GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. - Sébastien Aubourg; Véronique Brunaud; Clémence Bruyère; J. Mark Cock; Richard Cooke 003; Annick Cottet; Arnaud Couloux; Patrice Déhais; Gilbert Deléage; Aymeric Duclert; Manuel Echeverria; Aimée Eschbach; et al. (Nucleic Acids Res., 2005)

SmashCommunity: a metagenomic annotation and analysis tool. - Manimozhiyan Arumugam; Eoghan D. Harrington; Konrad U. Foerstner; Jeroen Raes; Peer Bork (Bioinform., 2010)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences. - Eoghan D. Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David A. Relman (Bioinform., 2010)

Microbial Co-occurrence Relationships in the Human Microbiome. - Karoline Faust; Jarupon Fah Sathirapongsasuti; Jacques Izard; Nicola Segata; Dirk Gevers; Jeroen Raes; Curtis Huttenhower (PLoS Comput. Biol., 2012)

Addendum: Enterotypes of the human gut microbiome. - Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R. Mende; Gabriel R. Fernandes; Julien Tap; Thomas Brüls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; et al. (Nat., 2014)

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. - Mohamed Mysara; Natalie Leys; Jeroen Raes; Pieter Monsieurs (BMC Bioinform., 2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle Krogh Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; et al. (Nat., 2015)

A web application for sample size and power calculation in case-control microbiome studies. - Federico Mattiello; Bie M. P. Verbist; Karoline Faust; Jeroen Raes; William D. Shannon; Luc Bijnens; Olivier Thas (Bioinform., 2016)

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. - Mohamed Mysara; Natalie Leys; Jeroen Raes; Pieter Monsieurs (BMC Bioinform., 2016)

CoNet app: inference of biological association networks using Cytoscape. - Karoline Faust; Jeroen Raes (F1000Research, 2016)