JBioWH: an open-source Java framework for bioinformatics data integration. - Roberto Vera; Yasset Pérez-Riverol; Sonia Pérez; Balázs Ligeti; Attila Kertész-Farkas; Sándor Pongor (Database J. Biol. Databases Curation, 2013)

Effectively addressing complex proteomic search spaces with peptide spectrum matching. - Diogo B. Lima; Yasset Pérez-Riverol; Fabio C. S. Nogueira; Gilberto B. Domont; Jesus Noda; Felipe da Veiga Leprevost; Vladimir Besada; Felipe M. G. França; Valmir Carneiro Barbosa; Aniel Sánchez; Paulo C. Carvalho (Bioinform., 2013)

A UML-based Approach to Design Parallel and Distributed Applications. - Yasset Pérez-Riverol; Roberto Vera Alvarez (CoRR, 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)

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)

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. - Enrique Audain; Yassel Ramos; Henning Hermjakob; Darren R. Flower; Yasset Pérez-Riverol (Bioinform., 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)

BioContainers: an open-source and community-driven framework for software standardization. - Felipe da Veiga Leprevost; Björn A. Grüning; Saulo Aflitos; Hannes L. Röst; Julian Uszkoreit; Harald Barsnes; Marc Vaudel; Pablo A. Moreno; Laurent Gatto; Jonas Weber; Mingze Bai; Rafael C. Jiménez; et al. (Bioinform., 2017)

Four simple recommendations to encourage best practices in research software. - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

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)

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)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

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)

Trends in Cuban research output: publications and patents. - Yasset Pérez-Riverol (CoRR, 2020)

The omics discovery REST interface. - Gaurhari Dass; Manh-Tu Vu; Pan Xu; Enrique Audain; Marc-Phillip Hitz; Björn A. Grüning; Henning Hermjakob; Yasset Pérez-Riverol (Nucleic Acids Res., 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)

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. - Husen M. Umer; Enrique Audain; Yafeng Zhu; Julianus Pfeuffer; Timo Sachsenberg; Janne Lehtiö; Rui Mamede Branca; Yasset Pérez-Riverol (Bioinform., 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)

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)

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)