Pycoevol - A Python Workflow to Study Protein-protein Coevolution. - Fábio Madeira; Ludwig Krippahl (BIOINFORMATICS, 2012)

Constraining Protein Docking with Coevolution Data for Medical Research. - Ludwig Krippahl; Fábio Madeira; Pedro Barahona (AIME, 2013)

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. - Michele Tinti; Fábio Madeira; Gavuthami Murugesan; Gerta Hoxhaj; Rachel Toth; Carol MacKintosh (Database J. Biol. Databases Curation, 2014)

14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. - Fábio Madeira; Michele Tinti; Gavuthami Murugesan; Emily Berrett; Margaret Stafford; Rachel Toth; Christian Cole; Carol MacKintosh; Geoffrey J. Barton (Bioinform., 2015)

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure. - Peter V. Troshin; James B. Procter; Alexander Sherstnev; Daniel L. Barton; Fábio Madeira; Geoffrey J. Barton (Bioinform., 2018)

Recommendations for the packaging and containerizing of bioinformatics software. - Björn A. Grüning; Olivier Sallou; Pablo A. Moreno; Felipe da Veiga Leprevost; Hervé Ménager; Dan Søndergaard; Hannes L. Röst; Timo Sachsenberg; Brian O'Connor; Fábio Madeira; Victoria Dominguez Del Angel; Michael R. Crusoe; et al. (F1000Research, 2018)

The EMBL-EBI search and sequence analysis tools APIs in 2019. - Fábio Madeira; Young Mi Park; Joon Lee; Nicola Buso; Tamer Gur; Nandana Madhusoodanan; Prasad Basutkar; Adrian R. N. Tivey; Simon C. Potter; Robert D. Finn; Rodrigo Lopez (Nucleic Acids Res., 2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations. - Alex L. Mitchell; Teresa K. Attwood; Patricia C. Babbitt; Matthias Blum; Peer Bork; Alan J. Bridge; Shoshana D. Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2019)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

The European Nucleotide Archive in 2021. - Carla A. Cummins; Alisha Ahamed; Raheela Aslam; Josephine Burgin; Rajkumar Devraj; Ossama Edbali; Dipayan Gupta; Peter W. Harrison; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; et al. (Nucleic Acids Res., 2022)

Search and sequence analysis tools services from EMBL-EBI in 2022. - Fábio Madeira; Matt Pearce; Adrian R. N. Tivey; Prasad Basutkar; Joon Lee; Ossama Edbali; Nandana Madhusoodanan; Anton Kolesnikov; Rodrigo Lopez (Nucleic Acids Res., 2022)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)

Taxonomy Resolver: A Python package for building and filtering taxonomy trees. - Fábio Madeira; Nandana Madhusoodanan; Joonheung Lee; Alberto Eusebi; Ania Niewielska; Sarah Butcher (J. Open Source Softw., 2025)