Rolf Apweiler

发表

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

Prudence Mutowo-Meullenet, Rachael P. Huntley, Emily Dimmer, 2013, Database J. Biol. Databases Curation.

The EBI SRS server-new features

Rolf Apweiler, Evgeny M. Zdobnov, Rodrigo Lopez, 2002, Bioinform..

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible

Rolf Apweiler, Henning Hermjakob, R. Apweiler, 2006, Expert review of proteomics.

The Rice Annotation Project Database (RAP-DB): 2008 update

Yoshihiro Kawahara, Yasuyuki Fujii, Rolf Apweiler, 2007, Nucleic Acids Res..

IntEnz - The Enzyme Database in Oracle

Rolf Apweiler, Astrid Fleischmann, Michael Darsow, 2001, German Conference on Bioinformatics.

The predictive power of the CluSTr database

Robert Petryszak, Rolf Apweiler, Ernst Kretschmann, 2005, Bioinform..

GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools

Emily Dimmer, Rolf Apweiler, Vivian Lee, 2004, Silico Biol..

Faculty Opinions recommendation of MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.

Rolf Apweiler, R. Apweiler, 2003 .

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Nigel W. Hardy, Chris F. Taylor, John M. Hancock, 2008, Nature Biotechnology.

Make Research Data Public?---Not Always so Simple: A Dialogue for Statisticians and Science Editors pdf

Rolf Apweiler, Deborah Nolan, Robert A. Moffitt, 2010, ArXiv.

Analyzing large-scale proteomics projects with latent semantic indexing.

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2008, Journal of proteome research.

Dasty and UniProt DAS: a perfect pair for protein feature visualization

Rolf Apweiler, Henning Hermjakob, Thomas A. Down, 2005, Bioinform..

Approaching clinical proteomics: current state and future fields of application in fluid proteomics

Helmut E Meyer, Michael Neumaier, Rolf Apweiler, 2009, Clinical chemistry and laboratory medicine.

Organisation and standardisation of information in SWISS_PROT and TrEMBL

Rolf Apweiler, Michele Magrane, M. Magrane, 2002, Data Sci. J..

TEMBLOR – Perspectives of EBI Database Services

Rolf Apweiler, Henning Hermjakob, 2002, Comparative and functional genomics.

Protein Family and Domain Signature Databases

Rolf Apweiler, R. Apweiler, 2004 .

PRIDE: The proteomics identifications database

Lennart Martens, Chris F. Taylor, Rolf Apweiler, 2005, Proteomics.

Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters

Rolf Apweiler, Florence Servant, Evgenia V. Kriventseva, 2003, Nucleic Acids Res..

The Universal Protein Resource (UniProt): an expanding universe of protein information

Cathy H. Wu, Maria Jesus Martin, Claire O'Donovan, 2005, Nucleic Acids Res..

Faculty Opinions recommendation of Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Rolf Apweiler, R. Apweiler, 2003 .

InterProScan - an integration platform for the signature-recognition methods in InterPro

Rolf Apweiler, Evgeny M. Zdobnov, R. Apweiler, 2001, Bioinform..

Cardiovascular GO Annotation Initiative Year 1 Report: Why Cardiovascular GO?

Rolf Apweiler, Emily Dimmer, Ruth C Lovering, 2008, Proteomics.

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative

Rolf Apweiler, Henning Hermjakob, Luisa Montecchi-Palazzi, 2003, Comparative and functional genomics.

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins

Rolf Apweiler, Evgeny M. Zdobnov, Evgenia V. Kriventseva, 2001, Nucleic Acids Res..

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2003, Nucleic Acids Res..

The Gene Ontology: enhancements for 2011

María Martín, Juancarlos Chan, Paul W. Sternberg, 2011, Nucleic Acids Res..

Further advances in the development of a data interchange standard for proteomics data

Rolf Apweiler, Henning Hermjakob, Randall K Julian, 2003, Proteomics.

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998

Rolf Apweiler, Amos Marc Bairoch, A. Bairoch, 1998, Nucleic Acids Res..

InterPro : An integrated documentation resource for protein families , domains and functional sites The InterPro Consortium :

Alex Bateman, Rolf Apweiler, Beate Marx, 2005 .

The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase

Emily Dimmer, Rolf Apweiler, Vivian Lee, 2003, Silico Biol..

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Kai Ye, Quan Long, Marcel H. Schulz, 2009, Bioinform..

EMBL Nucleotide Sequence Database in 2006

Dan Wu, Vincent Lombard, Rolf Apweiler, 2006, Nucleic Acids Res..

IntAct: an open source molecular interaction database

Martin Vingron, David James Sherman, Alfonso Valencia, 2004, Nucleic Acids Res..

The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments

Rolf Apweiler, Henning Hermjakob, Sandra E. Orchard, 2004, Pacific Symposium on Biocomputing.

Design, Implementation and Updating of Knowledge Bases

Rolf Apweiler, Sarah Hunter, María Martín, 2010 .

Verification of Uncurated Protein Annotations

Mário J. Silva, Emily Dimmer, Rolf Apweiler, 2009, Information Retrieval in Biomedicine.

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects

Oliver Hofmann, Chris F. Taylor, Rolf Apweiler, 2013 .

Managing core resources for genomics and proteomics.

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2003, Pharmacogenomics.

Source of annotations in the UniProt Knowledgebase

Rolf Apweiler, Benoit Bely, María Martín, 2010 .

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

Rolf Apweiler, Amos Marc Bairoch, A. Bairoch, 2000, Nucleic Acids Res..

Bioinformatics: Using the Molecular Biology Data

Rolf Apweiler, Rodrigo Lopez, Thure Etzold, 2007, Essentials of Genomics and Bioinformatics.

A collection of well characterised integral membrane proteins

Rolf Apweiler, Steffen Möller, Evgenia V. Kriventseva, 2000, Bioinform..

Data standardization and the HUPO proteomics standards initiative

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2005 .

Further Steps in Standardisation Report of the Second Annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17–20th April 2005)

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2005, Proteomics.

Faculty Opinions recommendation of DIAN: a novel algorithm for genome ontological classification.

Rolf Apweiler, R. Apweiler, 2001 .

Swissknife - 'lazy parsing' of SWISS-PROT entries

Rolf Apweiler, Henning Hermjakob, Wolfgang Fleischmann, 1999, Bioinform..

Evidence standards in experimental and inferential INSDC Third Party Annotation data.

Rolf Apweiler, Ilene Karsch Mizrachi, Yoshio Tateno, 2006, Omics : a journal of integrative biology.

Proteomic Data Exchange and Storage

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2007 .

Meeting Review: Progress in Establishing Common Standards for Exchanging Proteomics Data: the second meeting of the HUPO Proteomics Standards

Rolf Apweiler, Henning Hermjakob, Luisa Montecchi-Palazzi, 2003 .

The InterPro Database and Tools for Protein Domain Analysis

Rolf Apweiler, Nicola J Mulder, 2008, Current protocols in bioinformatics.

Advances in the development of common interchange standards for proteomic data

Rolf Apweiler, Henning Hermjakob, Chris F Taylor, 2004, Proteomics.

Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL

Sergio Contrino, Maria Jesus Martin, Claire O'Donovan, 1997, ISMB.

Linking publication, gene and protein data

Rolf Apweiler, Paul Kersey, P. Kersey, 2006, Nature Cell Biology.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

Rolf Apweiler, Henning Hermjakob, Richard G. Côté, 2006, BMC Bioinformatics.

The GOA database in 2009—an integrated Gene Ontology Annotation resource

Rachael P. Huntley, Emily Dimmer, Claire O'Donovan, 2008, Nucleic Acids Res..

InterPro: the integrative protein signature database

Robert D. Finn, Cathy H. Wu, Alex Bateman, 2008, Nucleic Acids Res..

InterPro and InterProScan

Rolf Apweiler, Nicola Mulder, N. Mulder, 2007 .

Gaining knowledge from previously unexplained spectra‐application of the PTM‐Explorer software to detect PTM in HUPO BPP MS/MS data

Helmut E Meyer, Gerhard Körting, Martin Blüggel, 2006, Proteomics.

The European Bioinformatics Institute in 2018: tools, infrastructure and training

Rolf Apweiler, Rodrigo Lopez, Guy Cochrane, 2018, Nucleic Acids Res..

Proteomics Data Collection – 4th ProDaC Workshop 15 August 2008, Amsterdam, The Netherlands

Lennart Martens, Harald Barsnes, Helmut E Meyer, 2009, Proteomics.

UniProtJAPI: a remote API for accessing UniProt data

Maria Jesus Martin, Rolf Apweiler, Ernst Kretschmann, 2008, Bioinform..

CARDIOVASCULAR GENE ONTOLOGY INITIATIVE

Rolf Apweiler, Peter J. Scambler, Mike Hubank, 2008 .

Approaching clinical proteomics: Current state and future fields of application in cellular proteomics

Helmut E Meyer, Michael Neumaier, Rolf Apweiler, 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

Representation of functional information in the SWISS-PROT Data Bank

Rolf Apweiler, Amos Bairoch, V. L. Junker, 1999, Bioinform..

The Gene Ontology Annotation (GOA) Database

Rachael P. Huntley, Emily Dimmer, Rolf Apweiler, 2009 .

Integrating Genomic and Proteomic Data: The Integr8 Project

Rolf Apweiler, Paul J. Kersey, Manuela Pruess, 2004, J. Integr. Bioinform..

SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 1998, German Conference on Bioinformatics.

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

Emily Dimmer, Rolf Apweiler, Rodrigo Lopez, 2004, Nucleic Acids Res..

InterProScan: protein domains identifier

Rolf Apweiler, Nicola J. Mulder, Rodrigo Lopez, 2005, Nucleic Acids Res..

A novel method for automatic and reliable functional annotation of proteins

Rolf Apweiler, Alain Gateau, Steffen Möller, 1998, German Conference on Bioinformatics.

InterPro, progress and status in 2005

Cathy H. Wu, Alex Bateman, Rolf Apweiler, 2004, Nucleic Acids Res..

Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al

Rolf Apweiler, Amos Bairoch, Paul J. Kersey, 2001, Bioinform..

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

Emily Dimmer, Rolf Apweiler, Vivian Lee, 2005, BMC Bioinformatics.

GOAnnotator: linking protein GO annotations to evidence text

Rolf Apweiler, Mário J. Silva, Evelyn Camon, 2006, Journal of biomedical discovery and collaboration.

The EMBL Nucleotide Sequence Database

Vincent Lombard, Rolf Apweiler, Peter Stoehr, 2004, Nucleic Acids Res..

New developments in the InterPro database

Robert D. Finn, Robert Petryszak, Cathy H. Wu, 2007, Nucleic Acids Res..

Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003

Rolf Apweiler, Henning Hermjakob, David Sherman, 2004, Proteomics.

Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25–27th October, 2004

Rolf Apweiler, Henning Hermjakob, Chris F Taylor, 2005, Proteomics.

Faculty Opinions recommendation of A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Rolf Apweiler, R. Apweiler, 2004 .

Focus on InterPro

Rolf Apweiler, R. Apweiler, 2002 .

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL

Rolf Apweiler, Henning Hermjakob, Paul J. Kersey, 2000, Bioinform..

The European Bioinformatics Institute in 2016: Data growth and integration

Robert D. Finn, Rolf Apweiler, Guy Cochrane, 2015, Nucleic Acids Res..

PRIDE: a public repository of protein and peptide identifications for the proteomics community

Lennart Martens, Chris F. Taylor, Rolf Apweiler, 2005, Nucleic Acids Res..

In Silico Characterization of Proteins InterPro and Proteome Analysis

Rolf Apweiler, Manuela Pruess, Nicola Mulder, 2005 .

The EMBL Nucleotide Sequence Database

Vincent Lombard, Rolf Apweiler, Guy Cochrane, 2005, Nucleic Acids Res..

Abstract P326: An Innovative Peptide Spectral Library Search Engine for Cardiovascular Proteomics

Huilong Duan, Haomin Li, Rolf Apweiler, 2011 .

Activities at the Universal Protein Resource (UniProt)

María Martín, Peter B. McGarvey, Y Wang, 2013, Nucleic Acids Res..

Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes

Rolf Apweiler, Nicola J. Mulder, Evgeny M. Zdobnov, 2000, German Conference on Bioinformatics.

The Gene Ontology Annotation (GOA) Project—Application of GO in SWISS-PROT, TrEMBL and InterPro

Rolf Apweiler, Catherine Brooksbank, Evelyn Camon, 2003, Comparative and functional genomics.

Chapter 59 – Bioinformatic Resources for in Silico Proteome Analysis

Rolf Apweiler, Manuela Pruess, 2006 .

Proteomics Data Collection – 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, Greece

Lennart Martens, Harald Barsnes, Helmut E Meyer, 2009, Proteomics.

IntAct—open source resource for molecular interaction data

Y. Zhang, Rachael P. Huntley, Emily Dimmer, 2006, Nucleic Acids Res..

Functional Information in SWISS-PROT: the Basis for Large-scale Characterisation of Protein Sequences

Rolf Apweiler, R. Apweiler, 2001, Briefings Bioinform..

The European Bioinformatics Institute's data resources

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2003, Nucleic Acids Res..

Proteomics Data Collection – 3rd ProDaC Workshop April 22nd 2008, Toledo, Spain

Lennart Martens, Helmut E Meyer, Martin Eisenacher, 2008, Proteomics.

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999

Claire O'Donovan, Rolf Apweiler, Amos Bairoch, 1999, Nucleic Acids Res..

Facilitating context-sensitive queries: A tool to rephrase SWISS-PROT

Michael Schroeder, Rolf Apweiler, Michael J. Wise, 1999, German Conference on Bioinformatics.

UniProt: A hub for protein information

María Martín, Peter B. McGarvey, Y Wang, 2015 .

Bioinformatics for Biologists

Rolf Apweiler, R. Apweiler, 2009 .

IntEnz, the integrated relational enzyme database

Rolf Apweiler, Kristian B. Axelsen, Amos Bairoch, 2004, Nucleic Acids Res..

An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2007, German Conference on Bioinformatics.

The European Bioinformatics Institute’s data resources 2014

Rolf Apweiler, Catherine Brooksbank, Janet M. Thornton, 2013, Nucleic Acids Res..

The Proteomics Standards Initiative

Rolf Apweiler, Henning Hermjakob, Sandra Orchard, 2003, Proteomics.

Filtering erroneous protein annotation

Rolf Apweiler, Ernst Kretschmann, Daniela Wieser, 2004, ISMB/ECCB.

Protein Information Resource (PIR)

Rolf Apweiler, R. Apweiler, 2004 .

The InterPro Database and Tools for Protein Domain Analysis

Rolf Apweiler, Nicola Mulder, 2003 .

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

Ingmar Reuter, Robert Petryszak, Rolf Apweiler, 2004, Nucleic Acids Res..

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care

Victor Maojo, Rolf Apweiler, Fernando Martín-Sánchez, 2004, J. Biomed. Informatics.

The EBI SRS Server: Recent Developments

Rolf Apweiler, Evgeny M. Zdobnov, Rodrigo Lopez, 2002, German Conference on Bioinformatics.

A common open representation of mass spectrometry data and its application to proteomics research

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2004, Nature Biotechnology.

Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science

Rolf Apweiler, Ewan Birney, Jessica Vamathevan, 2019 .

The European Bioinformatics Institute in 2017: data coordination and integration

Rolf Apweiler, Guy Cochrane, Ewan Birney, 2017, Nucleic Acids Res..

Proteomics and data standardisation

Rolf Apweiler, Henning Hermjakob, Sandra Orchard, 2004 .

Second Proteomics Standards Initiative Spring Workshop

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2005, Expert review of proteomics.

GOAnnotator: linking electronic protein GO annotation to evidence text

Dietrich Rebholz-Schuhmann, Emily Dimmer, Rolf Apweiler, 2006 .

Integration of biological databases: the example of InterPro.

Rolf Apweiler, Wolfgang Fleischmann, Alexander Kanapin, 2001 .

UniProt: the Universal Protein knowledgebase

Cathy H. Wu, Maria Jesus Martin, Claire O'Donovan, 2004, Nucleic Acids Res..

Erratum: Evaluation of methods for the prediction of membrane spanning regions

Rolf Apweiler, Steffen Möller, Michael D. R. Croning, 2002, Bioinform..

Prepublication data sharing

Christopher P Austin, Rolf Apweiler, Tatsuhiko Tsunoda, 2009, Nature.

Interactive InterPro-based comparisons of proteins in whole genomes

Rolf Apweiler, Nicola J. Mulder, Evgeny M. Zdobnov, 2002, Bioinform..

The minimum information required for reporting a molecular interaction experiment (MIMIx)

Peter Woollard, Mark Gerstein, Gary D Bader, 2007, Nature Biotechnology.

ProDac (Proteomics data collection); Coordinated action within the 6th EU framework programme

Martin Eisenacher, Martin Blüggel, Christian Stephan, 2006 .

UniProt archive

Rolf Apweiler, Rodrigo Lopez, Rasko Leinonen, 2004, Bioinform..

Ongoing and future developments at the Universal Protein Resource

María Martín, Peter B. McGarvey, Y Wang, 2010, Nucleic Acids Res..

A novel method for automatic functional annotation of proteins

Rolf Apweiler, Alain Gateau, Steffen Möller, 1999, Bioinform..

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

Lennart Martens, Helmut E Meyer, Martin Eisenacher, 2007, Proteomics.

Analysing latent topics in large-scale proteomics

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2007, LWA.

HUPO Brain Proteome Project pilot phase; Automated reprocessing pipeline for searching heterogenic data

Lennart Martens, Michael Müller, Gerhard Körting, 2006 .

The minimum information about a proteomics experiment (MIAPE)

Lennart Martens, Chris F. Taylor, John R Yates, 2007, Nature Biotechnology.

The Gene Ontology project in 2008

Giorgio Valle, Kimberly Van Auken, Paul W. Sternberg, 2007, Nucleic Acids Res..

Removing Redundancy in SWISS-PROT and TrEMBL

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 1999, German Conference on Bioinformatics.

Report of the second international nomenclature workshop

Lois J. Maltais, Sue Povey, Rolf Apweiler, 1999 .

Evaluation of methods for the prediction of membrane spanning regions

Rolf Apweiler, Steffen Möller, Michael D. R. Croning, 2001, Bioinform..

EMBL Nucleotide Sequence Database: developments in 2005

Dan Wu, Vincent Lombard, Rolf Apweiler, 2005, Nucleic Acids Res..

Proteomics and Beyond A report on the 3rd Annual Spring Workshop of the HUPO‐PSI 21–23 April 2006, San Francisco, CA, USA

Ruth McNally, Rolf Apweiler, Henning Hermjakob, 2006, Proteomics.

High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL

Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler, 2002, Briefings Bioinform..

Towards a New Curation Environment for the TrEMBL Database

Rolf Apweiler, Henning Hermjakob, Kai J. Runte, 2001, German Conference on Bioinformatics.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

Lennart Martens, Rolf Apweiler, Henning Hermjakob, 2007, BMC Bioinformatics.

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Alex Bateman, Rolf Apweiler, Henning Hermjakob, 2002, Briefings Bioinform..

The Integr8 project - a resource for genomic and proteomic data

Rolf Apweiler, Paul J. Kersey, Manuela Pruess, 2004, Silico Biol..

Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis

Rolf Apweiler, Nicola J. Mulder, Evgenia V. Kriventseva, 2002, Gene Regulations and Metabolism.

Automatic rule generation for protein annotation with the C4.5 data-mining algorithm applied on peptides in Ensembl

Rolf Apweiler, Ernst Kretschmann, R. Apweiler, 2001, German Conference on Bioinformatics.

QuickGO: a user tutorial for the web-based Gene Ontology browser

Rachael P. Huntley, Emily Dimmer, Claire O'Donovan, 2009, Database J. Biol. Databases Curation.

Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation

Rolf Apweiler, Henning Hermjakob, Arno Velds, 1999, German Conference on Bioinformatics.

The Universal Protein Resource (UniProt) in 2010

María Martín, Peter B. McGarvey, Cathy H. Wu, 2010 .

Databases and resources for in silico proteome analysis.

Rolf Apweiler, Manuela Pruess, Paul Kersey, 2006, Methods of biochemical analysis.

EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation

Ulf Leser, Rolf Apweiler, Steffen Möller, 1999, German Conference on Bioinformatics.

Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT

Rolf Apweiler, Ernst Kretschmann, Wolfgang Fleischmann, 2001, Bioinform..

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes

Rolf Apweiler, Nicola J. Mulder, Paul J. Kersey, 2003, Nucleic Acids Res..

The Gene Ontology in 2010: extensions and refinements

Giorgio Valle, Juancarlos Chan, Paul W. Sternberg, 2009, Nucleic Acids Res..

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2006, Omics : a journal of integrative biology.

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK – Setting the Analysis Frame

Lennart Martens, Helmut E Meyer, Kai A Reidegeld, 2005, Proteomics.

The SWISS-PROT protein sequence data bank and its new supplement TREMBL

Rolf Apweiler, Amos Bairoch, A. Bairoch, 1996, Nucleic Acids Res..

Practical Applications of the Gene Ontology Resource

Rachael P. Huntley, Emily Dimmer, Rolf Apweiler, 2010 .

Proteomics Data Collection – 2nd ProDaC Workshop 5 October 2007, Seoul, Korea

Lennart Martens, Helmut E Meyer, Martin Eisenacher, 2008, Proteomics.

A comparison of signal sequence prediction methods using a test set of signal peptides

Rolf Apweiler, Henning Hermjakob, Kerstin M. L. Menne, 2000, Bioinform..

Algorithms and databases.

Lennart Martens, Rolf Apweiler, R. Apweiler, 2009, Methods in molecular biology.

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

Dan Wu, Rolf Apweiler, Rodrigo Lopez, 2007, Nucleic Acids Res..

New Developments in the Linking of Biological Databases and Computer-Generation of Annotation

Claire O'Donovan, Rolf Apweiler, Amos Bairoch, 1996, German Conference on Bioinformatics.

The UniProt-GO Annotation database in 2011

Rachael P. Huntley, Emily Dimmer, Yasmin Alam-Faruque, 2011, Nucleic Acids Res..

The Gene Ontology − Providing a Functional Role in Proteomic Studies

Rachael P. Huntley, Rolf Apweiler, Sorin Draghici, 2008 .

Proteomics Data Collection – The 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France

Lennart Martens, Helmut E Meyer, Martin Eisenacher, 2007, Proteomics.

Do you do text?

Alfonso Valencia, Rolf Apweiler, Lynette Hirschman, 2005, Bioinform..

UniSave: the UniProtKB Sequence/Annotation Version database

Rolf Apweiler, Rasko Leinonen, Weimin Zhu, 2006, Bioinform..

Current status of proteomic standards development

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2004, Expert review of proteomics.

On the Importance of Comprehensible Classification Models for Protein Function Prediction

Alex Alves Freitas, Rolf Apweiler, Daniela Wieser, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The Universal Protein Resource (UniProt)

Cathy H. Wu, Rolf Apweiler, Darren A. Natale, 2006, Nucleic Acids Research.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries

Lennart Martens, Rolf Apweiler, Henning Hermjakob, 2008, Nucleic Acids Res..

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes

Rolf Apweiler, Nicola J. Mulder, Evgeny M. Zdobnov, 2001, Nucleic Acids Res..

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Alex Bateman, Rolf Apweiler, Beate Marx, 2001, Nucleic Acids Res..

The InterPro Database, 2003 brings increased coverage and new features

Alex Bateman, Rolf Apweiler, Nicola J. Mulder, 2003, Nucleic Acids Res..

The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies

Lennart Martens, Michael Müller, Helmut E Meyer, 2006, Proteomics.

Biological Databases: Infrastructure, Content and Integration

Rolf Apweiler, Manuela Pruess, Paul Kersey, 2005, Data Analysis and Visualization in Genomics and Proteomics.

QuickGO: a web-based tool for Gene Ontology searching

Rachael P. Huntley, Emily Dimmer, Claire O'Donovan, 2009, Bioinform..

Consistent Integration of Non-reliable Heterogeneous Information Resources Applied to the Annotation of Transmembrane Proteins

Michael Schroeder, Rolf Apweiler, Steffen Möller, 2001, Comput. Chem..

InterPro in 2011: new developments in the family and domain prediction database

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

Rolf Apweiler, Henning Hermjakob, Sandra Orchard, 2003, Comparative and functional genomics.

The SWISS-PROT protein sequence data bank and its supplement TrEMBL

Rolf Apweiler, Amos Bairoch, A. Bairoch, 1997, Nucleic Acids Res..

Cardiovascular Gene Ontology Annotation Initiative

Rolf Apweiler, Peter J. Scambler, Daniel Barrell, 2009 .

E-MSD: an integrated data resource for bioinformatics.

Rolf Apweiler, Sameer Velankar, A. Suarez, 2004, Nucleic acids research.

Applications of InterPro in Protein Annotation and Genome Analysis

Rolf Apweiler, Nicola J. Mulder, Paul J. Kersey, 2002, Briefings Bioinform..

Annotating the Human Proteome

Rolf Apweiler, Henning Hermjakob, Sandra Orchard, 2005, Molecular & Cellular Proteomics.

Genome Reviews: standardizing content and representation of information about complete genomes.

Rolf Apweiler, Peter Sterk, Paul J Kersey, 2006, Omics : a journal of integrative biology.

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.

Lennart Martens, Rolf Apweiler, Henning Hermjakob, 2007, Molecular & cellular proteomics : MCP.

Plant Protein Annotation in the UniProt Knowledgebase1

Cathy H. Wu, Rolf Apweiler, Michel Schneider, 2005, Plant Physiology.

Bioinformatics Resources for In Silico Proteome Analysis

Rolf Apweiler, Manuela Pruess, R. Apweiler, 2003, Journal of biomedicine & biotechnology.

Systematic comparison of the human saliva and plasma proteomes

Rolf Apweiler, Shen Hu, Weixia Yu, 2009, Proteomics. Clinical applications.

Human Proteome Organisation Proteomics Standards Initiative Pre‐Congress Initiative

Rolf Apweiler, Henning Hermjakob, Ruedi Aebersold, 2005, Proteomics.

Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria

Rolf Apweiler, Peipei Ping, Chenggong Zong, 2008, Proteomics.

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.

John R Yates, Rolf Apweiler, Henning Hermjakob, 2014, Journal of proteome research.

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

Johannes Griss, Juan Antonio Vizcaíno, Claire O'Donovan, 2011, Proteomics.

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study

Lennart Martens, Daniel Chamrad, Gerhard Körting, 2006, Proteomics.

Protein sequence databases.

Cathy H. Wu, Rolf Apweiler, Amos Bairoch, 2004, Current opinion in chemical biology.

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.

Phil Andrews, John R Yates, Rolf Apweiler, 2009, Journal of proteome research.

A large-scale protein-function database.

Christoph Steinbeck, Rolf Apweiler, Amos Bairoch, 2010, Nature chemical biology.

Proteomic data exchange and storage: the need for common standards and public repositories.

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2007, Methods in molecular biology.

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

Rolf Apweiler, Jasmin Fisher, Nicholas M Luscombe, 2013, eLife.

The power of cooperative investigation: Summary and comparison of the HUPO Brain Proteome Project pilot study results

Lennart Martens, Kai A Reidegeld, Gerhard Körting, 2006, Proteomics.

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) Geneva, September, 4–6, 2005

Chris F. Taylor, Rolf Apweiler, Henning Hermjakob, 2006, Proteomics.

InterPro as a new tool for complete genome analysis: An example of comparative analysis

Rolf Apweiler, Nicola Mulder, Wolfgang Fleischmann, 2006 .

A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies

Lennart Martens, Kai A Reidegeld, Martin Blüggel, 2006, Proteomics.

Increase of functional diversity by alternative splicing.

Martin Vingron, Rolf Apweiler, Peer Bork, 2003, Trends in genetics : TIG.

Whither systems medicine?

Ingo Roeder, Olaf Wolkenhauer, Nils Blüthgen, 2018, Experimental & Molecular Medicine.

ASTD: The Alternative Splicing and Transcript Diversity database.

Oliver Hofmann, Gautier Koscielny, William Ritchie, 2009, Genomics.

Mining Unique-m Substrings from Genomes

Rolf Apweiler, Zhenyu Jia, Paul Flicek, 2010, Journal of proteomics & bioinformatics.

The EMBL Nucleotide Sequence and Genome Reviews Databases.

Rolf Apweiler, Peter Sterk, Paul Kersey, 2007, Methods in molecular biology.

The speciation of the proteome

Rolf Apweiler, Peter R Jungblut, Hartmut Schlüter, 2008, Chemistry Central journal.

Altered proteome biology of cardiac mitochondria under stress conditions.

Rolf Apweiler, Peipei Ping, Chenggong Zong, 2008, Journal of proteome research.

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Lennart Martens, Kai Stühler, Martin Blüggel, 2006, Proteomics.

Building a biological space based on protein sequence similarities and biological ontologies.

Robert Petryszak, Rolf Apweiler, David Lonsdale, 2008, Combinatorial chemistry & high throughput screening.

A posteriori quality control for the curation and reuse of public proteomics data

Lennart Martens, Johannes Griss, Rolf Apweiler, 2011, Proteomics.

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

Lennart Martens, Chris F. Taylor, Kai A Reidegeld, 2006, Proteomics.

Annotating the human proteome: beyond establishing a parts list.

Lennart Martens, Rolf Apweiler, R. Apweiler, 2007, Biochimica et biophysica acta.

Bioinformatics database infrastructure for biotechnology research.

Rolf Apweiler, Manuela Pruess, R. Apweiler, 2006, Journal of biotechnology.

HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

Lennart Martens, Kai Stühler, Martin Blüggel, 2006 .

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

Lennart Martens, Harald Barsnes, Martin Eisenacher, 2009, Proteomics.

Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasets

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2008, Proteomics.

Proteome Analysis Database

Rolf Apweiler, R. Apweiler, 2004 .

The Renal Gene Ontology Annotation Initiative

Yasmin Alam-Faruque, Claire O'Donovan, Rolf Apweiler, 2010, Organogenesis.

A guide to UniProt for protein scientists.

Claire O'Donovan, Rolf Apweiler, R. Apweiler, 2011, Methods in molecular biology.