| Publication | Author position | Listed as |
|---|
| The EBI SRS server--recent developments. | 3 | Apweiler R |
| Interactive InterPro-based comparisons of proteins in whole genomes. | 2 | Apweiler R |
| The EBI SRS server-new features. | 3 | Apweiler R |
| InterPro: an integrated documentation resource for protein families, domains and functional sites. | 2 | Apweiler R |
| High-quality protein knowledge resource: SWISS-PROT and TrEMBL. | last | Apweiler R |
| Applications of InterPro in protein annotation and genome analysis. | last | Apweiler R |
| The European Bioinformatics Institute's data resources. | 10 | Apweiler R |
| The InterPro Database, 2003 brings increased coverage and new features. | 2 | Apweiler R |
| The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. | 3 | Apweiler R |
| Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. | last | Apweiler R |
| The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. | last | Apweiler R |
| Increase of functional diversity by alternative splicing. | 3 | Apweiler R |
| The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. | last | Apweiler R |
| Managing core resources for genomics and proteomics. | 1 | Apweiler R |
| Integr8: enhanced inter-operability of European molecular biology databases. | last | Apweiler R |
| The proteomics standards initiative. | last | Apweiler R |
| Further advances in the development of a data interchange standard for proteomics data. | last | Apweiler R |
| The EMBL Nucleotide Sequence Database. | last | Apweiler R |
| UniProt: the Universal Protein knowledgebase. | 1 | Apweiler R |
| The Gene Ontology (GO) database and informatics resource. | 39 | Apweiler R |
| The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. | last | Apweiler R |
| IntEnz, the integrated relational enzyme database. | last | Apweiler R |
| IntAct: an open source molecular interaction database. | last | Apweiler R |
| The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. | last | Apweiler R |
| Common interchange standards for proteomics data: Public availability of tools and schema. | last | Apweiler R |
| Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. | 9 | Apweiler R |
| Protein sequence databases. | 1 | Apweiler R |
| UniProt archive. | last | Apweiler R |
| The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase. | last | Apweiler R |
| Integrative annotation of 21,037 human genes validated by full-length cDNA clones. | 149 | Apweiler R |
| The International Protein Index: an integrated database for proteomics experiments. | last | Apweiler R |
| Filtering erroneous protein annotation. | last | Apweiler R |
| Towards data management of the HUPO Human Brain Proteome Project pilot phase. | 7 | Apweiler R |
| Advances in the development of common interchange standards for proteomic data. | last | Apweiler R |
| Protein sequence database methods. | last | Apweiler R |
| A common open representation of mass spectrometry data and its application to proteomics research. | 10 | Apweiler R |
| The Universal Protein Resource (UniProt). | 2 | Apweiler R |
| InterPro, progress and status in 2005. | 2 | Apweiler R |
| E-MSD: an integrated data resource for bioinformatics. | 6 | Apweiler R |
| The EMBL Nucleotide Sequence Database. | last | Apweiler R |
| Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. | last | Apweiler R |
| The importance of uniformity in reporting protein-function data. | 1 | Apweiler R |
| Annotating the human proteome. | last | Apweiler R |
| Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. | last | Apweiler R |
| The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. | last | Apweiler R |
| Plant protein annotation in the UniProt Knowledgebase. | last | Apweiler R |
| Dasty and UniProt DAS: a perfect pair for protein feature visualization. | last | Apweiler R |
| An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. | last | Apweiler R |
| The predictive power of the CluSTr database. | last | Apweiler R |
| Current status of proteomic standards development. | last | Apweiler R |
| Who tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools. | last | Apweiler R |
| The Integr8 project--a resource for genomic and proteomic data. | last | Apweiler R |
| InterProScan: protein domains identifier. | 6 | Apweiler R |
| Second proteomics standards initiative spring workshop. | last | Apweiler R |
| PRIDE: the proteomics identifications database. | last | Apweiler R |
| Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-... | 7 | Apweiler R |
| The transcriptional landscape of the mammalian genome. | 23 | Apweiler R |
| Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). | last | Apweiler R |
| 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. | last | Apweiler R |
| Do you do text? | 5 | Apweiler R |
| Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative. | last | Apweiler R |
| EMBL Nucleotide Sequence Database: developments in 2005. | last | Apweiler R |
| The Universal Protein Resource (UniProt): an expanding universe of protein information. | 2 | Apweiler R |
| PRIDE: a public repository of protein and peptide identifications for the proteomics community. | last | Apweiler R |
| Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. | last | Apweiler R |
| The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. | last | Apweiler R |
| The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. | 3 | Apweiler R |
| The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. | last | Apweiler R |
| UniSave: the UniProtKB sequence/annotation version database. | last | Apweiler R |
| Bioinformatics database infrastructure for biotechnology research. | last | Apweiler R |
| Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. | 2 | Apweiler R |
| Evidence standards in experimental and inferential INSDC Third Party Annotation data. | 3 | Apweiler R |
| Genome Reviews: standardizing content and representation of information about complete genomes. | last | Apweiler R |
| The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). | last | Apweiler R |
| Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data. | 6 | Apweiler R |
| Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. | last | Apweiler R |
| A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies. | last | Apweiler R |
| The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. | 10 | Apweiler R |
| Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. | 9 | Apweiler R |
| HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. | 2 | Apweiler R |
| Databases and resources for in silico proteome analysis. | last | Apweiler R |
| Linking publication, gene and protein data. | last | Apweiler R |
| IntAct--open source resource for molecular interaction data. | 23 | Apweiler R |
| EMBL Nucleotide Sequence Database in 2006. | last | Apweiler R |
| GOAnnotator: linking protein GO annotations to evidence text. | 6 | Apweiler R |
| Proteomic data exchange and storage: the need for common standards and public repositories. | last | Apweiler R |
| New developments in the InterPro database. | 2 | Apweiler R |
| Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. | 10 | Apweiler R |
| Annotating the human proteome: beyond establishing a parts list. | last | Apweiler R |
| High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK. | 15 | Apweiler R |
| Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Superieur, Lyon, France. | 7 | Apweiler R |
| The minimum information about a proteomics experiment (MIAPE). | 8 | Apweiler R |
| The minimum information required for reporting a molecular interaction experiment (MIMIx). | 35 | Apweiler R |
| Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. | 3 | Apweiler R |
| The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. | 4 | Apweiler R |
| Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. | 29 | Apweiler R |
| The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. | 8 | Apweiler R |
| InterPro and InterProScan: tools for protein sequence classification and comparison. | last | Apweiler R |
| Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. | 34 | Apweiler R |
| Analyzing large-scale proteomics projects with latent semantic indexing. | 6 | Apweiler R |
| The Rice Annotation Project Database (RAP-DB): 2008 update. | 49 | Apweiler R |
| Wiley-VCH and HUPO: a global effort to advance proteomic science. | last | Apweiler R |
| In silico characterization of proteins: UniProt, InterPro and Integr8. | last | Apweiler R |
| The EMBL Nucleotide Sequence and Genome Reviews Databases. | last | Apweiler R |
| Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. | 6 | Apweiler R |
| Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. | 7 | Apweiler R |
| Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. | 13 | Apweiler R |
| UniProtJAPI: a remote API for accessing UniProt data. | last | Apweiler R |
| The InterPro database and tools for protein domain analysis. | last | Apweiler R |
| The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. | 4 | Apweiler R |
| Altered proteome biology of cardiac mitochondria under stress conditions. | 13 | Apweiler R |
| Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? | 7 | Apweiler R |
| The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data. | last | Apweiler R |
| The Gene Ontology Annotation (GOA) Project-Application of GO in SWISS-PROT, TrEMBL and InterPro. | last | Apweiler R |
| Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. | last | Apweiler R |
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