A5011445829- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Bacterial biofilms and quorum sensing
- Research Data Management Practices
- SARS-CoV-2 and COVID-19 Research
- Antibiotic Resistance in Bacteria
- Astronomy and Astrophysical Research
- Adaptive optics and wavefront sensing
- Data Quality and Management
- Scientific Computing and Data Management
- Calibration and Measurement Techniques
- CRISPR and Genetic Engineering
- SARS-CoV-2 detection and testing
- RNA and protein synthesis mechanisms
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Machine Learning in Bioinformatics
Justus-Liebig-Universität Gießen
2021-2023
Giessen School of Theology
2023
Command-line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command-line pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and, nonetheless, fast Bakta conducts comprehensive workflow including detection small proteins taking into...
Abstract The EDGAR platform, a web server providing databases of precomputed orthology data for thousands microbial genomes, is one the most established tools in field comparative genomics and phylogenomics. Based on gene alignments, allows quick identification differential content, i.e. pan genome, core or singleton genes. Furthermore, features wide range analyses visualizations like Venn diagrams, synteny plots, phylogenetic trees, as well Amino Acid Identity (AAI) Average Nucleotide (ANI)...
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for world-wide spread multi- and pan-drug resistant bacteria. Aiding urgent demand novel therapeutic targets, comparative genomics studies between their apathogenic relatives shed light on genetic basis human-pathogen interaction. Yet, existing limited in taxonomic scope, sensing phylogenetic signal, resolution by largely analyzing genes independent organization functional gene clusters....
Abstract Command line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command pipelines heavily depend on taxon specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and nonetheless fast Bakta conducts comprehensive workflow including detection small proteins taking into...
Abstract Summary The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand evolution virus, monitor viral population, and plan epidemiological responses. Detailed analysis, easy visualization intuitive filtering latest sequences are powerful for this purpose. We present CovRadar, a tool Spike protein. CovRadar consists an analytical pipeline web application that enable analysis hundreds thousand sequences. First, extracts regions interest using...
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 Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for world-wide spread multi- and pan-drug resistant bacteria. Aiding urgent demand novel therapeutic targets, comparative genomics studies between their apathogenic relatives shed light on genetic basis human-pathogen interaction. Yet, existing limited in taxonomic scope, sensing phylogenetic signal, resolution by largely analyzing genes isolated from functional contexts. Here,...
ABSTRACT The SARS-CoV-2 pandemic underlined the importance of molecular surveillance to track evolution virus and inform public health interventions. Fast analysis, easy visualization convenient filtering latest sequences are essential for this purpose. However, access computational resources, lack bioinformatics expertise, sheer volume in databases complicate efforts. CovRadar combines an analytical pipeline a web application designed spike gene SARS-CoV-2, important vaccine target....
Microbes – bacteria, archaea, unicellular eukaryotes, and viruses play an important role in human environmental health. Growing awareness of this fact has led to a huge increase microbiological research applications variety fields. Driven by technological advances that allow high-throughput molecular characterization microbial species communities, now offers unparalleled opportunities address current emerging needs. As well as helping global health threats such antimicrobial resistance viral...
The exponential growth of scientific data has led to an increasing demand for effective management and storage solutions. Academic computing infrastructures are often fragmented, which can make it challenging researchers leverage cloud-native principles modern analysis tools. To address this challenge, a new distributed platform called Aruna Object Storage (AOS) was developed. AOS is cloud-native, scalable, domain-agnostic object system that provides S3-compatible interface variety tools...