A5059898325- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- Species Distribution and Climate Change
- Research Data Management Practices
- Scientific Computing and Data Management
- Veterinary Practice and Education Studies
- Regional Economic Development and Innovation
- Protist diversity and phylogeny
- Genetic diversity and population structure
- Medical and Biological Sciences
- Methane Hydrates and Related Phenomena
- Animal Disease Management and Epidemiology
- Marine and coastal ecosystems
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Peatlands and Wetlands Ecology
- Complex Network Analysis Techniques
- Data Quality and Management
- Bioinformatics and Genomic Networks
- Anaerobic Digestion and Biogas Production
- Biomedical Text Mining and Ontologies
- Metabolomics and Mass Spectrometry Studies
- Environmental and Biological Research in Conflict Zones
- Molecular Biology Techniques and Applications
Max Planck Institute for Marine Microbiology
2007-2022
Constructor University
2007-2016
University of South Australia
2014
Institut Català de Ciències del Clima
2013
Institut de Ciències del Mar
2013
Max Planck Society
2008-2009
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of marine microbial biodiversity and function world's oceans. It is simultaneous global mega-sequencing campaign aiming generate largest standardized data set in single day. This will be achievable only through coordinated efforts an Consortium, supportive partnerships networks between sites. commentary outlines establishment, aims Consortium...
Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts temperature, transformations land-use, or energy budget systems. While latter processes easily quantifiable, documentation loss biodiversity community structure is more difficult. Changes organismal abundance diversity barely documented. Censuses species usually fragmentary inferred often spatially, temporally ecologically unsatisfactory simple lists for individual study...
Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives not available for any three ANME clades. Therefore, a metagenomic approach was applied assess genetic potential ANME-1 archaea. In total, 3.4 Mbp sequence information generated based on fosmid libraries constructed directly from microbial mat in Black Sea. These data represent, 30...
While powerful and user-friendly software suites exist for phylogenetics, an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting diagnosing species, is still its infancy. Here we present a project to develop bioinformatic toolkit taxonomy, based on open-source Python code, including tools focusing delimitation diagnosis centered around specimen identifiers. At...
Genomic samples of non-model organisms are becoming increasingly important in a broad range studies from developmental biology, biodiversity analyses, to conservation. sample definition, description, quality, voucher information and metadata all need be digitized disseminated across scientific communities. This needs concise consistent today's ever-increasing bioinformatic era, for complementary data aggregators easily map databases one another. In order facilitate exchange on genomic their...
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...
Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data marine genome metagenome projects for microbial ecological genomics. All are stored in the Microbial Ecological Genomics DataBase (MegDB), which subdivided hold both sequence habitat global environmental layers. The extended system several hundreds of genomes metagenomes from prokaryotes phages, as well over million small large subunit ribosomal RNA sequences. With refined Genes...
Little research has assessed the fidelity, adaptation or integrity of activities implemented within community-based obesity prevention initiatives. To address this gap, a mixed-method process evaluation was undertaken in context South Australian Obesity Prevention and Lifestyle (OPAL) initiative. An ecological coding procedure fidelity activity settings, targets strategies second year four communities. Implementation reflected to local context, whereas efforts resulting significant...
Abstract The ability to rapidly generate and share molecular, visual, acoustic data, compare them with existing information, thereby detect name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms also impacting taxonomy. Harnessing taxonomic data for rapid, automated species identification by machine learning tools or DNA metabarcoding techniques has great potential but will require their review, accessible storage, comprehensive...
Marine metatranscriptome data was generated as part of a study investigating the bacterioplankton communities towards end diatom-dominated spring phytoplankton bloom. This genomic resource article reports metatranscriptomic dataset from amidst winter time prior to occurrence diatom Up 58% all sequences could be assigned predicted genes. Taxonomic analysis based on expressed 16S ribosomal RNA genes identified Alphaproteobacteria and Gammaproteobacteria most active community members.
Background The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies sequence and structural homology have indicated that many uncharacterized protein domain are variants functionally described domains. If these promote an organism's ecological fitness, they likely to be the genome its progeny population at large. genetic composition microbial communities their native ecosystems accessible through metagenomics. We hypothesize...
State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into ‘blueprints’ organisms from all domains life. Sequencing is carried out around globe and data submitted to public repositories International Nucleotide Sequence Database Collaboration. However, context which these are conducted often gets lost, because experimental data, as well information about environment rarely along with sequence data. If contextual or metadata missing, key opportunities comparison...
Abstract While powerful and user-friendly software suites exist for phylogenetics, an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting diagnosing species, is still its infancy. Here we present a project to develop bioinformatic toolkit taxonomy, based on open-source Python code, including tools focusing delimitation diagnosis centered around specimen...
DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often response to environmental stimuli. Thus, the environment exerts constant selective pressure on TF gene content of microbial communities. Recently a study marine Synechococcus strains detected differences their genomic related adaptation, but so far effect parameters TFs bacterial communities has not been systematically investigated.We quantified stability factor repertoire pelagic microbes from Global...
NFDI4Biodiversity is a consortium within the German National Research Data Infrastructure (NFDI) dedicated to data and services for biodiversity research ecology. In domain, well-developed international networks exist, with quite mature tools standards. These are used disseminated in project order mobilise publish collected by national stakeholders according FAIR Guiding Principles scientific management stewardship.The partners provide methods archiving, publishing, searching analysing that...
The concept of a "Research Data Commons" (RDC) established itself as an infrastructure ecosystem for science based on open standards and federated resources to facilitate the sharing research data services. consortia German National Research Infrastructure (NFDI) have identified collaborative provisioning services be key importance functioning efficient RDC are leveraging different corresponding measures establish sustainable in line with international developments.
Abstract Knowledge derived from nucleotide sequence data is increasing in importance the life sciences, as well decision making (mainly biodiversity policy). Metadata standards have been established to facilitate sustainable management according FAIR principles (Findability, Accessibility, Interoperability, Reusability). Here, we review status of metadata available for raw read Illumina amplicon and whole genome shotgun sequencing ecological metagenomic material that are accessible at...
The Nagoya Protocol on Access and Benefit Sharing is a transparent legal framework, which governs the access to genetic resources fair equitable sharing of benefits arising from their utilization. Complying with regulations ensures use re-use data resources. Providing detailed provenance information clear re-usage conditions plays key role in ensuring re-usability research according FAIR (findable, accessible, interoperable re-usable) Guiding Principles for scientific management stewardship....