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CONSENT

 Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre
2018, ⟨swh:1:dir:435ce7c73cfd3e0a70e78e70b324124b3a7b507b;origin=https://hal.archives-ouvertes.fr/hal-04442770;visit=swh:1:snp:8052f6a704123e9d53a08f2c142ebd6e9a29a800;anchor=swh:1:rel:29f2436e25a2800c24d0d26fdc90faa7cf0fe793;path=/⟩
Logiciel hal-04442770v1
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Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

 Camille Marchet , Antoine Limasset
Recomb 2022- 26th Annual International Conference on Research in Computational Molecular Biology, May 2022, La jolla, United States
Communication dans un congrès hal-03832918v1
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Simulation of RNA sequencIng with Oxford Nanopore Technologies

 Camille Marchet , Leandro Lima
JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2
Poster de conférence hal-01929917v1
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A de novo approach to disentangle partner identity and function in holobiont systems

 Arnaud Meng , Camille Marchet , Erwan Corre , Pierre Peterlongo , Adriana A. Alberti , et al.
Microbiome, 2018, pp.1-35. ⟨10.1186/s40168-018-0481-9⟩
Article dans une revue hal-01643153v2
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Read correction for non-uniform coverages

 Camille Marchet , Yoann Dufresne , Antoine Limasset
2021
Pré-publication, Document de travail pasteur-03263392v1
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Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching

 Timothé Rouzé , Igor Martayan , Camille Marchet , Antoine Limasset
23rd International Workshop on Algorithms in Bioinformatics (WABI 2023, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.15⟩
Communication dans un congrès hal-04279798v1
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supersampler Fractionnal hitting set implementation for lightweight genomic data sketching

 Antoine Limasset , Timothé Rouzé , Igor Martayan , Camille Marchet
2023, ⟨swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/⟩
Logiciel hal-04448163v1
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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

 Hélène Lopez-Maestre , Lilia Brinza , Camille Marchet , Janice Kielbassa , Sylvère Bastien , et al.
Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw655⟩
Article dans une revue hal-01352586v1

Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

 Camille Marchet , Antoine Limasset
2022
Pré-publication, Document de travail hal-03871213v1
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Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

 Clara Benoit-Pilven , Camille Marchet , Emilie Chautard , Leandro Lima , Marie-Pierre Lambert , et al.
2017
Pré-publication, Document de travail hal-01643169v1
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ELECTOR: EvaLuation of Error Correction Tools for lOng Reads

 Lolita Lecompte , Camille Marchet , Pierre Morisse , Antoine Limasset , Pierre Peterlongo , et al.
JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2
Poster de conférence hal-01929900v1
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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 , et al.
GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩
Article dans une revue hal-01280238v1
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BLIGHT

 Camille Marchet , Antoine Limasset , Maël Kerbiriou
2017, ⟨swh:1:dir:e5e5dfd7345c521e1c211a16ae14115996bb9b5f;origin=https://hal.archives-ouvertes.fr/hal-04489902;visit=swh:1:snp:320be2f68227ca53ed1aa7f637b1f79288e7b732;anchor=swh:1:rel:96d6fee08fa540b75008627d049844c320b17fc8;path=/⟩
Logiciel hal-04489902v1
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De Novo Clustering of Long Reads by Gene from Transcriptomics Data

 Camille Marchet , Lolita Lecompte , Corinne da Silva , Corinne Cruaud , Jean-Marc Aury , et al.
Nucleic Acids Research, In press, pp.1-12. ⟨10.1093/nar/gky834⟩
Article dans une revue hal-01643156v2
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Sneak peek at the -tig sequences: useful sequences built from nucleic acid data

 Camille Marchet
2022
Pré-publication, Document de travail hal-03768446v2
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A survey of mapping algorithms in the long-reads era

 Kristoffer Sahlin , Thomas Baudeau , Bastien Cazaux , Camille Marchet
2023
Pré-publication, Document de travail hal-03934299v1
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Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

 Clara Benoit-Pilven , Camille Marchet , Emilie Chautard , Leandro Lima , Marie-Pierre Lambert , et al.
Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-018-21770-7⟩
Article dans une revue hal-01924204v1

CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets

 Camille Marchet , Lolita Lecompte , Corinne da Silva , Corinne Cruaud , Jean-Marc Aury , et al.
RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Apr 2018, Paris, France. pp.1-2
Poster de conférence hal-04360334v1

A transcriptomic approach to study marine plankton holobionts

 Arnaud Meng , Erwan Corre , Pierre Peterlongo , Camille Marchet , Adriana A. Alberti , et al.
International Conference on Holobionts, Apr 2017, Paris, France
Communication dans un congrès hal-01575069v1

BLight: efficient exact associative structure for k-mers

 Antoine Limasset , Camille Marchet , Mael Kerbiriou
Bioinformatics, 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Article dans une revue hal-03443183v1

Data structures based on k -mers for querying large collections of sequencing data sets

 Camille Marchet , Christina Boucher , Simon Puglisi , Paul Medvedev , Mikaël Salson , et al.
Genome Research, 2021, 31 (1), pp.1-12. ⟨10.1101/gr.260604.119⟩
Article dans une revue hal-03165261v1
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Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

 Leandro Lima , Camille Marchet , Ségolène Caboche , Corinne da Silva , Benjamin Istace , et al.
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Article dans une revue hal-02394395v1
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Data structures based on k-mers for querying large collections of sequencing datasets

 Camille Marchet , Christina Boucher , Simon J Puglisi , Paul Medvedev , Mikaël Salson , et al.
2019
Pré-publication, Document de travail hal-02414162v1
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A survey of mapping algorithms in the long-reads era

 Kristoffer Sahlin , Thomas Baudeau , Bastien Cazaux , Camille Marchet
Genome Biology, 2023, 24 (1), pp.133. ⟨10.1186/s13059-023-02972-3⟩
Article dans une revue hal-04279817v1
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CONSENT: Scalable self-correction of long reads with multiple sequence alignment

 Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Washinton, United States. pp.1-9, ⟨10.1101/546630⟩
Communication dans un congrès hal-02435116v1
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From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.

 Camille Marchet
Bioinformatics [q-bio.QM]. Université de Rennes 1, 2018. English. ⟨NNT : ⟩
Thèse tel-01939193v1
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PAC (Partitionned Aggregated bloom Comb trees)

 Camille Marchet , Antoine Limasset
2021, ⟨swh:1:dir:71df7ad3c1d66b4989702820283a7cc3e9bfd5e5;origin=https://hal.archives-ouvertes.fr/hal-04441806;visit=swh:1:snp:5e96275dff1a0983e64f36993e8cfa6a2bf4ee9b;anchor=swh:1:rel:9d59c913641e1e548439d22aced030ded561a90e;path=/⟩
Logiciel hal-04441806v1
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Minimal perfect hash functions in large scale bioinformatics Problem

 Antoine Limasset , Camille Marchet , Pierre Peterlongo , Lucie Bittner
JOBIM 2016, Jun 2016, Lyon, France
Poster de conférence hal-01341718v1
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REINDEER

 Camille Marchet
2019, ⟨swh:1:dir:7ab009dfb65a96cb4bcf61732fd9a83184cf77e5;origin=https://hal.archives-ouvertes.fr/hal-04421684;visit=swh:1:snp:801d3f351fc1cab83bad4ca56df01f11103b5812;anchor=swh:1:rel:c07528eb6401c488758f9726dc6f4c1789719828;path=/⟩
Logiciel hal-04421684v1
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

 Camille Marchet , Zamin Iqbal , Daniel Gautheret , Mikaël Salson , Rayan Chikhi
Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩
Article dans une revue hal-03413006v1
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