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Yoann DUFRESNE
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Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring
T Cordier, D Forster, Y Dufresne, CIM Martins, T Stoeck, J Pawlowski
Molecular ecology resources 18 (6), 1381-1391, 2018
1462018
Norine: Update of the nonribosomal peptide resource
A Flissi, E Ricart, C Campart, M Chevalier, Y Dufresne, J Michalik, ...
Nucleic acids research 48 (D1), D465-D469, 2020
952020
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
Y Dufresne, F Lejzerowicz, LA Perret-Gentil, J Pawlowski, T Cordier
BMC bioinformatics 20, 1-6, 2019
782019
Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing
A Flissi, Y Dufresne, J Michalik, L Tonon, S Janot, L Noé, P Jacques, ...
Nucleic acids research 44 (D1), D1113-D1118, 2016
602016
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
P Pericard, Y Dufresne, L Couderc, S Blanquart, H Touzet
Bioinformatics 34 (4), 585-591, 2018
512018
Norine: A powerful resource for novel nonribosomal peptide discovery
M Pupin, Q Esmaeel, A Flissi, Y Dufresne, P Jacques, V Leclère
Synthetic and systems biotechnology 1 (2), 89-94, 2016
362016
Smiles2Monomers: a link between chemical and biological structures for polymers
Y Dufresne, L Noé, V Leclère, M Pupin
Journal of cheminformatics 7, 1-11, 2015
202015
The K-mer File Format: a standardized and compact disk representation of sets of k-mers
Y Dufresne, T Lemane, P Marijon, P Peterlongo, A Rahman, M Kokot, ...
Bioinformatics 38 (18), 4423-4425, 2022
122022
Comparing methods for constructing and representing human pangenome graphs
F Andreace, P Lechat, Y Dufresne, R Chikhi
Genome Biology 24 (1), 274, 2023
52023
Compression algorithm for colored de Bruijn graphs
A Rahman, Y Dufresne, P Medvedev
bioRxiv, 2023.05. 12.540616, 2023
32023
Construction and representation of human pangenome graphs
F Andreace, P Lechat, Y Dufresne, R Chikhi
bioRxiv, 2023.06. 02.542089, 2023
22023
A Graph-Theoretic Barcode Ordering Model for Linked-Reads
Y Dufresne, C Sun, P Marijon, D Lavenier, C Chauve, R Chikhi
WABI 2020-20th Workshop on Algorithms in Bioinformatics, 11-12, 2020
22020
BioConvert: a comprehensive format converter for life sciences
H Caro, S Dollin, A Biton, B Brancotte, D Desvillechabrol, Y Dufresne, B Li, ...
NAR Genomics and Bioinformatics 5 (3), lqad074, 2023
12023
Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics
P Pericard, Y Dufresne, S Blanquart, H Touzet
JOBIM 2017-Journées Ouvertes en Biologie, Informatique et Mathématiques, 2017
12017
Compression algorithm for colored de Bruijn graphs
A Rahman, Y Dufresne, P Medvedev
Algorithms for Molecular Biology 19 (1), 20, 2024
2024
The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k-mers with abundance.
V Levallois, F Andreace, B Le Gal, Y Dufresne, P Peterlongo
bioRxiv, 2024.02. 15.580441, 2024
2024
Efficient dynamic associative dictionary for large k-mer sets
Y Dufresne, C Marchet, R Chikhi, A Limasset
BMC BIOINFORMATICS 21 (SUPPL 20), 2020
2020
Read correction for non-uniform coverages
C Marchet, Y Dufresne, A Limasset
bioRxiv, 673624, 2019
2019
Norine, Florine, s2m: powerful bioinformatics resource and tools for the discovery of novel nonribosomal peptides, natural metabolites with versatile activities
Q Esmaeel, Y Dufresne, A Flissi, M Pupin, P Jacques, V Leclère
FEMS 2017-7th congress of Federation of European Microbiology societies, 2017
2017
Data updates on Norine, the reference Non-Ribosomal Peptide knowledge base
Y Dufresne, J Michalik, A Flissi, V Leclère, M Pupin
JOBIM 2017-Journées Ouvertes en Biologie, Informatique et Mathématiques, 2017
2017
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Articles 1–20