Laboratory of Bioinformatics and Protein Engineering

El Capo: Bioinformatics: Postdoctoral Researchers: Ph.D. students: Research Assistants: Undergraduate students: Molecular Biology: Research Coordinator: Ph.D. students: Undergraduate students: Office management: Computer administration: Alumni, former members, former students, visitors etc.:

Janusz M. Bujnicki (PhD, DHabil bioinformatics) Michal Boniecki (PhD chemistry) Marcin Pawlowski (PhD bioinformatics) Ewa Wywial (PhD bioinformatics) Katarzyna H. Kaminska (MSc bioinformatics) Iga Korneta (MSc cell biology) Lukasz Kozlowski (MSc genetics) Jerzy Orlowski (MSc bioinformatics) Michal Pietal (MSc mathematics) Wojciech Potrzebowski (MSc biophysics) Irina Tuszynska (MSc chemistry) Pawel Lukasz (MSc bioinformatics) Magdalena Mika Tomasz Stepniewski Krzysztof J. Skowronek (PhD microbiology) Elzbieta Purta (MSc biochemistry) Katarzyna Filip (MSc molecular biology) Agata Kamaszewska (MSc molecular biology) Maria Werner (MSc biotechnology) Dariusz Pianka (MSc biotechnology) Wojciech Siwek (MSc microbiology) Malgorzata Durawa (MSc molecular biology) Natalia Borkowska Agnieszka Faliszewska (MSc biology) Jan Kogut (BSc computer science) Tomasz Jarzynka Lukasz Munio (help-desk)   Janusz Debski (MSc bioinformatics 2003) Tomasz Jurkowski (MSc molecular biology/bioinformatics 2004) Laura Lopez Munoz (MSc bioinformatics 2007) Stanislaw Dunin-Horkawicz (MSc molecular evolution 2007) Pawel Sztromwasser (MSc bioinformatics 2007) Agnieszka Zylicz-Stachula (PhD biochemistry 2007) Agnieszka Chmiel (PhD biochemistry 2007) Malgorzata Figiel (research assistant 2007) Iwona A. Cymerman (PhD biochemistry 2008) Agata Parysz (MSc chemistry 2008) Krzysztof Nawara (MSc chemistry 2008) Michal Gajda (PhD bioinformatics 2009) Joanna M. Sasin-Kurowska (PhD bioinformatics 2009) Konrad Tomala (MSc biotechnology 2009) Kristian Rother (postdoc, 2006-2009) Jan Kosinski (PhD bioinformatics 2009) Agnieszka Obarska-Kosinska (PhD bioinformatics 2010)

Projects:

• - Development of tools for protein structure prediction. We develop software for protein structure prediction from sequence. The pipeline of methods developed in our laboratory, which includes the fold recognition metaserver, modeling tools, and model quality assessment tools is available via the GeneSilico TOOLKIT.

  - Development of tools for modeling and analysis of RNA and RNP 3D structures. We develop software for both comparative and de novo modeling of RNA and for prediction of RNA-ligand interactions. Our "flagship" method is ModeRNA, software for comparative modeling of RNA 3D structures.

  - Development of databases of nucleic acid metabolism. First, we developed and maintain the MODOMICS database of systems biology of posttrascriptional RNA modification. Currently, we are developing databases of DNA repair pathways, and RNA processing pathways.

  - RNA modification enzymes. We predict (using bioinformatics) and characterize experimentally novel RNA modification enzymes, in particular RNA methyltransferases.

  - Nucleases. We predict (using bioinformatics) and characterize experimentally novel RNAses and DNases, and we use protein engineering techniques to obtain enzymes with new functions, e.g. restriction enzymes with new substrate speificities.

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