Rolf Apweiler

Sarah Hunter, Philip Jones, Alex Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Muellenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong: InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40(Database-Issue): 306-312 (2012)

Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan Bridge, Elisabeth Coudert, Anne Estreicher, Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler: The UniProt-GO Annotation database in 2011. Nucleic Acids Research 40(Database-Issue): 565-570 (2012)

Alex Alves Freitas, Daniela Wieser, Rolf Apweiler: On the Importance of Comprehensible Classification Models for Protein Function Prediction. IEEE/ACM Trans. Comput. Biology Bioinform. 7(1): 172-182 (2010)

Nell Sedransk, Lawrence H. Cox, Deborah Nolan, Keith Soper, Cliff Spiegelman, Linda J. Young, Katrina L. Kelner, Robert A. Moffitt, Ani Thakar, Jordan Raddick, Edward J. Ungvarsky, Richard W. Carlson, Rolf Apweiler: Make Research Data Public?---Not Always so Simple: A Dialogue for Statisticians and Science Editors. CoRR abs/1011.0810 (2010)

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

David Binns, Emily Dimmer, Rachael P. Huntley, Daniel Barrell, Claire O'Donovan, Rolf Apweiler: QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 25(22): 3045-3046 (2009)

Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats: InterPro: the integrative protein signature database. Nucleic Acids Research 37(Database-Issue): 211-215 (2009)

Daniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O'Donovan, Rolf Apweiler: The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Research 37(Database-Issue): 396-403 (2009)

Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, Rolf Apweiler: UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics 24(10): 1321-1322 (2008)

Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Research 36(Database-Issue): 5-12 (2008)

Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, Henning Hermjakob: The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Research 36(Web-Server-Issue): 372-376 (2008)

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

Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler: EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Research 35(Database-Issue): 16-20 (2007)

Nicola 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: New developments in the InterPro database. Nucleic Acids Research 35(Database-Issue): 224-228 (2007)

Samuel Kerrien, Yasmin Alam-Faruque, Bruno Aranda, I. Bancarz, Alan Bridge, C. Derow, Emily Dimmer, Marc Feuermann, A. Friedrichsen, Rachael P. Huntley, C. Kohler, Jyoti Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, J. Risse, K. Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob: IntAct - open source resource for molecular interaction data. Nucleic Acids Research 35(Database-Issue): 561-565 (2007)

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

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

Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler: UniSave: the UniProtKB Sequence/Annotation Version database. Bioinformatics 22(10): 1284-1285 (2006)

Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7: 97 (2006)

Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler: EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Research 34(Database-Issue): 10-15 (2006)

Cathy 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: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research 34(Database-Issue): 187-191 (2006)

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

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

Robert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler: The predictive power of the CluSTr database. Bioinformatics 21(18): 3604-3609 (2005)

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

Evelyn Camon, Daniel Barrell, Emily Dimmer, Vivian Lee, Michele Magrane, John Maslen, David Binns, Rolf Apweiler: An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 6(S-1) (2005)

Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler: The EMBL Nucleotide Sequence Database. Nucleic Acids Research 33(Database-Issue): 29-33 (2005)

Amos Bairoch, Rolf Apweiler, 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: The Universal Protein Resource (UniProt). Nucleic Acids Research 33(Database-Issue): 154-159 (2005)

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu: InterPro, progress and status in 2005. Nucleic Acids Research 33(Database-Issue): 201-205 (2005)

Samir S. Velankar, P. McNeil, Virginie Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick: E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Research 33(Database-Issue): 262-265 (2005)

Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler: Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Research 33(Database-Issue): 297-302 (2005)

Emmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez: InterProScan: protein domains identifier. Nucleic Acids Research 33(Web-Server-Issue): 116-120 (2005)

Sandra E. Orchard, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler: The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments. Pacific Symposium on Biocomputing 2005

Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler: UniProt archive. Bioinformatics 20(17): 3236-3237 (2004)

Vivian Lee, Evelyn Camon, Emily Dimmer, Daniel Barrell, Rolf Apweiler: GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools. In Silico Biology 5 (2004)

Manuela Pruess, Paul Kersey, Rolf Apweiler: The Integr8 project - a resource for genomic and proteomic data. In Silico Biology 5 (2004)

Manuela Pruess, Paul Kersey, Rolf Apweiler: Integrating Genomic and Proteomic Data: The Integr8 Project. J. Integrative Bioinformatics 1(1) (2004)

Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler: The EMBL Nucleotide Sequence Database. Nucleic Acids Research 32(Database-Issue): 27-30 (2004)

Rolf 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: UniProt: the Universal Protein knowledgebase. Nucleic Acids Research 32(Database-Issue): 115-119 (2004)

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

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

Henning 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: IntAct: an open source molecular interaction database. Nucleic Acids Research 32(Database-Issue): 452-455 (2004)

Daniela Wieser, Ernst Kretschmann, Rolf Apweiler: Filtering erroneous protein annotation. ISMB/ECCB (Supplement of Bioinformatics) 2004: 342-347

Evelyn Camon, Daniel Barrell, Vivian Lee, Emily Dimmer, Rolf Apweiler: The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biology 4 (2003)

Catherine 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: The European Bioinformatics Institute's data resources. Nucleic Acids Research 31(1): 43-50 (2003)

Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov: The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research 31(1): 315-318 (2003)

Brigitte 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: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31(1): 365-370 (2003)

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

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

Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist: InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites. Briefings in Bioinformatics 3(3): 225-235 (2002)

Claire O'Donovan, Maria Jesus Martin, Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch, Rolf Apweiler: High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL. Briefings in Bioinformatics 3(3): 275-284 (2002)

Margaret 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: Applications of InterPro in Protein Annotation and Genome Analysis. Briefings in Bioinformatics 3(3): 285-295 (2002)

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

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

Alexander 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: Interactive InterPro-based comparisons of proteins in whole genomes. Bioinformatics 18(2): 374-375 (2002)

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

Steffen Möller, Michael Schroeder, Rolf Apweiler: Consistent Integration of Non-reliable Heterogeneous Information Resources Applied to the Annotation of Transmembrane Proteins. Computers & Chemistry 26(1): 41-49 (2002)

Michele Magrane, Rolf Apweiler: Organisation and standardisation of information in SWISS_PROT and TrEMBL. Data Science Journal 1(1): 13-18 (2002)

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

Rolf Apweiler: Functional Information in SWISS-PROT: the Basis for Large-scale Characterisation of Protein Sequences. Briefings in Bioinformatics 2(1): 9-18 (2001)

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

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

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

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

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

Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29(1): 37-40 (2001)

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

Ernst Kretschmann, Rolf Apweiler: Automatic rule generation for protein annotation with the C4.5 data-mining algorithm applied on peptides in Ensembl. German Conference on Bioinformatics 2001: 53-57

Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Rolf Apweiler: IntEnz - The Enzyme Database in Oracle. German Conference on Bioinformatics 2001: 148-149

Kai J. Runte, Henning Hermjakob, Rolf Apweiler: Towards a New Curation Environment for the TrEMBL Database. German Conference on Bioinformatics 2001: 220

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

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

Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov: InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16(12): 1145-1150 (2000)

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

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

Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold: The EBI SRS Server: Recent Developments. German Conference on Bioinformatics 2000: 139-148

Margaret 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: Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes. German Conference on Bioinformatics 2000: 149-158

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

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

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

Henning Hermjakob, Wolfgang Fleischmann, Rolf Apweiler: Swissknife - 'lazy parsing' of SWISS-PROT entries. Bioinformatics 15(9): 771-772 (1999)

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

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

Steffen Möller, Michael J. Wise, David P. Kreil, Michael Schroeder, D. Gilbest, Rolf Apweiler: Facilitating context-sensitive queries: A tool to rephrase SWISS-PROT. German Conference on Bioinformatics 1999: 216-218

Arno Velds, Henning Hermjakob, Rolf Apweiler: Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation. German Conference on Bioinformatics 1999: 229-230

Amos Bairoch, Rolf Apweiler: The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Research 26(1): 38-42 (1998)

Wolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler: A novel method for automatic and reliable functional annotation of proteins. German Conference on Bioinformatics 1998

Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Fiona Lang, Rolf Apweiler: SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world. German Conference on Bioinformatics 1998

Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler: EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation. German Conference on Bioinformatics 1998

Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler: Removing Redundancy in SWISS-PROT and TrEMBL. German Conference on Bioinformatics 1998

Amos Bairoch, Rolf Apweiler: The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Research 25(1): 31-36 (1997)

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

Amos Bairoch, Rolf Apweiler: The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Research 24(1): 21-25 (1996)

Rolf Apweiler, Vivien Junker, Alain Gateau, Claire O'Donovan, Fiona Lang, Amos Bairoch: New Developments in the Linking of Biological Databases and Computer-Generation of Annotation. German Conference on Bioinformatics 1996: 29-34

Rolf Apweiler, Vivien Junker, Alain Gateau, Claire O'Donovan, Fiona Lang, Amos Bairoch: New Developments in Linking of Biological Databases and Computer-Generation of Annotations: SWISS-PROT and Its Computer-Annotated Supplement TREMBL. German Conference on Bioinformatics - Selected Papers 1996: 44-51