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Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. Scalable long read self-correction and assembly polishing with multiple sequence alignment. Scientific Reports, Nature Publishing Group, 2021, 11 (1), pp.1-13. ⟨10.1038/s41598-020-80757-5⟩. ⟨hal-03210290⟩
Paul Simion, Jitendra Narayan, Antoine Houtain, Alessandro Derzelle, Lyam Baudry, et al.. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Science Advances , American Association for the Advancement of Science (AAAS), 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩. ⟨hal-03406292⟩
Samuel Alizon, Frédéric Cazals, Stéphane Guindon, Claire Lemaitre, Tristan Mary-Huard, et al.. 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. [Research Report] CNRS. 2021, pp.1-35. ⟨hal-03170023⟩
Asma S. Khelifa, Cecilia Guillen Sanchez, Kevin M. Lesage, Ludovic Huot, Thomas Mouveaux, et al.. TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii. Nature Communications, Nature Publishing Group, 2021, 12, pp.116. ⟨10.1038/s41467-020-20216-x⟩. ⟨hal-03107529v2⟩
Martin Frith, Laurent Noé, Gregory Kucherov. Minimally-overlapping words for sequence similarity search. Bioinformatics, Oxford University Press (OUP), 2020, ⟨10.1093/bioinformatics/btaa1054⟩. ⟨hal-03087470⟩
Camille Marchet, Pierre Morisse, Lolita Lecompte, Arnaud Lefebvre, Thierry Lecroq, et al.. ELECTOR : evaluator for long reads correction methods. NAR Genomics and Bioinformatics, Oxford University Press, 2020, 2 (1), pp.1-12. ⟨10.1093/nargab/lqz015⟩. ⟨hal-02371117⟩
Delphine Beury, Léa Fléchon, Florence Maurier, Ségolène Caboche, Jean-Stéphane Varré, et al.. Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit. Journal of Clinical Virology, Elsevier, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩. ⟨hal-02403094⟩
Pierre Marijon. Novel components at the periphery of long read genome assembly tools. Computer Science [cs]. University of Lille, 2019. English. ⟨tel-02441360⟩
Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, et al.. miRkwood: a tool for the reliable identification of microRNAs in plant genomes. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩. ⟨hal-02265367⟩
Nicolas Guillaudeux, Catherine Belleannée, Samuel Blanquart, Jean-Stéphane Varré. Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 8, pp.1, 2019, ⟨10.7490/f1000research.1117311.1⟩. ⟨hal-02267357⟩
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. Briefings in Bioinformatics, Oxford University Press (OUP), 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩. ⟨hal-02394395⟩
Enrico Petrucci, Laurent Noé, Cinzia Pizzi, Matteo Comin. Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing. 15th International Symposium on Bioinformatics Research and Applications (ISBRA), Jun 2019, Barcelona, Spain. pp.208-219, ⟨10.1007/978-3-030-20242-2_18⟩. ⟨hal-02146404⟩
Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. CONSENT: Scalable self-correction of long reads with multiple sequence alignment. Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Washinton, United States. pp.1-9, ⟨10.1101/546630⟩. ⟨hal-02435116⟩
Camille Marchet, Maël Kerbiriou, Antoine Limasset. Indexing De Bruijn graphs with minimizers. Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Whashinton, United States. pp.1-16, ⟨10.1101/546309⟩. ⟨hal-02435086v1⟩
Florence Maurier, Delphine Beury, Léa Fléchon, Jean-Stéphane Varré, Hélène Touzet, et al.. A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology, Elsevier, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩. ⟨hal-02167880⟩
Juraj Michalik. Non-redundant sampling in RNA Bioinformatics. Bioinformatics [q-bio.QM]. Université Paris Saclay (COmUE), 2019. English. ⟨NNT : 2019SACLX009⟩. ⟨tel-02124550⟩
Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz102⟩. ⟨hal-02407243⟩
Areski Flissi, Emma Ricart, Clémentine Campart, Mickael Chevalier, Yoann Dufresne, et al.. Norine: update of the nonribosomal peptide resource. Nucleic Acids Research, Oxford University Press, 2019, ⟨10.1093/nar/gkz1000⟩. ⟨hal-02376009⟩
Jean-Stéphane Varré, Nunzio d'Agostino, Pascal Touzet, Sophie Gallina, Rachele Tamburino, et al.. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. International Journal of Molecular Sciences, MDPI, 2019, 20, ⟨10.3390/ijms20194788⟩. ⟨hal-02298474⟩
Alan Kuhnle, Victoria G. Crawford, Christina Boucher, Rayan Chikhi, Travis Gagie. Practical dynamic de Bruijn graphs. Bioinformatics, Oxford University Press (OUP), 2018, ⟨10.1093/bioinformatics/bty500⟩. ⟨hal-01935559⟩

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