Rafael Jimenez

Rafael Jimenez

ELIXIR Chief Technical Officer - ELIXIR directorate

ORCID iD: 0000-0001-5404-7670

Tel:+44 (0)1223 492 574 / Fax:+44 (0)1223 494 468

Publications

2013

A new reference implementation of the PSICQUIC web service.
del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.
Nucleic Acids Res Volume 41 (2013) p.w601-6
DOI: 10.1093/nar/gkt392

Bioinformatics workflows and web services in systems biology made easy for experimentalists.
Jimenez RC, Corpas M.
Methods Mol Biol Volume 1021 (2013) p.299-310
DOI: 10.1007/978-1-62703-450-0_16

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics Volume 29 (2013) p.1103-1104
DOI: 10.1093/bioinformatics/btt100

Best practices in bioinformatics training for life scientists.
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.
Brief Bioinform Volume 14 (2013) p.528-537
DOI: 10.1093/bib/bbt043

iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.
Bioinformatics Volume 29 (2013) p.1919-1921
DOI: 10.1093/bioinformatics/btt306

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR 3rd, Apweiler R, Ge J, Hermjakob H, Ping P.
Circ Res Volume 113 (2013) p.1043-1053
DOI: 10.1161/circresaha.113.301151

Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez RC, Vizcaíno JA.
Methods Mol Biol Volume 1007 (2013) p.317-333
DOI: 10.1007/978-1-62703-392-3_14

2012

MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.
PLoS One Volume 7 (2012) p.e44180
DOI: 10.1371/journal.pone.0044180

The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.
Nucleic Acids Res Volume 40 (2012) p.d841-6
DOI: 10.1093/nar/gkr1088

Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC.
PLoS Comput Biol Volume 8 (2012) p.e1002789
DOI: 10.1371/journal.pcbi.1002789

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
Brief Bioinform Volume 13 (2012) p.383-389
DOI: 10.1093/bib/bbr064

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
Nat Methods Volume 8 (2011) p.528-529
DOI: 10.1038/nmeth.1637

easyDAS: automatic creation of DAS servers.
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.
BMC Bioinformatics Volume 12 (2011) p.23
DOI: 10.1186/1471-2105-12-23

Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.
Bioinformatics Volume 27 (2011) p.2616-2617
DOI: 10.1093/bioinformatics/btr433

myKaryoView: a light-weight client for visualization of genomic data.
Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, Corpas M.
PLoS One Volume 6 (2011) p.e26345
DOI: 10.1371/journal.pone.0026345

DAS writeback: a collaborative annotation system.
Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.
BMC Bioinformatics Volume 12 (2011) p.143
DOI: 10.1186/1471-2105-12-143

2008

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.
Bioinformatics Volume 24 (2008) p.2767-2772
DOI: 10.1093/bioinformatics/btn528

Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.
BMC Bioinformatics Volume 9 Suppl 8 (2008) p.s3
DOI: 10.1186/1471-2105-9-s8-s3

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H.
BMC Bioinformatics Volume 9 (2008) p.437
DOI: 10.1186/1471-2105-9-437

Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H.
Bioinformatics Volume 24 (2008) p.2119-2121
DOI: 10.1093/bioinformatics/btn387