Bioinformatics
In a modern Microbiology lab large amount of data e.g. from genome sequencing and transcriptomics accumulate from various experiments that needs to be directly analyzed in the context of the experiments. Using bioinformatic command line software as well as my own Python scripts and Java software I have the ability to do my own analysis of our data, such as:
- Analysis of genome data and strain comparison
- Analysis of data from functional genomics analysis such as transcriptomics
- Quantifications from image analysis
- Metabolic reconstruction from whole genome data
Additionally pure Bioinformatic projects were done in the lab such as developing a Java database software for comparative genome analysis of apathogenic and pathogenic Clostridia that we applied for analyzing 48 Clostridium difficile genomes and the genomes of several solventogenic Clostridia. Conserved genes and pathogenicity factors were extracted and linked to described phenotypes.
My major current bioinformatic interest is to explore new concepts for a metabolic reconstruction from whole genome data. The existing bioinformatic approaches have the problem that they are mainly based on data structures and concepts from computer science such as simply storing sequence homologies in relational or object oriented databases or modelling metabolism as graphs. The disadvantage of those approaches is that genetic, physiological, biochemical, and energetic concepts are not adequately incorporated and errors and inaccuracies in annotations accumulate. I want to apply combined biological knowledge with modern concepts from computer science to allow analysis of whole genome sequences to reconstruct the metabolism of the respective organism with increasing quality and thereby also improve the raw data of the project.
