Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet. A survey of mapping algorithms in the long-reads era. 2023. ⟨hal-03934299⟩

Camille Marchet. Sneak peek at the -tig sequences: useful sequences built from nucleic acid data. 2022. ⟨hal-03768446v2⟩

Clément Agret, Bastien Cazaux, Antoine Limasset. Toward Optimal Fingerprint Indexing for Large Scale Genomics. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Sep 2022, Postdam, Germany. ⟨10.1101/2021.11.04.467355v1⟩. ⟨hal-03832910⟩

Loïc Couderc, Erwan Gueguen, Maxime Brunin, Areski Flissi, Guillemette Marot, et al.. TnSeek : analysing Tn-seq data for multiple conditions and multiple species. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2022), Jul 2022, Rennes, France. ⟨hal-03827389⟩

Julie Baltenneck, Ben Moussa, Loïc Couderc, Areski Flissi, Jacques Pédron, et al.. Tn-phyto: essential genomes of nine bacterial phytopathogens. 4. International Ewinia workshop (IEW), Jul 2022, Assise, Italy. ⟨hal-03721522⟩

Hélène Touzet, Mikaël Salson, Claire Lemaitre. Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2. Interstices, 2022. ⟨hal-03750389⟩

Claire Lemaitre, Mikaël Salson, Hélène Touzet. Comment la bioinformatique a résolu le puzzle du génome du SARS-CoV-2. Interstices, 2022. ⟨hal-03896532⟩

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, et al.. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩. ⟨hal-03832903⟩

Patrick Villarese, Chrystelle Abdo, Matthieu Bertrand, Florian Thonier, Mathieu Giraud, et al.. One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia. Anton W. Langerak. Immunogenetics. Methods and Protocols, 2453, Springer, pp.43-59, 2022, Methods in Molecular Biology, 978-1-0716-2115-8. ⟨10.1007/978-1-0716-2115-8_3⟩. ⟨hal-03684695⟩

Anne Langlois de Septenville, Myriam Boudjoghra, Clotilde Bravetti, Marine Armand, Mikaël Salson, et al.. Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia. Anton W. Langerak. Immunogenetics, 2453, Springer, pp.153-167, 2022, Methods in Molecular Biology, 978-1-0716-2115-8. ⟨10.1007/978-1-0716-2115-8_10⟩. ⟨hal-03684717⟩

Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. Scalable long read self-correction and assembly polishing with multiple sequence alignment. Scientific Reports, 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 , 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩. ⟨hal-03406292⟩

Antoine Limasset, Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, et al.. STRONG: metagenomics strain resolution on assembly graphs. Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩. ⟨hal-03443171⟩

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, 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, 2020, ⟨10.1093/bioinformatics/btaa1054⟩. ⟨hal-03087470⟩

Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi. REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩. ⟨hal-03413006⟩

Camille Marchet, Pierre Morisse, Lolita Lecompte, Arnaud Lefebvre, Thierry Lecroq, et al.. ELECTOR : evaluator for long reads correction methods. NAR Genomics and Bioinformatics, 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, 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. ⟨NNT : ⟩. ⟨tel-02441360⟩