An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. - Sebastian Klie; Lennart Martens; Juan Antonio Vizcaíno; Richard G. Côté; Philip Jones; Rolf Apweiler; Alexander Hinneburg; Henning Hermjakob (German Conference on Bioinformatics, 2007)

Analysing latent topics in large-scale proteomics. - Sebastian Klie; Alexander Hinneburg; Lennart Martens; Juan Antonio Vizcaíno; Richard G. Côté; Philip Jones; Rolf Apweiler; Henning Hermjakob (LWA, 2007)

The Ontology Lookup Service: bigger and better. - Richard G. Côté; Florian Reisinger; Lennart Martens; Harald Barsnes; Juan Antonio Vizcaíno; Henning Hermjakob (Nucleic Acids Res., 2010)

The Proteomics Identifications database: 2010 update. - Juan Antonio Vizcaíno; Richard G. Côté; Florian Reisinger; Harald Barsnes; Joseph M. Foster; Jonathan Rameseder; Henning Hermjakob; Lennart Martens (Nucleic Acids Res., 2010)

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. - Nelson Ndegwa; Richard G. Côté; David Ovelleiro; Peter D'Eustachio; Henning Hermjakob; Juan Antonio Vizcaíno; David Croft 001 (Database J. Biol. Databases Curation, 2011)

PRIDE: Quality control in a proteomics data repository. - Attila Csordas; David Ovelleiro; Rui Wang; Joseph M. Foster; Daniel Rios; Juan Antonio Vizcaíno; Henning Hermjakob (Database J. Biol. Databases Curation, 2012)

Improvements in the protein identifier cross-reference service. - Samuel P. Wein; Richard G. Côté; Marine Dumousseau; Florian Reisinger; Henning Hermjakob; Juan Antonio Vizcaíno (Nucleic Acids Res., 2012)

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. - Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R. Jones; Pierre-Alain Binz; Eric W. Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra E. Orchard; Juan Antonio Vizcaíno; et al. (Database J. Biol. Databases Curation, 2013)

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. - Juan Antonio Vizcaíno; Richard G. Côté; Attila Csordas; José A. Dianes; Antonio Fabregat; Joseph M. Foster; Johannes Griss; Emanuele Alpi; Melih Birim; Javier Contell; Gavin O'Kelly; Andreas Schoenegger; et al. (Nucleic Acids Res., 2013)

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets. - Alejandro Barrera; Ana Alastruey-Izquierdo; María J. Martín; Isabel Cuesta; Juan Antonio Vizcaíno (PLoS Comput. Biol., 2014)

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. - Yasset Pérez-Riverol; Julian Uszkoreit; Aniel Sánchez; Tobias Ternent; Noemi del-Toro; Henning Hermjakob; Juan Antonio Vizcaíno; Rui Wang (Bioinform., 2015)

Development of data representation standards by the human proteome organization proteomics standards initiative. - Eric W. Deutsch; Juan P. Albar; Pierre-Alain Binz; Martin Eisenacher; Andrew R. Jones; Gerhard Mayer; Gilbert S. Omenn; Sandra E. Orchard; Juan Antonio Vizcaíno; Henning Hermjakob (J. Am. Medical Informatics Assoc., 2015)

Introducing the PRIDE Archive RESTful web services. - Florian Reisinger; Noemi del-Toro; Tobias Ternent; Henning Hermjakob; Juan Antonio Vizcaíno (Nucleic Acids Res., 2015)

Chapter 11. Data Formats of the Proteomics Standards Initiative. - Juan Antonio Vizcaíno; Simon Perkins; Andrew R. Jones; Eric W. Deutsch (Proteome Informatics, 2016)

2016 update of the PRIDE database and its related tools. - Juan Antonio Vizcaíno; Attila Csordas; Noemi del-Toro; José A. Dianes; Johannes Griss; Ilias Lavidas; Gerhard Mayer; Yasset Pérez-Riverol; Florian Reisinger; Tobias Ternent; Qing-Wei Xu; Rui Wang; et al. (Nucleic Acids Res., 2016)

Ten Simple Rules for Taking Advantage of Git and GitHub. - Yasset Pérez-Riverol; Laurent Gatto; Rui Wang; Timo Sachsenberg; Julian Uszkoreit; Felipe da Veiga Leprevost; Christian Fufezan; Tobias Ternent; Stephen J. Eglen; Daniel S. Katz; Tom J. Pollard; Alexander Konovalov 001; et al. (PLoS Comput. Biol., 2016)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

Expression Atlas: gene and protein expression across multiple studies and organisms. - Irene Papatheodorou; Nuno A. Fonseca; Maria Keays; Y. Amy Tang; Elisabet Barrera; Wojciech Bazant; Melissa L. Burke; Anja Füllgrabe; Alfonso Muñoz-Pomer Fuentes; Nancy George; Laura Huerta; Satu Koskinen; et al. (Nucleic Acids Res., 2018)

The SysteMHC Atlas project. - Wenguang Shao; Patrick G. A. Pedrioli; Witold Wolski; Christian Scurtescu; Emanuel Schmid; Juan Antonio Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S. Lindestam Arlehamn; Kerrie Vaughan; et al. (Nucleic Acids Res., 2018)

The PRIDE database and related tools and resources in 2019: improving support for quantification data. - Yasset Pérez-Riverol; Attila Csordas; Jingwen Bai 003; Manuel Bernal Llinares; Suresh Hewapathirana; Deepti Jaiswal Kundu; Avinash Inuganti; Johannes Griss; Gerhard Mayer; Martin Eisenacher; Enrique Pérez; Julian Uszkoreit; et al. (Nucleic Acids Res., 2019)

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. - Rachel Drysdale; Charles E. Cook; Robert Petryszak; Vivienne Baillie Gerritsen; Mary Barlow; Elisabeth Gasteiger; Franziska Gruhl; Jürgen Haas; Jerry Lanfear; Rodrigo Lopez; Nicole Redaschi; Heinz Stockinger; et al. (Bioinform., 2020)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

Expression Atlas update: from tissues to single cells. - Irene Papatheodorou; Pablo A. Moreno; Jonathan R. Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A. Fonseca; Anja Füllgrabe; Matthew Green 005; Ni Huang; Laura Huerta; Haider Iqbal; et al. (Nucleic Acids Res., 2020)

Expression Atlas update: gene and protein expression in multiple species. - Pablo A. Moreno; Silvie Fexova; Nancy George; Jonathan R. Manning; Zhichao Miao; Suhaib Mohammed; Alfonso Muñoz-Pomer Fuentes; Anja Füllgrabe; Yalan Bi; Natassja Bush; Haider Iqbal; Upendra Kumbham; et al. (Nucleic Acids Res., 2022)

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. - Yasset Pérez-Riverol; Jingwen Bai 003; Chakradhar Bandla; David García-Seisdedos; Suresh Hewapathirana; Selvakumar Kamatchinathan; Deepti Jaiswal Kundu; Ananth Prakash; Anika Frericks-Zipper; Martin Eisenacher; Mathias Walzer; Shengbo Wang; et al. (Nucleic Acids Res., 2022)

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. - Shengbo Wang; David García-Seisdedos; Ananth Prakash; Deepti Jaiswal Kundu; Andrew Collins 003; Nancy George; Silvie Fexova; Pablo A. Moreno; Irene Papatheodorou; Andrew R. Jones; Juan Antonio Vizcaíno (PLoS Comput. Biol., 2022)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. - Matthew Thakur; Alex Bateman; Cath Brooksbank; Mallory Ann Freeberg; Melissa Harrison; Matthew Hartley; Thomas M. Keane; Gerard J. Kleywegt; Andrew Leach; Maria Levchenko; Sarah L. Morgan; Ellen M. McDonagh; et al. (Nucleic Acids Res., 2023)

Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. - Javier Robles; Ananth Prakash; Juan Antonio Vizcaíno; J. Ignacio Casal (PLoS Comput. Biol., 2024)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)

pridepy: A Python package to download and search data from PRIDE database. - Selvakumar Kamatchinathan; Suresh Hewapathirana; Chakradhar Bandla; Santiago Insua; Juan Antonio Vizcaíno; Yasset Pérez-Riverol (J. Open Source Softw., 2025)