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Janusz-M-Bujnicki

Research Focus

Our laboratory is multidisciplinary and comprises three sections, devoted to: development of bioinformatic methods and databases, application of computational tools to study particular macromolecules, and experimental research on protein-nucleic acid interactions. In the past, our group has developed software tools for protein structure prediction, including the GeneSilico meta-server for protein 3D structure prediction, and TOOLKIT, a set of online tools for generation, validation and experimental probing of structural models. On the RNA side, we developed the first database of RNA modification pathways MODOMICS. Currently we are involved in modeling studies on a number of proteins important for splicing regulation, and we are developing new tools for structure prediction of RNA and protein-RNA complexes.

Publications

  1. Palfi, Z., Jaé, N., Preusser, C., Kaminska, K.H., Bujnicki, J.M., Lee, J.H., Günzl, A., Kambach, C., Urlaub, H., Bindereif, A. (2009). SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes and Development 23(14), 1650-64.
  2. Pietal M, Tuszynska I, Bujnicki JM (2007). PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure.. Bioinformatics 23(11), 1429-30.
  3. Bujnicki, J.M. (2006). Protein-structure prediction by recombination of fragments. Chembiochem 7, 19-27.
  4. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H. and Bujnicki, J.M. (2006). MODOMICS: a database of RNA modification pathways. Nucleic Acids Research 34, D145-149.
  5. Kosinski, J., Cymerman, I.A., Feder, M., Kurowski, M.A., Sasin, J.M. and Bujnicki, J.M. (2003). A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53 Suppl 6, 369-379.
  6. Kurowski, M.A. and Bujnicki, J.M. (2003). GeneSilico protein structure prediction meta-server. Nucleic Acids Research 31, 3305-3307.

Key lab techniques: Algorithms for protein and RNA structure prediction, modeling of protein-protein and protein-nucleic acid complexes, protein and RNA biochemistry.

Key lab reagents: Protein and RNA sequences and structures, Python programming language.

Interest in alternative splicing: I am fascinated by the complexity of the spliceosome. Currently there is no single technique with which to determine its detailed structure and dynamics and mechanism of function. I believe structural bioinformatics will be the key approach to integrate the available data for different forms and parts of the spliceosome, to provide useful working models.

Lab contact: Olga Babcka: ola@genesilico.pl

Lab website: http://genesilico.pl