Rafael C. Jimenez

Publication Activity (10 Years)

Years Active: 2008-2021
Publications (10 Years): 13

Top Topics

Biological Data

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Maria Victoria Schneider, Rafael C. Jimenez
Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era. Briefings Bioinform. 22 (1) (2021)
Leyla J. García, Erick Antezana, Alexander García Castro, Evan Bolton, Rafael C. Jimenez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama
Ten simple rules to run a successful BioHackathon. PLoS Comput. Biol. 16 (5) (2020)
Daniel S. Katz, Lois Curfman McInnes, David E. Bernholdt, Abigail Cabunoc Mayes, Neil P. Chue Hong, Jonah Duckles, Sandra Gesing, Michael A. Heroux, Simon Hettrick, Rafael C. Jimenez, Marlon E. Pierce, Belinda Weaver, Nancy Wilkins-Diehr
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained. Comput. Sci. Eng. 21 (2) (2019)
Daniel S. Katz, Lois Curfman McInnes, David E. Bernholdt, Abigail Cabunoc Mayes, Neil P. Chue Hong, Jonah Duckles, Sandra Gesing, Michael A. Heroux, Simon Hettrick, Rafael C. Jimenez, Marlon E. Pierce, Belinda Weaver, Nancy Wilkins-Diehr
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained. CoRR (2018)
Mateusz Kuzak, Jen Harrow, Rafael C. Jimenez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via
Lesson Development for Open Source Software Best Practices Adoption. eScience (2018)
Haydee Artaza, John M. Hancock, Rafael C. Jimenez, Manuel Corpas
PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics. PeerJ Prepr. 5 (2017)
Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol
BioContainers: an open-source and community-driven framework for software standardization. Bioinform. 33 (16) (2017)
Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck
The future of metabolomics in ELIXIR. F1000Research 6 (2017)
Carlos Horro, Martin Cook, Teresa K. Attwood, Michelle D. Brazas, John M. Hancock, Patricia M. Palagi, Manuel Corpas, Rafael C. Jimenez
BioCIDER: a Contextualisation InDEx for biological Resources discovery. Bioinform. 33 (16) (2017)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Haydee Artaza, Neil Chue Hong, Manuel Corpas, Angel Corpuz, Rob W. W. Hooft, Rafael C. Jimenez, Brane Leskosek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vareková, Thomas Van Parys, Daniel Vaughan
Top 10 metrics for life science software good practices. F1000Research 5 (2016)
Jose M. Villaveces, Rafael C. Jimenez, Pablo Porras, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Sandra E. Orchard, H. Choi, Peipei Ping, N. C. Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database J. Biol. Databases Curation 2015 (2015)
Manuel Corpas, Rafael C. Jimenez, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas, Pedro L. Fernandes, Bruno A. Gaëta, Celia W. G. van Gelder, Eija Korpelainen, Fran Lewitter, Annette McGrath, Daniel MacLean, Patricia M. Palagi, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson, Maria Victoria Schneider, Teresa K. Attwood
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers. Bioinform. 31 (1) (2015)
Sandra E. Orchard, Mais G. Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Eugenia Galeota, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jimenez, Jyoti Khadake, Astrid Lægreid, Luana Licata, Ruth C. Lovering, Birgit Meldal, Anna N. Melidoni, Mila Milagros, Daniele Peluso, Livia Perfetto, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli, Kim Van Roey, Gianni Cesareni, Henning Hermjakob
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42 (Database-Issue) (2014)
Rafael C. Jimenez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas
iAnn: an event sharing platform for the life sciences. Bioinform. 29 (15) (2013)
John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jimenez
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29 (8) (2013)
Allegra Via, Thomas Blicher, Erik Bongcam-Rudloff, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Pedro L. Fernandes, Celia W. G. van Gelder, Joachim Jacob, Rafael C. Jimenez, Jane E. Loveland, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood
Best practices in bioinformatics training for life scientists. Briefings Bioinform. 14 (5) (2013)
Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Rafael C. Jimenez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwínski, Henning Hermjakob
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Maria Victoria Schneider, Rafael C. Jimenez
Teaching the Fundamentals of Biological Data Integration Using Classroom Games. PLoS Comput. Biol. 8 (12) (2012)
Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro L. Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jimenez, Jane E. Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. Briefings Bioinform. 13 (3) (2012)
Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan Bridge, Fiona Broackes-Carter, Carol Chen, Margaret J. Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits, Rafael C. Jimenez, Jyoti Khadake, Usha Mahadevan, Patrick Masson, Ivo Pedruzzi, Eric Pfeiffenberger, Pablo Porras, Arathi Raghunath, Bernd Roechert, Sandra E. Orchard, Henning Hermjakob
The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40 (Database-Issue) (2012)
Bernat Gel, Andrew M. Jenkinson, Rafael C. Jimenez, Xavier Messeguer Peypoch, Henning Hermjakob
easyDAS: Automatic creation of DAS servers. BMC Bioinform. 12 (2011)
Gustavo A. Salazar, Rafael C. Jimenez, Alexander García Castro, Henning Hermjakob, Nicola J. Mulder, Edwin H. Blake
DAS Writeback: A Collaborative Annotation System. BMC Bioinform. 12 (2011)
Jose M. Villaveces, Rafael C. Jimenez, Leyla J. García, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob
Dasty3, a WEB framework for DAS. Bioinform. 27 (18) (2011)
Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic
Integrating biological data - the Distributed Annotation System. BMC Bioinform. 9 (S-8) (2008)
Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinform. 24 (23) (2008)
Kieran O'Neill, Alexander García Castro, Anita Schwegmann, Rafael C. Jimenez, Dan Jacobson, Henning Hermjakob
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinform. 9 (2008)
Rafael C. Jimenez, Antony F. Quinn, Alexander García Castro, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, Henning Hermjakob
Dasty2, an Ajax protein DAS client. Bioinform. 24 (18) (2008)