We formulate (mathematic) hypotheses for the experimental research into fungi
The Research Group Systems Biology/Bioinformatics is dedicated to the integrated computational analysis of genome, transcriptome, proteome and metabolome as well as microbiological and clinical data. A central task is the gene expression analysis of fungi producing secondary metabolites as well as of the pathogenic fungi Candida albicans and Aspergillus fumigatus and their interaction with the human immune system by microarray and RNA-Seq data.
The data analysis comprises the management of heterogeneous large-scale experimental data in a data warehouse, pre-processing, discovery of the main features and patterns by data mining techniques and – finally – prediction of experimentally testable hypotheses. Hypotheses of interest concern molecular interactions between host and pathogen, or between transcription factors and their target genes within the host or the pathogen or the fungus that produces an natural product.
The hypotheses have been embedded in predictive mathematical and computational models that represent both prior knowledge available from experts or extracted from biomolecular databases or by text mining in research papers and the pattern found by the computational analysis of experimentally measured data.
We are developing and applying novel bioinformatic tools that identify the structure and parameter values of network models of gene regulation and signaling. In addition, we are developing and applying bioinformatic tools of genome sequence analysis to predict protein coding genes, transcription factor binding sites and secondary metabolite synthesis gene clusters.