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List of works by Rolf Apweiler

"4D Biology for health and disease" workshop report

scientific article published on 15 October 2010

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame

scientific article

A Guide to UniProt for Protein Scientists ⬇️

scientific article published on January 1, 2011

A collection of well characterised integral membrane proteins

scientific article published in December 2000

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

scientific article

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

scientific article

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

scientific article published in September 2006

A large-scale protein-function database

scientific article published on November 2010

A novel method for automatic functional annotation of proteins

scientific article published on 01 March 1999

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

scientific article

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

Advances in the development of common interchange standards for proteomic data

scientific article

Algorithms and databases

scientific article published on January 2009

Altered proteome biology of cardiac mitochondria under stress conditions

scientific article

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

scientific article published on 24 May 2005

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

article

Analyzing large-scale proteomics projects with latent semantic indexing

scientific article

Annotating the human proteome

scientific article

Annotating the human proteome: beyond establishing a parts list

scientific article

Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL.

scientific article published in June 2001

Applications of InterPro in protein annotation and genome analysis

scientific article published on September 2002

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

scientific article published on October 2009

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

scientific article

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

scientific article

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

scientific article

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

article

Bioinformatics Resources for In Silico Proteome Analysis

scientific article

Bioinformatics database infrastructure for biotechnology research

scientific article

Bioinformatics: Using the Molecular Biology Data

scholarly article

Biological Databases: Infrastructure, Content and Integration

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

scientific article

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

scientific article published on September 2008

Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?

scientific article published on May 2008

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

scientific article published on 06 August 2013

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

scientific article

Classification of proteins into families

Clinical proteomics: A need to define the field and to begin to set adequate standards

scientific article published on 22 January 2007

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

scientific article

Clustering and analysis of protein families

scientific article

Common interchange standards for proteomics data: Public availability of tools and schema

scientific article

Comparative Proteomics Profiling Reveals Role of Smooth Muscle Progenitors in Extracellular Matrix Production

article

Comparative genomics of the eukaryotes

scientific article (publication date: 24 March 2000)

Computational Methods and Bioinformatic Tools

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

scientific article published on 17 October 2011

Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins.

scientific article published on December 2001

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

scientific article

Current status of proteomic standards development

scientific article

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

scientific article published on 19 May 2005

Data standardization and the HUPO proteomics standards initiative

Databases and resources for in silico proteome analysis

scientific article published on January 2006

Design, Implementation and Updating of Knowledge Bases

Development of glucose intolerance in obese (fa/fa) Zucker rats

article

Do you do text?

scientific article published on 29 September 2005

E-MSD: an integrated data resource for bioinformatics

scientific article

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

scientific article published in March 1999

EMBL Nucleotide Sequence Database in 2006.

scientific article published on 05 December 2006

EMBL Nucleotide Sequence Database: developments in 2005

scientific article

Effect of the new oral antidiabetic agent (−)-BM 13.0913.Na on insulin resistance in lean and obese zucker rats

scientific article published on 01 May 1995

Evaluation of methods for the prediction of membrane spanning regions

scientific article

Evidence standards in experimental and inferential INSDC Third Party Annotation data

scientific article

Filtering erroneous protein annotation

scientific article published in August 2004

Finding one's way in proteomics: a protein species nomenclature

scientific article published on 9 September 2009

Focus on InterPro

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

scientific article published in September 2006

Functional information in SWISS-PROT: The basis for large-scale characterisation of protein sequences

article

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

scientific article published in October 2003

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

scientific article published in September 2005

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.

scientific article published in February 2005

GOAnnotator: linking protein GO annotations to evidence text

scientific article published on 20 December 2006

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

scientific article

Gene Ontology annotations and resources

scientific article

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

scientific article published in January 2006

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

scientific article

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

scientific article

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

scientific article published in August 2007

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

scientific article

Human Proteome Organisation Proteomics Standards Initiative Pre-Congress Initiative

article

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

scientific article

Identifying ELIXIR Core Data Resources

scientific article

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

scientific article

In Silico Characterization of Proteins InterPro and Proteome Analysis

In silico characterization of proteins: UniProt, InterPro and Integr8.

scientific article published on 04 October 2007

In vitro poly-(ADP-ribosyl)ation of chromatin proteins in the rat tapeworm, Hymenolepis diminuta

scientific article published on 01 April 1993

Increase of functional diversity by alternative splicing

scientific article

IntAct--open source resource for molecular interaction data

scientific article (publication date: 2007)

IntAct: an open source molecular interaction database

scientific article

IntEnz, the integrated relational enzyme database

scientific article

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

scientific article

Integr8: enhanced inter-operability of European molecular biology databases

scientific article

Integration of cardiac proteome biology and medicine by a specialized knowledgebase

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

InterPro and InterProScan: tools for protein sequence classification and comparison

scientific article

InterPro and Proteome Analysis — In silico Analysis of Proteins and Proteomes

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

scientific article

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

scientific article published on 19 May 2012

InterPro, progress and status in 2005

scientific article

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

scientific article (publication date: December 2000)

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

scientific article

InterPro: the integrative protein signature database

scientific article

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

scientific article (publication date: September 2001)

InterProScan: protein domains identifier

scientific article

Interactive InterPro-based comparisons of proteins in whole genomes

scientific article published in February 2002

Know your limits: assumptions, constraints and interpretation in systems biology

scientific article published on 09 May 2009

Linking publication, gene and protein data

scientific article

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics

scientific article published on 7 May 2013

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

scientific article

Managing core resources for genomics and proteomics

scientific article

Mining Unique-m Substrings from Genomes.

scientific article published in March 2010

Missing in action: enzyme functional annotations in biological databases

scientific article published on August 2009

Mus musculus in the SWISS-PROT database: its relevance to developmental research

scientific article published in January 2000

New developments in linking of biological databases and computer-generation of annotation: SWISS-PROT and its computer-annotated supplement TREMBL

New developments in the InterPro database

scientific article

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database

scientific journal article

On the importance of comprehensible classification models for protein function prediction

scientific article published on January 2010

Ongoing and future developments at the Universal Protein Resource

scientific article

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-available database

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-available database

scientific article published in August 2005

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

scientific article published in January 2006

PRIDE: the proteomics identifications database

scientific article

Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria

scientific article

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

scientific article (publication date: November 2009)

Plant protein annotation in the UniProt knowledgebase

scientific article

Practical Applications of the Gene Ontology Resource

article

Prepublication data sharing

scientific article

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

scientific article (publication date: 2008)

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

scientific article

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

scientific article (publication date: August 2008)

Protein Sequence Databases

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

scientific article published in January 1997

Protein sequence database methods.

scientific article published in January 2004

Protein sequence databases

scientific article

Protein sequence databases

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

scientific article

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic Data Standardization, Deposition and Exchange

article published in 2006

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

scientific article

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

scientific article published in April 2008

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

scientific article published in October 2008

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.

scientific article published in July 2009

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

article

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

scientific article published on August 2006

Proteomics and data standardisation

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands

scientific article

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

scientific article published on 29 September 2009

QuickGO: a web-based tool for Gene Ontology searching

scientific article published on 10 September 2009

Recommendations for biomarker identification and qualification in clinical proteomics

scientific article published in August 2010

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

scientific article (publication date: July 2009)

Removing redundancy in SWISS-PROT and TrEMBL.

scientific article published in March 1999

Reorganizing the protein space at the Universal Protein Resource (UniProt)

scientific article (publication date: 2012)

Report of the Second International Nomenclature Workshop. Cambridge, United Kingdom, May 1-2, 1999.

scientific article published in December 1999

Representation of functional information in the SWISS-PROT data bank

scientific article

Representing kidney development using the gene ontology

scientific article

Second Proteomics Standards Initiative Spring Workshop

article

Swissknife - 'lazy parsing' of SWISS-PROT entries

article

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

scientific article published on February 2004

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

scientific article

Systematic comparison of the human saliva and plasma proteomes

scientific article published on January 2009

TEMBLOR - Perspectives of EBI Database Services

scientific article

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

scientific article (publication date: 23 February 2017)

The EBI Metagenomics Archive, Integration and Analysis Resource

The EBI SRS server--recent developments

scientific article published on February 2002

The EBI SRS server-new features

scientific article

The EMBL Nucleotide Sequence Database

scientific article (published 2005-01-01)

The EMBL Nucleotide Sequence Database.

scientific article published in January 2004

The EMBL Nucleotide Sequence and Genome Reviews Databases

scientific article

The European Bioinformatics Institute in 2016: Data growth and integration

scientific article

The European Bioinformatics Institute in 2017: data coordination and integration

scientific article published on 25 November 2017

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

scientific article published on 01 January 2019

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

scientific article published on 01 January 2020

The European Bioinformatics Institute's data resources 2014

scientific article

The European Bioinformatics Institute's data resources.

scientific article

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis

scientific article published on 27 November 2020

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

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

scientific article

The Gene Ontology (GO) database and informatics resource

scientific article (publication date: 2004)

The Gene Ontology - Providing a Functional Role in Proteomic Studies

article

The Gene Ontology Annotation (GOA) Database

article

The Gene Ontology Annotation (GOA) Database

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

scientific article published on December 2003

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

scientific article (publication date: 2004)

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

scientific article published on January 2003

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro

scientific article published on 12 March 2003

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies

scientific article published in March 2006

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

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

scientific article

The HUPO initiative on Model Organism Proteomes, iMOP.

scientific article published in February 2012

The Integr8 project--a resource for genomic and proteomic data

scientific article

The InterPro Database and Tools for Protein Domain Analysis

The InterPro database and tools for protein domain analysis

scientific article

The InterPro database, 2003 brings increased coverage and new features

scientific article (publication date: 2003)

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

scientific article (publication date: 2001)

The International Protein Index: an integrated database for proteomics experiments

scientific article (publication date: July 2004)

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

scientific article published on 28 February 2006

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

scientific article

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

scientific article (publication date: 18 October 2007)

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

scientific article published on January 2003

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

scientific article

The Renal Gene Ontology Annotation Initiative

scientific article

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

scientific article

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

scientific article (publication date: 2003)

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

scientific article

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

scientific article

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

scientific article published on January 1, 1998

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

scientific article

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

scientific article

The SWISS-PROT protein sequence database: its relevance to human molecular medical research.

scientific article published in May 1997

The UniProt-GO Annotation database in 2011.

scientific article published on 28 November 2011

The Universal Protein Resource (UniProt)

scientific article

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

scientific article

The human proteomics initiative (HPI).

scientific article

The impact of focused Gene Ontology curation of specific mammalian systems

scientific article

The importance of uniformity in reporting protein-function data

scientific article

The minimum information about a proteomics experiment (MIAPE)

scientific article (publication date: August 2007)

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

scientific article published on August 2007

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

scientific article published in September 2006

The predictive power of the CluSTr database

scientific article published on 16 June 2005

The proteomics standards initiative

scientific article

The role SWISS-PROT and TrEMBL play in the genome research environment.

scientific article

The speciation of the proteome

scientific article published on 18 July 2008

The transcriptional landscape of the mammalian genome

scientific article

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments

scientific article

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

scientific article published on January 2006

Tools and resources for identifying protein families, domains and motifs

scientific article

Towards data management of the HUPO Human Brain Proteome Project pilot phase

scientific article

UniProt archive

scientific article

UniProt: the Universal Protein knowledgebase

scientific article from 2004

UniProtJAPI: a remote API for accessing UniProt data

scientific article

UniSave: the UniProtKB sequence/annotation version database

scientific article published on 21 March 2006

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

scientific article published on 17 January 2013

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

article

Whither systems medicine?

scientific article published on 2 March 2018

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

scientific article

Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science

Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science

scholarly article by Peipei Ping published in January 2008

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