Data Analysis Using a Learning Program, a Case Study: An Application of PLAGE to a Biological Sequence Analysis. - Olivier Gascuel; Antoine Danchin (ECAI, 1988)

METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database. - T. Rouxel; Antoine Danchin; Alain Hénaut (Comput. Appl. Biosci., 1993)

Cooperative Computer System For Genome Sequence Analysis. - Claudine Médigue; Thierry Vermat; Gilles Bisson; Alain Viari; Antoine Danchin (ISMB, 1995)

Imagene: an integrated computer environment for sequence annotation and analysis. - Claudine Médigue; François Rechenmann; Antoine Danchin; Alain Viari (Bioinform., 1999)

A brief history of genome research and bioinformatics in France. - Antoine Danchin (Bioinform., 2000)

Application Domains: Genome Projects of Model Organisms. - Alfred Pühler; Doris Jording; Jörn Kalinowski; Detlev Buttgereit; Renate Renkawitz-Pohl; Lothar Altschmied; Antoine Danchin; Horst Feldmann; Hans-Peter Klenk; Manfred Krüger (Essentials of Genomics and Bioinformatics, 2002)

Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes. - Stéphanie Bocs; Antoine Danchin; Claudine Médigue (BMC Bioinform., 2002)

SubtiList: the reference database for the Bacillus subtilis genome. - Ivan Moszer; Louis M. Jones; Sandrine Moreira; Cécilia Fabry; Antoine Danchin (Nucleic Acids Res., 2002)

Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling. - Yee Leng Yap; Xue Wu Zhang; Antoine Danchin (BMC Bioinform., 2003)

Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". - Etienne Larsabal; Antoine Danchin (BMC Bioinform., 2005)

Codon Usage Domains over Bacterial Chromosomes. - Marc Bailly-Bechet; Antoine Danchin; Mudassar Iqbal; Matteo Marsili; Massimo Vergassola (PLoS Comput. Biol., 2006)

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. - Yuko Makita; Michiel J. L. de Hoon; Antoine Danchin (BMC Bioinform., 2007)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)