A5086334945- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Microbial Natural Products and Biosynthesis
- Biomedical Text Mining and Ontologies
- Methane Hydrates and Related Phenomena
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Protist diversity and phylogeny
- Machine Learning in Bioinformatics
- Environmental DNA in Biodiversity Studies
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Biofuel production and bioconversion
- Molecular Biology Techniques and Applications
- Microbial infections and disease research
- Research Data Management Practices
- Geology and Paleoclimatology Research
- Scientific Computing and Data Management
- Bacteriophages and microbial interactions
- Semantic Web and Ontologies
- Plant biochemistry and biosynthesis
- Enzyme Catalysis and Immobilization
- Natural Language Processing Techniques
SIB Swiss Institute of Bioinformatics
2014-2021
Max Planck Institute for Marine Microbiology
2003-2008
Constructor University
2008
Max Planck Society
2004-2008
Max Planck Institute for Molecular Genetics
2003
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...
Pirellula sp. strain 1 (“ Rhodopirellula baltica ”) is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales . Here we report complete genome sequence member this independent phylum. With 7.145 megabases, has largest circular sequenced so far. The presence all genes required for heterolactic acid fermentation, key interconversion C1 compounds, 110 sulfatases were unexpected aerobic heterotrophic isolate. Although proteinaceous cell...
Abstract Background In the emerging field of environmental genomics, direct cloning and sequencing genomic fragments from complex microbial communities has proven to be a valuable source new enzymes, expanding knowledge basic biological processes. The central problem this so called metagenome-approach is that cloned often lack suitable phylogenetic marker genes, rendering identification clones are likely originate same genome difficult or impossible. such cases, analysis intrinsic...
Summary Members of the Bacteroidetes , formerly known as Cytophaga‐Flavobacteria‐Bacteroides (CFB) phylum, are among major taxa marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part free‐living microbial assemblages in nutrient‐rich microenvironments. Their abundance and distribution pattern combination with enzymatic activity studies has led notion that organisms...
Summary Desulfotalea psychrophila is a marine sulfate‐reducing δ‐proteobacterium that able to grow at in situ temperatures below 0°C. As abundant members of the microbial community permanently cold sediments, D. ‐like bacteria contribute global cycles carbon and sulfur. Here, we describe genome sequence strain LSv54, which consists 3 523 383 bp circular chromosome with 3118 predicted genes two plasmids 121 586 14 663 bp. Analysis gave insight into metabolic properties organism, e.g. presence...
Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic prokaryotes with unique intracellular organelle, the magnetosome, which orients cell along magnetic field lines. Magnetotaxis is complex phenotype, depends on coordinate synthesis magnetosomes and ability to swim orient direction caused by interaction Earth's field. Although number putative magnetotaxis genes were recently identified within conserved genomic magnetosome island (MAI) several MTB, their functions have remained...
To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants the ChEBI (Chemical Entities Biological Interest) ontology.We replaced existing textual descriptions with their equivalents from is now standard for enzymatic UniProtKB. We developed improved search and query facilities UniProt website, REST API SPARQL endpoint that leverage chemical structure...
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction participants. Originally designed as an annotation vocabulary for UniProt Knowledgebase (UniProtKB), also provides data range other core knowledgebases repositories including MetaboLights. Here we describe recent developments in Rhea, focusing on new description framework representation SPARQL...
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation enzymes description metabolic networks. describes enzyme-catalyzed covering IUBMB Enzyme Nomenclature list as well additional reactions, including spontaneously occurring using entities from ChEBI (Chemical Entities Biological Interest) ontology small molecules. Here we describe developments in since our last report database issue Nucleic...
Summary The anaerobic oxidation of methane is a globally significant process which mediated by consortia yet uncultivated methanotrophic archaea (ANME) and sulfate‐reducing bacteria. In order to gain deeper insights into genome characteristics the different ANME groups, large‐insert genomic libraries were constructed using DNA extracted from microbial mat growing in anoxic part Black Sea, sediments above gas hydrates at Hydrate Ridge off coast Oregon. Analysis these fosmid with respect...
The Genomic Contextual Data Markup Language (GCDML) is a core project of the Standards Consortium (GSC) that implements "Minimum Information about Genome Sequence" (MIGS) specification and its extension, Metagenome (MIMS). GCDML an XML Schema for generating MIGS/MIMS compliant reports data entry, exchange, storage. When mature, this sample-centric, strongly-typed schema will provide diverse set descriptors describing exact origin processing biological sample, from sampling to sequencing,...
Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities Biological Interest) ontology small molecules. has been designed for functional annotation enzymes description genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed (covering IUBMB Enzyme Nomenclature list additional reactions), transport spontaneously occurring reactions. are...
ABSTRACT The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers single genes rather than a not-yet-identified “metabolic island.” Here we provide evidence that the transfer gene cluster may indeed be responsible for patchy sulfate-reducing prokaryotes (SRP) phylogenetic tree. We isolated...
Abstract Background Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided the centers. Although, standardised workflows are desirable useful in many respects, rational mining, comparative genomics, especially interpretation of biological context, demands intuitive, flexible, extendable solutions. Results The JCoast software tool was primarily...
In recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. The form an independent within bacterial domain, whose exact phylogenetic position remains controversial. With completion sequencing genome ‘Rhodopirellula baltica’ SH 1, it is now possible re-evaluate phylogeny based on multiple genes trees in addition single like 16S rRNA or elongation factor Tu. Here, evidence...
Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of first marine bacterial genome 2003, number fully sequenced bacteria has grown rapidly. Concurrently, studies are performed on a regular basis, resulting sequences growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces regional differences cycling nutrients, it necessary couple sequence data with geographical...
Rhodopirellula baltica SH1(T), which was isolated from the water column of Kieler Bight, a bay in southwestern Baltic Sea, is marine aerobic, heterotrophic representative ubiquitous bacterial phylum Planctomycetes. We analyzed R. proteome by applying different preanalytical protein as well peptide separation techniques (1-D and 2-DE, HPLC separation) prior to MS. That way, we could identify total 1115 nonredundant proteins intracellular cell wall fractions. With contribution 709 novel...
The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization biomass in natural environment. On basis its recently determined complete genome we investigated proteome by 2-DE established reference gel for soluble protein fraction. Approximately 1000 spots were excised from colloidal Coomassie-stained (pH 4–7), analyzed MALDI-MS identified PMF. non-redundant data set contained 626 spots,...
UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute this with a FAIRness assessment our UniProtKB dataset followed by critical reflection on challenges and future directions adoption validation FAIR principles metrics.
Rhodopirellula baltica (strain SH 1T) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum Planctomycetes. Little known about regulatory strategies bacteria with large (7.15 Mb) genomes. Therefore, consistent, quantitative qualitative description was produced by comparing R. baltica's transcriptional regulator pool that 123 publicly available bacterial The overall results are congruous earlier observations in Bacteria, proportion...
Modern sequencing technologies allow rapid and bioinformatic analysis of genomes metagenomes. With every new project a vast number proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities alone. Extending similarity searches gene pattern approaches, defined as sharing distinct genomic neighbourhood, have shown to significantly improve the functional assignments. Further can be gained by correlating these patterns prevailing...
Abstract Motivation To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants the ontology ChEBI (Chemical Entities Biological Interest). Results We replaced existing textual descriptions with their equivalents from is now standard for enzymatic UniProtKB. developed improved search and query facilities UniProt website, REST API, SPARQL endpoint that...