• 2025
  Vicedomini R, Andreace F, Dufresne Y, Chikhi R, Duitama González C, MUSET: Set of utilities for constructing abundance unitig matrices from sequencing data., Bioinformatics 2025 Feb; (): .
• 2024
  Victor Levallois, Francesco Andreace, Bertrand Le Gal, Yoann Dufresne, Pierre Peterlongo, The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k -mers with abundance, iScience, 2024, pp.111435. ⟨10.1016/j.isci.2024.111435⟩.
• 2024
  Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González, MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data, 2024.
• 2023
  Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi, Comparing methods for constructing and representing human pangenome graphs, Genome Biology, 2023, 24 (1), pp.274. ⟨10.1186/s13059-023-03098-2⟩.
• 2023
  Hugo Caro, Sulyvan Dollin, Anne Biton, Bryan Brancotte, Dimitri Desvillechabrol, Yoann Dufresne, Blaise Li, Etienne Kornobis, Frédéric Lemoine, Nicolas Maillet, Amandine Perrin, Nicolas Traut, Bertrand Néron, Thomas Cokelaer, BioConvert: a comprehensive format converter for life sciences, NAR Genomics and Bioinformatics, 2023, 5 (3), ⟨10.1093/nargab/lqad074⟩.
• 2023
  Amatur Rahman, Yoann Dufresne, Paul Medvedev, Compression Algorithm for Colored de Bruijn Graphs, Leibniz International Proceedings in Informatics , 273 (17), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp.1-14, 2023, 978-3-95977-294-5. ⟨10.4230/LIPIcs.WABI.2023.17⟩.
• 2023
  Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi, Construction and representation of human pangenome graphs, 2023.
• 2022
  Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi, The K-mer File Format: a standardized and compact disk representation of sets of k-mers, Bioinformatics, 2022, 38 (18), pp.4423-4425. ⟨10.1093/bioinformatics/btac528⟩.
• 2020
  Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, Rayan Chikhi, A Graph-Theoretic Barcode Ordering Model for Linked-Reads, WABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩.
• 2020
  Areski Flissi, Emma Ricart, Clémentine Campart, Mickael Chevalier, Yoann Dufresne, Juraj Michalik, Philippe Jacques, Christophe Flahaut, Frederique Lisacek, Valérie Leclère, Maude Pupin, Norine: update of the nonribosomal peptide resource, Nucleic Acids Research, 2019, ⟨10.1093/nar/gkz1000⟩.
• 2019
  Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier, SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data, BMC Bioinformatics, 2019, 20 (1), pp.88. ⟨10.1186/s12859-019-2663-2⟩.
• 2018
  Tristan Cordier, Dominik Forster, Yoann Dufresne, Catarina Martins, Thorsten Stoeck, Jan Pawlowski, Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring, Molecular Ecology Resources, 2018, 18 (6), pp.1381-1391. ⟨10.1111/1755-0998.12926⟩.
• 2018
  Pericard P, Dufresne Y, Couderc L, Blanquart S, Touzet H, MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes, Bioinformatics 2018 02;34(4):585-591.
• 2016
  Pupin M, Esmaeel Q, Flissi A, Dufresne Y, Jacques P, Leclère V, Norine: A powerful resource for novel nonribosomal peptide discovery, Synth Syst Biotechnol 2016 Jun;1(2):89-94.
• 2015
  Dufresne Y, Noé L, Leclère V, Pupin M, Smiles2Monomers: a link between chemical and biological structures for polymers, J Cheminform 2015;7:62.
• 2015
  Flissi A, Dufresne Y, Michalik J, Tonon L, Janot S, Noé L, Jacques P, Leclère V, Pupin M, Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing, Nucleic Acids Res. 2016 Jan;44(D1):D1113-8.