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Journal Biologia[IF: 0.696]
Biologia
Laboratory of BioinformaticsKlucar_2014.jpg
Dr. Lubos Klucar
head of laboratory

The Laboratory of Bioinformatics mostly focuses on building and maintaining new and unique biological databases. It maintains phiSITE, a database holding data on regulation of gene expression and general genomics of bacteriophages. Its integrated visualisation tool phiGENOME is optimised for visualising phage genomes, especially their gene regulatory elements. phiBIOTICS is phage-related database which collects information on representative enzybiotics and relevant research studies on their practical application in the field of phage therapy. The accompanying tool phiBiScan can reliably predict potential new enzybiotics based on their primary structure. viruSITE is a unique viral database which was developed to bring together high-value information on viruses compiled from various sources. The Laboiratory also touches the field of theoretical biology. A mathematical model simulating the interaction between bacteriophages and their bacterial hosts was developed based on other known models describing these types of interactions, but enhanced by the ability to model the system when influenced by environmental factors such as pH and temperature.

The lab also cooperates with a number of other research groups in Slovakia, mainly using its skills in DNA arrays and NGS data analysis. These include the study of the silkworm Bombyx mori neuroendocrine system (collaboration with the Insititute of Zoology SAS) and cancer research (collaboration with the Institute of Virology SAS, the Institute of Experimental Oncology SAS, and the National Institute of Oncology and Jessenius Faculty of Medicine in Martin). The group uses its broad knowledge of advanced analysis pipelines together with its available computing infrastructure to interpret the large data sets produced by these cutting edge technologies. In addition, the group is also involved in extensive international collaborations (running the national EMBnet node, participating in the preliminary phase of the ELIXIR consortium foundation, and participating in the COST SeqAhead project), teaching activities at Comenius University, and training Ph.D. students and young scientists (e.g. the DNA arrays and NGS data analysis workshop organised in 2015).

Staff
Research fellows:
     Klucar_2014.jpgDr. Lubos Klucar
     Stano_2014.jpgDr. Matej Stano
PhD students:
     Matus Hajduk
     gabor_2.jpgGabor Beke
     Zizkovicova.jpgPatricia Žizkovicova
Undergraduate students:
     Jana_Terenova.jpgJana Terenova
International scientific co-operation
  1. CNR, Institute for Biomedical Technologies, Bari, Italy
  2. Sweden Biomedical Centre, Uppsala, Sweeden
Scientific projects
  • Web atlas of neuroendocrine system in insect.
    (VEGA 2/0164/15, Jan 2015 - Dec 2017)
    Principal investigator: Matej Stano
Selected Publications
  1. Beke, G., Stano, M., Klucar, L.
    Modelling the interaction between bacteriophages and their bacterial hosts.
    (2016) Math. Biosci. 279: 27-32.
  2. Hojckova, K., Stano, M., Klucar, L.
    phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications.
    (2013) BMC Microbiol. 13: 53-.
  3. Stano, M., Klucar, L.
    phiGENOME: An integrative navigation throughout bacteriophage genomes .
    (2011) Genomics 98(5): 376-380.
  4. Klucar, L., Stano, M., Hajduk, M.
    phiSITE: database of gene regulation in bacteriophages.
    (2010) Nucleic Acids Res. 38(Database issue): D366-D370.
  5. D'Elia, D., Gisel, A., Eriksson, N.E., Kossida, S., Mattila, K., Klucar, L., Bongcam-Rudloff, E.
    The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community.
    (2009) BMC Bioinformatics 10(Suppl 6): S1-.
  6. Bukovska, G., Klucar, L., Vlcek, C., Adamovic, J., Turna, J., Timko, J.
    Complete nucleotide sequence and genome analysis of bacteriophage BFK20 - A lytic phage of the industrial producer Brevibacterium flavum.
    (2006) Virology 348(1): 57-71.
  7. Kormutakova, R., Klucar, L., Turna, J.
    DNA sequence analysis of the tellurite-resistance determinant from clinical strain of Escherichia coli and identification of essential genes.
    (2000) Biometals 13(2): 135-139.