José María Fernández

According to our database, José María Fernández authored at least 19 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

WorkflowHub: a registry for computational workflows.

Johan Gustafsson, Sean R. Wilkinson, Finn Bacall, Luca Pireddu, Stian Soiland-Reyes, Simone Leo, Stuart Owen, Nick S. Juty, José María Fernández, Björn A. Grüning, Tom Brown, Hervé Ménager, Salvador Capella-Gutiérrez, Frederik Coppens, Carole A. Goble

CoRR, 2024

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

Proceedings of the 3rd Workshop on Metadata and Research (objects) Management for Linked Open Science, 2023

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, Björn A. Grüning, Simone Leo, Luca Pireddu, Michael R. Crusoe, Johan Gustafsson, Salvador Capella-Gutiérrez, Frederik Coppens

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

2022

Packaging research artefacts with RO-Crate.

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José María Fernández, Daniel Garijo, Björn A. Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole A. Goble

Data Sci., 2022

Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows.

Raül Sirvent, Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodríguez-Navas, José María Fernández, Salvador Capella-Gutiérrez, Rosa M. Badia

Proceedings of the IEEE/ACM Workshop on Workflows in Support of Large-Scale Science, 2022

2020

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, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz

Nucleic Acids Res., 2020

2017

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, Coral Fustero Torre, Florentino Fdez-Riverola, Daniel Glez-Peña

Comput. Methods Programs Biomed., 2017

2016

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, Florentino Fdez-Riverola, Daniel Glez-Peña, David G. Pisano

Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016

2015

FUN-L: gene prioritization for RNAi screens.

Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José María Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. G. Ranea, Christine A. Orengo

Bioinform., 2015

2013

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.

Miriam Rubio-Camarillo, Gonzalo Gómez-López, José María Fernández, Alfonso Valencia, David G. Pisano

Bioinform., 2013

2011

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, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

J. Biomed. Semant., 2011

2010

The EMBRACE web service collection.

Steve Pettifer, Jon C. Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José María Fernández, Jose Manuel Rodriguez, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter M. Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten L. Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, Gert Vriend

Nucleic Acids Res., 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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

J. Biomed. Semant., 2010

Bioinformatic Software Developments in Spain.

José María Fernández, Alfonso Valencia

Proceedings of the Bioinformatics for Personalized Medicine, 2010

iHOP Web Services Family.

José María Fernández, Robert Hoffmann, Alfonso Valencia

Proceedings of the Bioinformatics for Personalized Medicine, 2010

2007

iHOP web services.

José María Fernández, Robert Hoffmann, Alfonso Valencia

Nucleic Acids Res., 2007

CARGO: a web portal to integrate customized biological information.

Ildefonso Cases, David G. Pisano, Eduardo Andrés León, Angel Carro, José María Fernández, Gonzalo Gómez-López, Jose Manuel Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas

Nucleic Acids Res., 2007

2004

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

José María Fernández, Alfonso Valencia

Bioinform., 2004

XML Databases, are Ready for Bioinformatics?

José María Fernández, Alfonso Valencia

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004