XML Databases, are Ready for Bioinformatics? - José María Fernández 001; Alfonso Valencia (Spanish Bioinformatics Conference, 2004)

YAdumper: extracting and translating large information volumes from relational databases to structured flat files. - José María Fernández 001; Alfonso Valencia (Bioinform., 2004)

CARGO: a web portal to integrate customized biological information. - Ildefonso Cases; David G. Pisano; Eduardo Andrés León; Angel Carro; José María Fernández 001; Gonzalo Gómez-López; José Manuel Rodriguez; Jaime F. Vera; Alfonso Valencia; Ana María Rojas (Nucleic Acids Res., 2007)

iHOP web services. - José María Fernández 001; Robert Hoffmann; Alfonso Valencia (Nucleic Acids Res., 2007)

iHOP Web Services Family. - José María Fernández 001; Robert Hoffmann; Alfonso Valencia (JBI, 2010)

Bioinformatic Software Developments in Spain. - José María Fernández 001; Alfonso Valencia (JBI, 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

The EMBRACE web service collection. - Steve Pettifer; Jon C. Ison; Matús Kalas; Dave Thorne; Philip McDermott; Inge Jonassen; Ali Liaquat; José María Fernández 001; José Manuel Rodriguez; David G. Pisano; Christophe Blanchet; Mahmut Uludag; et al. (Nucleic Acids Res., 2010)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. - Miriam Rubio-Camarillo; Gonzalo Gómez-López; José María Fernández 001; Alfonso Valencia; David G. Pisano (Bioinform., 2013)

FUN-L: gene prioritization for RNAi screens. - Jonathan G. Lees; Jean-Karim Hériché; Ian Morilla; José María Fernández 001; Priit Adler; Martin Krallinger; Jaak Vilo; Alfonso Valencia; Jan Ellenberg; Juan A. G. Ranea; Christine A. Orengo (Bioinform., 2015)

RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data. - Miriam Rubio-Camarillo; Hugo López-Fernández; Gonzalo Gómez-López; Angel Carro; José María Fernández 001; Florentino Fdez-Riverola; Daniel Glez-Peña; David G. Pisano (PACBB, 2016)

RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. - Miriam Rubio-Camarillo; Hugo López-Fernández; Gonzalo Gómez-López; Angel Carro; José María Fernández 001; Coral Fustero Torre; Florentino Fdez-Riverola; Daniel Glez-Peña (Comput. Methods Programs Biomed., 2017)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows. - Raül Sirvent; Javier Conejero; Francesc Lordan; Jorge Ejarque; Laura Rodríguez-Navas; José María Fernández 001; Salvador Capella-Gutiérrez; Rosa M. Badia (WORKS@SC, 2022)

Packaging research artefacts with RO-Crate. - Stian Soiland-Reyes; Peter Sefton; Mercè Crosas; Leyla Jael Castro; Frederik Coppens; José María Fernández 001; Daniel Garijo; Björn A. Grüning; Marco La Rosa; Simone Leo; Eoghan Ó Carragáin; Marc Portier; et al. (Data Sci., 2022)

The EOSC-Life Workflow Collaboratory for the Life Sciences. - Carole A. Goble; Finn Bacall; Stian Soiland-Reyes; Stuart Owen; Ignacio Eguinoa; Bert Droesbeke; Hervé Ménager; Laura Rodríguez-Navas; José María Fernández 001; Björn A. Grüning; Simone Leo; Luca Pireddu; et al. (CoRDI, 2023)

A metadata schema for machine-actionable Software Management Plans. - Leyla Jael Castro; Dietrich Rebholz-Schuhmann; Nelson Quiñones; Dimitrios Bampalikis; Olga L. Giraldo; Eva Martin Del Pico; Allegra Via; Dhwani Solanki; Lukas Geist; Fotis E. Psomopoulos; Renato Alves; José María Fernández González (DaMaLOS, 2023)

WorkflowHub: a registry for computational workflows. - Johan Gustafsson 001; Sean R. Wilkinson; Finn Bacall; Luca Pireddu; Stian Soiland-Reyes; Simone Leo; Stuart Owen; Nick S. Juty; José María Fernández 001; Björn A. Grüning; Tom Brown; Hervé Ménager; et al. (CoRR, 2024)

An Ecosystem of Services for FAIR Computational Workflows. - Sean R. Wilkinson; Johan Gustafsson 001; Finn Bacall; Khalid Belhajjame; Salvador Capella; José María Fernández González; Jacob Fosso Tande; Luiz Gadelha; Daniel Garijo; Patricia Grubel; Björn A. Grüning; Farah Zaib Khan; et al. (CoRR, 2025)