• 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
  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
  Duitama González C, Vicedomini R, Lemane T, Rascovan N, Richard H, Chikhi R, decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods., Microbiome 2023 Nov; 11(1): 243.
• 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; (): .
• 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
  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; (): .
• 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, 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
  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;.