The iRMSD: a local measure of sequence alignment accuracy using structural information. - Fabrice Armougom; Sébastien Moretti; Vladimir Keduas; Cédric Notredame (ISMB (Supplement of Bioinformatics), 2006)

APDB: a web server to evaluate the accuracy of sequence alignments using structural information. - Fabrice Armougom; Olivier Poirot; Sébastien Moretti; Desmond G. Higgins; Phillip Bucher; Vladimir Keduas; Cédric Notredame (Bioinform., 2006)

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. - Fabrice Armougom; Sébastien Moretti; Olivier Poirot; Stéphane Audic; Pierre Dumas; Basile Schaeli; Vladimir Keduas; Cédric Notredame (Nucleic Acids Res., 2006)

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. - Sébastien Moretti; Frédéric Reinier; Olivier Poirot; Fabrice Armougom; Stéphane Audic; Vladimir Keduas; Cédric Notredame (Nucleic Acids Res., 2006)

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. - Sébastien Moretti; Fabrice Armougom; Iain M. Wallace; Desmond G. Higgins; C. Victor Jongeneel; Cédric Notredame (Nucleic Acids Res., 2007)

Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. - Frederic B. Bastian; Gilles Parmentier; Julien Roux; Sébastien Moretti; Vincent Laudet; Marc Robinson-Rechavi (DILS, 2008)

R-Coffee: a web server for accurately aligning noncoding RNA sequences. - Sébastien Moretti; Andreas Wilm; Desmond G. Higgins; Ioannis Xenarios; Cédric Notredame (Nucleic Acids Res., 2008)

Selectome: a database of positive selection. - Estelle Proux-Wéra; Romain A. Studer; Sébastien Moretti; Marc Robinson-Rechavi (Nucleic Acids Res., 2009)

Phylogenetic Code in the Cloud - Can it Meet the Expectations? - Adam Kraut; Sébastien Moretti; Marc Robinson-Rechavi; Heinz Stockinger; Dean Flanders (HealthGrid, 2010)

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. - Paolo Di Tommaso; Sébastien Moretti; Ioannis Xenarios; Miquel Orobitg; Alberto Montanyola; Jia-Ming Chang; Jean-François Taly; Cédric Notredame (Nucleic Acids Res., 2011)

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. - Sébastien Moretti; Riccardo Murri; Sergio Maffioletti; Arnold Kuzniar; Briséïs Castella; Nicolas Salamin; Marc Robinson-Rechavi; Heinz Stockinger (HealthGrid, 2012)

ExPASy: SIB bioinformatics resource portal. - Panu Artimo; Manohar Jonnalagedda; Konstantin Arnold; Delphine Baratin; Gábor Csárdi; Edouard De Castro; Severine Duvaud; Volker Flegel; Arnaud Fortier; Elisabeth Gasteiger; Aurélien Grosdidier; Céline Hernandez; et al. (Nucleic Acids Res., 2012)

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. - Mathias Ganter; Thomas Bernard; Sébastien Moretti; Jörg Stelling; Marco Pagni (Bioinform., 2013)

Reconciliation of metabolites and biochemical reactions for metabolic networks. - Thomas Bernard; Alan J. Bridge; Anne Morgat; Sébastien Moretti; Ioannis Xenarios; Marco Pagni (Briefings Bioinform., 2014)

Selectome update: quality control and computational improvements to a database of positive selection. - Sébastien Moretti; Balazs Laurenczy; Walid H. Gharib; Briséïs Castella; Arnold Kuzniar; Hannes Schabauer; Romain A. Studer; Mario Valle; Nicolas Salamin; Heinz Stockinger; Marc Robinson-Rechavi (Nucleic Acids Res., 2014)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. - Sébastien Moretti; Olivier Martin 002; T. Van Du Tran; Alan J. Bridge; Anne Morgat; Marco Pagni (Nucleic Acids Res., 2016)

Updates in Rhea - an expert curated resource of biochemical reactions. - Anne Morgat; Thierry Lombardot; Kristian B. Axelsen; Lucila Aimo; Anne Niknejad; Nevila Hyka-Nouspikel; Elisabeth Coudert; Monica Pozzato; Marco Pagni; Sébastien Moretti; Steven Rosanoff; Joseph Onwubiko; et al. (Nucleic Acids Res., 2017)

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. - T. Van Du Tran; Sébastien Moretti; Alix T. Coste; Sara Amorim-Vaz; Dominique Sanglard; Marco Pagni (Bioinform., 2019)

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. - Frederic B. Bastian; Julien Roux; Anne Niknejad; Aurélie Comte; Sara S. Fonseca Costa; Tarcisio Mendes de Farias; Sébastien Moretti; Gilles Parmentier; Valentine Rech de Laval; Marta Rosikiewicz; Julien Wollbrett; Amina Echchiki; et al. (Nucleic Acids Res., 2021)

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. - Sébastien Moretti; T. Van Du Tran; Florence Mehl; Mark Ibberson; Marco Pagni (Nucleic Acids Res., 2021)

Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a collaborative research project. - Frédéric Burdet; Luis-Manuel Quiros-Guerrero; Olivier Kirchhoffer; Jahn Nitschke; Pierre-Marie Allard; Louis-Félix Nothias; Arnaud Gaudry; Sébastien Moretti; Robin Engler; Emerson Ferreira Queiroz; Nabil Hanna; Chunyan Wu; et al. (SWAT4HCLS, 2024)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. - Jerven T. Bolleman; Vincent Emonet; Adrian M. Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan J. Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-André Michel; Anne Morgat; et al. (CoRR, 2024)