Elisabeth Gasteiger
A5051386555- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Mass Spectrometry Techniques and Applications
- Glycosylation and Glycoproteins Research
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Scientific Computing and Data Management
- Research Data Management Practices
- Identification and Quantification in Food
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Structure and Function
- Carbohydrate Chemistry and Synthesis
- Gene expression and cancer classification
- Genomics and Rare Diseases
- Microbial Community Ecology and Physiology
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Protein Structure and Dynamics
- Ubiquitin and proteasome pathways
- Natural Language Processing Techniques
- Metabolism and Genetic Disorders
SIB Swiss Institute of Bioinformatics
2014-2024
European Bioinformatics Institute
2024
University of Geneva
1996-2017
Battelle
2017
University of Basel
2012
University of Lausanne
2005
University Hospital of Geneva
1996-2001
Zimmer Biomet (Switzerland)
1996
Université Claude Bernard Lyon 1
1996
Centre National de la Recherche Scientifique
1996
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, Swiss-Prot, TrEMBL PIR database activities have united to form Universal Protein Knowledgebase (UniProt) consortium. Our mission is comprehensive, fully classified, richly accurately annotated sequence knowledgebase, extensive cross-references query interfaces. The central will two sections, corresponding familiar Swiss-Prot (fully manually curated entries)...
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this article, we describe significant updates that have made over last two years resource. number in UniProtKB has risen approximately 190 million, despite continued work reduce sequence redundancy at proteome level. We adopted new methods assessing completeness quality. continue extract detailed annotations from...
The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by multidisciplinary team at Swiss Institute of Bioinformatics (SIB). It provides access variety databases and analytical tools dedicated proteins proteomics. include SWISS-PROT TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME SWISS-MODEL repository. are available for specific tasks relevant proteomics, similarity searches, pattern profile...
Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication we describe enhancements made our data processing pipeline website adapt an ever-increasing information content. number in UniProtKB has risen over 227 million are working towards including reference proteome for each taxonomic group. We continue extract detailed annotations from literature...
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in Life Sciences. Each entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features sometimes even contradictory conclusions. Detailed expertise that goes beyond scope is made available via direct links to specialised databases. annotated entries for all species,...
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases software tools in different areas life sciences. Scientists can henceforth access seamlessly a wide range domains, such proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual (databases, web-based...
ScanProsite— http://www.expasy.org/tools/scanprosite/ —is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For number profiles, now makes use ProRules—context-dependent annotation templates—to detect functional structural intra-domain residues. The detection those features enhances power function prediction based on profiles. Both user-defined sequences from UniProt Knowledgebase can be matched against custom patterns, or...
The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references querying interfaces freely accessible the scientific community. UniProt produced Consortium which consists groups from European Bioinformatics Institute (EBI), Swiss (SIB) Information (PIR). comprised four major components, each optimized for...
Abstract Background The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), European (EBI) and Protein Information Resource (PIR) at Georgetown University, soon afterwards website http://www.uniprot.org set up as a central entry point to resources. Requests this address were redirected one three organisations' websites. While these sites shared static pages with general information about UniProt, their for searching viewing data different. To...
GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of glycan structure from its experimentally determined mass. The program can be used predict the composition any glycoprotein-derived oligosaccharide comprised either underivatised, methylated or acetylated monosaccharides, with derivatised reducing terminus. attached peptide computed if sequence mass known. In addition, protein known and contained in SWISS-PROT TrEMBL databases,...
Abstract Motivation To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities Biological Interest), to better support efforts study and predict functionally interactions between protein sequences structures small molecule ligands. Results We structured data model cognate ligand site annotations performed a complete reannotation all stable unique identifiers from...
Abstract Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number key developments in since our last report database issue Nucleic Acids Research 2019. These include improved reaction coverage Rhea, adoption as reference vocabulary for enzyme annotation UniProt UniProtKB (https://www.uniprot.org), development new...
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication, we describe ongoing changes our production pipeline limit available in UniProtKB high-quality, non-redundant reference proteomes. We continue manually curate scientific literature add latest data use machine learning techniques. also encourage community curation...
Abstract In peptide mass fingerprinting, there are frequently peptides whose masses cannot be explained. These usually attributed to either a missed cleavage site during the chemical or enzymatic cutting process, lack of reduction and alkylation protein, protein modifications like oxidation methionine, presence post‐translational modifications. However, they could equally due database errors, unusual splicing events, variants in population, artifactual Unfortunately verification each these...
Abstract Summary: Protein tyrosine sulfation is an important post-translational modification of proteins that go through the secretory pathway. No clear-cut acceptor motif can be defined allows prediction sites in polypeptide chains. The Sulfinator a software tool used to predict protein sequences with overall accuracy 98%. Four different Hidden Markov Models were constructed, each them specialized recognize sulfated residues depending on their location within sequence: near N-terminus,...
Abstract Two‐dimensional (2‐D) gel electrophoresis is often used in proteome projects to provide a global view of the proteins expressed any cell or tissue type. Here we have investigated effects protein hydrophobicity and cellular copy number on protein's presence absence two‐dimensional gel. The average hydropathy values all known from Bacillus subtilis, Escherichia coli Saccharomyces cerevisiae were calculated, thus defining range hydrophilicity these organisms. then calculated for total...
The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures glycoproteins. UniCarbKB is an international effort that aims further our understanding structures, pathways and networks involved in glycosylation glyco-mediated processes by integrating structural, experimental functional glycoscience information. This initiative builds upon success structure GlycoSuiteDB, together with informatic standards...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...