A5053452109- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Trace Elements in Health
- Microbial Fuel Cells and Bioremediation
- Machine Learning in Bioinformatics
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Bacterial biofilms and quorum sensing
Technische Universität Braunschweig
2020-2023
Helmholtz Centre for Infection Research
2020-2021
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy reliability of annotations, particularly small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized flexible bioinformatics workflow proteogenomics covering all steps (i) generation...
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of cognate open-reading frames (smORFs) remains challenging both experimentally computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing ribosome-protected fragments) enables detecting actively translated (ORFs) empirical coding sequences (CDSs) using in-register translation pattern that characteristic...
ABSTRACT Emerging evidence places small proteins (≤ 50 amino acids) more centrally in physiological processes. Yet, the identification of functional and systematic genome annotation their cognate open reading frames (smORFs) remains challenging both experimentally computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing ribosome-protected fragments) enables detecting actively translated open-reading (ORFs) empirical coding sequences (CDSs) using in-register translation...
Abstract Small proteins play diverse and essential roles in bacterial physiology virulence. Despite their importance, automated genome annotation algorithms still cannot accurately annotate all respective small open reading frames (sORFs), as they usually provide insufficient sequence information for domain homology searches, tend to be species specific only a few experimentally validated examples are covered standard proteomics studies. The accuracy reliability of annotations, particularly...
Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed adaptation D . different kinds oxidative stress using a GeLC-MS/MS approach. was grown artificial seawater medium dark with succinate as sole carbon source and hydrogen peroxide, paraquat or diamide. We quantified 2580 proteins. 75 proteins changed significantly response peroxide stress, while 220 207 were differently regulated by...