Bioinformatics and Proteogenomics Group
Agroscope research program on microbial biodiversity
Main domain of activity:
Domains of application:
- Basic research
What do we do?
Our research revolves around the bioinformatic integration and analysis of datasets from state-of-the-art omics technologies, which we obtain through close collaboration with experimental biologists. These datasets include genome sequences, gene and protein expression, as well as metabolomics data. One particular focus is to exploit the unique advantages of proteomics data, including strategies to identify all proteins encoded in a genome (proteogenomics). Recently, we started to study the role of microbiomes – e.g. for plant protection – by applying metagenomics, genomics and transcriptomics approaches.
We developed a novel, integrative strategy to identify previously missed protein-coding genes in prokaryotes by proteogenomics. We released a public web server, where researchers can create such integrated proteogenomics search databases (iPtgxDBs) themselves, as well as GFF files that integrate different annotations, transparently capturing overlap and differences. We furthermore contributed our expertise in de novo genome assembly to a collaboration with Profs. Laure Weisskopf (Univ. Fribourg), Rolf Müller (Helmholtz Centre for Infection research) and Stefan Schulz (TU Braunschweig), who identified a novel chemical class of volatile long-chain alkyl cyanides in bacterial isolates from soil. Finally, we helped to sequence and annotate yeast strains from soil, which showed antagonistic activity against a number of soil-borne plant pathogens, aiming to provide the basis for identifying the mechanism of action of these protective effects.
Main publications 2017
- Omasits U et al. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res. 2017. 27(12):2083- 2095.
- Montes Vidal D et al. Long-Chain Alkyl Cyanides: Unprecedented Volatile Compounds Released by Pseudomonas and Micromonospora Bacteria. Angew Chem Int Ed Engl. 2017. 56(15):4342-4346.
- Hilber-Bodmer M et al. Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi. BMC Microbiol. 2017. 17(1):4.