PipeAlign: a new toolkit for protein family analysis. - Frédéric Plewniak; Laurent Bianchetti; Yann Brelivet; Annaick Carles; Frédéric Chalmel; Odile Lecompte; Thiebaut Mochel; Luc Moulinier; Arnaud Muller; Jean Muller; Veronique Prigent; Raymond Ripp; et al. (Nucleic Acids Res., 2003)

GOAnno: GO annotation based on multiple alignment. - Frédéric Chalmel; Aurélie Lardenois; Julie Dawn Thompson; Jean Muller; José-Alain Sahel; Thierry Léveillard; Olivier Poch (Bioinform., 2005)

ICDS database: interrupted CoDing sequences in prokaryotic genomes. - Emmanuel Perrodou; Caroline Deshayes; Jean Muller; Christine Schaeffer; Alain Van Dorsselaer; Raymond Ripp; Olivier Poch; Jean-Marc Reyrat; Odile Lecompte (Nucleic Acids Res., 2006)

A maximum likelihood approximation method for Dirichlet's parameter estimation. - Nicolas Wicker; Jean Muller; Ravi Kiran Reddy Kalathur; Olivier Poch (Comput. Stat. Data Anal., 2008)

eggNOG: automated construction and annotation of orthologous groups of genes. - Lars Juhl Jensen; Philippe Julien; Michael Kuhn 004; Christian von Mering; Jean Muller; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2008)

STRING 8 - a global view on proteins and their functional interactions in 630 organisms. - Lars Juhl Jensen; Michael Kuhn 004; Manuel Stark; Samuel Chaffron; Christopher J. Creevey; Jean Muller; Tobias Doerks; Philippe Julien; Alexander Roth 001; Milan Simonovic; Peer Bork; Christian von Mering (Nucleic Acids Res., 2009)

AQUA: automated quality improvement for multiple sequence alignments. - Jean Muller; Christopher J. Creevey; Julie Dawn Thompson; Detlev Arendt; Peer Bork (Bioinform., 2010)

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. - Jean Muller; Damian Szklarczyk; Philippe Julien; Ivica Letunic; Alexander Roth 001; Michael Kuhn 004; Sean Powell; Christian von Mering; Tobias Doerks; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2010)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. - Damian Szklarczyk; Andrea Franceschini; Michael Kuhn 004; Milan Simonovic; Alexander Roth 001; Pablo Minguez; Tobias Doerks; Manuel Stark; Jean Muller; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2011)

Identifying Single Copy Orthologs in Metazoa. - Christopher J. Creevey; Jean Muller; Tobias Doerks; Julie Dawn Thompson; Detlev Arendt; Peer Bork (PLoS Comput. Biol., 2011)

MSV3d: database of human MisSense variants mapped to 3D protein structure. - Tien-Dao Luu; Alin-Mihai Rusu; Vincent Walter; Raymond Ripp; Luc Moulinier; Jean Muller; Thierry Toursel; Julie Dawn Thompson; Olivier Poch; Hoan Nguyen (Database J. Biol. Databases Curation, 2012)

KD4v: comprehensible knowledge discovery system for missense variant. - Tien-Dao Luu; Alin Rusu; Vincent Walter; Benjamin Linard; Laetitia Poidevin; Raymond Ripp; Luc Moulinier; Jean Muller; Wolfgang Raffelsberger; Nicolas Wicker; Odile Lecompte; Julie Dawn Thompson; et al. (Nucleic Acids Res., 2012)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. - Sean Powell; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Michael Kuhn 004; Jean Muller; Roland Arnold; Thomas Rattei; Ivica Letunic; Tobias Doerks; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2012)

AnnotSV: an integrated tool for structural variations annotation. - Véronique Geoffroy; Yvan Herenger; Arnaud Kress; Corinne Stoetzel; Amélie Piton; Hélène Dollfus; Jean Muller (Bioinform., 2018)

AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis. - Véronique Geoffroy; Thomas Guignard; Arnaud Kress; Jean-Baptiste Gaillard; Tor Solli-Nowlan; Audrey Schalk; Vincent Gatinois; Hélène Dollfus; Sophie Scheidecker; Jean Muller (Nucleic Acids Res., 2021)

The AnnotSV webserver in 2023: updated visualization and ranking. - Véronique Geoffroy; Jean-Baptiste Lamouche; Thomas Guignard; Samuel Nicaise; Arnaud Kress; Sophie Scheidecker; Antony Le Béchec; Jean Muller (Nucleic Acids Res., 2023)