• 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
  Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M, Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
• 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
  Duitama González C, Rangavittal S, Vicedomini R, Chikhi R, Richard H, aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets., iScience 2023 Nov; 26(11): 108057.
• 2023
  Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi, decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods, Microbiome, 2023, 11 (1), pp.1-12. ⟨10.1186/s40168-023-01670-3⟩.
• 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
  Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R, Efficient mapping of accurate long reads in minimizer space with mapquik., Genome Res 2023 Jun; (): .
• 2023
  Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi, Construction and representation of human pangenome graphs, 2023.
• 2022
  Denti L, Khorsand P, Bonizzoni P, Hormozdiari F, Chikhi R, SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads., Nat Methods 2022 Dec; (): .
• 2022
  Blassel L, Medvedev P, Chikhi R, , Mapping-friendly sequence reductions: Going beyond homopolymer compression., iScience 2022 Nov; 25(11): 105305.
• 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⟩.
• 2021
  Ekim B, Berger B, Chikhi R, , Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer., Cell Syst 2021 Sep; (): .
• 2021
  Vicedomini R, Quince C, Darling AE, Chikhi R, , Strainberry: automated strain separation in low-complexity metagenomes using long reads., Nat Commun 2021 07; 12(1): 4485.
• 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
  Lima L, Marchet C, Caboche S, Da Silva C, Istace B, Aury JM, Touzet H, Chikhi R, Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data, Brief. Bioinformatics 2019 Jun;.
• 2019
  Maël Kerbiriou, Rayan Chikhi, Parallel decompression of gzip-compressed files and random access to DNA sequences, HiCOMB'19, Proceedings of IPDPS 2019.
• 2019
  Marijon P, Chikhi R, Varré JS, Graph analysis of fragmented long-read bacterial genome assemblies, Bioinformatics 2019 Mar;.
• 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⟩.