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Rolf Apweiler

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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TOP 3
Binns David; Dimmer Emily; Huntley Rachael; Barrell Daniel; O'Donovan Claire; Apweiler Rolf
QuickGO: a web-based tool for Gene Ontology searching.
Ye Kai; Schulz Marcel H; Long Quan; Apweiler Rolf; Ning Zemin
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ilsley Garth R; Luscombe Nicholas M; Apweiler Rolf
Know your limits: assumptions, constraints and interpretation in systems biology.

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All Publications

2009: Binns David; Dimmer Emily; Huntley Rachael; Barrell Daniel; O'Donovan Claire; Apweiler Rolf
QuickGO: a web-based tool for Gene Ontology searching.
Bioinformatics (Oxford, England) 2009;25(22):3045-6.
2009: Ye Kai; Schulz Marcel H; Long Quan; Apweiler Rolf; Ning Zemin
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Bioinformatics (Oxford, England) 2009;25(21):2865-71.
2009: Ilsley Garth R; Luscombe Nicholas M; Apweiler Rolf
Know your limits: assumptions, constraints and interpretation in systems biology.
Biochimica et biophysica acta 2009;1794(9):1280-7.
2009: Eisenacher Martin; Martens Lennart; Hardt Tanja; Kohl Michael; Barsnes Harald; Helsens Kenny; Häkkinen Jari; Levander Fredrik; Aebersold Ruedi; Vandekerckhove Joël; Dunn Michael J; Lisacek Frederique; Siepen Jennifer A; Hubbard Simon J; Binz Pierre-Alain; Blüggel Martin; Thiele Herbert; Cottrell John; Meyer Helmut E; Apweiler Rolf; Stephan Christian
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Proteomics 2009;9(15):3928-33.
2009: Furnham Nicholas; Garavelli John S; Apweiler Rolf; Thornton Janet M
Missing in action: enzyme functional annotations in biological databases.
Nature chemical biology 2009;5(8):521-5.
2009: Eisenacher Martin; Martens Lennart; Barsnes Harald; Hardt Tanja; Kohl Michael; Häkkinen Jari; Apweiler Rolf; Meyer Helmut E; Stephan Christian
Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
Proteomics 2009;9(14):3626-9.
2009: Rodriguez Henry; Snyder Mike; Uhlén Mathias; Andrews Phil; Beavis Ronald; Borchers Christoph; Chalkley Robert J; Cho Sang Yun; Cottingham Katie; Dunn Michael; Dylag Tomasz; Edgar Ron; Hare Peter; Heck Albert J R; Hirsch Roland F; Kennedy Karen; Kolar Patrik; Kraus Hans-Joachim; Mallick Parag; Nesvizhskii Alexey; Ping Peipei; Pontén Fredrik; Yang Liming; Yates John R; Stein Stephen E; Hermjakob Henning; Kinsinger Christopher R; Apweiler Rolf
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Journal of proteome research 2009;8(7):3689-92.
2009: Koscielny Gautier; Le Texier Vincent; Gopalakrishnan Chellappa; Kumanduri Vasudev; Riethoven Jean-Jack; Nardone Francesco; Stanley Eleanor; Fallsehr Christine; Hofmann Oliver; Kull Meelis; Harrington Eoghan; Boué Stéphanie; Eyras Eduardo; Plass Mireya; Lopez Fabrice; Ritchie William; Moucadel Virginie; Ara Takeshi; Pospisil Heike; Herrmann Alexander; G Reich Jens; Guigó Roderic; Bork Peer; Doeberitz Magnus von Knebel; Vilo Jaak; Hide Winston; Apweiler Rolf; Thanaraj Thangavel Alphonse; Gautheret Daniel
ASTD: The Alternative Splicing and Transcript Diversity database.
Genomics 2009;93(3):213-20.
2009: Eisenacher Martin; Kohl Michael; Martens Lennart; Barsnes Harald; Hardt Tanja; Levander Fredrik; Häkkinen Jari; Apweiler Rolf; Meyer Helmut E; Stephan Christian
Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
Proteomics 2009;9(2):218-22.
2009: Schlüter Hartmut; Apweiler Rolf; Holzhütter Hermann-Georg; Jungblut Peter R
Finding one's way in proteomics: a protein species nomenclature.
Chemistry Central journal 2009;3():11.
2009: Martens Lennart; Apweiler Rolf
Algorithms and databases.
Methods in molecular biology (Clifton, N.J.) 2009;564():245-59.
2008: Kersey Paul; Lonsdale David; Mulder Nicky J; Petryszak Robert; Apweiler Rolf
Building a biological space based on protein sequence similarities and biological ontologies.
Combinatorial chemistry & high throughput screening 2008;11(8):653-60.
2008: Côté Richard G; Jones Philip; Martens Lennart; Apweiler Rolf; Hermjakob Henning
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Nucleic acids research 2008;36(Web Server issue):W372-6.
2008: Zhang Jun; Liem David A; Mueller Michael; Wang Yueju; Zong Chenggong; Deng Ning; Vondriska Thomas M; Korge Paavo; Drews Oliver; Maclellan W Robb; Honda Henry; Weiss James N; Apweiler Rolf; Ping Peipei
Altered proteome biology of cardiac mitochondria under stress conditions.
Journal of proteome research 2008;7(6):2204-14.
2008: Lovering Ruth C; Dimmer Emily; Khodiyar Varsha K; Barrell Daniel G; Scambler Peter; Hubank Mike; Apweiler Rolf; Talmud Philippa J
Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?
Proteomics 2008;8(10):1950-3.
2008: Patient Samuel; Wieser Daniela; Kleen Michael; Kretschmann Ernst; Jesus Martin Maria; Apweiler Rolf
UniProtJAPI: a remote API for accessing UniProt data.
Bioinformatics (Oxford, England) 2008;24(10):1321-2.
2008: Zhang Jun; Li Xiaohai; Mueller Michael; Wang Yueju; Zong Chenggong; Deng Ning; Vondriska Thomas M; Liem David A; Yang Jeong-In; Korge Paavo; Honda Henry; Weiss James N; Apweiler Rolf; Ping Peipei
Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.
Proteomics 2008;8(8):1564-75.
2008: Eisenacher Martin; Hardt Tanja; Hamacher Michael; Martens Lennart; Häkkinen Jari; Levander Fredrik; Apweiler Rolf; Meyer Helmut E; Stephan Christian
Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
Proteomics 2008;8(7):1326-30.
2008: Mulder Nicola J; Apweiler Rolf
The InterPro database and tools for protein domain analysis.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 2():Unit 2.7.
2008: Mueller Michael; Vizcaíno Juan Antonio; Jones Philip; Côté Richard; Thorneycroft David; Apweiler Rolf; Hermjakob Henning; Martens Lennart
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Proteomics 2008;8(6):1138-48.
2008: Mulder Nicola Jane; Kersey Paul; Pruess Manuela; Apweiler Rolf
In silico characterization of proteins: UniProt, InterPro and Integr8.
Molecular biotechnology 2008;38(2):165-77.
2008: Ping Peipei; Bergeron John; Apweiler Rolf
Wiley-VCH and HUPO: a global effort to advance proteomic science.
Proteomics 2008;8(1):4-6.
2008: Klie Sebastian; Martens Lennart; Vizcaíno Juan Antonio; Côté Richard; Jones Phil; Apweiler Rolf; Hinneburg Alexander; Hermjakob Henning
Analyzing large-scale proteomics projects with latent semantic indexing.
Journal of proteome research 2008;7(1):182-91.
2008: Chatr-aryamontri Andrew; Kerrien Samuel; Khadake Jyoti; Orchard Sandra; Ceol Arnaud; Licata Luana; Castagnoli Luisa; Costa Stefano; Derow Cathy; Huntley Rachael; Aranda Bruno; Leroy Catherine; Thorneycroft Dave; Apweiler Rolf; Cesareni Gianni; Hermjakob Henning
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Genome biology 2008;9 Suppl 2():S5.
2008: Jungblut Peter R; Holzhütter Hermann G; Apweiler Rolf; Schlüter Hartmut
The speciation of the proteome.
Chemistry Central journal 2008;2():16.
2007: Jones Andrew R; Miller Michael; Aebersold Ruedi; Apweiler Rolf; Ball Catherine A; Brazma Alvis; Degreef James; Hardy Nigel; Hermjakob Henning; Hubbard Simon J; Hussey Peter; Igra Mark; Jenkins Helen; Julian Randall K; Laursen Kent; Oliver Stephen G; Paton Norman W; Sansone Susanna-Assunta; Sarkans Ugis; Stoeckert Christian J; Taylor Chris F; Whetzel Patricia L; White Joseph A; Spellman Paul; Pizarro Angel
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: Martens Lennart; Orchard Sandra; Apweiler Rolf; Hermjakob Henning
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Molecular & cellular proteomics : MCP 2007;6(9):1666-7.
2007: Eisenacher Martin; Hardt Tanja; Hamacher Michael; Martens Lennart; Häkkinen Jari; Levander Fredrik; Apweiler Rolf; Meyer Helmut E; Stephan Christian
Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Proteomics 2007;7(17):3034-7.
2007: Taylor Chris F; Paton Norman W; Lilley Kathryn S; Binz Pierre-Alain; Julian Randall K; Jones Andrew R; Zhu Weimin; Apweiler Rolf; Aebersold Ruedi; Deutsch Eric W; Dunn Michael J; Heck Albert J R; Leitner Alexander; Macht Marcus; Mann Matthias; Martens Lennart; Neubert Thomas A; Patterson Scott D; Ping Peipei; Seymour Sean L; Souda Puneet; Tsugita Akira; Vandekerckhove Joel; Vondriska Thomas M; Whitelegge Julian P; Wilkins Marc R; Xenarios Ioannnis; Yates John R; Hermjakob Henning
The minimum information about a proteomics experiment (MIAPE).
Nature biotechnology 2007;25(8):887-93.
2007: Hamacher Michael; Stephan Christian; Eisenacher Martin; Lewczuk Piotr; Wiltfang Jens; Martens Lennart; Vizcaíno Juan Antonio; Kwon Kyung-Hoon; Yoo Jong Shin; Park Young Mok; Beckers Johannes; Horsch Marion; de Angelis Martin Hrabé; Cho Zang-Hee; Apweiler Rolf; Meyer Helmut E
High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Proteomics 2007;7(15):2490-6.
2007: Mueller Michael; Martens Lennart; Apweiler Rolf
Annotating the human proteome: beyond establishing a parts list.
Biochimica et biophysica acta 2007;1774(2):175-91.
2007: 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
IntAct--open source resource for molecular interaction data.
Nucleic acids research 2007;35(Database issue):D561-5.
2007: Sterk Peter; Kulikova Tamara; Kersey Paul; Apweiler Rolf
The EMBL Nucleotide Sequence and Genome Reviews Databases.
Methods in molecular biology (Clifton, N.J.) 2007;406():1-21.
2007: Mulder Nicola; Apweiler Rolf
InterPro and InterProScan: tools for protein sequence classification and comparison.
Methods in molecular biology (Clifton, N.J.) 2007;396():59-70.
2007: Côté Richard G; Jones Philip; Martens Lennart; Kerrien Samuel; Reisinger Florian; Lin Quan; Leinonen Rasko; Apweiler Rolf; Hermjakob Henning
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
BMC bioinformatics 2007;8():401.
2007: Kerrien Samuel; Orchard Sandra; Montecchi-Palazzi Luisa; Aranda Bruno; Quinn Antony F; Vinod Nisha; Bader Gary D; Xenarios Ioannis; Wojcik Jérôme; Sherman David; Tyers Mike; Salama John J; Moore Susan; Ceol Arnaud; Chatr-Aryamontri Andrew; Oesterheld Matthias; Stümpflen Volker; Salwinski Lukasz; Nerothin Jason; Cerami Ethan; Cusick Michael E; Vidal Marc; Gilson Michael; Armstrong John; Woollard Peter; Hogue Christopher; Eisenberg David; Cesareni Gianni; Apweiler Rolf; Hermjakob Henning
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
BMC biology 2007;5():44.
2007: Orchard Sandra; Jones Philip; Taylor Chris; Zhu Weimin; Julian Randall K; Hermjakob Henning; Apweiler Rolf
Proteomic data exchange and storage: the need for common standards and public repositories.
Methods in molecular biology (Clifton, N.J.) 2007;367():261-70.
2006: Kersey Paul; Apweiler Rolf
Linking publication, gene and protein data.
Nature cell biology 2006;8(11):1183-9.
2006: Stephan Christian; Reidegeld Kai A; Hamacher Michael; van Hall André; Marcus Katrin; Taylor Chris; Jones Philip; Müller Michael; Apweiler Rolf; Martens Lennart; Körting Gerhard; Chamrad Daniel C; Thiele Herbert; Blüggel Martin; Parkinson David; Binz Pierre-Alain; Lyall Andrew; Meyer Helmut E
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
Proteomics 2006;6(18):5015-29.
2006: Reidegeld Kai A; Müller Michael; Stephan Christian; Blüggel Martin; Hamacher Michael; Martens Lennart; Körting Gerhard; Chamrad Daniel C; Parkinson David; Apweiler Rolf; Meyer Helmut E; Marcus Katrin
The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.
Proteomics 2006;6(18):4997-5014.
2006: Martens Lennart; Müller Michael; Stephan Christian; Hamacher Michael; Reidegeld Kai A; Meyer Helmut E; Blüggel Martin; Vandekerckhove Joël; Gevaert Kris; Apweiler Rolf
A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Proteomics 2006;6(18):5076-86.
2006: Mueller Michael; Martens Lennart; Reidegeld Kai A; Hamacher Michael; Stephan Christian; Blüggel Martin; Körting Gerhard; Chamrad Daniel; Scheer Christian; Marcus Katrin; Meyer Helmut E; Apweiler Rolf
Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.
Proteomics 2006;6(18):5059-75.
2006: Chamrad Daniel C; Körting Gerhard; Schäfer Heike; Stephan Christian; Thiele Herbert; Apweiler Rolf; Meyer Helmut E; Marcus Katrin; Blüggel Martin
Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
Proteomics 2006;6(18):5048-58.
2006: Orchard Sandra; Apweiler Rolf; Barkovich Robert; Field Dawn; Garavelli John S; Horn David; Jones Andy; Jones Philip; Julian Randall; McNally Ruth; Nerothin Jason; Paton Norman; Pizarro Angel; Seymour Sean; Taylor Chris; Wiemann Stefan; Hermjakob Henning
Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Proteomics 2006;6(16):4439-43.
2006: Whitfield Eleanor J; Pruess Manuela; Apweiler Rolf
Bioinformatics database infrastructure for biotechnology research.
Journal of biotechnology 2006;124(4):629-39.
2006: Leinonen Rasko; Nardone Francesco; Zhu Weimin; Apweiler Rolf
UniSave: the UniProtKB sequence/annotation version database.
Bioinformatics (Oxford, England) 2006;22(10):1284-5.
2006: Hamacher Michael; Stephan Christian; Blüggel Martin; Chamrad Daniel; Körting Gerhard; Martens Lennart; Müller Michael; Hermjakob Henning; Parkinson David; Dowsey Andrew; Reidegeld Kai A; Marcus Katrin; Dunn Michael J; Meyer Helmut E; Apweiler Rolf
The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Proteomics 2006;6(6):1719-21.
2006: Hermjakob Henning; Apweiler Rolf
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Expert review of proteomics 2006;3(1):1-3.
2006: Orchard Sandra; Hermjakob Henning; Taylor Chris; Binz Pierre-Alain; Hoogland Christine; Julian Randall; Garavelli John S; Aebersold Ruedi; Apweiler Rolf
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Proteomics 2006;6(3):738-41.
2006: Jones Philip; Côté Richard G; Martens Lennart; Quinn Antony F; Taylor Chris F; Derache William; Hermjakob Henning; Apweiler Rolf
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Nucleic acids research 2006;34(Database issue):D659-63.
2006: Wu Cathy H; Apweiler Rolf; Bairoch Amos; Natale Darren A; Barker Winona C; Boeckmann Brigitte; Ferro Serenella; Gasteiger Elisabeth; Huang Hongzhan; Lopez Rodrigo; Magrane Michele; Martin Maria J; Mazumder Raja; O'Donovan Claire; Redaschi Nicole; Suzek Baris
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic acids research 2006;34(Database issue):D187-91.
2006: Couto Francisco M; Silva Mário J; Lee Vivian; Dimmer Emily; Camon Evelyn; Apweiler Rolf; Kirsch Harald; Rebholz-Schuhmann Dietrich
GOAnnotator: linking protein GO annotations to evidence text.
Journal of biomedical discovery and collaboration 2006;1():19.
2006: Pruess Manuela; Kersey Paul; Kulikova Tamara; Apweiler Rolf
Databases and resources for in silico proteome analysis.
Methods of biochemical analysis 2006;49():397-414.
2006: Taylor Chris F; Hermjakob Henning; Julian Randall K; Garavelli John S; Aebersold Ruedi; Apweiler Rolf
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Omics : a journal of integrative biology 2006;10(2):145-51.
2006: Sterk Peter; Kersey Paul J; Apweiler Rolf
Genome Reviews: standardizing content and representation of information about complete genomes.
Omics : a journal of integrative biology 2006;10(2):114-8.
2006: Cochrane Guy; Bates Kirsty; Apweiler Rolf; Tateno Yoshio; Mashima Jun; Kosuge Takehide; Mizrachi Ilene Karsch; Schafer Susan; Fetchko Michael
Evidence standards in experimental and inferential INSDC Third Party Annotation data.
Omics : a journal of integrative biology 2006;10(2):105-13.
2006: Côté Richard G; Jones Philip; Apweiler Rolf; Hermjakob Henning
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
BMC bioinformatics 2006;7():97.
2005: Orchard Sandra; Hermjakob Henning; Taylor Chris; Aebersold Ruedi; Apweiler Rolf
Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Proteomics 2005;5(18):4651-2.
2005: Blaschke Christian; Yeh Alexander; Camon Evelyn; Colosimo Marc; Apweiler Rolf; Hirschman Lynette; Valencia Alfonso
Do you do text?
Bioinformatics (Oxford, England) 2005;21(23):4199-200.
2005: Stephan Christian; Hamacher Michael; Blüggel Martin; Körting Gerhard; Chamrad Daniel; Scheer Christian; Marcus Katrin; Reidegeld Kai A; Lohaus Christiane; Schäfer Heike; Martens Lennart; Jones Philip; Müller Michael; Auyeung Kevin; Taylor Chris; Binz Pierre-Alain; Thiele Herbert; Parkinson David; Meyer Helmut E; Apweiler Rolf
5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.
Proteomics 2005;5(14):3560-2.
2005: Orchard Sandra; Hermjakob Henning; Taylor Chris F; Potthast Frank; Jones Phil; Zhu Weimin; Julian Randall K; Apweiler Rolf
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
Proteomics 2005;5(14):3552-5.
2005: Petryszak Robert; Kretschmann Ernst; Wieser Daniela; Apweiler Rolf
The predictive power of the CluSTr database.
Bioinformatics (Oxford, England) 2005;21(18):3604-9.
2005: Martens Lennart; Hermjakob Henning; Jones Philip; Adamski Marcin; Taylor Chris; States David; Gevaert Kris; Vandekerckhove Joël; Apweiler Rolf
PRIDE: the proteomics identifications database.
Proteomics 2005;5(13):3537-45.
2005: Quevillon E; Silventoinen V; Pillai S; Harte N; Mulder N; Apweiler R; Lopez R
InterProScan: protein domains identifier.
Nucleic acids research 2005;33(Web Server issue):W116-20.
2005: Jones Philip; Vinod Nisha; Down Thomas; Hackmann Andre; Kahari Andreas; Kretschmann Ernst; Quinn Antony; Wieser Daniela; Hermjakob Henning; Apweiler Rolf
Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Bioinformatics (Oxford, England) 2005;21(14):3198-9.
2005: Orchard Sandra; Hermjakob Henning; Taylor Chris F; Potthast Frank; Jones Phil; Zhu Weimin; Julian Randall K; Apweiler Rolf
Second proteomics standards initiative spring workshop.
Expert review of proteomics 2005;2(3):287-9.
2005: Schneider Michel; Bairoch Amos; Wu Cathy H; Apweiler Rolf
Plant protein annotation in the UniProt Knowledgebase.
Plant physiology 2005;138(1):59-66.
2005: Orchard Sandra; Hermjakob Henning; Apweiler Rolf
Annotating the human proteome.
Molecular & cellular proteomics : MCP 2005;4(4):435-40.
2005: Orchard Sandra; Hermjakob Henning; Binz Pierre-Alain; Hoogland Christine; Taylor Chris F; Zhu Weimin; Julian Randall K; Apweiler Rolf
Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
Proteomics 2005;5(2):337-9.
2005: Apweiler Rolf; Cornish-Bowden Athel; Hofmeyr Jan-Hendrik S; Kettner Carsten; Leyh Thomas S; Schomburg Dietmar; Tipton Keith
The importance of uniformity in reporting protein-function data.
Trends in biochemical sciences 2005;30(1):11-2.
2005: Kersey Paul; Bower Lawrence; Morris Lorna; Horne Alan; Petryszak Robert; Kanz Carola; Kanapin Alexander; Das Ujjwal; Michoud Karine; Phan Isabelle; Gattiker Alexandre; Kulikova Tamara; Faruque Nadeem; Duggan Karyn; Mclaren Peter; Reimholz Britt; Duret Laurent; Penel Simon; Reuter Ingmar; Apweiler Rolf
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Nucleic acids research 2005;33(Database issue):D297-302.
2005: Velankar S; McNeil P; Mittard-Runte V; Suarez A; Barrell D; Apweiler R; Henrick K
E-MSD: an integrated data resource for bioinformatics.
Nucleic acids research 2005;33(Database issue):D262-5.
2005: Bairoch Amos; Apweiler Rolf; Wu Cathy H; Barker Winona C; Boeckmann Brigitte; Ferro Serenella; Gasteiger Elisabeth; Huang Hongzhan; Lopez Rodrigo; Magrane Michele; Martin Maria J; Natale Darren A; O'Donovan Claire; Redaschi Nicole; Yeh Lai-Su L
The Universal Protein Resource (UniProt).
Nucleic acids research 2005;33(Database issue):D154-9.
2005: Pruess Manuela; Kersey Paul; Apweiler Rolf
The Integr8 project--a resource for genomic and proteomic data.
In silico biology 2005;5(2):179-85.
2005: Lee Vivian; Camon Evelyn; Dimmer Emily; Barrell Daniel; Apweiler Rolf
Who tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools.
In silico biology 2005;5(1):5-8.
2005: Camon Evelyn B; Barrell Daniel G; Dimmer Emily C; Lee Vivian; Magrane Michele; Maslen John; Binns David; Apweiler Rolf
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
BMC bioinformatics 2005;6 Suppl 1():S17.
2005: Orchard Sandra; Montecchi-Palazzi Luisa; Hermjakob Henning; Apweiler Rolf
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():186-96.
2004: Pedrioli Patrick G A; Eng Jimmy K; Hubley Robert; Vogelzang Mathijs; Deutsch Eric W; Raught Brian; Pratt Brian; Nilsson Erik; Angeletti Ruth H; Apweiler Rolf; Cheung Kei; Costello Catherine E; Hermjakob Henning; Huang Sequin; Julian Randall K; Kapp Eugene; McComb Mark E; Oliver Stephen G; Omenn Gilbert; Paton Norman W; Simpson Richard; Smith Richard; Taylor Chris F; Zhu Weimin; Aebersold Ruedi
A common open representation of mass spectrometry data and its application to proteomics research.
Nature biotechnology 2004;22(11):1459-66.
2004: Leinonen Rasko; Diez Federico Garcia; Binns David; Fleischmann Wolfgang; Lopez Rodrigo; Apweiler Rolf
UniProt archive.
Bioinformatics (Oxford, England) 2004;20(17):3236-7.
2004: Orchard Sandra; Taylor Chris; Hermjakob Henning; Zhu Weimin; Julian Randall; Apweiler Rolf
Current status of proteomic standards development.
Expert review of proteomics 2004;1(2):179-83.
2004: Orchard Sandra; Taylor Chris F; Hermjakob Henning; Weimin-Zhu; Julian Randall K; Apweiler Rolf
Advances in the development of common interchange standards for proteomic data.
Proteomics 2004;4(8):2363-5.
2004: Blüggel Martin; Bailey Sonja; Körting Gerhard; Stephan Christian; Reidegeld Kai A; Thiele Herbert; Apweiler Rolf; Hamacher Michael; Meyer Helmut E
Towards data management of the HUPO Human Brain Proteome Project pilot phase.
Proteomics 2004;4(8):2361-2.
2004: Wieser D; Kretschmann E; Apweiler R
Filtering erroneous protein annotation.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i342-7.
2004: Kersey Paul J; Duarte Jorge; Williams Allyson; Karavidopoulou Youla; Birney Ewan; Apweiler Rolf
The International Protein Index: an integrated database for proteomics experiments.
Proteomics 2004;4(7):1985-8.
2004: Apweiler Rolf; Bairoch Amos; Wu Cathy H
Protein sequence databases.
Current opinion in chemical biology 2004;8(1):76-80.
2004: Orchard Sandra; Hermjakob Henning; Julian Randall K; Runte Kai; Sherman David; Wojcik Jérôme; Zhu Weimin; Apweiler Rolf
Common interchange standards for proteomics data: Public availability of tools and schema.
Proteomics 2004;4(2):490-1.
2004: Hermjakob Henning; Montecchi-Palazzi Luisa; Lewington Chris; Mudali Sugath; Kerrien Samuel; Orchard Sandra; Vingron Martin; Roechert Bernd; Roepstorff Peter; Valencia Alfonso; Margalit Hanah; Armstrong John; Bairoch Amos; Cesareni Gianni; Sherman David; Apweiler Rolf
IntAct: an open source molecular interaction database.
Nucleic acids research 2004;32(Database issue):D452-5.
2004: Fleischmann Astrid; Darsow Michael; Degtyarenko Kirill; Fleischmann Wolfgang; Boyce Sinéad; Axelsen Kristian B; Bairoch Amos; Schomburg Dietmar; Tipton Keith F; Apweiler Rolf
IntEnz, the integrated relational enzyme database.
Nucleic acids research 2004;32(Database issue):D434-7.
2004: Camon Evelyn; Magrane Michele; Barrell Daniel; Lee Vivian; Dimmer Emily; Maslen John; Binns David; Harte Nicola; Lopez Rodrigo; Apweiler Rolf
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
Nucleic acids research 2004;32(Database issue):D262-6.
2004: Apweiler Rolf; Bairoch Amos; Wu Cathy H; Barker Winona C; Boeckmann Brigitte; Ferro Serenella; Gasteiger Elisabeth; Huang Hongzhan; Lopez Rodrigo; Magrane Michele; Martin Maria J; Natale Darren A; O'Donovan Claire; Redaschi Nicole; Yeh Lai-Su L
UniProt: the Universal Protein knowledgebase.
Nucleic acids research 2004;32(Database issue):D115-9.
2004: Kulikova Tamara; Aldebert Philippe; Althorpe Nicola; Baker Wendy; Bates Kirsty; Browne Paul; van den Broek Alexandra; Cochrane Guy; Duggan Karyn; Eberhardt Ruth; Faruque Nadeem; Garcia-Pastor Maria; Harte Nicola; Kanz Carola; Leinonen Rasko; Lin Quan; Lombard Vincent; Lopez Rodrigo; Mancuso Renato; McHale Michelle; Nardone Francesco; Silventoinen Ville; Stoehr Peter; Stoesser Guenter; Tuli Mary Ann; Tzouvara Katerina; Vaughan Robert; Wu Dan; Zhu Weimin; Apweiler Rolf
The EMBL Nucleotide Sequence Database.
Nucleic acids research 2004;32(Database issue):D27-30.
2004: Martin Maria Jesus; O'Donovan Claire; Apweiler Rolf
Protein sequence database methods.
Genetic engineering 2004;26():13-7.
2004: Camon Evelyn; Barrell Daniel; Lee Vivian; Dimmer Emily; Apweiler Rolf
The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase.
In silico biology 2004;4(1):5-6.
2003: Orchard Sandra; Zhu Weimin; Julian Randall K; Hermjakob Henning; Apweiler Rolf
Further advances in the development of a data interchange standard for proteomics data.
Proteomics 2003;3(10):2065-6.
2003: Orchard Sandra; Hermjakob Henning; Apweiler Rolf
The proteomics standards initiative.
Proteomics 2003;3(7):1374-6.
2003: Apweiler Rolf; Martin Maria Jesus; O'Donovan Claire; Pruess Manuela
Managing core resources for genomics and proteomics.
Pharmacogenomics 2003;4(3):343-50.
2003: Camon Evelyn; Magrane Michele; Barrell Daniel; Binns David; Fleischmann Wolfgang; Kersey Paul; Mulder Nicola; Oinn Tom; Maslen John; Cox Anthony; Apweiler Rolf
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Genome research 2003;13(4):662-72.
2003: Kriventseva Evgenia V; Koch Ina; Apweiler Rolf; Vingron Martin; Bork Peer; Gelfand Mikhail S; Sunyaev Shamil
Increase of functional diversity by alternative splicing.
Trends in genetics : TIG 2003;19(3):124-8.
2003: Pruess Manuela; Fleischmann Wolfgang; Kanapin Alexander; Karavidopoulou Youla; Kersey Paul; Kriventseva Evgenia; Mittard Virginie; Mulder Nicola; Phan Isabelle; Servant Florence; Apweiler Rolf
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
Nucleic acids research 2003;31(1):414-7.
2003: Kriventseva E V; Servant F; Apweiler R
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.
Nucleic acids research 2003;31(1):388-9.
2003: Boeckmann Brigitte; Bairoch Amos; Apweiler Rolf; Blatter Marie-Claude; Estreicher Anne; Gasteiger Elisabeth; Martin Maria J; Michoud Karine; O'Donovan Claire; Phan Isabelle; Pilbout Sandrine; Schneider Michel
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Nucleic acids research 2003;31(1):365-70.
2003: Brooksbank Catherine; Camon Evelyn; Harris Midori A; Magrane Michele; Martin Maria Jesus; Mulder Nicola; O'Donovan Claire; Parkinson Helen; Tuli Mary Ann; Apweiler Rolf; Birney Ewan; Brazma Alvis; Henrick Kim; Lopez Rodrigo; Stoesser Guenter; Stoehr Peter; Cameron Graham
The European Bioinformatics Institute's data resources.
Nucleic acids research 2003;31(1):43-50.
2003: Orchard Sandra; Kersey Paul; Zhu Weimin; Montecchi-Palazzi Luisa; Hermjakob Henning; Apweiler Rolf
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Comparative and functional genomics 2003;4(2):203-6.
2003: Camon Evelyn; Barrell Daniel; Brooksbank Catherine; Magrane Michele; Apweiler Rolf
The Gene Ontology Annotation (GOA) Project-Application of GO in SWISS-PROT, TrEMBL and InterPro.
Comparative and functional genomics 2003;4(1):71-4.
2003: Orchard Sandra; Kersey Paul; Hermjakob Henning; Apweiler Rolf
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Comparative and functional genomics 2003;4(1):16-9.
2003: Kersey P J; Morris L; Hermjakob H; Apweiler R
Integr8: enhanced inter-operability of European molecular biology databases.
Methods of information in medicine 2003;42(2):154-60.
2002: Biswas Margaret; O'Rourke John F; Camon Evelyn; Fraser Gill; Kanapin Alexander; Karavidopoulou Youla; Kersey Paul; Kriventseva Evgenia; Mittard Virginie; Mulder Nicola; Phan Isabelle; Servant Florence; Apweiler Rolf
Applications of InterPro in protein annotation and genome analysis.
Briefings in bioinformatics 2002;3(3):285-95.
2002: O'Donovan Claire; Martin Maria Jesus; Gattiker Alexandre; Gasteiger Elisabeth; Bairoch Amos; Apweiler Rolf
High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
Briefings in bioinformatics 2002;3(3):275-84.
2002: Zdobnov Evgeny M; Lopez Rodrigo; Apweiler Rolf; Etzold Thure
The EBI SRS server-new features.
Bioinformatics (Oxford, England) 2002;18(8):1149-50.
2002: Kanapin A; Apweiler R; Biswas M; Fleischmann W; Karavidopoulou Y; Kersey P; Kriventseva E V; Mittard V; Mulder N; Oinn T; Phan I; Servant F; Zdobnov E
Interactive InterPro-based comparisons of proteins in whole genomes.
Bioinformatics (Oxford, England) 2002;18(2):374-5.
2002: Zdobnov Evgeni M; Lopez Rodrigo; Apweiler Rolf; Etzold Thure
The EBI SRS server--recent developments.
Bioinformatics (Oxford, England) 2002;18(2):368-73.
2002: Hermjakob Henning; Apweiler Rolf
TEMBLOR - Perspectives of EBI Database Services.
Comparative and functional genomics 2002;3(1):47-50.
2002: Mulder Nicola J; Apweiler Rolf
Tools and resources for identifying protein families, domains and motifs.
Genome biology 2002;3(1):REVIEWS2001.
2001: Kretschmann E; Fleischmann W; Apweiler R
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT.
Bioinformatics (Oxford, England) 2001;17(10):920-6.
2001: Zdobnov E M; Apweiler R
InterProScan--an integration platform for the signature-recognition methods in InterPro.
Bioinformatics (Oxford, England) 2001;17(9):847-8.
2001: Möller S; Croning M D; Apweiler R
Evaluation of methods for the prediction of membrane spanning regions.
Bioinformatics (Oxford, England) 2001;17(7):646-53.
2001: Biswas M; Kanapin A; Apweiler R
Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL.
Journal of biosciences 2001;26(2):277-84.
2001: Kriventseva E V; Biswas M; Apweiler R
Clustering and analysis of protein families.
Current opinion in structural biology 2001;11(3):334-9.
2001: O'Donovan C; Apweiler R; Bairoch A
The human proteomics initiative (HPI).
Trends in biotechnology 2001;19(5):178-81.
2001: Apweiler R
Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences.
Briefings in bioinformatics 2001;2(1):9-18.
2001: Apweiler R; Biswas M; Fleischmann W; Kanapin A; Karavidopoulou Y; Kersey P; Kriventseva E V; Mittard V; Mulder N; Phan I; Zdobnov E
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Nucleic acids research 2001;29(1):44-8.
2001: Apweiler R; Attwood T K; Bairoch A; Bateman A; Birney E; Biswas M; Bucher P; Cerutti L; Corpet F; Croning M D; 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 N J; Oinn T M; Pagni M; Servant F; Sigrist C J; Zdobnov E M
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic acids research 2001;29(1):37-40.
2001: Kriventseva E V; Fleischmann W; Zdobnov E M; Apweiler R
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.
Nucleic acids research 2001;29(1):33-6.
2000: Apweiler R; Attwood T K; Bairoch A; Bateman A; Birney E; Biswas M; Bucher P; Cerutti L; Corpet F; Croning M D; 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 N J; Oinn T M; Pagni M; Servant F; Sigrist C J; Zdobnov E M;
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics (Oxford, England) 2000;16(12):1145-50.
2000: Kersey P; Hermjakob H; Apweiler R
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Bioinformatics (Oxford, England) 2000;16(11):1048-9.
2000: Menne K M; Hermjakob H; Apweiler R
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics (Oxford, England) 2000;16(8):741-2.
2000: Junker V; Contrino S; Fleischmann W; Hermjakob H; Lang F; Magrane M; Martin M J; Mitaritonna N; O'Donovan C; Apweiler R
The role SWISS-PROT and TrEMBL play in the genome research environment.
Journal of biotechnology 2000;78(3):221-34.
2000: Magrane M; Apweiler R
Mus musculus in the SWISS-PROT database: its relevance to developmental research.
Genesis (New York, N.Y. : 2000) 2000;26(1):1-4.
2000: Bairoch A; Apweiler R
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
Nucleic acids research 2000;28(1):45-8.
1999: Junker V L; Apweiler R; Bairoch A
Representation of functional information in the SWISS-PROT data bank.
Bioinformatics (Oxford, England) 1999;15(12):1066-7.
1999: Apweiler R; Hermjakob H; Sharon N
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Biochimica et biophysica acta 1999;1473(1):4-8.
1999: Hermjakob H; Fleischmann W; Apweiler R
Swissknife - 'lazy parsing' of SWISS-PROT entries.
Bioinformatics (Oxford, England) 1999;15(9):771-2.
1999: O'Donovan C; Martin M J; Glemet E; Codani J J; Apweiler R
Removing redundancy in SWISS-PROT and TrEMBL.
Bioinformatics (Oxford, England) 1999;15(3):258-9.
1999: Fleischmann W; Möller S; Gateau A; Apweiler R
A novel method for automatic functional annotation of proteins.
Bioinformatics (Oxford, England) 1999;15(3):228-33.
1999: Möller S; Leser U; Fleischmann W; Apweiler R
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation.
Bioinformatics (Oxford, England) 1999;15(3):219-27.
1999: Bairoch A; Apweiler R
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Nucleic acids research 1999;27(1):49-54.
1998: Bairoch A; Apweiler R
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.
Nucleic acids research 1998;26(1):38-42.
1997: Bairoch A; Apweiler R
The SWISS-PROT protein sequence database: its relevance to human molecular medical research.
Journal of molecular medicine (Berlin, Germany) 1997;75(5):312-6.
1997: Bairoch A; Apweiler R
The SWISS-PROT protein sequence data bank and its supplement TrEMBL.
Nucleic acids research 1997;25(1):31-6.
1997: Apweiler R; Gateau A; Contrino S; Martin M J; Junker V; O'Donovan C; Lang F; Mitaritonna N; Kappus S; Bairoch A
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():33-43.
1996: Bairoch A; Apweiler R
The SWISS-PROT protein sequence data bank and its new supplement TREMBL.
Nucleic acids research 1996;24(1):21-5.
1993: Kappus S; Apweiler R; White C J; Whish W J
In vitro poly-(ADP-ribosyl)ation of chromatin proteins in the rat tapeworm, Hymenolepis diminuta.
Comparative biochemistry and physiology. B, Comparative biochemistry 1993;104(4):711-6.
1990: Alsharif M; Apweiler R; Whish W J; Branford White C J; Brunt R V
Identification of ADPR-transferase activity in the rat tapeworm, Hymenolepis diminuta.
Comparative biochemistry and physiology. B, Comparative biochemistry 1990;96(3):527-31.

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