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2020 – today
- 2022
[j86]Gaia Cantelli
, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna R. McEntyre:
The European Bioinformatics Institute (EMBL-EBI) in 2021. Nucleic Acids Res. 50(D1): 11-19 (2022)- 2021
- [j85]Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen M. McDonagh, Paul Flicek, Johanna R. McEntyre, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. Nucleic Acids Res. 49(Database-Issue): D29-D37 (2021) - [j84]Peter W. Harrison, Rodrigo Lopez, Nadim Rahman, Stefan Gutnick Allen, Raheela Aslam, Nicola Buso, Carla A. Cummins, Yasmin Fathy, Eloy Felix, Mihai Glont, Suran Jayathilaka, Sandeep Kadam, Manish Kumar, Katharina B. Lauer, Geetika Malhotra, Abayomi Mosaku, Ossama Edbali, Young Mi Park, Andrew Parton, Matt Pearce, Jose Francisco Estrada pena, Joseph Rossetto, Craig Russell, Sandeep Selvakumar, Xènia Pérez Sitjà, Alexey Sokolov, Ross Thorne, Marianna Ventouratou, Peter Walter, Galabina Yordanova, Amonida Zadissa, Guy Cochrane, Niklas Blomberg, Rolf Apweiler:
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res. 49(Webserver-Issue): 619-623 (2021) - 2020
- [j83]Charles E. Cook, Oana Stroe, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. Nucleic Acids Res. 48(Database-Issue): D17-D23 (2020)
2010 – 2019
- 2019
- [j82]Charles E. Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic Acids Res. 47(Database-Issue): D15-D22 (2019) - 2018
- [j81]Charles E. Cook, Mary Todd Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney:
The European Bioinformatics Institute in 2017: data coordination and integration. Nucleic Acids Res. 46(Database-Issue): D21-D29 (2018) - 2016
- [j80]Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Res. 44(Database-Issue): 20-26 (2016) - 2014
- [j79]Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet M. Thornton:
The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res. 42(Database-Issue): 18-25 (2014) - 2013
- [j78]Prudence Mutowo-Meullenet, Rachael P. Huntley, Emily C. Dimmer, Yasmin Alam-Faruque, Tony Sawford, Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler:
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database J. Biol. Databases Curation 2013 (2013) - 2012
- [j77]Sarah Hunter, Philip Jones, Alex L. 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 C. 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-Meullenet, 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 Res. 40(Database-Issue): 306-312 (2012) - [j76]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 Y. 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, Maria 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 Res. 40(Database-Issue): 565-570 (2012) - 2010
- [j75]Alex Alves Freitas, Daniela Wieser, Rolf Apweiler:
On the Importance of Comprehensible Classification Models for Protein Function Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 7(1): 172-182 (2010) - [i1]Nell Sedransk, Lawrence H. Cox, Deborah Nolan, Keith Soper, Clifford H. Spiegelman, Linda J. Young, Katrina L. Kelner, Robert A. Moffitt, Ani Thakar, M. 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)
2000 – 2009
- 2009
- [j74]Rachael P. Huntley, David Binns, Emily Dimmer, Daniel Barrell, Claire O'Donovan, Rolf Apweiler:
QuickGO: a user tutorial for the web-based Gene Ontology browser. Database J. Biol. Databases Curation 2009 (2009) - [j73]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. Bioinform. 25(21): 2865-2871 (2009) - [j72]David Binns, Emily Dimmer, Rachael P. Huntley, Daniel Barrell, Claire O'Donovan, Rolf Apweiler:
QuickGO: a web-based tool for Gene Ontology searching. Bioinform. 25(22): 3045-3046 (2009) - [j71]Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise C. 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 L. 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 Res. 37(Database-Issue): 211-215 (2009) - [j70]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 Res. 37(Database-Issue): 396-403 (2009) - [p3]Francisco M. Couto, Mário J. Silva, Vivian Lee, Emily Dimmer, Evelyn Camon, Rolf Apweiler:
Verification of Uncurated Protein Annotations. Information Retrieval in Biomedicine 2009: 301-314 - 2008
- [j69]Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, Rolf Apweiler:
UniProtJAPI: a remote API for accessing UniProt data. Bioinform. 24(10): 1321-1322 (2008) - [j68]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 Y. 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 Res. 36(Database-Issue): 5-12 (2008) - [j67]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 Res. 36(Web-Server-Issue): 372-376 (2008) - 2007
- [j66]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 Bioinform. 8 (2007) - [j65]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 Y. 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 Res. 35(Database-Issue): 16-20 (2007) - [j64]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 C. 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 L. 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 Res. 35(Database-Issue): 224-228 (2007) - [j63]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, Judith E. Risse, Karine Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob:
IntAct - open source resource for molecular interaction data. Nucleic Acids Res. 35(Database-Issue): 561-565 (2007) - [c19]Sebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, 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 - [c18]Sebastian Klie, Alexander Hinneburg, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
Analysing latent topics in large-scale proteomics. LWA 2007: 73-80 - 2006
- [j62]Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler:
UniSave: the UniProtKB Sequence/Annotation Version database. Bioinform. 22(10): 1284-1285 (2006) - [j61]Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinform. 7: 97 (2006) - [j60]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 Y. 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 Res. 34(Database-Issue): 10-15 (2006) - [j59]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 Res. 34(Database-Issue): 187-191 (2006) - [j58]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 Res. 34(Database-Issue): 659-663 (2006) - 2005
- [j57]Philip Jones, Nisha Vinod, Thomas A. 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. Bioinform. 21(14): 3198-3199 (2005) - [j56]Robert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler:
The predictive power of the CluSTr database. Bioinform. 21(18): 3604-3609 (2005) - [j55]Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc E. Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia:
Do you do text? Bioinform. 21(23): 4199-4200 (2005) - [j54]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 Bioinform. 6(S-1) (2005) - [j53]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 Y. 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 Res. 33(Database-Issue): 29-33 (2005) - [j52]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 Res. 33(Database-Issue): 154-159 (2005) - [j51]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 L. 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 Res. 33(Database-Issue): 201-205 (2005) - [j50]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 Res. 33(Database-Issue): 262-265 (2005) - [j49]Paul J. 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 Res. 33(Database-Issue): 297-302 (2005) - [j48]Emmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez:
InterProScan: protein domains identifier. Nucleic Acids Res. 33(Web-Server-Issue): 116-120 (2005) - [c17]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 - [p2]Allyson L. Williams, Paul J. Kersey, Manuela Pruess, Rolf Apweiler:
Biological Databases: Infrastructure, Content and Integration. Data Analysis and Visualization in Genomics and Proteomics 2005: 11-28 - 2004
- [j47]Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler:
UniProt archive. Bioinform. 20(17): 3236-3237 (2004) - [j46]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. Silico Biol. 5(1): 5-8 (2004) - [j45]Manuela Pruess, Paul J. Kersey, Rolf Apweiler:
The Integr8 project - a resource for genomic and proteomic data. Silico Biol. 5(2): 179-185 (2004) - [j44]Fernando Martín-Sánchez, Ilias Iakovidis, S. Nørager, Victor Maojo, Piet C. de Groen, Johan van der Lei, T. Jones, Klaus Abraham-Fuchs, Rolf Apweiler, Ankica Babic:
Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. J. Biomed. Informatics 37(1): 30-42 (2004) - [j43]Manuela Pruess, Paul J. Kersey, Rolf Apweiler:
Integrating Genomic and Proteomic Data: The Integr8 Project. J. Integr. Bioinform. 1(1) (2004) - [j42]Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Y. 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 Res. 32(Database-Issue): 27-30 (2004) - [j41]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 Res. 32(Database-Issue): 115-119 (2004) - [j40]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 Res. 32(Database-Issue): 262-266 (2004) - [j39]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 Res. 32(Database-Issue): 434-437 (2004) - [j38]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 Res. 32(Database-Issue): 452-455 (2004) - [c16]Daniela Wieser, Ernst Kretschmann, Rolf Apweiler:
Filtering erroneous protein annotation. ISMB/ECCB (Supplement of Bioinformatics) 2004: 342-347 - 2003
- [j37]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. Silico Biol. 4(1): 5-6 (2003) - [j36]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 Res. 31(1): 43-50 (2003) - [j35]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 Res. 31(1): 315-318 (2003) - [j34]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 Res. 31(1): 365-370 (2003) - [j33]Evgenia V. Kriventseva, Florence Servant, Rolf Apweiler:
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. Nucleic Acids Res. 31(1): 388-389 (2003) - [j32]Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. 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 Res. 31(1): 414-417 (2003) - 2002
- [j31]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 Bioinform. 3(3): 225-235 (2002) - [j30]Claire O'Donovan, Maria Jesus Martin, Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch, Rolf Apweiler:
High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL. Briefings Bioinform. 3(3): 275-284 (2002) - [j29]Margaret Biswas, Joseph F. O'Rourke, Evelyn Camon, Gillian Fraser, Alexander Kanapin, Youla Karavidopoulou, Paul J. 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 Bioinform. 3(3): 285-295 (2002) - [j28]Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
Erratum: Evaluation of methods for the prediction of membrane spanning regions. Bioinform. 18(1): 218 (2002) - [j27]Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
The EBI SRS server-recent developments. Bioinform. 18(2): 368-373 (2002) - [j26]Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul J. 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. Bioinform. 18(2): 374-375 (2002) - [j25]Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
The EBI SRS server-new features. Bioinform. 18(8): 1149-1150 (2002) - [j24]Steffen Möller, Michael Schroeder, Rolf Apweiler:
Consistent Integration of Non-reliable Heterogeneous Information Resources Applied to the Annotation of Transmembrane Proteins. Comput. Chem. 26(1): 41-49 (2002) - [j23]Michele Magrane, Rolf Apweiler:
Organisation and standardisation of information in SWISS_PROT and TrEMBL. Data Sci. J. 1(1): 13-18 (2002) - [c15]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 - [p1]Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
Bioinformatics: Using the Molecular Biology Data. Essentials of Genomics and Bioinformatics 2002: 265-284 - 2001
- [j22]Rolf Apweiler:
Functional Information in SWISS-PROT: the Basis for Large-scale Characterisation of Protein Sequences. Briefings Bioinform. 2(1): 9-18 (2001) - [j21]Rolf Apweiler, Paul J. Kersey, Vivien Junker, Amos Bairoch:
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al. Bioinform. 17(6): 533-534 (2001) - [j20]Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
Evaluation of methods for the prediction of membrane spanning regions. Bioinform. 17(7): 646-653 (2001) - [j19]Evgeni M. Zdobnov, Rolf Apweiler:
InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinform. 17(9): 847-848 (2001) - [j18]Ernst Kretschmann, Wolfgang Fleischmann, Rolf Apweiler:
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinform. 17(10): 920-926 (2001) - [j17]Evgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov, Rolf Apweiler:
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res. 29(1): 33-36 (2001) - [j16]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 Res. 29(1): 37-40 (2001) - [j15]Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. 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 Res. 29(1): 44-48 (2001) - [c14]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 - [c13]Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Rolf Apweiler:
IntEnz - The Enzyme Database in Oracle. German Conference on Bioinformatics 2001: 148-149 - [c12]Kai J. Runte, Henning Hermjakob, Rolf Apweiler:
Towards a New Curation Environment for the TrEMBL Database. German Conference on Bioinformatics 2001: 220 - 2000
- [j14]Kerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler:
A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinform. 16(8): 741-742 (2000) - [j13]Paul J. Kersey, Henning Hermjakob, Rolf Apweiler:
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinform. 16(11): 1048-1049 (2000) - [j12]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. Bioinform. 16(12): 1145-1150 (2000) - [j11]