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ORCIDJosé María Fernández 0001
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- affiliation: Barcelona Supercomputing Center, Barcelona, Spain
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2020 – today
- 2024
[i2]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:
WorkflowHub: a registry for computational workflows. CoRR abs/2410.06941 (2024)- 2023
- [c7]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:
The EOSC-Life Workflow Collaboratory for the Life Sciences. CoRDI 2023 - [c6]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:
A metadata schema for machine-actionable Software Management Plans. DaMaLOS 2023 - 2022
- [j11]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:
Packaging research artefacts with RO-Crate. Data Sci. 5(2): 97-138 (2022) - [c5]Raül Sirvent, Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodríguez-Navas, José María Fernández, Salvador Capella-Gutiérrez, Rosa M. Badia:
Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows. WORKS@SC 2022: 1-9 - 2021
- [i1]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:
Packaging research artefacts with RO-Crate. CoRR abs/2108.06503 (2021) - 2020
- [j10]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:
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48(Webserver-Issue): W538-W545 (2020)
2010 – 2019
- 2017
- [j9]Miriam Rubio-Camarillo, Hugo López-Fernández, Gonzalo Gómez-López, Angel Carro, José María Fernández, Coral Fustero Torre, Florentino Fdez-Riverola, Daniel Glez-Peña:
RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. Comput. Methods Programs Biomed. 138: 73-81 (2017) - 2016
- [c4]Miriam Rubio-Camarillo, Hugo López-Fernández, Gonzalo Gómez-López, Angel Carro, José María Fernández, Florentino Fdez-Riverola, Daniel Glez-Peña, David G. Pisano:
RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data. PACBB 2016: 141-149 - 2015
- [j8]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:
FUN-L: gene prioritization for RNAi screens. Bioinform. 31(12): 2052-2053 (2015) - 2013
- [j7]Miriam Rubio-Camarillo, Gonzalo Gómez-López, José María Fernández, Alfonso Valencia, David G. Pisano:
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinform. 29(13): 1687-1689 (2013) - 2011
- [j6]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:
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semant. 2: 4 (2011) - 2010
- [j5]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:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010) - [j4]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:
The EMBRACE web service collection. Nucleic Acids Res. 38(Web-Server-Issue): 683-688 (2010) - [c3]José María Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP Web Services Family. JBI 2010: 102-107 - [c2]José María Fernández, Alfonso Valencia:
Bioinformatic Software Developments in Spain. JBI 2010: 108-120
2000 – 2009
- 2007
- [j3]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:
CARGO: a web portal to integrate customized biological information. Nucleic Acids Res. 35(Web-Server-Issue): 16-20 (2007) - [j2]José María Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP web services. Nucleic Acids Res. 35(Web-Server-Issue): 21-26 (2007) - 2004
- [j1]José María Fernández, Alfonso Valencia:
YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinform. 20(15): 2455-2457 (2004) - [c1]José María Fernández, Alfonso Valencia:
XML Databases, are Ready for Bioinformatics? Spanish Bioinformatics Conference 2004: 166-170
Coauthor Index
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