• 2023
  Andreace F, Lechat P, Dufresne Y, Chikhi R, Comparing methods for constructing and representing human pangenome graphs., Genome Biol 2023 Nov; 24(1): 274.
• 2023
  Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y, Li B, Kornobis E, Lemoine F, Maillet N, Perrin A, Traut N, Néron B, Cokelaer T, BioConvert: a comprehensive format converter for life sciences., NAR Genom Bioinform 2023 Sep; 5(3): 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⟩.
• 2022
  Dufresne Y, Lemane T, Marijon P, Peterlongo P, Rahman A, Kokot M, Medvedev P, Deorowicz S, Chikhi R, , The K-mer File Format: a standardized and compact disk representation of sets of k-mers., Bioinformatics 2022 Jul; (): .
• 2020
  Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, RayanChikhi, A Graph-Theoretic Barcode Ordering Model forLinked-Reads, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020).
• 2020
  Flissi A, Ricart E, Campart C, Chevalier M, Dufresne Y, Michalik J, Jacques P, Flahaut C, Lisacek F, Leclère V, Pupin M, , Norine: update of the nonribosomal peptide resource., Nucleic Acids Res. 2020 01; 48(D1): D465-D469.
• 2019
  Dufresne Y, Lejzerowicz F, Perret-Gentil LA, Pawlowski J, Cordier T, SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data, BMC Bioinformatics 2019 Feb;20(1):88.
• 2018
  Cordier T, Forster D, Dufresne Y, Martins CI, Stoeck T, Pawlowski J, Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring, Mol Ecol Resour 2018 Jul;.
• 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.