Publications

Article dans des revues

  • 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. Scientific Reports, Nature Publishing Group, 2018, 8 (1), ⟨10.1038/s41598-018-21770-7⟩. ⟨hal-01924204⟩
  • Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, et al.. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome, BioMed Central, 2018, pp.1-35. ⟨10.1101/221424⟩. ⟨hal-01643153v2⟩
  • Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in bioinformatics. Discrete Applied Mathematics, Elsevier, 2018, pp.1-11. ⟨10.1016/j.dam.2018.03.035⟩. ⟨hal-01873312⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. De Novo Clustering of Long Reads by Gene from Transcriptomics Data. Nucleic Acids Research, Oxford University Press, In press, pp.1-12. ⟨10.1093/nar/gky834⟩. ⟨hal-01643156v2⟩
  • Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, et al.. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, BioMed Central, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩. ⟨hal-01280238⟩
  • Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, et al.. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Research, Oxford University Press, 2016, ⟨10.1093/nar/gkw655⟩. ⟨hal-01352586⟩
  • Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, et al.. Navigating in a Sea of Repeats in RNA-seq without Drowning. Lecture Notes in Bioinformatics, Springer, 2014, Proceedings of 14th Workshop on Algorithms in Bioinformatics, 8701, pp.82-96. ⟨10.1007/978-3-662-44753-6_7⟩. ⟨hal-01079947⟩

Communication dans un congrès

  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads. JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-3. ⟨hal-01930211⟩
  • Arnaud Meng, Erwan Corre, Pierre Peterlongo, Camille Marchet, Adriana Alberti, et al.. A transcriptomic approach to study marine plankton holobionts . International Conference on Holobionts, Apr 2017, Paris, France. ⟨hal-01575069⟩
  • Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. Prageu Stringology Conference , Aug 2016, Prague, Czech Republic. ⟨hal-01386744⟩

Poster

  • Lolita Lecompte, Camille Marchet, Pierre Morisse, Antoine Limasset, Pierre Peterlongo, et al.. ELECTOR: EvaLuation of Error Correction Tools for lOng Reads. JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2. ⟨hal-01929900⟩
  • Camille Marchet, Leandro Lima. Simulation of RNA sequencIng with Oxford Nanopore Technologies. JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2. ⟨hal-01929917⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets. RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Apr 2018, Paris, France. pp.1-2. ⟨hal-01929963⟩
  • Antoine Limasset, Camille Marchet, Pierre Peterlongo, Lucie Bittner. Minimal perfect hash functions in large scale bioinformatics Problem. JOBIM 2016, Jun 2016, Lyon, France. ⟨hal-01341718⟩

Pré-publication, Document de travail

  • Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, et al.. Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data. 2017. ⟨hal-01643169⟩
  • Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. 2016. ⟨hal-01322440⟩

Thèse

  • 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. ⟨tel-01939193⟩