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Publications on UniProt

Last modified February 22, 2016

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If you find UniProt useful, please consider citing our latest publication:

The UniProt Consortium
UniProt: a hub for protein information
Nucleic Acids Res. 43: D204-D212 (2015)

...or choose the publication that best covers the UniProt aspects or components you used in your work:

Publications on UniProt databases

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
Database (Oxford) bav043 (2016)

Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I.
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View
Methods Mol. Biol. 1374:23-54 (2016)

Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Rios D, O’Donovan C, Vizcaino JA, Martin MJ.
Analysis of the tryptic search space in UniProt databases
Proteomics 15:48-57 (2015)

Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.
Representing virus-host interactions and other multi-organism processes in the Gene Ontology
BMC Microbiol. 15:146 (2015)

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O’Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.
Key challenges for the creation and maintenance of specialist protein resources
Proteins 83:1005-1013 (2015)

Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O’Donovan C.
The GOA database: gene Ontology annotation updates for 2015
Nucleic Acids Res. 43:d1057-1063 (2015)

Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A.
HAMAP in 2015: updates to the protein family classification and annotation system
Nucleic Acids Res. 43:D1064-1070 (2015)

Pundir S, Magrane M, Martin MJ, O’Donovan C, UniProt Consortium.
Searching and Navigating UniProt Databases
Curr. Protoc. Bioinformatics 50:1.27.1-1.27.10 (2015)

Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium.
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Bioinformatics 31:926-32 (2015)

Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I.
Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation.
Hum. Mutat. 35:927-935 (2014)

Huntley RP, Sawford T, Martin MJ, O?Donovan C.
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt
Gigascience 3:4 (2014)

Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P.
An Integrated Ontology Resource to Explore and Study Host-Virus Relationships
PLoS One 9(9):e108075 (2014)

Poux S, Magrane M, Arighi CN, Bridge A, O?Donovan C, Laiho K, The UniProt Consortium.
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data
Database (Oxford) bau016 (2014)

Chen C, Li Z, Huang H, Suzek BE, Wu CH; UniProt Consortium.
A fast Peptide Match service for UniProt Knowledgebase
Bioinformatics 29:2808-2809 (2013)

Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Martin MJ, O?Donovan C, Apweiler R.
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans
Database (Oxford) bas062 (2013)

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

Jain E., Bairoch A., Duvaud S., Phan I., Redaschi N., Suzek B.E., Martin M.J., McGarvey P., Gasteiger E.
Infrastructure for the life sciences: design and implementation of the UniProt website
BMC Bioinformatics 10:136 (2009)

Suzek B.E., Huang H., McGarvey P., Mazumder R., Wu C.H.
UniRef: Comprehensive and Non-Redundant UniProt Reference Clusters
Bioinformatics 23:1282-1288 (2007)

Leinonen R., Nardone F., Zhu W., Apweiler R.
UniSave: the UniProtKB Sequence/Annotation Version database
Bioinformatics 22:1284-1285 (2006)

Boeckmann B., Blatter M.-C., Famiglietti L., Hinz U., Lane L., Roechert B., Bairoch A.
Protein variety and functional diversity: Swiss-Prot annotation in its biological context
C. R. Biol. 328:882-899 (2005)

Apweiler R., Bairoch A., Wu C.H.
Protein sequence databases
Curr. Opin. Chem. Biol. 8:76-80 (2004)

Bairoch A., Boeckmann B., Ferro S., Gasteiger E.
Swiss-Prot: juggling between evolution and stability
Brief. Bioinform. 5:39-55 (2004)

Leinonen R., Diez F.G., Binns D., Fleischmann W., Lopez R., Apweiler R.
UniProt Archive
Bioinformatics 20:3236-3237 (2004)

Publications on annotation projects

Pedruzzi I., Rivoire C., Auchincloss A.H., Coudert E., Keller G., de Castro E., Baratin D., Cuche B.A., Bougueleret L., Poux S., Redaschi N., Xenarios I., Bridge A.; UniProt Consortium
HAMAP in 2013, new developments in the protein family classification and annotation system.
Nucleic Acids Res. 41:D584-D589 (2013)

Schneider M., Poux S., UniProt Consortium.
UniProtKB amid the turmoil of plant proteomics research front
Front. Plant Sci. 3:270-270 (2012)

Jungo F., Bougueleret L., Xenarios I., Poux S.
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data
Toxicon 60:551-557 (2012)

Hinz U., UniProt Consortium.
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase
Cell. Mol. Life Sci. 67:1049-1064 (2010)

Lima T., Auchincloss A.H., Coudert E., Keller G., Michoud K., Rivoire C., Bulliard V., de Castro E., Lachaize C., Baratin D., Phan I., Bougueleret L., Bairoch A.
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Nucleic Acids Res. 37:D471-D478 (2009)

Braconi Quintaje S., Orchard S.
The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes
Mol. Cell. Proteomics 7:1409-1419 (2008)

Farriol-Mathis N., Garavelli J.S., Boeckmann B., Duvaud S., Gasteiger E., Gateau A., Veuthey A.-L., Bairoch A.
Annotation of post-translational modifications in the Swiss-Prot knowledgebase
Proteomics 4:1537-1550 (2004)

Yip Y.L., Scheib H., Diemand A.V., Gattiker A., Famiglietti L.M., Gasteiger E., Bairoch A.
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants
Hum. Mutat. 23:464-470 (2004)

Gattiker A., Michoud K., Rivoire C., Auchincloss A.H., Coudert E., Lima T., Kersey P., Pagni M., Sigrist C.J., Lachaize C., Veuthey A.-L., Gasteiger E., Bairoch A.
Automated annotation of microbial proteomes in Swiss-Prot
Comput. Biol. Chem. 27:49-58 (2003)

See also: Past publications