Comparing methods for constructing and representing human pangenome graphs

Autor: Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi

Publikováno v: Genome Biology, Vol 24, Iss 1, Pp 1-19 (2023)

Abstract Background As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several

Externí odkaz: https://doaj.org/article/75120c1ff0e047c09e3f59223dc3ef0f

BioConvert: a comprehensive format converter for life sciences

Autor: 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

Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They consta

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a7a2cefc8b4c2ab1f4662fb4c9d396e
https://doi.org/10.1101/2023.03.13.532455

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

Autor: Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier, Yoann Dufresne

Publikováno v: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2019, 20 (1), pp.88. ⟨10.1186/s12859-019-2663-2⟩
BMC Bioinformatics, 2019, 20 (1), pp.88. ⟨10.1186/s12859-019-2663-2⟩
BMC Bioinformatics, Vol 20, Iss 1, Pp 1-6 (2019)

High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR amplification, it is possible to multip

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::53d84ff7f441a3358e7e342fefbd2832
https://hal-pasteur.archives-ouvertes.fr/pasteur-03263390/file/s12859-019-2663-2.pdf

MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

Autor: Samuel Blanquart, Yoann Dufresne, Loïc Couderc, Hélène Touzet, Pierre Pericard

Publikováno v: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2018, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩
Bioinformatics, Oxford University Press (OUP), 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩
Bioinformatics, 2018, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩
Bioinformatics, 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩

Motivation Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bb6c6d5c76c59db079a6f15a0bb7810c
https://hal-pasteur.archives-ouvertes.fr/pasteur-03263400

Norine: a powerful resource for novel nonribosomal peptide discovery

Autor: Valérie Leclère, Qassim Esmaeel, Maude Pupin, Yoann Dufresne, Philippe Jacques, Areski Flissi

Publikováno v: Synthetic and Systems Biotechnology
Synthetic and Systems Biotechnology, KeAi, 2015, ⟨10.1016/j.synbio.2015.11.001⟩
Synthetic and Systems Biotechnology, 2015, ⟨10.1016/j.synbio.2015.11.001⟩
Synthetic and Systems Biotechnology, Vol 1, Iss 2, Pp 89-94 (2016)

International audience; Since its first release in 2008, Norine remains the unique resource completely devoted to nonribosomal peptides (NRPs). They are very attractive microbial secondary metabolites, displaying a remarkable diversity of structure a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::66dd550857517d3afa456ab9e53cc1c7
https://hal.inria.fr/hal-01250614/file/ssb2015.pdf