Works by Jimenez, Rafael C.

Results: 22

A new reference implementation of the PSICQUIC web service.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W601, doi. 10.1093/nar/gkt392

By:

del-Toro, Noemi;
Dumousseau, Marine;
Orchard, Sandra;
Jimenez, Rafael C.;
Galeota, Eugenia;
Launay, Guillaume;
Goll, Johannes;
Breuer, Karin;
Ono, Keiichiro;
Salwinski, Lukasz;
Hermjakob, Henning

Publication type:

Article

The IntAct molecular interaction database in 2012.

Published in:

Nucleic Acids Research, 2012, p. D841, doi. 10.1093/nar/gkr1088

By:

Kerrien, Samuel;
Aranda, Bruno;
Breuza, Lionel;
Bridge, Alan;
Broackes-Carter, Fiona;
Chen, Carol;
Duesbury, Margaret;
Dumousseau, Marine;
Feuermann, Marc;
Hinz, Ursula;
Jandrasits, Christine;
Jimenez, Rafael C.;
Khadake, Jyoti;
Mahadevan, Usha;
Masson, Patrick;
Pedruzzi, Ivo;
Pfeiffenberger, Eric;
Porras, Pablo;
Raghunath, Arathi;
Roechert, Bernd

Publication type:

Article

Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 610, doi. 10.1093/bib/bbaa106

By:

Schneider, Maria Victoria;
Jimenez, Rafael C

Publication type:

Article

Bioinformatics: scalability, capabilities and training in the data-driven era.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 2, p. 735, doi. 10.1093/bib/bbz053

By:

Schneider, Maria Victoria;
Jimenez, Rafael C.

Publication type:

Article

Best practices in bioinformatics training for life scientists.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 528, doi. 10.1093/bib/bbt043

By:

Via, Allegra;
Blicher, Thomas;
Bongcam-Rudloff, Erik;
Brazas, Michelle D.;
Brooksbank, Cath;
Budd, Aidan;
De Las Rivas, Javier;
Dreyer, Jacqueline;
Fernandes, Pedro L.;
van Gelder, Celia;
Jacob, Joachim;
Jimenez, Rafael C.;
Loveland, Jane;
Moran, Federico;
Mulder, Nicola;
Nyrönen, Tommi;
Rother, Kristian;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

Published in:

Briefings in Bioinformatics, 2012, v. 13, n. 3, p. 383, doi. 10.1093/bib/bbr064

By:

Schneider, Maria V.;
Walter, Peter;
Blatter, Marie-Claude;
Watson, James;
Brazas, Michelle D.;
Rother, Kristian;
Budd, Aidan;
Via, Allegra;
van Gelder, Celia W. G.;
Jacob, Joachim;
Fernandes, Pedro;
Nyrönen, Tommi H.;
De Las Rivas, Javier;
Blicher, Thomas;
Jimenez, Rafael C.;
Loveland, Jane;
McDowall, Jennifer;
Jones, Phil;
Vaughan, Brendan W.;
Lopez, Rodrigo

Publication type:

Article

BioContainers: an open-source and community-driven framework for software standardization.

Published in:

Bioinformatics, 2017, v. 33, n. 16, p. 2580, doi. 10.1093/bioinformatics/btx192

By:

Leprevost, Felipe da Veiga;
Grüning, Björn A.;
Aflitos, Saulo Alves;
Röst, Hannes L.;
Uszkoreit, Julian;
Barsnes, Harald;
Vaudel, Marc;
Moreno, Pablo;
Gatto, Laurent;
Weber, Jonas;
Mingze Bai;
Jimenez, Rafael C.;
Sachsenberg, Timo;
Pfeuffer, Julianus;
Alvarez, Roberto Vera;
Griss, Johannes;
Nesvizhskii, Alexey I.;
Perez-Riverol, Yasset

Publication type:

Article

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 140, doi. 10.1093/bioinformatics/btu601

By:

Corpas, Manuel;
Jimenez, Rafael C.;
Bongcam-Rudloff, Erik;
Budd, Aidan;
Brazas, Michelle D.;
Fernandes, Pedro L.;
Gaeta, Bruno;
van Gelder, Celia;
Korpelainen, Eija;
Lewitter, Fran;
McGrath, Annette;
MacLean, Daniel;
Palagi, Patricia M.;
Rother, Kristian;
Taylor, Jan;
Via, Allegra;
Watson, Mick;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

iAnn: an event sharing platform for the life sciences.

Published in:

Bioinformatics, 2013, v. 29, n. 15, p. 1919, doi. 10.1093/bioinformatics/btt306

By:

Jimenez, Rafael C.;
Albar, Juan P.;
Bhak, Jong;
Blatter, Marie-Claude;
Blicher, Thomas;
Brazas, Michelle D.;
Brooksbank, Cath;
Budd, Aidan;
De Las Rivas, Javier;
Dreyer, Jacqueline;
van Driel, Marc A.;
Dunn, Michael J.;
Fernandes, Pedro L.;
van Gelder, Celia W. G.;
Hermjakob, Henning;
Ioannidis, Vassilios;
Judge, David P.;
Kahlem, Pascal;
Korpelainen, Eija;
Kraus, Hans-Joachim

Publication type:

Article

BioJS: an open source JavaScript framework for biological data visualization.

Published in:

Bioinformatics, 2013, v. 29, n. 8, p. 1103, doi. 10.1093/bioinformatics/btt100

By:

Gómez, John;
García, Leyla J.;
Salazar, Gustavo A.;
Villaveces, Jose;
Gore, Swanand;
García, Alexander;
Martín, Maria J.;
Launay, Guillaume;
Alcántara, Rafael;
del-Toro, Noemi;
Dumousseau, Marine;
Orchard, Sandra;
Velankar, Sameer;
Hermjakob, Henning;
Zong, Chenggong;
Ping, Peipei;
Corpas, Manuel;
Jiménez, Rafael C.

Publication type:

Article

Dasty3, a WEB framework for DAS.

Published in:

Bioinformatics, 2011, v. 27, n. 18, p. 2616, doi. 10.1093/bioinformatics/btr433

By:

Villaveces, Jose M.;
Jimenez, Rafael C.;
Garcia, Leyla J.;
Salazar, Gustavo A.;
Gel, Bernat;
Mulder, Nicola;
Martin, Maria;
Garcia, Alexander;
Hermjakob, Henning

Publication type:

Article

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Published in:

Bioinformatics, 2008, v. 24, n. 23, p. 2767, doi. 10.1093/bioinformatics/btn528

By:

Gabrielle A. Reeves;
Karen Eilbeck;
Michele Magrane;
Claire ODonovan;
Luisa Montecchi-Palazzi;
Midori A. Harris;
Sandra Orchard;
Rafael C. Jimenez;
Andreas Prlic;
Tim J. P. Hubbard;
Henning Hermjakob;
Janet M. Thornton

Publication type:

Article

Dasty2, an Ajax protein DAS client.

Published in:

Bioinformatics, 2008, v. 24, n. 18, p. 2119, doi. 10.1093/bioinformatics/btn387

By:

Rafael C. Jimenez;
Antony F. Quinn;
Alexander Garcia;
Alberto Labarga;
Kieran ONeill;
Fernando Martinez;
Gustavo A. Salazar;
Henning Hermjakob

Publication type:

Article

DAS Writeback: A Collaborative Annotation System.

Published in:

2011

By:

Salazar, Gustavo A.;
Jimenez, Rafael C.;
Garcia, Alexander;
Hermjakob, Henning;
Mulder, Nicola;
Blake, Edwin

Publication type:

Product Review

easyDAS: Automatic creation of DAS servers.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 1, doi. 10.1186/1471-2105-12-23

By:

Moreno, Bernat Gel;
Jenkinson, Andrew M.;
Jimenez, Rafael C.;
Peypoch, Xavier Messeguer;
Hermjakob, Henning

Publication type:

Article

Integrating biological data -- the Distributed Annotation System.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S8-S3

By:

Jenkinson, Andrew M.;
Albrecht, Mario;
Birney, Ewan;
Blankenburg, Hagen;
Down, Thomas;
Finn, Robert D.;
Hermjakob, Henning;
Hubbard, Tim J. P.;
Jimenez, Rafael C.;
Jones, Philip;
Kähäri, Andreas;
Kulesha, Eugene;
Macías, José R.;
Reeves, Gabrielle A.;
Prlić, Andreas

Publication type:

Article

Teaching the Fundamentals of Biological Data Integration Using Classroom Games.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002789

By:

Schneider, Maria Victoria;
Jimenez, Rafael C.

Publication type:

Article

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Published in:

Frontiers in Genetics, 2015, p. 1, doi. 10.3389/fgene.2015.00197

By:

Duarte, Afonso M. S.;
Psomopoulos, Fotis E.;
Blanchet, Christophe;
Bonvin, Alexandre M. J. J.;
Corpas, Manuel;
Franc, Alain;
Jimenez, Rafael C.;
de Lucas, Jesus Marco;
Nyrönen, Tommi;
Sipos, Gergely;
Suhr, Stephanie B.

Publication type:

Article

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Published in:

2011

By:

Aranda, Bruno;
Blankenburg, Hagen;
Kerrien, Samuel;
Brinkman, Fiona S. L.;
Ceol, Arnaud;
Chautard, Emilie;
Dana, Jose M.;
De Las Rivas, Javier;
Dumousseau, Marine;
Galeota, Eugenia;
Gaulton, Anna;
Goll, Johannes;
Hancock, Robert E. W.;
Isserlin, Ruth;
Jimenez, Rafael C.;
Kerssemakers, Jules;
Khadake, Jyoti;
Lynn, David J.;
Michaut, Magali;
O'Kelly, Gavin

Publication type:

Letter to the Editor

MyDas, an Extensible Java DAS Server.

Published in:

PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0044180

By:

Salazar, Gustavo A.;
García, Leyla J.;
Jones, Philip;
Jimenez, Rafael C.;
Quinn, Antony F.;
Jenkinson, Andrew M.;
Mulder, Nicola;
Martin, Maria;
Hunter, Sarah;
Hermjakob, Henning;
Haslam, Niall James

Publication type:

Article

myKaryoView: A Light-Weight Client for Visualization of Genomic Data.

Published in:

PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0026345

By:

Jimenez, Rafael C.;
Salazar, Gustavo A.;
Gel, Bernat;
Dopazo, Joaquin;
Mulder, Nicola;
Corpas, Manuel

Publication type:

Article

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

Published in:

PLoS Biology, 2017, v. 15, n. 6, p. 1, doi. 10.1371/journal.pbio.2001414

By:

McMurry, Julie A.;
Juty, Nick;
Blomberg, Niklas;
Burdett, Tony;
Conlin, Tom;
Conte, Nathalie;
Courtot, Mélanie;
Deck, John;
Dumontier, Michel;
Fellows, Donal K.;
Gonzalez-Beltran, Alejandra;
Gormanns, Philipp;
Grethe, Jeffrey;
Hastings, Janna;
Hériché, Jean-Karim;
Hermjakob, Henning;
Ison, Jon C.;
Jimenez, Rafael C.;
Jupp, Simon;
Kunze, John

Publication type:

Article