Rolf Apweiler

Rolf Apweiler

Joint Associate Director and Senior Scientist

Dr Apweiler is Joint Associate Director of EMBL-EBI, and together with Ewan Birney has strategic oversight of all EMBL-EBI services. Prior to taking on this position he led protein resources, including the team responsible for EMBL-EBI's contribution to the UniProt Consortium. Dr Apweiler has made a major contribution to methods for the automatic annotation of proteins, making it possible to add relevant information to proteome sets for entire organisms. Dr Apweiler has spearheaded the development of standards for proteomics data, and his teams have maintained major collections of protein identifications from proteomics experiments (PRIDE) and molecular interactions (IntAct). He also leads EMBL-EBI’s contribution to the Gene Ontology. Rolf received his PhD from the University of Heidelberg in 1994, and has been at EMBL since 1987. His major contribution to the field of proteomics was recognised by his election to President of the Human Proteomics Organisation, which he held in 2007 and 2008. Also, in 2012 he has been elected as a member of EMBO.

ORCID iD: 0000-0001-7078-200X

Tel:+44 (0)1223 494 435 (Internal 8701) / Fax:+44 (0)1223 494 468

Apweiler projects

Publications

2014

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic Acids Res Volume 42 (2014) p.d18-25
DOI: 10.1093/nar/gkt1206

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR 3rd, Apweiler R, Ping P.
J Proteome Res Volume 13 (2014) p.433-446
DOI: 10.1021/pr400539j

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 42 (2014) p.d191-8
DOI: 10.1093/nar/gkt1140

2013

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.
Database (Oxford) Volume 2013 (2013) p.bas062
DOI: 10.1093/database/bas062

Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Ilsley GR, Fisher J, Apweiler R, Depace AH, Luscombe NM.
Elife Volume 2 (2013) p.e00522
DOI: 10.7554/elife.00522

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

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA.
PLoS One Volume 8 (2013) p.e61951
DOI: 10.1371/journal.pone.0061951

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic Acids Res Volume 41 (2013) p.d530-5
DOI: 10.1093/nar/gks1050

Maximising proteomics data for the scientific community
Hermjakob H, Apweiler R.
European Pharmaceutical Review Volume 9 (2013) p.23-29

2012

The HUPO initiative on Model Organism Proteomes, iMOP.
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.
Proteomics Volume 12 (2012) p.340-345
DOI: 10.1002/pmic.201290014

InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong S.
Nucleic Acids Res Volume 40 (2012) p.4725-4725

InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.
Nucleic Acids Res Volume 40 (2012) p.d306-12
DOI: 10.1093/nar/gkr948

Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 40 (2012) p.d71-5
DOI: 10.1093/nar/gkr981

Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, Quest for Orthologs Consortium.
Bioinformatics Volume 28 (2012) p.900-904
DOI: 10.1093/bioinformatics/bts050

The UniProt-GO Annotation database in 2011.
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.
Nucleic Acids Res Volume 40 (2012) p.d565-70
DOI: 10.1093/nar/gkr1048

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic Acids Res Volume 40 (2012) p.d559-64
DOI: 10.1093/nar/gkr1028

2011

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res Volume 39 (2011) p.d214-9
DOI: 10.1093/nar/gkq1020

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods Mol Biol Volume 694 (2011) p.25-35
DOI: 10.1007/978-1-60761-977-2_2

The impact of focused Gene Ontology curation of specific mammalian systems.
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.
PLoS One Volume 6 (2011) p.e27541
DOI: 10.1371/journal.pone.0027541

The EBI Metagenomics Archive, Integration and Analysis resource
Hunter C, Cochrane G, Apweiler R, Hunter S.
Volume (2011) p.333–340
DOI: 10.1002/9781118010518.ch38

Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria.
Deng N, Zhang J, Zong C, Wang Y, Lu H, Yang P, Wang W, Young GW, Wang Y, Korge P, Lotz C, Doran P, Liem DA, Apweiler R, Weiss JN, Duan H, Ping P.
Mol Cell Proteomics Volume 10 (2011) p.m110.000117
DOI: 10.1074/mcp.m110.000117

A posteriori quality control for the curation and reuse of public proteomics data.
Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L.
Proteomics Volume 11 (2011) p.2182-2194
DOI: 10.1002/pmic.201000602

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 11 (2011) p.4434-4438
DOI: 10.1002/pmic.201100363

"4D Biology for health and disease" workshop report.
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ.
N Biotechnol Volume 28 (2011) p.291-293
DOI: 10.1016/j.nbt.2010.10.003

2010

Recommendations for biomarker identification and qualification in clinical proteomics.
Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J, Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP, Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina F, Monsarrat B, Novak J, Peter K, Rossing P, Sánchez-Carbayo M, Schanstra JP, Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra TD, Weissinger E, Yamamoto T, Vlahou A.
Sci Transl Med Volume 2 (2010) p.46ps42
DOI: 10.1126/scitranslmed.3001249

Design, Implementation and Updating of Knowledge Bases
Hunter S, Apweiler R, Martin MJ.
Volume (2010) p.87–105
DOI: 10.1002/9780470669716.ch4

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cell Mol Life Sci Volume 67 (2010) p.1049-1064
DOI: 10.1007/s00018-009-0229-6

The Renal Gene Ontology Annotation Initiative.
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.
Organogenesis Volume 6 (2010) p.71-75
DOI: 10.4161/org.6.2.11294

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic Acids Res Volume 38 (2010) p.d331-5
DOI: 10.1093/nar/gkp1018

On the importance of comprehensible classification models for protein function prediction.
Freitas AA, Wieser DC, Apweiler R.
IEEE/ACM Trans Comput Biol Bioinform Volume 7 (2010) p.172-182
DOI: 10.1109/tcbb.2008.47

Comparative proteomics profiling reveals role of smooth muscle progenitors in extracellular matrix production.
Simper D, Mayr U, Urbich C, Zampetaki A, Prokopi M, Didangelos A, Saje A, Mueller M, Benbow U, Newby AC, Apweiler R, Rahman S, Dimmeler S, Xu Q, Mayr M.
Arterioscler Thromb Vasc Biol Volume 30 (2010) p.1325-1332
DOI: 10.1161/atvbaha.110.204651

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res Volume 38 (2010) p.d142-8
DOI: 10.1093/nar/gkp846

A large-scale protein-function database.
Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K.
Nat Chem Biol Volume 6 (2010) p.785
DOI: 10.1038/nchembio.460

Mining Unique-m Substrings from Genomes
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R.
J Proteomics Bioinform Volume 3 (2010) p.99-100
DOI: 10.4172/jpb.1000127

Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure
Cochrane G, Martin MJ, Apweiler R.
Volume (2010) p.79

2009

QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R.
Database (Oxford) Volume 2009 (2009) p.bap010
DOI: 10.1093/database/bap010

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.
Bioinformatics Volume 25 (2009) p.2865-2871
DOI: 10.1093/bioinformatics/btp394

Systematic comparison of the human saliva and plasma proteomes.
Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT.
Proteomics Clin Appl Volume 3 (2009) p.116-134
DOI: 10.1002/prca.200800140

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.
Bioinformatics Volume 25 (2009) p.3045-3046
DOI: 10.1093/bioinformatics/btp536

Know your limits: assumptions, constraints and interpretation in systems biology.
Ilsley GR, Luscombe NM, Apweiler R.
Biochim Biophys Acta Volume 1794 (2009) p.1280-1287
DOI: 10.1016/j.bbapap.2009.05.002

Algorithms and databases.
Martens L, Apweiler R.
Methods Mol Biol Volume 564 (2009) p.245-259
DOI: 10.1007/978-1-60761-157-8_14

Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature Volume 461 (2009) p.168-170
DOI: 10.1038/461168a

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 9 (2009) p.218-222
DOI: 10.1002/pmic.200800732

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.
Nucleic Acids Res Volume 37 (2009) p.d396-403
DOI: 10.1093/nar/gkn803

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R.
J Proteome Res Volume 8 (2009) p.3689-3692
DOI: 10.1021/pr900023z

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 9 (2009) p.3626-3629
DOI: 10.1002/pmic.200900205

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res Volume 37 (2009) p.d169-74
DOI: 10.1093/nar/gkn664

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Reference Genome Group of the Gene Ontology Consortium.
PLoS Comput Biol Volume 5 (2009) p.e1000431
DOI: 10.1371/journal.pcbi.1000431

ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D.
Genomics Volume 93 (2009) p.213-220
DOI: 10.1016/j.ygeno.2008.11.003

InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res Volume 37 (2009) p.d211-5
DOI: 10.1093/nar/gkn785

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.
Proteomics Volume 9 (2009) p.3928-3933
DOI: 10.1002/pmic.200900247

Approaching clinical proteomics: current state and future fields of application in fluid proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G.
Clin Chem Lab Med Volume 47 (2009) p.724-744
DOI: 10.1515/cclm.2009.167

Approaching clinical proteomics: current state and future fields of application in cellular proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G.
Cytometry A Volume 75 (2009) p.816-832
DOI: 10.1002/cyto.a.20779

Finding one's way in proteomics: a protein species nomenclature.
Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR.
Chem Cent J Volume 3 (2009) p.11
DOI: 10.1186/1752-153x-3-11

Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM.
Nat Chem Biol Volume 5 (2009) p.521-525
DOI: 10.1038/nchembio0809-521

2008

UniProtJAPI: a remote API for accessing UniProt data.
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R.
Bioinformatics Volume 24 (2008) p.1321-1322
DOI: 10.1093/bioinformatics/btn122

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Mol Biotechnol Volume 38 (2008) p.165-177
DOI: 10.1007/s12033-007-9003-x

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.
Nucleic Acids Res Volume 36 (2008) p.w372-6
DOI: 10.1093/nar/gkn252

The speciation of the proteome.
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H.
Chem Cent J Volume 2 (2008) p.16
DOI: 10.1186/1752-153x-2-16

The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.
Nucleic Acids Res Volume 36 (2008) p.d1028-33
DOI: 10.1093/nar/gkm978

The InterPro database and tools for protein domain analysis.
Mulder NJ, Apweiler R.
Curr Protoc Bioinformatics Volume Chapter 2 (2008) p.unit 2.7
DOI: 10.1002/0471250953.bi0207s21

Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.
Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P.
Proteomics Volume 8 (2008) p.1564-1575
DOI: 10.1002/pmic.200700851

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Comb Chem High Throughput Screen Volume 11 (2008) p.653-660
DOI: 10.2174/138620708785739925

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 8 (2008) p.1326-1330
DOI: 10.1002/pmic.200701098

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain.
Eisenacher M, Hardt T, Martens L, Häkkinen J, Apweiler R, Hamacher M, Meyer HE, Stephan C.
Proteomics Volume 8 (2008) p.4163-4167
DOI: 10.1002/pmic.200800515

Altered proteome biology of cardiac mitochondria under stress conditions.
Zhang J, Liem DA, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Korge P, Drews O, Maclellan WR, Honda H, Weiss JN, Apweiler R, Ping P.
J Proteome Res Volume 7 (2008) p.2204-2214
DOI: 10.1021/pr070371f

Wiley-VCH and HUPO: a global effort to advance proteomic science.
Ping P, Bergeron J, Apweiler R.
Proteomics Volume 8 (2008) p.4-6
DOI: 10.1002/pmic.200790108

Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?
Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ.
Proteomics Volume 8 (2008) p.1950-1953
DOI: 10.1002/pmic.200800078

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L.
Proteomics Volume 8 (2008) p.1138-1148
DOI: 10.1002/pmic.200700761

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects
Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J.
Volume (2008) p.

Analyzing large-scale proteomics projects with latent semantic indexing.
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H.
J Proteome Res Volume 7 (2008) p.182-191
DOI: 10.1021/pr070461k

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.
Nat Biotechnol Volume 26 (2008) p.889-896
DOI: 10.1038/nbt.1411

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E.
Nucleic Acids Res Volume 36 (2008) p.d5-12
DOI: 10.1093/nar/gkm1018

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.
Genome Biol Volume 9 Suppl 2 (2008) p.s5
DOI: 10.1186/gb-2008-9-s2-s5

2007

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.
BMC Biol Volume 5 (2007) p.44
DOI: 10.1186/1741-7007-5-44

The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.
Nat Biotechnol Volume 25 (2007) p.887-893
DOI: 10.1038/nbt1329

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.
BMC Bioinformatics Volume 8 (2007) p.401
DOI: 10.1186/1471-2105-8-401

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, Meyer HE.
Proteomics Volume 7 (2007) p.2490-2496
DOI: 10.1002/pmic.200700449

New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res Volume 35 (2007) p.d224-8
DOI: 10.1093/nar/gkl841

Annotating the human proteome: beyond establishing a parts list.
Mueller M, Martens L, Apweiler R.
Biochim Biophys Acta Volume 1774 (2007) p.175-191
DOI: 10.1016/j.bbapap.2006.11.011

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Mol Cell Proteomics Volume 6 (2007) p.1666-1667

Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 7 (2007) p.3034-3037
DOI: 10.1002/pmic.200700554

IntAct--open source resource for molecular interaction data.
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.
Nucleic Acids Res Volume 35 (2007) p.d561-5
DOI: 10.1093/nar/gkl958

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods Mol Biol Volume 406 (2007) p.1-21
DOI: 10.1007/978-1-59745-535-0_1

The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
Nat Biotechnol Volume 25 (2007) p.894-898
DOI: 10.1038/nbt1324

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
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.
Genome Res Volume 17 (2007) p.175-183
DOI: 10.1101/gr.5509507

Clinical proteomics: A need to define the field and to begin to set adequate standards.
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.
Proteomics Clin Appl Volume 1 (2007) p.148-156
DOI: 10.1002/prca.200600771

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nat Biotechnol Volume 25 (2007) p.1127-1133
DOI: 10.1038/nbt1347

InterPro and InterProScan: tools for protein sequence classification and comparison.
Mulder N, Apweiler R.
Methods Mol Biol Volume 396 (2007) p.59-70
DOI: 10.1007/978-1-59745-515-2_5

Proteomic data exchange and storage: the need for common standards and public repositories.
Orchard S, Jones P, Taylor C, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R.
Methods Mol Biol Volume 367 (2007) p.261-270
DOI: 10.1385/1-59745-275-0:261

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, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 35 (2007) p.d16-20
DOI: 10.1093/nar/gkl913

2006

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.
Mueller M, Martens L, Reidegeld KA, Hamacher M, Stephan C, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Meyer HE, Apweiler R.
Proteomics Volume 6 (2006) p.5059-5075
DOI: 10.1002/pmic.200600194

The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.
Reidegeld KA, Müller M, Stephan C, Blüggel M, Hamacher M, Martens L, Körting G, Chamrad DC, Parkinson D, Apweiler R, Meyer HE, Marcus K.
Proteomics Volume 6 (2006) p.4997-5014
DOI: 10.1002/pmic.200600305

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

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Müller M, Apweiler R, Martens L, Körting G, Chamrad DC, Thiele H, Blüggel M, Parkinson D, Binz PA, Lyall A, Meyer HE.
Proteomics Volume 6 (2006) p.5015-5029
DOI: 10.1002/pmic.200600294

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert Rev Proteomics Volume 3 (2006) p.1-3
DOI: 10.1586/14789450.3.1.1

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, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 34 (2006) p.d10-5
DOI: 10.1093/nar/gkj130

UniSave: the UniProtKB sequence/annotation version database.
Leinonen R, Nardone F, Zhu W, Apweiler R.
Bioinformatics Volume 22 (2006) p.1284-1285
DOI: 10.1093/bioinformatics/btl105

Evidence standards in experimental and inferential INSDC Third Party Annotation data.
Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M.
OMICS Volume 10 (2006) p.105-113
DOI: 10.1089/omi.2006.10.105

HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.
Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Kretzschmar H, Lewczuk P, Lubec G, Marcus K, Martens L, Palacios Bustamante N, Park YM, Pennington SR, Robben J, Stühler K, Reidegeld KA, Riederer P, Rossier J, Sanchez JC, Schrader M, Stephan C, Tagle D, Thiele H, Wang J, Wiltfang J, Yoo JS, Zhang C, Klose J, Meyer HE.
Proteomics Volume 6 (2006) p.4890-4898
DOI: 10.1002/pmic.200600295

A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Martens L, Müller M, Stephan C, Hamacher M, Reidegeld KA, Meyer HE, Blüggel M, Vandekerckhove J, Gevaert K, Apweiler R.
Proteomics Volume 6 (2006) p.5076-5086
DOI: 10.1002/pmic.200600291

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R.
Proteomics Volume 6 (2006) p.1719-1721
DOI: 10.1002/pmic.200600069

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
Chamrad DC, Körting G, Schäfer H, Stephan C, Thiele H, Apweiler R, Meyer HE, Marcus K, Blüggel M.
Proteomics Volume 6 (2006) p.5048-5058
DOI: 10.1002/pmic.200600189

Proteomic Data Standardization, Deposition and Exchange
Orchard S, Hermjakob H, Pruess M, Apweiler R.
Volume (2006) p.19–30
DOI: 10.1002/3527608230.ch2

GOAnnotator: linking protein GO annotations to evidence text.
Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D.
J Biomed Discov Collab Volume 1 (2006) p.19
DOI: 10.1186/1747-5333-1-19

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.
Proteomics Volume 6 (2006) p.738-741
DOI: 10.1002/pmic.200500868

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Taylor CF, Hermjakob H, Julian RK Jr, Garavelli JS, Aebersold R, Apweiler R.
OMICS Volume 10 (2006) p.145-151
DOI: 10.1089/omi.2006.10.145

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H.
Proteomics Volume 6 (2006) p.4439-4443
DOI: 10.1002/pmic.200600452

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
OMICS Volume 10 (2006) p.114-118
DOI: 10.1089/omi.2006.10.114

PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.
Nucleic Acids Res Volume 34 (2006) p.d659-63
DOI: 10.1093/nar/gkj138

Bioinformatics database infrastructure for biotechnology research.
Whitfield EJ, Pruess M, Apweiler R.
J Biotechnol Volume 124 (2006) p.629-639
DOI: 10.1016/j.jbiotec.2006.04.006

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nat Cell Biol Volume 8 (2006) p.1183-1189
DOI: 10.1038/ncb1495

The Universal Protein Resource (UniProt): an expanding universe of protein information.
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.
Nucleic Acids Res Volume 34 (2006) p.d187-91
DOI: 10.1093/nar/gkj161

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
Côté RG, Jones P, Apweiler R, Hermjakob H.
BMC Bioinformatics Volume 7 (2006) p.97
DOI: 10.1186/1471-2105-7-97

2005

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM.
Proteomics Volume 5 (2005) p.3226-3245
DOI: 10.1002/pmic.200500358

The transcriptional landscape of the mammalian genome.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
Science Volume 309 (2005) p.1559-1563
DOI: 10.1126/science.1112014

The predictive power of the CluSTr database.
Petryszak R, Kretschmann E, Wieser D, Apweiler R.
Bioinformatics Volume 21 (2005) p.3604-3609
DOI: 10.1093/bioinformatics/bti542

E-MSD: an integrated data resource for bioinformatics.
Velankar S, McNeil P, Mittard-Runte V, Suarez A, Barrell D, Apweiler R, Henrick K.
Nucleic Acids Res Volume 33 (2005) p.d262-5
DOI: 10.1093/nar/gki058

The importance of uniformity in reporting protein-function data.
Apweiler R, Cornish-Bowden A, Hofmeyr JH, Kettner C, Leyh TS, Schomburg D, Tipton K.
Trends Biochem Sci Volume 30 (2005) p.11-12
DOI: 10.1016/j.tibs.2004.11.002

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK Jr, Apweiler R.
Proteomics Volume 5 (2005) p.337-339
DOI: 10.1002/pmic.200401158

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, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez FG, Harte N, Kulikova T, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Sobhany S, Stoehr P, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 33 (2005) p.d29-33
DOI: 10.1093/nar/gki098

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.
Stephan C, Hamacher M, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schäfer H, Martens L, Jones P, Müller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R.
Proteomics Volume 5 (2005) p.3560-3562
DOI: 10.1002/pmic.200500580

The Integr8 project--a resource for genomic and proteomic data.
Pruess M, Kersey P, Apweiler R.
In Silico Biol Volume 5 (2005) p.179-185

PRIDE: the proteomics identifications database.
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R.
Proteomics Volume 5 (2005) p.3537-3545
DOI: 10.1002/pmic.200401303

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
Nucleic Acids Res Volume 33 (2005) p.d297-302
DOI: 10.1093/nar/gki039

Protein Sequence Databases
Magrane M, Martin MJ, O’Donovan C, Apweiler R.
Volume (2005) p.609-618
DOI: 10.1385/1-59259-890-0:609

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.
BMC Bioinformatics Volume 6 Suppl 1 (2005) p.s17
DOI: 10.1186/1471-2105-6-s1-s17

InterProScan: protein domains identifier.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
Nucleic Acids Res Volume 33 (2005) p.w116-20
DOI: 10.1093/nar/gki442

Second proteomics standards initiative spring workshop.
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.
Expert Rev Proteomics Volume 2 (2005) p.287-289
DOI: 10.1586/14789450.2.3.287

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.
Proteomics Volume 5 (2005) p.3552-3555
DOI: 10.1002/pmic.200500626

The Universal Protein Resource (UniProt).
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.
Nucleic Acids Res Volume 33 (2005) p.d154-9
DOI: 10.1093/nar/gki070

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Pac Symp Biocomput Volume (2005) p.186-196

Annotating the human proteome.
Orchard S, Hermjakob H, Apweiler R.
Mol Cell Proteomics Volume 4 (2005) p.435-440
DOI: 10.1074/mcp.r500003-mcp200

Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R.
Proteomics Volume 5 (2005) p.4651-4652
DOI: 10.1002/pmic.200500727

Plant protein annotation in the UniProt Knowledgebase.
Schneider M, Bairoch A, Wu CH, Apweiler R.
Plant Physiol Volume 138 (2005) p.59-66
DOI: 10.1104/pp.104.058933

Biological Databases: Infrastructure, Content and Integration
Williams AL, Kersey PJ, Pruess M, Apweiler R.
Volume (2005) p.11–28
DOI: 10.1002/0470094419.ch2

Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Jones P, Vinod N, Down T, Hackmann A, Kahari A, Kretschmann E, Quinn A, Wieser D, Hermjakob H, Apweiler R.
Bioinformatics Volume 21 (2005) p.3198-3199
DOI: 10.1093/bioinformatics/bti506

InterPro, progress and status in 2005.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH.
Nucleic Acids Res Volume 33 (2005) p.d201-5
DOI: 10.1093/nar/gki106

Do you do text?
Blaschke C, Yeh A, Camon E, Colosimo M, Apweiler R, Hirschman L, Valencia A.
Bioinformatics Volume 21 (2005) p.4199-4200
DOI: 10.1093/bioinformatics/bti695

Who tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools.
Lee V, Camon E, Dimmer E, Barrell D, Apweiler R.
In Silico Biol Volume 5 (2005) p.5-8

2004

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, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d262-6
DOI: 10.1093/nar/gkh021

IntAct: an open source molecular interaction database.
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d452-5
DOI: 10.1093/nar/gkh052

A common open representation of mass spectrometry data and its application to proteomics research.
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Nat Biotechnol Volume 22 (2004) p.1459-1466
DOI: 10.1038/nbt1031

Filtering erroneous protein annotation.
Wieser D, Kretschmann E, Apweiler R.
Bioinformatics Volume 20 Suppl 1 (2004) p.i342-7
DOI: 10.1093/bioinformatics/bth938

Current status of proteomic standards development.
Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R.
Expert Rev Proteomics Volume 1 (2004) p.179-183
DOI: 10.1586/14789450.1.2.179

Protein sequence database methods.
Martin MJ, O'Donovan C, Apweiler R.
Genet Eng (N Y) Volume 26 (2004) p.13-17
DOI: 10.2478/v10050-008-0057-3

Advances in the development of common interchange standards for proteomic data.
Orchard S, Taylor CF, Hermjakob H, Weimin-Zhu, Julian RK Jr, Apweiler R.
Proteomics Volume 4 (2004) p.2363-2365
DOI: 10.1002/pmic.200400884

Common interchange standards for proteomics data: Public availability of tools and schema.
Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R.
Proteomics Volume 4 (2004) p.490-491
DOI: 10.1002/pmic.200300694

Towards data management of the HUPO Human Brain Proteome Project pilot phase.
Blüggel M, Bailey S, Körting G, Stephan C, Reidegeld KA, Thiele H, Apweiler R, Hamacher M, Meyer HE.
Proteomics Volume 4 (2004) p.2361-2362
DOI: 10.1002/pmic.200400867

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, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d27-30
DOI: 10.1093/nar/gkh120

The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase.
Camon E, Barrell D, Lee V, Dimmer E, Apweiler R.
In Silico Biol Volume 4 (2004) p.5-6

IntEnz, the integrated relational enzyme database.
Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d434-7
DOI: 10.1093/nar/gkh119

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R.
Proteomics Volume 4 (2004) p.1985-1988
DOI: 10.1002/pmic.200300721

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nat Biotechnol Volume 22 (2004) p.177-183
DOI: 10.1038/nbt926

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
PLoS Biol Volume 2 (2004) p.e162
DOI: 10.1371/journal.pbio.0020162

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care.
Martin-Sanchez F, Iakovidis I, Nørager S, Maojo V, de Groen P, Van der Lei J, Jones T, Abraham-Fuchs K, Apweiler R, Babic A, Baud R, Breton V, Cinquin P, Doupi P, Dugas M, Eils R, Engelbrecht R, Ghazal P, Jehenson P, Kulikowski C, Lampe K, De Moor G, Orphanoudakis S, Rossing N, Sarachan B, Sousa A, Spekowius G, Thireos G, Zahlmann G, Zvárová J, Hermosilla I, Vicente FJ.
J Biomed Inform Volume 37 (2004) p.30-42
DOI: 10.1016/j.jbi.2003.09.003

UniProt archive.
Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R.
Bioinformatics Volume 20 (2004) p.3236-3237
DOI: 10.1093/bioinformatics/bth191

Protein sequence databases.
Apweiler R, Bairoch A, Wu CH.
Curr Opin Chem Biol Volume 8 (2004) p.76-80
DOI: 10.1016/j.cbpa.2003.12.004

UniProt: the Universal Protein knowledgebase.
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.
Nucleic Acids Res Volume 32 (2004) p.d115-9
DOI: 10.1093/nar/gkh131

2003

The InterPro Database, 2003 brings increased coverage and new features.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM.
Nucleic Acids Res Volume 31 (2003) p.315-318
DOI: 10.1093/nar/gkg046

Bioinformatics Resources for In Silico Proteome Analysis.
Pruess M, Apweiler R.
J Biomed Biotechnol Volume 2003 (2003) p.231-236
DOI: 10.1155/s1110724303209219

Managing core resources for genomics and proteomics.
Apweiler R, Martin MJ, O'Donovan C, Pruess M.
Pharmacogenomics Volume 4 (2003) p.343-350
DOI: 10.1517/phgs.4.3.343.22689

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.203-206
DOI: 10.1002/cfg.279

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.16-19
DOI: 10.1002/cfg.232

Integr8: enhanced inter-operability of European molecular biology databases.
Kersey PJ, Morris L, Hermjakob H, Apweiler R.
Methods Inf Med Volume 42 (2003) p.154-160

The proteomics standards initiative.
Orchard S, Hermjakob H, Apweiler R.
Proteomics Volume 3 (2003) p.1374-1376
DOI: 10.1002/pmic.200300496

Further advances in the development of a data interchange standard for proteomics data.
Orchard S, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R.
Proteomics Volume 3 (2003) p.2065-2066
DOI: 10.1002/pmic.200300588

Increase of functional diversity by alternative splicing.
Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S.
Trends Genet Volume 19 (2003) p.124-128
DOI: 10.1016/s0168-9525(03)00023-4

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.
Genome Res Volume 13 (2003) p.662-672
DOI: 10.1101/gr.461403

The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro.
Camon E, Barrell D, Brooksbank C, Magrane M, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.71-74
DOI: 10.1002/cfg.235

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M.
Nucleic Acids Res Volume 31 (2003) p.365-370
DOI: 10.1093/nar/gkg095

The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic Acids Res Volume 31 (2003) p.43-50
DOI: 10.1093/nar/gkg066

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Nucleic Acids Res Volume 31 (2003) p.414-417
DOI: 10.1093/nar/gkg105

2002

Tools and resources for identifying protein families, domains and motifs.
Mulder NJ, Apweiler R.
Genome Biol Volume 3 (2002) p.reviews2001

Computational Methods and Bioinformatic Tools
Cullen P, Lorkowski S, Hennig S, Poustka A, Panopoulou G, Lehrach H, Korsching E, Pickeral O, Herwig R, Kel A, Tchekmenev D, Wingender E, Streicher J, Müller GB, Kawashima T, Makabe KW, Dubchak I, Ji H, Okubo K, Kawamoto S, Fricke E, Karas D, Haubrock M, Land S, Rotert S, Chen X, Pontius J, Eveno E, Auffray C, Decraene C, Chelala C, Piétu G, Devignes M-D, Mariage-Samson R, Imbeaud S, Bortoli S, Amit A, Ringwald M, de Veer MJ, Williams BRG, Walker EM, Davies JA, Grunau C, Baldock R, Davidson DR, Stoeckert CJ Jr., Pizarro A, Manduchi E, Grant GR, Crabtree J, Liu J, Le PV, McWeeney SK, Welle S, Ball CA, Botstein D, Binkley G, Sherlock GJ, Cherry JM, Dolinski K, Issel-Tarver L, Schroeder M, Dwight SS, Wenig S, Matese JC, Jin H, Gollub J, Hebert J, Kaloper M, Brown PO, Hernandez-Boussard T, Kumar A, Cheung K, Marenco L, Snyder M, Tosches N, Bertone P, Miller P, Masiar P, Liu Y, Pesole G, Marc P, Biswas M, Kersey P, Apweiler R, Hoogland C.
Volume (2002) p.769–904
DOI: 10.1002/352760149x.ch7

Applications of InterPro in protein annotation and genome analysis.
Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Brief Bioinform Volume 3 (2002) p.285-295
DOI: 10.1093/bib/3.3.285

TEMBLOR - Perspectives of EBI Database Services.
Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 3 (2002) p.47-50
DOI: 10.1002/cfg.133

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R.
Brief Bioinform Volume 3 (2002) p.275-284
DOI: 10.1093/bib/3.3.275

Bioinformatics: Using the Molecular Biology Data
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Volume (2002) p.265–284
DOI: 10.1002/9783527612642.ch11

The EBI SRS server-new features.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.1149-1150
DOI: 10.1093/bioinformatics/18.8.1149

The EBI SRS server--recent developments.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.368-373
DOI: 10.1093/bioinformatics/18.2.368

Interactive InterPro-based comparisons of proteins in whole genomes.
Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics Volume 18 (2002) p.374-375
DOI: 10.1093/bioinformatics/18.2.374

InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium.
Brief Bioinform Volume 3 (2002) p.225-235
DOI: 10.1093/bib/3.3.225

2001

InterProScan--an integration platform for the signature-recognition methods in InterPro.
Zdobnov EM, Apweiler R.
Bioinformatics Volume 17 (2001) p.847-848
DOI: 10.1093/bioinformatics/17.9.847

Evaluation of methods for the prediction of membrane spanning regions.
Möller S, Croning MD, Apweiler R.
Bioinformatics Volume 17 (2001) p.646-653
DOI: 10.1093/bioinformatics/17.7.646

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic Acids Res Volume 29 (2001) p.44-48
DOI: 10.1093/nar/29.1.44

The human proteomics initiative (HPI).
O'Donovan C, Apweiler R, Bairoch A.
Trends Biotechnol Volume 19 (2001) p.178-181
DOI: 10.1016/s0167-7799(01)01598-0

Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences.
Apweiler R.
Brief Bioinform Volume 2 (2001) p.9-18
DOI: 10.1093/bib/2.1.9

Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins.
Möller S, Schroeder M, Apweiler R.
Comput Chem Volume 26 (2001) p.41-49
DOI: 10.1016/s0097-8485(01)00098-5

Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT.
Kretschmann E, Fleischmann W, Apweiler R.
Bioinformatics Volume 17 (2001) p.920-926
DOI: 10.1093/bioinformatics/17.10.920

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.
Nucleic Acids Res Volume 29 (2001) p.37-40
DOI: 10.1093/nar/29.1.37

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.
Kriventseva EV, Fleischmann W, Zdobnov EM, Apweiler R.
Nucleic Acids Res Volume 29 (2001) p.33-36
DOI: 10.1093/nar/29.1.33

Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL.
Biswas M, Kanapin A, Apweiler R.
J Biosci Volume 26 (2001) p.277-284
DOI: 10.1007/bf02703652

Clustering and analysis of protein families.
Kriventseva EV, Biswas M, Apweiler R.
Curr Opin Struct Biol Volume 11 (2001) p.334-339
DOI: 10.1016/s0959-440x(00)00211-6

2000

Comparative genomics of the eukaryotes.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S.
Science Volume 287 (2000) p.2204-2215
DOI: 10.1126/science.287.5461.2204

InterPro--an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, InterPro Consortium.
Bioinformatics Volume 16 (2000) p.1145-1150
DOI: 10.1093/bioinformatics/16.12.1145

A comparison of signal sequence prediction methods using a test set of signal peptides.
Menne KM, Hermjakob H, Apweiler R.
Bioinformatics Volume 16 (2000) p.741-742
DOI: 10.1093/bioinformatics/16.8.741

Mus musculus in the SWISS-PROT database: its relevance to developmental research.
Magrane M, Apweiler R.
Genesis Volume 26 (2000) p.1-4
DOI: 10.1002/(sici)1526-968x(200001)26:1<1::aid-gene2>3.0.co;2-f

The role SWISS-PROT and TrEMBL play in the genome research environment.
Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R.
J Biotechnol Volume 78 (2000) p.221-234
DOI: 10.1016/s0168-1656(00)00198-x

Protein sequence databases.
Apweiler R.
Adv Protein Chem Volume 54 (2000) p.31-71
DOI: 10.1016/s0065-3233(00)54002-9

A collection of well characterised integral membrane proteins.
Möller S, Kriventseva EV, Apweiler R.
Bioinformatics Volume 16 (2000) p.1159-1160
DOI: 10.1093/bioinformatics/16.12.1159

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Kersey P, Hermjakob H, Apweiler R.
Bioinformatics Volume 16 (2000) p.1048-1049
DOI: 10.1093/bioinformatics/16.11.1048

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
Bairoch A, Apweiler R.
Nucleic Acids Res Volume 28 (2000) p.45-48
DOI: 10.1093/nar/28.1.45

1999

A novel method for automatic functional annotation of proteins.
Fleischmann W, Möller S, Gateau A, Apweiler R.
Bioinformatics Volume 15 (1999) p.228-233
DOI: 10.1093/bioinformatics/15.3.228

Representation of functional information in the SWISS-PROT data bank.
Junker VL, Apweiler R, Bairoch A.
Bioinformatics Volume 15 (1999) p.1066-1067
DOI: 10.1093/bioinformatics/15.12.1066

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Bairoch A, Apweiler R.
Nucleic Acids Res Volume 27 (1999) p.49-54
DOI: 10.1093/nar/27.1.49

Report of the Second International Nomenclature Workshop. Cambridge, United Kingdom, May 1-2, 1999.
White JA, Apweiler R, Blake JA, Eppig JT, Maltais LJ, Povey S.
Genomics Volume 62 (1999) p.320-323
DOI: 10.1006/geno.1999.6013

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Apweiler R, Hermjakob H, Sharon N.
Biochim Biophys Acta Volume 1473 (1999) p.4-8
DOI: 10.1016/s0304-4165(99)00165-8

Removing redundancy in SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R.
Bioinformatics Volume 15 (1999) p.258-259
DOI: 10.1093/bioinformatics/15.3.258

EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation.
Möller S, Leser U, Fleischmann W, Apweiler R.
Bioinformatics Volume 15 (1999) p.219-227
DOI: 10.1093/bioinformatics/15.3.219

Swissknife - 'lazy parsing' of SWISS-PROT entries.
Hermjakob H, Fleischmann W, Apweiler R.
Bioinformatics Volume 15 (1999) p.771-772
DOI: 10.1093/bioinformatics/15.9.771

1998

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.
Bairoch A, Apweiler R.
Nucleic Acids Res Volume 26 (1998) p.38-42
DOI: 10.1093/nar/26.1.38

1997

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
Apweiler R, Gateau A, Contrino S, Martin MJ, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Bairoch A.
Proc Int Conf Intell Syst Mol Biol Volume 5 (1997) p.33-43

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

The SWISS-PROT protein sequence data bank and its supplement TrEMBL.
Bairoch A, Apweiler R.
Nucleic Acids Res Volume 25 (1997) p.31-36
DOI: 10.1093/nar/25.1.31

1996

The SWISS-PROT protein sequence data bank and its new supplement TREMBL.
Bairoch A, Apweiler R.
Nucleic Acids Res Volume 24 (1996) p.21-25
DOI: 10.1093/nar/24.1.21

1995

Effect of the new oral antidiabetic agent (-)-BM 13.0913.Na on insulin resistance in lean and obese Zucker rats.
Apweiler R, Kühnle HF, Ritter G, Schell R, Freund P.
Metabolism Volume 44 (1995) p.577-583
DOI: 10.1016/0026-0495(95)90113-2

1993

Development of glucose intolerance in obese (fa/fa) Zucker rats.
Apweiler R, Freund P.
Horm Metab Res Volume 25 (1993) p.521-524

In vitro poly-(ADP-ribosyl)ation of chromatin proteins in the rat tapeworm, Hymenolepis diminuta.
Kappus S, Apweiler R, White CJ, Whish WJ.
Comp Biochem Physiol B Volume 104 (1993) p.711-716

1990

Identification of ADPR-transferase activity in the rat tapeworm, Hymenolepis diminuta.
Alsharif M, Apweiler R, Whish WJ, Branford White CJ, Brunt RV.
Comp Biochem Physiol B Volume 96 (1990) p.527-531

Team members

Jason Mundin