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Publications on UniProt

Last modified October 17, 2017

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

The UniProt Consortium
UniProt: the universal protein knowledgebase
Nucleic Acids Res. 45: D158-D169 (2017)

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


Chen C, Huang H, Wu CH.
Protein Bioinformatics Databases and Resources
Methods Mol. Biol. 1558:3-39 (2017)

Nightingale A, Antunes R, Alpi E, Bursteinas B, Gonzales L, Liu W, Luo J, Qi G, Turner E, Martin M.
The Proteins API: accessing key integrated protein and genome information
Nucleic Acids Res. 45: W539-W544 (2017)

Poux S, Arighi, CN, Magrane M, Bateman A, Wei C-H, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B.
On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
bioRxiv (2017)

Pundir S, Martin MJ, O’Donovan C.
UniProt Protein Knowledgebase
Methods Mol. Biol. 1558:41-55 (2017)

Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium
ProtVista: visualization of protein sequence annotations
Bioinformatics 33:2040-2041 (2017)

Zaru R, Magrane M, O’Donovan C, UniProt Consortium
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB
Biochem J. 474(4):493-515 (2017)


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)

Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium
The UniProtKB guide to the human proteome
Database (Oxford) (2016)

Bursteinas B, Britto R, Bely B, Auchincloss A, Rivoire C, Redaschi N, O’Donovan C, Martin MJ.
Minimizing proteome redundancy in the UniProt Knowledgebase
Database (Oxford) (2016)

Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH, UniProt Consortium.
Computational Clustering for Viral Reference Proteomes
Bioinformatics 32:2041-2043 (2016)

Dogan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O’Donovan C, Martin MJ.
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB
Bioinformatics 32:2264-2271 (2016)

Kilic S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O’Donovan C, Chibucos MC, Martin MJ, Erill I.
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
Database (Oxford) (2016)

Pundir S, Martin MJ, O’Donovan C, UniProt Consortium
UniProt Tools
Curr. Protoc. Bioinformatics 53:1.29.1-1.29.15 (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)

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 (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 31:926-932 (2015)

The UniProt Consortium
UniProt: a hub for protein information
Nucleic Acids Res. 43:D204-212 (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)

The UniProt Consortium
Activities at the Universal Protein Resource (UniProt)
Nucl. Acids Res. 42:D191-D198 (2014)

Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Nucleic Acids Res. 42:D1001-D1006 (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)

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, UniProt Consortium
HAMAP in 2013, new developments in the protein family classification and annotation system
Nucl. Acids Res. 41:D584-D589 (2013)

The UniProt Consortium
Update on activities at the Universal Protein Resource (UniProt) in 2013
Nucleic Acids Res. 41: D43-D47 (2013)

Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O’Donovan C, Martin MJ, Kleywegt GJ.
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
Nucleic Acids Res. 41:D483-D4839 (2013)

Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I.
Application of text-mining for updating protein post-translational modification annotation in UniProtKB
BMC Bioinformatics 14:104 (2013)


Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O’Donovan C, Xenarios I, Gaudet P.
Biocurators and Biocuration: surveying the 21st century challenges
Database (Oxford) (2012)

Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O’Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R.
The UniProt-GO Annotation database in 2011
Nucleic Acids Res. 40:D565-D570 (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)

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

Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Rendino MF, Thomas WK, Udwary DW, Wu CH.
North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees
Database (Oxford) (2012)

The UniProt Consortium
Reorganizing the protein space at the Universal Protein Resource (UniProt)
Nucleic Acids Res. 40: D71-D75 (2012)


Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O’Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC.
The impact of focused Gene Ontology curation of specific mammalian systems
Plos One (2011)

Burmester A, Shelest E, Glockner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh V, Hertweck C, Hube B, White TC, Platzer M, Guthke R, Heitman J, Wostemeyer J, Zipfel PF, Monod M, Brakhage AA.
Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
Genome Biol. 12:R7 (2011)

Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R.
Representative Proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation
PLOS One (2011)

Griss J, Martin M, O’Donovan C, Apweiler R, Hermjakob H, Vizcaino JA.
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets
Proteomics 11:4434-4438 (2011)

Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH.
A comprehensive protein-centric ID mapping service for molecular data integration
Bioinformatics 27:1190-1191 (2011)

Klimke W, O’Donovan C, White O, Brister JR, Clark K, Fedorov B, Mizrachi I, Pruitt KD, Tatusova T.
Solving the Problem: Genome Annotation Standards before the Data Deluge
Stand. Genomic Sci. 5:168-193 (2011)

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

O’Donovan C, Apweiler R.
A guide to UniProt for protein scientists
Methods Mol. Biol. 694:25-35 (2011)

Patient S, Martin M.
Annotating UniProt metagenomic and environmental sequences in UniMES
In: Bioinformatics 2011 – Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress 367-368 (2011)

The UniProt Consortium
Ongoing and future developments at the Universal Protein Resource
Nucleic Acids Res. 39:D214-D219 (2011)

Vasudevan S, Vinayaka CR, Natale DA, Huang H, Kahsay RY, Wu CH.
Structure-guided rule-based annotation of protein functional sites in UniProt Knowledgebase
Methods Mol. Biol. 694:91-105 (2011)


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)

Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I.
Animal Toxins: How is complexity represented in databases?
Toxins 2:262-282 (2010)

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


Cochrane G, Martin MJ, Apweiler R.
Public data resources as a foundation for a worldwide genomics data infrastructure
In: Metagenomics: Theory, methods, and applications. Marco D (Ed), pp 79-105 (2011)

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

Lima T, Auchincloss AH, 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)

Schneider M, Lane L, Boutet E, Lieberherr D, Tognolli M, Bougueleret L, Bairoch A.
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
J. Proteomics 72:567-573 (2009)

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Res. 37:D169-D174 (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)

Bridge A, Veuthey A-L.
Resources for functional annotation
In: Modern genome annotation: The biosapiens network. Frishman D, Valencia A (eds), pp 139-64, Springer, Cambridge, UK (2008)

David FP, Yip YL.
SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
BMC Bioinformatics 23:391 (2008)

Hinz U, Bairoch A.
The impact of 3d structures on a protein knowledgebase: From proteins to systems
In: Structural proteomics and its impact on the life sciences. Sussman JL, Silman I (eds), World Scientific Publishing, Israel (2008)

Mottaz A, Yip YL, Ruch P, Veuthey AL.
Mapping proteins to disease terminologies: from UniProt to MeSH
BMC Bioinformatics 29:S3 (2008)

Mulder NJ, Kersey P, Pruess M, Apweiler R.
In silico characterization of proteins: UniProt, InterPro and Integr8
Mol. Biotechnol. 38:165-177 (2008)

Patient S, Wieser D, Kleen M, Kretschmann E, Martin M, Apweiler R.
UniProtJAPI: a remote API for accessing UniProt data
Bioinformatics 24:1321-1322 (2008)

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Res. 36:D190-D195 (2008)

Yip YL, Famiglietti M, Gos A, Duek PD, David FP, Gateau A, Bairoch A.
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase
Hum. Mutat. 29:361-366 (2008)


Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A.
Methods Mol. Biol. 406:89-112 (2007)

Hu ZZ, Valencia JC, Huang H, Chi A, Shabanowitz J, Hearing VJ, Appella E, Wu C.
Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes
Int. J. Mass Spectrom. 259:147-160 (2007)

Mueller M, Martens L, Apweiler R.
Annotating the human proteome: beyond establishing a parts list
Biochim. Biophys. Acta 1774:175-191 (2007)

Qiu P, Wang J, Ray Liu KJ, Hu ZZ, Wu CH.
Dependence network modeling for biomarker identification
Bioinformatics 23:198-206 (2007)

Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O’Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
Genome Res. 17:175-183 (2007)

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

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Res. 35:D193-D197 (2007)

Yip YL, Lachenal N, Pillet V, Veuthey AL.
Retrieving mutation-specific information for human proteins in UniProt/Swiss-Prot Knowledgebase
J. Bioinform. Comput. Biol. 5:1215-1231 (2007)


Chi A, Valencia JC, Hu ZZ, Watabe H, Yamaguchi H, Mangini NJ, Huang H, Canfield VA, Cheng KC, Yang F, Abe R, Yamagishi S, Shabanowitz J, Hearing VJ, Wu C, Appella E, Hunt DF.
Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes
J. Proteome Res. 5:3135-3144 (2006)

Han B, Obradovic Z, Hu ZZ, Wu CH, Vucetic S.
Substring selection for biomedical document classification
Bioinformatics 22:2136-2142 (2006)

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

Liu H, Hu ZZ, Torii M, Wu C, Friedman CJ.
Quantitative assessment of dictionary-based protein named entity tagging
Am. Med. Inform. Assoc. 13:497-507 (2006)

Liu HF, Hu ZZ, Zhang J, Wu CH.
BioThesaurus: a web-based thesaurus of protein and gene names
Bioinformatics 22:103-105 (2006)

Nikolskaya AN, Arighi C, Huang H, Barker WC, Wu CH.
PIRSF family classification system for protein functional and evolutionary analysis
Evolutionary Bioinformatics Online 2:209-221 (2006)

Petrova NV, Wu CH.
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
BMC Bioinformatics 7:312 (2006)

Pruess M, Kersey P, Kulikova T, Apweiler R.
Databases and resources for in silico proteome analysis
Methods Biochem. Anal. 49:397-414 (2006)

Schneider M, Bairoch A, Wu CH, Apweiler R.
Plant Protein Annotation in the UniProt Knowledgebase
Plant Physiology 138:59-66 (2006)

Whitfield EJ, Pruess M, Apweiler R.
Bioinformatics database infrastructure for biotechnology research
Biotechnol. 124:629-639 (2006)

Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O’Donovan C, Redaschi N, Suzek B.
The Universal Protein Resource (UniProt): an expanding universe of protein information
Nucleic Acids Res. 34:D187-D191 (2006)

Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.
An online literature mining tool for protein phosphorylation
Bioinformatics 22:1668-1669 (2006)


Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS.
The Universal Protein Resource (UniProt)
Nucleic Acids Res. 33:D154-D159 (2005)

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)

Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.
Literature mining and database annotation of protein phosphorylation using a rule-based system
Bioinformatics 21:2759-2765 (2005)

Jones P, Vinod N, Down T, Hackmann A, Kahari A, Kretschmann E, Wieder D, Hermjakob H, Apweiler R.
Dasty and UniProt DAS: a perfect pair for protein feature visualization
Bioinformatics 21:3198-3199 (2005)

Jungo F, Bairoch A.
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase
Toxicon 45:293-301 (2005)

Schneider M, Bairoch A, Wu CH, Apweiler R.
Plant Protein Annotation in the UniProt Knowledgebase
Plant Physiol. 138:59-66 (2005)


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

Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS.
UniProt: the Universal Protein knowledgebase
Nucleic Acids Res. 32:D115-D119 (2004)

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

Farriol-Mathis N, Garavelli JS, 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)

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

Wieser D, Kretschmann E, Apweiler R.
Filtering Erroneous Protein Annotation
Bioinformatics 20:i342-i347 (2004)

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, 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)

2003 and earlier

Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, Phan I, Pilbout S, Schneider M.
The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003
Nucleic Acids Res. 31:365-370 (2003)

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

Wu CH, Huang H, Yeh L-S, Barker WC.
Protein family classification and functional annotation
Computational Biology and Chemistry 27:37-47 (2003)

O’Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R.
High-quality protein knowledge resource: Swiss-Prot and TrEMBL
Brief. Bioinform. 3:275-284 (2002)

Apweiler R.
Functional information in Swiss-Prot: the basis for large-scale characterisation of protein sequences
Brief. Bioinform. 2:9-18 (2001)

Gasteiger E, Jung E, Bairoch A.
Swiss-Prot: connecting biomolecular knowledge via a protein database
Curr. Issues Mol. Biol. 3:47-55 (2001)

Jung E, Veuthey A-L, Gasteiger E, Bairoch A.
Annotation of glycoproteins in the Swiss-Prot database
Proteomics 1:262-268 (2001)

O’Donovan C, Apweiler R, Bairoch A.
The human proteomics initiative (HPI)
Trends Biotechnol. 19:178-181 (2001)

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

Fleischmann W, Moeller S, Gateau A, Apweiler R.
A novel method for automatic functional annotation of proteins
Bioinformatics 15:228-233 (1999)

Junker VL, Apweiler R, Bairoch A.
Representation of functional information in the Swiss-Prot data bank
Bioinformatics 15:1066-1067 (1999)

Moeller S, Leser U, Fleischmann W, Apweiler R.
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation
Bioinformatics 15:219-227 (1999)

O’Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R.
Removing redundancy in Swiss-Prot and TrEMBL
Bioinformatics 15:258-259 (1999)

Bairoch A, Apweiler R.
The Swiss-Prot protein sequence database: its relevance to human molecular medical research
J. Mol. Med. 75:312-316 (1997)