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ORCIDRafael C. Jimenez
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2020 – today
- 2020
[j22]Leyla J. Garcia
, 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)
2010 – 2019
- 2019
- [j21]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): 8-24 (2019) - 2018
- [c1]Mateusz Kuzak, Jen Harrow, Rafael C. Jimenez, Paula Andrea Martinez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via:
Lesson Development for Open Source Software Best Practices Adoption. eScience 2018: 19-20 - [i2]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 abs/1811.08473 (2018) - 2017
- [j20]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): 2580-2582 (2017) - [j19]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): 2607-2608 (2017) - [i1]Haydee Artaza, John M. Hancock, Rafael C. Jimenez, Manuel Corpas:
PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics. PeerJ Prepr. 5: e3112 (2017) - 2016
- [j18]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): 38-47 (2016) - 2015
- [j17]Jose M. Villaveces, Rafael C. Jimenez, Pablo Porras, Noemi del-Toro, Margaret 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) - [j16]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): 140-142 (2015) - 2014
- [j15]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 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): 358-363 (2014) - 2013
- [j14]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 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): 528-537 (2013) - [j13]John Gómez, Leyla J. Garcia, 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): 1103-1104 (2013) - [j12]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 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): 1919-1921 (2013) - [j11]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): 601-606 (2013) - 2012
- [j10]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 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): 383-389 (2012) - [j9]Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan Bridge, Fiona Broackes-Carter, Carol Chen, Margaret 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): 841-846 (2012) - [j8]Maria Victoria Schneider, Rafael C. Jimenez:
Teaching the Fundamentals of Biological Data Integration Using Classroom Games. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j7]Jose M. Villaveces, Rafael C. Jimenez, Leyla J. Garcia, 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): 2616-2617 (2011) - [j6]Bernat Gel, Andrew M. Jenkinson, Rafael C. Jimenez, Xavier Messeguer Peypoch, Henning Hermjakob:
easyDAS: Automatic creation of DAS servers. BMC Bioinform. 12: 23 (2011) - [j5]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: 143 (2011)
2000 – 2009
- 2008
- [j4]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): 2119-2121 (2008) - [j3]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): 2767-2772 (2008) - [j2]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) - [j1]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)
Coauthor Index
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