InterPro-an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Bioinform., 2000)

Dotlet: diagonal plots in a Web browser. - Thomas Junier; Marco Pagni (Bioinform., 2000)

Making Sense of Score Statistics for Sequence Alignments. - Marco Pagni; C. Victor Jongeneel (Briefings Bioinform., 2001)

mmsearch: a motif arrangement language and search program. - Thomas Junier; Marco Pagni; Philipp Bucher (Bioinform., 2001)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Nucleic Acids Res., 2001)

trEST, trGEN and Hits: access to databases of predicted protein sequences. - Marco Pagni; Christian Iseli; Thomas Junier; Laurent Falquet; C. Victor Jongeneel; Philipp Bucher (Nucleic Acids Res., 2001)

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; Emmanuel Courcelle; et al. (Briefings Bioinform., 2002)

PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors. - Christian J. A. Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher (Briefings Bioinform., 2002)

The PROSITE database, its status in 2002. - Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J. A. Sigrist; Kay Hofmann; Amos Bairoch (Nucleic Acids Res., 2002)

Automated annotation of microbial proteomes in SWISS-PROT. - Alexandre Gattiker; Karine Michoud; Catherine Rivoire; Andrea H. Auchincloss; Elisabeth Coudert; Tania Lima; Paul J. Kersey; Marco Pagni; Christian J. A. Sigrist; Corinne Lachaize; Anne-Lise Veuthey; Elisabeth Gasteiger; et al. (Comput. Biol. Chem., 2003)

Swiss EMBnet node web server. - Laurent Falquet; Lorenza Bordoli; Vassilios Ioannidis; Marco Pagni; C. Victor Jongeneel (Nucleic Acids Res., 2003)

The InterPro Database, 2003 brings increased coverage and new features. - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; et al. (Nucleic Acids Res., 2003)

MyHits: a new interactive resource for protein annotation and domain identification. - Marco Pagni; Vassilios Ioannidis; Lorenzo Cerutti; Monique Zahn-Zabal; C. Victor Jongeneel; Laurent Falquet (Nucleic Acids Res., 2004)

trome, trEST and trGEN: databases of predicted protein sequences. - Peter Sperisen; Christian Iseli; Marco Pagni; Brian J. Stevenson; Philipp Bucher; C. Victor Jongeneel (Nucleic Acids Res., 2004)

JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture. - Peter Sperisen; Marco Pagni (BMC Bioinform., 2005)

InterPro, progress and status in 2005. - Nicola J. Mulder; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Paul Bradley; Peer Bork; Phillip Bucher; Lorenzo Cerutti; Richard R. Copley; Emmanuel Courcelle; et al. (Nucleic Acids Res., 2005)

Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems. - Heinz Stockinger; Marco Pagni; Lorenzo Cerutti; Laurent Falquet (e-Science, 2006)

The PROSITE database. - Nicolas Hulo; Amos Bairoch; Virginie Bulliard; Lorenzo Cerutti; Edouard De Castro; Petra S. Langendijk-Genevaux; Marco Pagni; Christian J. A. Sigrist (Nucleic Acids Res., 2006)

MyHits: improvements to an interactive resource for analyzing protein sequences. - Marco Pagni; Vassilios Ioannidis; Lorenzo Cerutti; Monique Zahn-Zabal; C. Victor Jongeneel; Jörg Hau; Olivier Martin 002; Dmitri Kuznetsov; Laurent Falquet (Nucleic Acids Res., 2007)

HitKeeper, a generic software package for hit list management. - Jörg Hau; Michael Muller; Marco Pagni (Source Code Biol. Medicine, 2007)

A Multi-protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go with HTML. - Marco Pagni; Jörg Hau; Heinz Stockinger (CCGRID, 2008)

Experience using web services for biological sequence analysis. - Heinz Stockinger; Teresa K. Attwood; Shahid Nadeem Chohan; Richard G. Côté; Philippe Cudré-Mauroux; Laurent Falquet; Pedro L. Fernandes; Robert D. Finn; Taavi Hupponen; Eija Korpelainen; Alberto Labarga; Aurélie Laugraud; et al. (Briefings Bioinform., 2008)

The Microbe browser for comparative genomics. - Alexandre Gattiker; Christophe Dessimoz; Adrian Schneider; Ioannis Xenarios; Marco Pagni; Jacques Rougemont (Nucleic Acids Res., 2009)

A Preliminary Study on the Prediction of Human Protein Functions. - Guido Bologna; Anne-Lise Veuthey; Marco Pagni; Lydie Lane; Amos Bairoch (IWINAC (1), 2011)

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)

Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. - Marco Pagni; Hélène Niculita-Hirzel; Loïc Pellissier; Anne Dubuis; Ioannis Xenarios; Antoine Guisan; Ian R. Sanders; Jérôme Goudet; Nicolas Guex (Bioinform., 2013)

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. - Thierry Schüpbach; Marco Pagni; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Lorenzo Cerutti (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)

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)

Inferring gene expression networks with hubs using a degree weighted Lasso approach. - Nurgazy Sulaimanov; Sunil Kumar; Frédéric Burdet; Mark Ibberson; Marco Pagni; Heinz Koeppl (Bioinform., 2019)

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)

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)

CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods. - Jerven T. Bolleman; Elias Crum; Iulian Dragan; Jakub Galgonek; Mark Ibberson; Tarcisio Mendes de Farias; Marek Moos; Marco Pagni; Ruben Taelman; Jirí Vondrásek; Ana Claudia Sima (SWAT4HCLS, 2024)

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)