Coralie Rohmer. Alignement multiple et séquençage de troisième génération. Bio-informatique [q-bio.QM]. Université de Lille, 2023. Français. ⟨NNT : ⟩. ⟨tel-04455674v1⟩

Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet. A survey of mapping algorithms in the long-reads era. Genome Biology, 2023, 24 (1), pp.133. ⟨10.1186/s13059-023-02972-3⟩. ⟨hal-04279817⟩

Mikaël Salson. Méthodes sans alignement et indexation pour l'analyse de données nucléiques massives. Informatique [cs]. Université de lille, 2023. ⟨tel-04362289⟩

Anthony Turpin, Carine Delliaux, Pauline Parent, Hortense Chevalier, Carmen Escudero-Iriarte, et al.. Fascin-1 expression is associated with neuroendocrine prostate cancer and directly suppressed by androgen receptor. British Journal of Cancer, 2023, ⟨10.1038/s41416-023-02449-x⟩. ⟨hal-04308764⟩

Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.15⟩. ⟨hal-04279798⟩

Blaise Waongo, Maude Pupin, Matthieu Duban, Gabrielle Chataigne, Oumarou Zongo, et al.. Kawal: A fermented food as a source of Bacillus strain producing antimicrobial peptides. Scientific African, 2023, 20, pp.e01714. ⟨10.1016/j.sciaf.2023.e01714⟩. ⟨hal-04426241⟩

Antoine Limasset, Timothé Rouzé, Igor Martayan, Camille Marchet. supersampler Fractionnal hitting set implementation for lightweight genomic data sketching. 2023, ⟨swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/⟩. ⟨hal-04448163⟩

Camille Marchet, Antoine Limasset. Scalable sequence database search using partitioned aggregated Bloom comb trees. Bioinformatics, 2023, 39 (Supplement_1), pp.i252-i259. ⟨10.1093/bioinformatics/btad225⟩. ⟨hal-04279824⟩

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

Zoé Postel, Daniel B. Sloan, Sophie Gallina, Cécile Godé, Eric Schmitt, et al.. The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process. New Phytologist, 2023, ⟨10.1111/nph.18966⟩. ⟨hal-04105655⟩

Hélène Touzet, Mikaël Salson, Claire Lemaitre, Florence Débarre. Le SARS-CoV-2 : une expérience inédite de surveillance génomique mondiale. 2023. ⟨hal-04155812⟩

Areski Flissi, Matthieu Duban, Philippe Jacques, Valérie Leclère, Maude Pupin. Norine: Bioinformatics Methods and Tools for the Characterization of Newly Discovered Nonribosomal Peptides. Michael Burkart; Fumihiro Ishikawa. Non-Ribosomal Peptide Biosynthesis and Engineering. Methods and Protocols, 2670, Springer US, pp.303-318, 2023, Methods in Molecular Biology, 978-1-0716-3214-7. ⟨10.1007/978-1-0716-3214-7_16⟩. ⟨hal-04119620⟩

Clément Agret, Annie Chateau, Gaetan Droc, Gautier Sarah, Manuel Ruiz, et al.. RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes. Journal of Open Source Software, 2022, 7 (80), pp.4363. ⟨10.21105/joss.04363⟩. ⟨lirmm-03920648⟩

Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, et al.. Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics, 2022, 23 (1), pp.448. ⟨10.1186/s12859-022-04983-6⟩. ⟨hal-03920854⟩

Quentin Bonenfant, Laurent Noé, Hélène Touzet. Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinformatics Advances, 2022, 3 (1), pp.vbac085. ⟨10.1093/bioadv/vbac085⟩. ⟨hal-03932719⟩

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. WABI 2022 - 22nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Postdam, Germany. pp.25:1-25:15, ⟨10.4230/LIPIcs.WABI.2022.25⟩. ⟨hal-04121819⟩

Sasha Darmon, Augustin Boudry, Mikaël Salson. FiLT3r. 2022, ⟨swh:1:dir:02f92eaac11f24854ffd36ed603827b6d41cc905;origin=https://gitlab.univ-lille.fr/filt3r/filt3r.git;visit=swh:1:snp:09358583d48462e9fe5ada490b97d16b1939c3bc;anchor=swh:1:rev:b87ce1839f7742ad0fff744f9fea96940ddcde8b⟩. ⟨hal-04398608⟩

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, Hajar 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⟩