Laboratory members:
Josef Pánek, PhD.
Research scientist. He is interested in computational biology of proteins. How properties of the protein sequence derived from the physico-chemical properties of amino acids code for similarities in structures and function of proteins, i.e. for protein families. He developed original computational method for identification of protein families in a set of proteins using hydropathy features.
Also computational biology of genomic sequences. This is aimed at inferring non coding RNAs in Streptomyces. It includes using BLAST and other standard tools of bioinformatics, together with various sources of bioinformatical data.
Jan Bobek, PhD.
Post doc. Focused on studies of gene expression and activity of translational system during cell
differentiation. Together with former supervisor, Dr. Mikulik, published new findings about molecular
mechanisms involved in spore germination and phosphorylation activities of cells during
differentiation. Identified and analyzed proteins expressed during spore germination in
Streptomyces granaticolor. Two new studies about functions of trans-translational system
in differentiating bacteria and its possible role in mechanisms of resistance against antibiotics
interfering with translational system were submitted. Analysed sequences of tmRNAs from four species
of streptomycetes (data deposited in GenBank). Nowadays, pays attention to identification of non-coding
RNAs and their regulatory role during differentiation of streptomycetes.
Since 2011 Jan got a job in the 1. Medical Faculty of the Charles University, Prague. Now he works here part time.
Eva Straková
PhD. student. Studied biophysics at the Charles University in Prague. Now focuses on systems biology of streptomycetes germination and inference of regulatory networks associated with germination.
Alice Ziková, Bc.
Technician. Responsible for all wet lab work. Works with Jan on snRNAs and with Eva on germination.
Former members
Aleš Ulrych
PhD. student of microbiology with experiences in molecular biology methods, microarrays, proteomic and mass spectrometry. His research is focused on the physiology and the molecular genetics of Streptomyces producing secondary metabolites. Currently he works on study of influence of WD-40 domain protein on production of antibiotics.
Aleš moved, currently he is a member of the lab 127 of Pavel Branny.
Tra Thi Vu
PhD student. Works on the neural network model of genetic networks. She focuses on development of algorithms for simulation of genetic networks and methods of reverse engineering of the network structure from experimental data. She developed software tool GenExp (http://proteom.biomed.cas.cz/genexp/) for simulation of arbitrarily defined genetic networks.
Tra finished her thesis in March 2006 and moved back home.
Here thesis can be downloaded here.
Cuong Chieu To
PhD. student. Works on algorithms for data mining of complex proteomic, transcriptomic and metabolic developmental databases. Currently focuses on supervised identification of similar kinetic patterns in proteomic and transcriptomic data using methods of evolutionary computing.
Cuong finished his thesis on October 2006 and is now back home. His thesis can
be downloaded here.
Jana Novotná, PhD.
Senior scientist. Works on the proteomic and biochemical part of the project. Her all-life scientific interests are in physiology and biochemistry of streptomycetes producing secondary metabolites. During last years she has been engaged in the study of stress responses of these and other bacteria using global approaches to microbial adaptation. She leads 2-D gel electrophoresis techniques, optimizes methods of bacterial sample preparation, isoelectric focusing, fluorescent labeling and preparative gels for mass spectrometry.
Jana moved in March 2007 to the Institute of Molecular Genetics, Prague.