Rolf Apweiler - researchr alias

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2010

On the Importance of Comprehensible Classification Models for Protein Function PredictionAlex Alves Freitas, Daniela Wieser, Rolf Apweiler. tcbb, 7(1):172-182, 2010. [doi]

2009

The GOA database in 2009 - an integrated Gene Ontology Annotation resourceDaniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O Donovan, Rolf Apweiler. nar, 37(Database-Issue):396-403, 2009. [doi]

QuickGO: a web-based tool for Gene Ontology searchingDavid Binns, Emily Dimmer, Rachael P. Huntley, Daniel Barrell, Claire O Donovan, Rolf Apweiler. bioinformatics, 25(22):3045-3046, 2009. [doi]

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short readsKai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning. bioinformatics, 25(21):2865-2871, 2009. [doi]

2008

The Ontology Lookup Service: more data and better tools for controlled vocabulary queriesRichard G. CÃ´tÃ©, Philip Jones, Lennart Martens, Rolf Apweiler, Henning Hermjakob. nar, 36(Web-Server-Issue):372-376, 2008. [doi]

UniProtJAPI: a remote API for accessing UniProt dataSamuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, Rolf Apweiler. bioinformatics, 24(10):1321-1322, 2008. [doi]

2007

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databasesRichard G. Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob. bmcbi, 8, 2007. [doi]

Analysing latent topics in large-scale proteomicsSebastian Klie, Alexander Hinneburg, Lennart Martens, Juan Antonio Vizcaino, Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob. lwa 2007: 73-80

An Application of Latent Topic Document Analysis to Large-Scale Proteomics DatabasesSebastian Klie, Lennart Martens, Juan Antonio Vizcaino, Richard G. Côté, Philip Jones, Rolf Apweiler, Alexander Hinneburg, Henning Hermjakob. gcb 2007: 174-184

New developments in the InterPro databaseNicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats. nar, 35(Database-Issue):224-228, 2007. [doi]

2006

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queriesRichard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob. bmcbi, 7:97, 2006. [doi]

PRIDE: a public repository of protein and peptide identifications for the proteomics communityPhilip Jones, Richard G. Côté, Lennart Martens, Antony F. Quinn, Chris F. Taylor, William Derache, Henning Hermjakob, Rolf Apweiler. nar, 34(Database-Issue):659-663, 2006. [doi]

UniSave: the UniProtKB Sequence/Annotation Version databaseRasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler. bioinformatics, 22(10):1284-1285, 2006. [doi]

The Universal Protein Resource (UniProt): an expanding universe of protein informationCathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O Donovan, Nicole Redaschi, Baris E. Suzek. nar, 34(Database-Issue):187-191, 2006. [doi]

2005

The Universal Protein Resource (UniProt)Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, María J. Martín, Darren A. Natale, Claire O Donovan, Nicole Redaschi, Lai-Su L. Yeh. nar, 33(Database-Issue):154-159, 2005. [doi]

Do you do text?Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc E. Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia. bioinformatics, 21(23):4199-4200, 2005. [doi]

An evaluation of GO annotation retrieval for BioCreAtIvE and GOAEvelyn Camon, Daniel Barrell, Emily Dimmer, Vivian Lee, Michele Magrane, John Maslen, David Binns, Rolf Apweiler. bmcbi, 6(S-1), 2005. [doi]

Dasty and UniProt DAS: a perfect pair for protein feature visualizationPhilip Jones, Nisha Vinod, Thomas Down, Andre Hackmann, Andreas Kähäri, Ernst Kretschmann, Antony F. Quinn, Daniela Wieser, Henning Hermjakob, Rolf Apweiler. bioinformatics, 21(14):3198-3199, 2005. [doi]

The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic ExperimentsSandra E. Orchard, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler. psb 2005: [doi]

The predictive power of the CluSTr databaseRobert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler. bioinformatics, 21(18):3604-3609, 2005. [doi]

InterProScan: protein domains identifierEmmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez. nar, 33(Web-Server-Issue):116-120, 2005. [doi]

E-MSD: an integrated data resource for bioinformaticsSamir S. Velankar, P. McNeil, V. Mittard-Runte, A. Suárez, Daniel Barrell, Rolf Apweiler, Kim Henrick. nar, 33(Database-Issue):262-265, 2005. [doi]

2004

UniProt: the Universal Protein knowledgebaseRolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O Donovan, Nicole Redaschi, Lai-Su L. Yeh. nar, 32(Database-Issue):115-119, 2004.

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyEvelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, Rolf Apweiler. nar, 32(Database-Issue):262-266, 2004.

IntEnz, the integrated relational enzyme databaseAstrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, Rolf Apweiler. nar, 32(Database-Issue):434-437, 2004.

IntAct: an open source molecular interaction databaseHenning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler. nar, 32(Database-Issue):452-455, 2004.

GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of -omics data and for validation of automatic annotation toolsVivian Lee, Evelyn Camon, Emily Dimmer, Daniel Barrell, Rolf Apweiler. isb, 5, 2004. [doi]

UniProt archiveRasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler. bioinformatics, 20(17):3236-3237, 2004. [doi]

The Integr8 project - a resource for genomic and proteomic dataManuela Pruess, Paul Kersey, Rolf Apweiler. isb, 5, 2004. [doi]

Integrating Genomic and Proteomic Data: The Integr8 ProjectManuela Pruess, Paul Kersey, Rolf Apweiler. jib, 1(1), 2004. [doi]

Filtering erroneous protein annotationDaniela Wieser, Ernst Kretschmann, Rolf Apweiler. ismb 2004: 342-347 [doi]

2003

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria Jesus Martin, Karine Michoud, Claire O Donovan, Isabelle Phan, Sandrine Pilbout, Michel Schneider. nar, 31(1):365-370, 2003.

The European Bioinformatics Institute s data resourcesCatherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron. nar, 31(1):43-50, 2003.

The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt KnowledgebaseEvelyn Camon, Daniel Barrell, Vivian Lee, Emily Dimmer, Rolf Apweiler. isb, 4, 2003. [doi]

Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clustersEvgenia V. Kriventseva, Florence Servant, Rolf Apweiler. nar, 31(1):388-389, 2003.

The Proteome Analysis database: a tool for the in silico analysis of whole proteomesManuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler. nar, 31(1):414-417, 2003.

2002

Automation of Protein Sequence Characterization and Its Application in Whole Proteome AnalysisRolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Evgenia V. Kriventseva, Nicola J. Mulder. dagstuhl 2002: 19-47

Applications of InterPro in Protein Annotation and Genome AnalysisMargaret Biswas, Joseph F. O Rourke, Evelyn Camon, Gillian Fraser, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler. bib, 3(3):285-295, 2002.

High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBLClaire O Donovan, Maria Jesus Martin, Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch, Rolf Apweiler. bib, 3(3):275-284, 2002.

Interactive InterPro-based comparisons of proteins in whole genomesAlexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Florence Servant, Evgeni M. Zdobnov. bioinformatics, 18(2):374-375, 2002.

Organisation and standardisation of information in SWISS_PROT and TrEMBLMichele Magrane, Rolf Apweiler. datascience, 1(1):13-18, 2002.

Consistent Integration of Non-reliable Heterogeneous Information Resources Applied to the Annotation of Transmembrane ProteinsSteffen Möller, Michael Schroeder, Rolf Apweiler. CANDC, 26(1):41-49, 2002. [doi]

Erratum: Evaluation of methods for the prediction of membrane spanning regionsSteffen Möller, Michael D. R. Croning, Rolf Apweiler. bioinformatics, 18(1):218, 2002.

The EBI SRS server-new featuresEvgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold. bioinformatics, 18(8):1149-1150, 2002.

The EBI SRS server-recent developmentsEvgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold. bioinformatics, 18(2):368-373, 2002.

2001

Functional Information in SWISS-PROT: the Basis for Large-scale Characterisation of Protein SequencesRolf Apweiler. bib, 2(1):9-18, 2001.

Technical comment to Database verification studies of SWISS-PROT and GenBank by Karp et alRolf Apweiler, Paul Kersey, Vivien Junker, Amos Bairoch. bioinformatics, 17(6):533-534, 2001.

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomesRolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Evgeni M. Zdobnov. nar, 29(1):44-48, 2001.

IntEnz - The Enzyme Database in OracleAstrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Rolf Apweiler. gcb 2001: 148-149

Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROTErnst Kretschmann, Wolfgang Fleischmann, Rolf Apweiler. bioinformatics, 17(10):920-926, 2001.

Automatic rule generation for protein annotation with the C4.5 data-mining algorithm applied on peptides in EnsemblErnst Kretschmann, Rolf Apweiler. gcb 2001: 53-57

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteinsEvgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov, Rolf Apweiler. nar, 29(1):33-36, 2001.

Evaluation of methods for the prediction of membrane spanning regionsSteffen Möller, Michael D. R. Croning, Rolf Apweiler. bioinformatics, 17(7):646-653, 2001.

Towards a New Curation Environment for the TrEMBL DatabaseKai J. Runte, Henning Hermjakob, Rolf Apweiler. gcb 2001: 220

InterProScan - an integration platform for the signature-recognition methods in InterProEvgeni M. Zdobnov, Rolf Apweiler. bioinformatics, 17(9):847-848, 2001.

2000

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000Amos Bairoch, Rolf Apweiler. nar, 28(1):45-48, 2000.

Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole GenomesMargaret Biswas, Rolf Apweiler, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Evgeni M. Zdobnov. gcb 2000: 149-158

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBLPaul Kersey, Henning Hermjakob, Rolf Apweiler. bioinformatics, 16(11):1048-1049, 2000.

A comparison of signal sequence prediction methods using a test set of signal peptidesKerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler. bioinformatics, 16(8):741-742, 2000.

A collection of well characterised integral membrane proteinsSteffen Möller, Evgenia V. Kriventseva, Rolf Apweiler. bioinformatics, 16(12):1159-1160, 2000.

The EBI SRS Server: Recent DevelopmentsEvgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold. gcb 2000: 139-148

1999

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999Amos Bairoch, Rolf Apweiler. nar, 27(1):49-54, 1999.

Removing redundancy in SWISS-PROT and TrEMBLClaire O Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler. bioinformatics, 15(3):258-259, 1999.

A novel method for automatic functional annotation of proteinsWolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler. bioinformatics, 15(3):228-233, 1999.

Swissknife - lazy parsing of SWISS-PROT entriesHenning Hermjakob, Wolfgang Fleischmann, Rolf Apweiler. bioinformatics, 15(9):771-772, 1999.

Representation of functional information in the SWISS-PROT Data BankV. L. Junker, Rolf Apweiler, Amos Bairoch. bioinformatics, 15(12):1066-1067, 1999.

Facilitating context-sensitive queries: A tool to rephrase SWISS-PROTSteffen Möller, Michael J. Wise, David P. Kreil, Michael Schroeder, D. Gilbest, Rolf Apweiler. gcb 1999: 216-218

EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotationSteffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler. bioinformatics, 15(3):219-227, 1999.

Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotationArno Velds, Henning Hermjakob, Rolf Apweiler. gcb 1999: 229-230

1998

1997

Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBLRolf Apweiler, Alain Gateau, Sergio Contrino, Maria Jesus Martin, Vivien Junker, Claire O Donovan, Fiona Lang, Nicoletta Mitaritonna, Stephanie Kappus, Amos Bairoch. ismb 1997: 33-43

The SWISS-PROT protein sequence data bank and its supplement TrEMBLAmos Bairoch, Rolf Apweiler. nar, 25(1):31-36, 1997.

1996