Rodrigo Lopez

Rodrigo Lopez

Head of Web Production - Web production

Vet. Med Degree 1984, Oslo Vet.Hoyskole and NASAS Cand. Scient. Molecular Toxicology and Informatics 1987, University of Oslo.At EMBL-EBI since 1995.

Tel:+44 (0)1223 494 423 / Fax:+44 (0)1223 494 468

Web production

The Web production team, led by Rodrigo Lopez, focuses on three major areas of service: developing and providing platforms for web services; maintaining web infrastructure; and providing robust and secure frameworks for deploying public bioinformatics services. The team maintains and develops the EBI search engine and job dispatcher framework as well as their corresponding SOAP/REST Web Services. Web production also provides access to core services for project management (document management, project documentation and issue tracking, source code control) and user support.

Publications

2013

The Annotation-enriched non-redundant patent sequence databases
Li, W., Kondratowicz B., McWilliam H., Nauche S., and Lopez R.
Database: The Journal of Biological Databases and Curation. Volume 2013, (2013), doi:
Facing growth in the European Nucleotide Archive
Cochrane, G., ALAKO B., Amid C., Bower L., Cerdeño-Tárraga A., Cleland I., Gibson R., Goodgame N., JANG M., Kay S., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D30–D35
The EBI enzyme portal
Alcántara, R., ONWUBIKO J., CAO H., De Matos P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D773–D780 doi:
EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats
Ison, Jon, Kalaš Matúš, Jonassen Inge, Bolser Dan, Uludag Mahmut, McWilliam Hamish, Malone James, Lopez Rodrigo, Pettifer Steve, and Rice Peter
Bioinformatics. (2013), doi:
The IMGT/HLA database
Robinson, James, Halliwell Jason A., McWilliam Hamish, Lopez Rodrigo, Parham Peter, and Marsh Steven G. E.
Nucleic acids research. Volume 41, Number D1, (2013), p.D1222–D1227 doi:
IPD—the Immuno Polymorphism Database
Robinson, James, Halliwell Jason A., McWilliam Hamish, Lopez Rodrigo, and Marsh Steven G. E.
Nucleic acids research. Volume 41, Number D1, (2013), p.D1234–D1240 doi:
Analysis Tool Web Services from the EMBL-EBI
McWilliam, Hamish, Li Weizhong, Uludag Mahmut, Squizzato Silvano, Park Young Mi, Buso Nicola, Cowley Andrew Peter, and Lopez Rodrigo
Nucleic acids research. (2013), doi: 10.1093/nar/gkt376
Update on activities at the Universal Protein Resource (UniProt) in 2013
Apweiler, Rolf, Martin Maria Jesus, O'Donovan Claire, Magrane Michele, Alam-Faruque Yasmin, Alpi Emanuele, Antunes Ricardo, Arganiska Joanna, Casanova Elisabet Barrera, Bely Benoit, et al.
NUCLEIC ACIDS RESEARCH. Volume 41, Number D 1, (2013), p.D43–D47 doi:

2012

PSI-Search: iterative HOE-reduced profile SSEARCH searching
Li, W., McWilliam H., GOUJON M., Cowley A., Lopez R., and Pearson W. R.
Bioinformatics. Volume 28, Number 12, (2012), p.1650–1651
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers
Schneider, M. V., Walter P., Blatter M. C., Watson J., Brazas M. D., Rother K., Budd A., Via A., van Gelder C. W. G., Jacob J., et al.
Briefings in bioinformatics. Volume 13, Number 3, (2012), p.383–389
InterPro in 2011: new developments in the family and domain prediction database
HUNTER, S., Jones P., Mitchell A., Apweiler R., Attwood T. K., Bateman A., Bernard T., Binns D., Bork P., BURGE S., et al.
Nucleic acids research. Volume 40, Number D1, (2012), p.D306–D312 doi:

2011

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm A., Dineen D., Gibson T. J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., et al.
Molecular systems biology. Volume 7, Number 1, (2011),

2010

Non-redundant patent sequence databases with value-added annotations at two levels
Li, W., McWilliam H., de la Torre A. R., Grodowski A., Benediktovich I., GOUJON M., Nauche S., and Lopez R.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D52–D56
Fast and efficient searching of biological data resources—using EB-eye
Valentin, F., Squizzato S., GOUJON M., McWilliam H., Paern J., and Lopez R.
Briefings in bioinformatics. Volume 11, Number 4, (2010), p.375–384
IPD—the immuno polymorphism database
Robinson, J., Mistry K., McWilliam H., Lopez R., and Marsh S. G. E.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D863–D869
BioCatalogue: a universal catalogue of web services for the life sciences
Bhagat, J., Tanoh F., NZUOBONTANE E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S., et al.
Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W689–W694
A new bioinformatics analysis tools framework at EMBL–EBI
GOUJON, M., McWilliam H., Li W., Valentin F., Squizzato S., Paern J., and Lopez R.
Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W695–W699

2009

BioCatalogue: a curated Web Service registry for the Life Science community
Goble, C. A., Belhajjame K., Tanoh F., Bhagat J., Wolstencroft K., Stevens R., NZUOBONTANE E., McWilliam H., Laurent T., and Lopez R.
(2009),
The imgt/hla database
Robinson, J., Waller M. J., Fail S. C., McWilliam H., Lopez R., Parham P., and Marsh S. G. E.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D1013–D1017
InterPro: the integrative protein signature database
HUNTER, S., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Bork P., Das U., Daugherty L., Duquenne L., et al.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D211–D215 doi:
Web services at the european bioinformatics institute-2009
McWilliam, H., Valentin F., GOUJON M., Li W., Narayanasamy M., Martin J., Miyar T., and Lopez R.
Nucleic acids research. Volume 37, Number suppl 2, (2009), p.W6–W10

2008

Using the molecular biology data
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Biotechnology Set, Second Edition. (2008), p.281–300
Data curation+ process curation= data integration+ science
Goble, C., Stevens R., Hull D., Wolstencroft K., and Lopez R.
Briefings in bioinformatics. Volume 9, Number 6, (2008), p.506–517
Herramientas para el manejo de datos biológicos en el EMBL-EBI
Lopez, R.
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
Biological Data Resources at the EMBL-EBI
Lopez, R.
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
Chica, C., LABARGA A., Gould C. M., López R., and Gibson T. J.
BMC bioinformatics. Volume 9, Number 1, (2008), p.229

2007

Bioinformatics: Using the Molecular Biology Data
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Essentials of Genomics and Bioinformatics. (2007), p.265–284
New developments in the InterPro database
Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., et al.
Nucleic Acids Research. Volume 35, Number suppl 1, (2007), p.D224–D228 doi:
Web services at the European bioinformatics institute
LABARGA, A., Valentin F., Anderson M., and Lopez R.
Nucleic acids research. Volume 35, Number suppl 2, (2007), p.W6–W11
EMBL nucleotide sequence database in 2006
Kulikova, T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D16–D20
Clustal W and Clustal X version 2.0
Larkin, MA, Blackshields G., Brown N. P., Chenna R., McGettigan PA, McWilliam H., Valentin F., Wallace IM, Wilm A., Lopez R., et al.
Bioinformatics. Volume 23, Number 21, (2007), p.2947–2948

2006

The Universal Protein Resource (UniProt): an expanding universe of protein information
Wu, C. H., Apweiler R., Bairoch A., NATALE D. A., Barker W. C., BOECKMANN B., Ferro S., GASTEIGER E., HUANG H., Lopez R., et al.
Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D187–D191
EMBL nucleotide sequence database: developments in 2005
Cochrane, G., Aldebert P., Althorpe N., Andersson M., Baker W., Baldwin A., Bates K., Bhattacharyya S., Browne P., van den Broek A., et al.
Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D10–D15

2005

The EMBL nucleotide sequence database
Kanz, C., Aldebert P., Althorpe N., Baker W., Baldwin A., Bates K., Browne P., van den Broek A., CASTRO M., Cochrane G., et al.
Nucleic Acids Research. Volume 33, Number suppl 1, (2005), p.D29–D33
InterPro, progress and status in 2005
Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., et al.
Nucleic acids research. Volume 33, Number suppl 1, (2005), p.D201–D205
The universal protein resource (UniProt)
Bairoch, A., Apweiler R., Wu C. H., Barker W. C., BOECKMANN B., Ferro S., GASTEIGER E., HUANG H., Lopez R., Magrane M., et al.
Nucleic acids research. Volume 33, Number suppl 1, (2005), p.D154–D159
SOAP-based services provided by the European Bioinformatics Institute
Pillai, S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., VELANKAR S., Golovin A., Henrick K., Rice P., et al.
Nucleic acids research. Volume 33, Number suppl 2, (2005), p.W25–W28

2004

Public web-based services from the European Bioinformatics Institute
Harte, N., Silventoinen V., Quevillon E., ROBINSON S., Kallio K., Fustero X., Patel P., Jokinen P., and Lopez R.
Nucleic acids research. Volume 32, Number suppl 2, (2004), p.W3–W9
Gene-Ontology analysis reveals association of tissue-specific 5′ CpG-island genes with development and embryogenesis
Robinson, P. N., Böhme U., Lopez R., Mundlos S., and Nürnberg P.
Human molecular genetics. Volume 13, Number 17, (2004), p.1969–1978
The EMBL nucleotide sequence database
Kulikova, T., Aldebert P., Althorpe N., Baker W., Bates K., Browne P., van den Broek A., Cochrane G., Duggan K., EBERHARDT R., et al.
Nucleic Acids Research. Volume 32, Number suppl 1, (2004), p.D27–D30
The Gene Ontology annotation (GOA) database: sharing knowledge in Uniprot with Gene Ontology
Camon, E., Magrane M., Barrell D., LEE V., DIMMER E., Maslen J., Binns D., Harte N., Lopez R., and Apweiler R.
Nucleic acids research. Volume 32, Number suppl 1, (2004), p.D262–D266
UniProt: the universal protein knowledgebase
Apweiler, R., Bairoch A., Wu C. H., Barker W. C., BOECKMANN B., Ferro S., GASTEIGER E., HUANG H., Lopez R., Magrane M., et al.
Nucleic acids research. Volume 32, Number suppl 1, (2004), p.D115–D119
UniProt archive
Leinonen, R., Diez F. G., Binns D., Fleischmann W., Lopez R., and Apweiler R.
Bioinformatics. Volume 20, Number 17, (2004), p.3236–3237

2003

The European Bioinformatics Institute web site: a new view
Lopez, R., ROBINSON S., Kibria A., Harte N., Patel G., Harper R., Quevillon E., Silventoinen V., Kallio K., and Jokinen P.
Bioinformatics. Volume 19, Number 4, (2003), p.546–547
Public services from the European Bioinformatics Institute
Lopez, R., Duggan K., Harte N., and Kibria A.
Briefings in bioinformatics. Volume 4, Number 4, (2003), p.332–340
[Initial analysis of complete genome sequences of SARS coronavirus]
Chen, Y. J., Gao G., Bao Y. M., Lopez R., Wu J. M., Cai T., Ye Z. Q., Gu X. C., Luo J. C., and others
Yi chuan xue bao= Acta genetica Sinica. Volume 30, Number 6, (2003), p.493
Initial Analysis of Complete Genome Sequences of SARS Coronavirus
YunHJia, C., Ge GAO, YiHMing BAO, Lopez R., JianHMin WU, Tao CAI, ZhiHQiang YE, XiaoHCheng GU, and JingHChu LUO
遗传学报. Volume 30, Number 6, (2003),
Multiple sequence alignment with the Clustal series of programs
Chenna, R., Sugawara H., Koike T., Lopez R., Gibson T. J., Higgins D. G., and Thompson J. D.
Nucleic acids research. Volume 31, Number 13, (2003), p.3497–3500
The EMBL nucleotide sequence database: major new developments
Stoesser, G., Baker W., van den Broek A., Garcia-Pastor M., Kanz C., Kulikova T., Leinonen R., LIN Q., Lombard V., Lopez R., et al.
Nucleic Acids Research. Volume 31, Number 1, (2003), p.17–22
WU-Blast2 server at the European bioinformatics institute
Lopez, R., Silventoinen V., ROBINSON S., Kibria A., and Gish W.
Nucleic acids research. Volume 31, Number 13, (2003), p.3795–3798

2002

11 Using the Molecular Biology Data
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Essentials of Genomics and Bioinformatics. (2002), p.265
The EMBL nucleotide sequence database
Stoesser, G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Leinonen R., LIN Q., Lombard V., et al.
Nucleic acids research. Volume 30, Number 1, (2002), p.21–26
The EBI SRS server—new features
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Bioinformatics. Volume 18, Number 8, (2002), p.1149–1150
The EBI SRS server—recent developments
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Bioinformatics. Volume 18, Number 2, (2002), p.368–373

2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Apweiler, R., Attwood T. K., Bairoch A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. R., Durbin R., et al.
Nucleic acids research. Volume 29, Number 1, (2001), p.37–40
The EMBL nucleotide sequence database
Stoesser, G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Lombard V., Lopez R., Parkinson H., et al.
Nucleic Acids Research. Volume 29, Number 1, (2001), p.17–21

1999

Introduction to Molecular Biology Databases
Apweiler, R., Lopez R., Marx B., and Apweiler R.
{INTERNET ARTICLE (THE EBI ONLINE MANUAL ON MOLECULAR BIOLOGY DATABASES), ÄOnlineÜ. (1999), p.1–26
The EMBL nucleotide sequence database
Stoesser, G., Tuli M. A., Lopez R., and Sterk P.
Nucleic Acids Research. Volume 27, Number 1, (1999), p.18–24

1994

Evaluation of the exon predictions of the GRAIL software
Lopez, R., Larsen F., and Prydz H.
Genomics. Volume 24, Number 1, (1994), p.133–136

1993

An estimate of the sequencing error frequency in the DNA sequence databases
Kristensen, T., Lopez R., and Prydz H.
Mitochondrial DNA. Volume 3, Number 5, (1993), p.337–337

1992

A type-III DNA restriction and modification system in< i> Bacillus cereus?
Hegna, I. K., Karlstrøm E. S., Lopez R., Kristensen T., and KolstØ A. B.
Gene. Volume 114, Number 1, (1992), p.149–150
Cloning of a gene from< i> Bacillus cereus with homology to the< i> mreB gene from< i> Escherichia coli
Ayako, N., Naterstad K., Kristensen T., Lopez R., Bork P., and KolstØ A. B.
Gene. Volume 122, Number 1, (1992), p.181–185
Database contamination.
Lopez, R., Kristensen T., and Prydz H.
Nature. Volume 355, Number 6357, (1992), p.211
Cloning of a gene from Bacillus cereus with homology to the mreb gene of Echerichia coli
Nahara, A., Naterstad K., Kristensen T., Lopez R., Bork P., and Kolsto AB
Gene. Volume 122, (1992), p.181–185
CpG islands as gene markers in the human genome
Larsen, F., Gundersen G., Lopez R., and Prydz H.
Genomics. Volume 13, Number 4, (1992), p.1095–1107
An estimate of the sequencing error frequency in the DNA sequence databases
Kristensen, T., Lopez R., and Prydz H.
Mitochondrial DNA. Volume 2, Number 6, (1992), p.343–346

1989

New nudeotide sequence data on the EMBL Fife Server
Knack, G., Kloppstech K., Voytas DF, Ausubel FM, Alexander LJ, Stewart A. F., Mackinlay AG, Kapelinskaya TV, Tkach TM, Gorodetsky SI, et al.
Nucl. Acids Res. Volume 17, (1989), p.5380–5380

Submitted

embnet. news
BLEASBY, A., Doelz R., Herzog R., Lloyd A., and Lopez R.
(Submitted),
Adams, MD, Kerlavage, AR, Fleischmann, RD, Fuldner, RA, Bult, CJ, Lee, NH, Kirkness, EF, Weinstock, KG, Gocayne, JD and White, O.[1995],Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence',
Altschul, SF, Gish W., Miller W., Myers E. W., Lipman DJ, Araya N., Hirota K., Shimamoto Y., Miyagishi M., Yoshida E., et al.
Cancer. Volume 45, Number 1, (Submitted), p.136–139
NAR Molecular Biology Database Collection entry number 207
HUNTER, S., Jones P., Mitchell A., Apweiler R., Attwood T. K., Bateman A., Bernard T., Binns D., Bork P., BURGE S., et al.
(Submitted),
Managing BioTech Patent Texts Using XML Technology
Wang, L., Lopez R., and Stoehr P.
(Submitted),
Nucleic acids research Volume: 33 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2005 Jan
Bairoch, A., Apweiler R., Wu C. H., Barker W. C., BOECKMANN B., Ferro S., GASTEIGER E., HUANG H., Lopez R., Magrane M., et al.
Detail:. (Submitted), doi:
EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Type: Abstract Highlight Terms Highlight biological terms.
Zdobnov, E. M., Lopez R., and Apweiler R.
(Submitted),
FASTA3, BLASTs and Smith&Waterman Services at the EBI
Lopez, R.
(Submitted),

Team members

Pedro Albuquerque
Nicola Buso
Andrew Cowley
Tamer Gur
Kelly Hughes
Robert Langlois
Philip Lewis
Weizhong Li
Hamish McWilliam
Youngmi Park
Silvano Squizzato
Dietmar Sturmayr
Mahmut Uludag