Scope of Research
Our main objective is to computationally analyse, model, and simulate regulatory processes in the cell, identify and predict function of RNAs, and provide bioinformatics processing of measured data. We develop deterministic and probabilistic models of regulation of gene expression and we use statistics and artificial intelligence for analysis of large scale gene expression data.
We also computationally predict new ncRNAs and identify their function using structure similarity to already functionally characterized ncRNAs, employing the fact that function of biological molecules depends on their structure. In collaboration with Lab. of regulation of gene expression and Lab. of RNA biology at IMG of the ASCR we predict function of mRNA, rRNA and snRNAs in eukaryotic gene expression.
The lab is divided into two parts – computational and a wet lab, which in collaboration with the laboratories of Microbial Genetics and Gene Expression and Dr. J. Bobek, (1st Medical fckulty, Charles University, Prague) , prepares most of the data processed in the lab.
For storage of large scale proteomics data we have established a database and a proteomics server SWICZ (originally with Biozentrum, Univ. Basel) . The server hosts the databases for streptomycetes, meningococus and caulobacter species, and is equipped with graphical interface and search engines which allow retrieving relevant information. The databases are linked with other data sources as GeneBank, and KEGG metabolic pathway servers. Laboratory runs two servers for analysis of RNA secondary structures cpPredictor and rPredictor. We also provide tools for simulation of kinetics of genetic networks, package GenExpi running under Cytoscape environment, as an R package, and at command line.
The laboratory is involved in the large European infrastructural projects ESFRI, ERIC, namely ELIXIR-CZ, a member of the Large European infrastructure ELIXIR – European Life Science Infrastructure for Biological Information, and C4SYS, the Czech node of ISBE – Infrastructure for Systems Biology Europe, where J. Vohradsky is the member of the board of both infrastructures.
The lab was a member of the consortium ActinoGEN of the EU 6th framework program.