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UniProt References

2011

Alam-Faruque, Y., Huntley, R.P., et al. (2011)
The impact of focused gene ontology curation of specific Mammalian systems.
PLoS One 6 (12), e27541.

Griss, J., Martin, M., et al. (2011)
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Proteomics 11 (22), 4434-8.

Magrane, M. and UniProt Consortium (2011)
UniProt Knowledgebase: a hub of integrated protein data.
Database (Oxford) 2011, bar009.

Patient, S. and Martin, M. (2011)
Annotating UniProt metagenomic and environmental sequences in UniMES. In: Bioinformatics 2011 – Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms.
SciTePress, pp. 367-8.

The UniProt Consortium. (2011)
Ongoing and future developments at the Universal Protein Resource.
Nucleic Acids Res. 39 (Database issue), D214-9.

Villaveces, J.M., Jimenez, R.C., et al. (2011)
Dasty3, a WEB Framework for DAS.
Bioinformatics 27 (18), 2616-7.

2010

Alam-Faruque, Y., et al. (2010).
The Renal Gene Ontology Annotation Initiative.
Organogenesis 6, 71-75.

Cochrane, G., Martin, M.J. and Apweiler, R. (2010)
Public data resources as a foundation for a worldwide metagenomics data infrastructure.
In: Metagenomics: theory, methods, and applications. Chapter 5. Marco, D., Ed. Norwich, UK: Caister Academic Press, 212 pp.

The Gene Ontology Consortium. (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Res. 38 (Database issue), 331-D335.

The UniProt Consortium. (2010).
The Universal Protein Resource (UniProt) in 2010.
Nucleic Acids Res. 38 (Database issue), D142-D148.

2009

Binns, D., et al. (2009). QuickGO: a web-based tool for Gene Ontology searching.
Bioinformatics 25, 3045-3046.
Jain, E., et al. (2009) Infrastructure for the life sciences: design and implementation of the UniProt website.
BMC Bioinformatics 10, 136.

Patient S., Wieser D., Kleen M., Kretschmann E., Jesus Martin M., Apweiler R. (2009)
UniProtJAPI: a remote API for accessing UniProt data.
Bioinformatics 24(10): 1321-1322.
abstract full-text PDF

The Universal Protein Resource (UniProt) 2009. (2009)
The UniProt Consortium
Nucleic Acids Research 37: D169-D174.
abstract full-text PDF

2008

The UniProt Consortium. (2008)
The Universal Protein Resource (UniProt).
Nucleic Acids Research 36: D190-D195.
abstract full-text PDF

2007

The UniProt Consortium. (2007)
The Universal Protein Resource (UniProt).
Nucleic. Acids Research 35: D193-D197.
abstract full-text PDF

2006

Wu C.H., Apweiler R., Bairoch A., Natale D.A, Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Mazumder R., O'Donovan C., Redaschi N. and Suzek B. (2006)
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic Acids Research 34: D187-D191.
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Leinonen R., Nardone F., Zhu W., Apweiler R. (2006)
UniSave: the UniProtKB Sequence/Annotation Version database.
Bioinformatics 22: 1284-1285.
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Magrane M., O'Donovan C. (2006)
Curator-Driven Protein Sequence Analysis and Annotation.
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 55-70, Nova Science Publishers, Inc, New York (2006).
more info

Wieser D., Kretschmann E. (2006)
Automated Annotation of Proteins.
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 71-78, Nova Science Publishers, Inc, New York (2006).
more info

2005

Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'donovan C., Redaschi N., Yeh L.S. (2005)
The Universal Protein Resource (UniProt).
Nucleic Acids Research 33: D154-D159.
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Magrane M., Martin M.J., O'Donovan C., Apweiler R. (2005)
Protein Sequence Databases.
In: Proteomics Protocols Handbook, Walker J.M. (ed.), pp. 609-618, Humana Press Inc., NJ, USA (2005).
abstract

Schneider M., Bairoch A., Wu C.H., Apweiler R. (2005)
Plant Protein Annotation in the UniProt Knowledgebase.
Plant Physiology 138(1): 59-66.
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2004

Apweiler R., Bairoch A., Wu C. H. (2004)
Protein sequence databases.
Current Opinion in Chemical Biology 8: 76-80.
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Apweiler R., Bairoch A., Wu C. H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M. J., Natale D. A., O'Donovan C., Redaschi N. and Yeh L. L. (2004)
UniProt: the Universal Protein knowledgebase
Nucleic Acids Research 32: D115-D119.
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Leinonen R., Diez F.G., Binns D., Fleischmann W., Lopez R., Apweiler R. (2004)
UniProt Archive
Bioinformatics 20: 3236-3237.
abstract full-text PDF

Martin M.J., O'Donovan C, Apweiler R. (2004)
Protein sequence database methods.
Genetic Engineering (NY) 26: 13-17.
no abstract available

Wieser D., Kretschmann E. and Apweiler R. (2004)
Filtering erroneous protein annotation.
Bioinformatics 20(1): i342–i347.
abstract full-text PDF

2003

Apweiler R., O'Donovan C., Martin M.J. (2003)
Protein Sequence Database Resources.
Screening Trends in Drug Discovery 4: 33-35.
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Boeckmann B., Bairoch A., Apweiler R., Blatter M., Estreicher A., Gasteiger E., Martin M. J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. (2003)
The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003.
Nucleic Acids Research 31: 365-370.
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2002

Magrane M., Apweiler R. (2002)
Organisation and standardisation of information in Swiss-Prot and TrEMBL.
Data Science Journal 1(1): 13-18.
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O'Donovan C., Martin M.J., Gattiker A., Gasteiger E., Bairoch A., Apweiler R. (2002)
High-quality protein knowledge resource: Swiss-Prot and TrEMBL.
Briefings in Bioinformatics 3(3): 275-284.
abstract full-text PDF

2001

Apweiler R. (2001)
Functional information in Swiss-Prot: The basis for large-scale characterisation of protein sequences.
Briefings in Bioinformatics 2: 9-18.
abstract full-text PDF

Apweiler R., Kersey P., Junker V., Bairoch A (2001)
Technical comment to "Database verification studies of Swiss-Prot and GenBank" by Karp et al.
Bioinformatics 17: 533-534.
full-text PDF

Biswas M., Kanapin A., Apweiler R. (2001)
Application of InterPro for the functional classification of the proteins of fish origin in Swiss-Prot and TrEMBL.
Journal of Bioscience 26(2): 277-284.
abstract

Kretschmann E., Fleischmann W., Apweiler R. (2001)
Automatic rule generation for protein annotation with the C4.5 data mining algorith applied on Swiss-Prot.
Bioinformatics 17: 920-926.
abstract full-text PDF

Kriventseva E.V., Fleischmann W., Zdobnov E.M., Apweiler R. (2001)
CluSTr: a database of clusters of Swiss-Prot+TrEMBL proteins.
Nucleic Acids Research 29(1): 33-36.
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O'Donovan C., Apweiler R., Bairoch A. (2001)
The human proteomics initiative (HPI).
Trends in Biotechnology 19(5): 178-181.
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2000 and earlier

Apweiler, R. (2000)
Protein sequence databases.
In: Advances in Protein Chemistry, Richards F.M., Eisenberg D.S., Kim P.S.(eds.); pp. 54:31-71, Academic Press, New York (2000).
abstract

Bairoch A., Apweiler R. (2000)
The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000.
Nucleic Acids Research 28: 45-48.
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Junker V., Contrino S., Fleischmann W., Hermjakob H., Lang F., Magrane M., Martin M.J., Mitaritonna N., O'Donovan C., Apweiler R. (2000)
The role Swiss-Prot and TrEMBL play in the genome research environment.
Journal of Biotechnology 78: 221-234.
abstract

Kersey P., Hermjakob H., Apweiler R. (2000)
VARSPLIC: alternatively-spliced protein sequences derived from Swiss-Prot and TrEMBL.
Bioinformatics 16(11): 1048-1049.
abstract full-text PDF

Magrane M., Apweiler R. (2000)
Mus musculus in the Swiss-Prot database: its relevance to developmental research.
Genesis: The Journal of Genetics and Development 26: 1-4.
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Apweiler R. (1999)
Introduction to Molecular Biology Databases.
In: The EBI Online Manual on Molecular Biology Databases, Apweiler R., Lopez R., Marx B. (1999).
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Apweiler R., Bairoch A. (1999)
The Human Proteomics Initiative of SIB and EBI.
The Bioinformer 5.
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Apweiler R., Hermjakob H., Sharon N. (1999)
On the frequency of protein glycosylation, as deduced from analysis of the Swiss-Prot database.
Biochimica et Biophysica Acta 1473: 4-8.
abstract

Bairoch A., Apweiler R. (1999)
The Swiss-Prot protein sequence data bank and its supplement TrEMBL in 1999.
Nucleic Acids Research 27: 49-54.
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Fleischmann W., Möeller S., Gateau A., Apweiler R. (1999)
A novel method for automatic functional annotation of proteins.
Bioinfomatics 15: 228-233.
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Hermjakob H., Fleischmann W., Apweiler R. (1999)
Swissknife - 'lazy parsing' of Swiss-Prot entries.
Bioinfomatics 15: 771-772.
abstract full-text PDF

Junker V., Apweiler R., Bairoch A. (1999)
Representation of functional information in the Swiss-Prot data bank.
Bioinfomatics 15: 1066-1067.
abstract full-text PDF

Möeller S., Leser U., Fleischmann W., Apweiler R. (1999)
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation.
Bioinfomatics 15: 219-227.
abstract full-text PDF

O'Donovan C., Martin M.J., Glemet E., Codani J., Apweiler R. (1999)
Removing redundancy in Swiss-Prot and TrEMBL.
Bioinfomatics 15: 258-259.
abstract full-text PDF

Apweiler R., O'Donovan C., Martin M.J., Fleischmann W., Hermjakob H., Möeller S., Contrino S. (1998)
Swiss-Prot and its computer-annotated supplement TREMBL: How to produce high quality automatic annotation.
In: Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics (SCI '98 / ISAS '98), Callaos N., Holmes L., Osers R. (eds.); Vol 4 pp. 184-191, Orlando, Florida, USA (1998).
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Apweiler R. (1998)
The Swiss-Prot + TrEMBL protein sequence database as a tool to model regulatory and metabolic pathways.
In: Modelling and Simulation of Gene Regulation and Metabolic Pathways, Collado-Vides J., Hofestaedt R., Mavrovouniotis M., Michal G. (eds.); Dagstuhl-Seminar-Report 215 pp. 23-26, Schloss Dagstuhl, Germany (1998).
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Bairoch A., Apweiler R. (1998)
The Swiss-Prot protein sequence databank and its supplement TrEMBL in 1998.
Nucleic Acids Research 26: 38-42.
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Fleischmann W., Möeller S., Gateau A., Apweiler R. (1998)
A novel method for automatic and reliable functional annotation.
In: Proceedings of the German Conference on Bioinformatics (GCB'98), Zimmermann O., Schomburg D. (eds.); Koeln, Germany (1998).


Hermjakob H., Lang F., Apweiler A. (1998)
SPTR - A comprehensive, non-redundant and up-to-date view of the protein sequence world.
CCP11 Newsletter Vol. 2.3 (July) 1998.
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Hermjakob H., Lang F., Apweiler R. (1998)
SPTR - A comprehensive, non-redundant and up-to-date protein sequence database.
The Bioinformer 4.
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Möeller S., Leser U., Fleischmann W., Apweiler R. (1998)
EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation.
In: Proceedings of the German Conference on Bioinformatics (GCB'98), Zimmermann O., Schomburg D. (eds.); Koeln, Germany (1998).
abstract

O'Donovan C., Martin M.J., Glemet E., Codani J.-J., Apweiler R. (1998)
Removing redundancy in Swiss-Prot and TrEMBL.
In: Proceedings of the German remoConference on Bioinformatics (GCB'98), Zimmermann O., Schomburg D. (eds.); Koeln, Germany (1998).
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O'Donovan C., Mitaritonna N., Apweiler R., Junker V., Gateau A., Lang F. (1998)
Glycosyltransferases in Swiss-Prot.
Glycoconjugate Journal 15: 507-509.
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Apweiler R., Gateau A., Contrino S., Martin M.J., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Bairoch A. (1997)
Protein Sequence Annotation in the Genome Era:The Annotation Concept of Swiss-Prot + TREMBL.
In: Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB), Gaasterland T., Karp P., Karplus K., Ouzounis C., Sander C., Valencia A., eds., pp. 33-43, Halkidiki, Greece (1997).
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Apweiler R., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Contrino S., Martin M. (1997)
New Developments in Biological Databases: Swiss-Prot and its Computer-annotated Supplement TREMBL.
Protein Science 6(Suppl.): 56-56.


Bairoch A., Apweiler R. (1997)
The Swiss-Prot protein sequence database: its relevance to human molecular medical research.
Journal of Molecular Medicine 75: 312-316.
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Bairoch A., Apweiler R. (1997)
The Swiss-Prot protein sequence data bank and its supplement TREMBL.
Nucleic Acids Research 25: 31-36.
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Lang F. (1997)
Swiss-Prot + TREMBL
Trends in Genetics 13: 417.
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Magrane M., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Apweiler R. (1997)
Representation of mouse data in Swiss-Prot and TrEMBL.
Mouse Genome 95: 701-703.
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Apweiler R., Gateau A., Junker V. (1996)
Swiss-Prot and its computer-annotated supplement TREMBL: New developments in the linking of biological databases and computer-generation of annotation.
Folding and Design 1(Suppl.): 3-4.


Apweiler R., Junker V., Gateau A., O'Donovan C., Lang F., Bairoch A. (1996)
New Developments in Linking of Biological Databases and Computer-Generation of Annotation: Swiss-Prot and its Computer-annotated Supplement TREMBL.
In: Lecture notes in Computer Science, Proceedings of the German Conference on Bioinformatics (GCB96), Hofestaedt R., Lengauer T., Loeffler M., Schomburg D., (eds.), 1278 pp. 44-51, Leipzig, Germany (1996).
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Apweiler R., Junker V., Gateau A., O'Donovan C., Lang F., Mitaritonna N. (1996)
The EBIs Nucleotide and Protein Sequence Databases and services: Current Developments.
In: Perspectives on Protein Engineering 3, CD-ROM edition, Geisow M.J. (eds.), BIODIGM Ltd, Nottingham, UK (1996).


Apweiler R. (1996)
Swiss-Prot and SP-TREMBL: Linking to biological database entries and features.
Report of a meeting supported by the Commission of the European Union (DG XII: 042-CM) (1996).


Bairoch A., Apweiler R. (1996)
The Swiss-Prot protein sequence data bank and its new supplement TREMBL.
Nucleic Acids Research 24: 21-25.
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Junker V., Apweiler R. (1996)
Introduction: Internet resources for biologists.
In: Perspectives on Protein Engineering 3, CD-ROM edition, Geisow M.J. (eds.), BIODIGM Ltd, Nottingham, UK (1996)


Apweiler, R. (1995)
European Protein and DNA Data Library Resources.
In: Perspectives on Protein Engineering and complementary technologies, Geisow M.J. and Epton R. (eds.), BIODIGM Ltd, Mayflower World-Wide, Birmingham, UK (1995).


Emmert D.B., Stoehr P.J., Stoesser G., Cameron G.N. (1994)
The European Bioinformatics Institute (EBI) databases.
Nucleic Acids Research 26(1): 3445-3449.
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