://pasteur.hal.science/pasteur-03263392\">⟨pasteur-03263392⟩</a>",
"title_s":["Read correction for non-uniform coverages"],
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"Yoann Dufresne",
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"citationRef_s":"<i>Genome Research</i>, 2021, 31 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1101/gr.260604.119\">⟨10.1101/gr.260604.119⟩</a>",
"citationFull_s":"Camille Marchet, Christina Boucher, Simon Puglisi, Paul Medvedev, Mikaël Salson, et al.. Data structures based on k -mers for querying large collections of sequencing data sets. <i>Genome Research</i>, 2021, 31 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1101/gr.260604.119\">⟨10.1101/gr.260604.119⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03165261\">⟨hal-03165261⟩</a>",
"title_s":["Data structures based on k -mers for querying large collections of sequencing data sets"],
"authFullName_s":["Camille Marchet",
"Christina Boucher",
"Simon Puglisi",
"Paul Medvedev",
"Mikaël Salson",
"Rayan Chikhi"],
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"citationFull_s":"Antoine Limasset, Camille Marchet, Mael Kerbiriou. BLight: efficient exact associative structure for k-mers. <i>Bioinformatics</i>, 2021, 37 (18), pp.2858-2865. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btab217\">⟨10.1093/bioinformatics/btab217⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03443183\">⟨hal-03443183⟩</a>",
"title_s":["BLight: efficient exact associative structure for k-mers"],
"authFullName_s":["Antoine Limasset",
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"Mael Kerbiriou"],
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"citationRef_s":"<i>Bioinformatics</i>, 2020, 36 (Supplement_1), pp.i177-i185. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btaa487\">⟨10.1093/bioinformatics/btaa487⟩</a>",
"citationFull_s":"Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi. REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. <i>Bioinformatics</i>, 2020, 36 (Supplement_1), pp.i177-i185. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btaa487\">⟨10.1093/bioinformatics/btaa487⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03413006\">⟨hal-03413006⟩</a>",
"title_s":["REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets"],
"authFullName_s":["Camille Marchet",
"Zamin Iqbal",
"Daniel Gautheret",
"Mikaël Salson",
"Rayan Chikhi"],
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"citationRef_s":"<i>Discrete Applied Mathematics</i>, 2020, 92-102 (Volume 274), <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.dam.2018.03.035\">⟨10.1016/j.dam.2018.03.035⟩</a>",
"citationFull_s":"Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in bioinformatics. <i>Discrete Applied Mathematics</i>, 2020, 92-102 (Volume 274), <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.dam.2018.03.035\">⟨10.1016/j.dam.2018.03.035⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01322440\">⟨hal-01322440⟩</a>",
"title_s":["A resource-frugal probabilistic dictionary and applications in bioinformatics"],
"authFullName_s":["Camille Marchet",
"Lolita Lecompte",
"Antoine Limasset",
"Lucie Bittner",
"Pierre Peterlongo"],
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"citationRef_s":"<i>NAR Genomics and Bioinformatics</i>, 2020, 2 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nargab/lqz015\">⟨10.1093/nargab/lqz015⟩</a>",
"citationFull_s":"Camille Marchet, Pierre Morisse, Lolita Lecompte, Arnaud Lefebvre, Thierry Lecroq, et al.. ELECTOR : evaluator for long reads correction methods. <i>NAR Genomics and Bioinformatics</i>, 2020, 2 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nargab/lqz015\">⟨10.1093/nargab/lqz015⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-02371117\">⟨hal-02371117⟩</a>",
"title_s":["ELECTOR : evaluator for long reads correction methods"],
"authFullName_s":["Camille Marchet",
"Pierre Morisse",
"Lolita Lecompte",
"Arnaud Lefebvre",
"Thierry Lecroq",
"Pierre Peterlongo",
"Antoine Limasset"],
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"citationFull_s":"Camille Marchet, Christina Boucher, Simon J Puglisi, Paul Medvedev, Mikaël Salson, et al.. Data structures based on k-mers for querying large collections of sequencing datasets. 2019. <a target=\"_blank\" href=\"https://hal.science/hal-02414162\">⟨hal-02414162⟩</a>",
"title_s":["Data structures based on k-mers for querying large collections of sequencing datasets"],
"authFullName_s":["Camille Marchet",
"Christina Boucher",
"Simon J Puglisi",
"Paul Medvedev",
"Mikaël Salson",
"Rayan Chikhi"],
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"citationFull_s":"Camille Marchet. REINDEER. 2019, <a target=\"_blank\" style=\"word-break: break-all;\" href=\"https://archive.softwareheritage.org/browse/swh:1:dir:7ab009dfb65a96cb4bcf61732fd9a83184cf77e5;origin=https://hal.archives-ouvertes.fr/hal-04421684;visit=swh:1:snp:801d3f351fc1cab83bad4ca56df01f11103b5812;anchor=swh:1:rel:c07528eb6401c488758f9726dc6f4c1789719828;path=/\">⟨swh:1:dir:7ab009dfb65a96cb4bcf61732fd9a83184cf77e5;origin=https://hal.archives-ouvertes.fr/hal-04421684;visit=swh:1:snp:801d3f351fc1cab83bad4ca56df01f11103b5812;anchor=swh:1:rel:c07528eb6401c488758f9726dc6f4c1789719828;path=/⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04421684\">⟨hal-04421684⟩</a>",
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"citationRef_s":"<i>Briefings in Bioinformatics</i>, 2019, pp.1-18. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bib/bbz058\">⟨10.1093/bib/bbz058⟩</a>",
"citationFull_s":"Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne da Silva, Benjamin Istace, et al.. Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data. <i>Briefings in Bioinformatics</i>, 2019, pp.1-18. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bib/bbz058\">⟨10.1093/bib/bbz058⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02394395\">⟨hal-02394395⟩</a>",
"title_s":["Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data"],
"authFullName_s":["Leandro Lima",
"Camille Marchet",
"Ségolène Caboche",
"Corinne da Silva",
"Benjamin Istace",
"Jean-Marc Aury",
"Hélène Touzet",
"Rayan Chikhi"],
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"citationFull_s":"Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. CONSENT: Scalable self-correction of long reads with multiple sequence alignment. <i>Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing</i>, May 2019, Washinton, United States. pp.1-9, <a target=\"_blank\" href=\"https://dx.doi.org/10.1101/546630\">⟨10.1101/546630⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02435116\">⟨hal-02435116⟩</a>",
"title_s":["CONSENT: Scalable self-correction of long reads with multiple sequence alignment"],
"authFullName_s":["Pierre Morisse",
"Camille Marchet",
"Antoine Limasset",
"Thierry Lecroq",
"Arnaud Lefebvre"],
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"citationFull_s":"Camille Marchet, Maël Kerbiriou, Antoine Limasset. Efficient exact associative structure for sequencing data. <i>Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing</i>, May 2019, Whashinton, United States. pp.1-16. <a target=\"_blank\" href=\"https://hal.science/hal-02435086v2\">⟨hal-02435086v2⟩</a>",
"title_s":["Efficient exact associative structure for sequencing data",
"Indexation de graphe de De Bruijn basee sur les minimisers"],
"authFullName_s":["Camille Marchet",
"Maël Kerbiriou",
"Antoine Limasset"],
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"citationRef_s":"<i>Scientific Reports</i>, 2018, 8 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41598-018-21770-7\">⟨10.1038/s41598-018-21770-7⟩</a>",
"citationFull_s":"Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, et al.. Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data. <i>Scientific Reports</i>, 2018, 8 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41598-018-21770-7\">⟨10.1038/s41598-018-21770-7⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01924204\">⟨hal-01924204⟩</a>",
"title_s":["Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data"],
"authFullName_s":["Clara Benoit-Pilven",
"Camille Marchet",
"Emilie Chautard",
"Leandro Lima",
"Marie-Pierre Lambert",
"Gustavo Sacomoto",
"Amandine Rey",
"Audric Cologne",
"Sophie Terrone",
"Louis Dulaurier",
"Jean-Baptiste Claude",
"Cyril Bourgeois",
"Didier Auboeuf",
"Vincent Lacroix"],
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"citationRef_s":"Bioinformatics [q-bio.QM]. Université de Rennes 1, 2018. English. <a target=\"_blank\" href=\"https://www.theses.fr/\">⟨NNT : ⟩</a>",
"citationFull_s":"Camille Marchet. From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.. Bioinformatics [q-bio.QM]. Université de Rennes 1, 2018. English. <a target=\"_blank\" href=\"https://www.theses.fr/\">⟨NNT : ⟩</a>. <a target=\"_blank\" href=\"https://theses.hal.science/tel-01939193\">⟨tel-01939193⟩</a>",
"title_s":["From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.",
"Des lectures aux transcrits : méthodes de novo pour l’analyse du séquençage des transcriptomes de deuxième et troisième génération."],
"authFullName_s":["Camille Marchet"],
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