Name:
Sikosek, Tobias
Status: Postdoc
Email: t.sikosek@uni-muenster.de
Tel.: +49-(0)251-83-21086
Room: 205
http://www.researchgate.net/profile/Tobias_Sikosek
Current research interests ( also see research page )
Current research interests ( also see research page )
- evolution of protein structure and function
- evolution by gene duplication (neo-/subfunctionalisation)
- evolutionary computer simulations, lattice proteins
- protein stability/disorder/folding
- structural bioinformatics
- catalytic promiscuity and experimental evolution of enzymes
- evolution of miRNAs
Curriculum
- 2000-2006: studies in biology, philosophy and computer sciences at the University of Muenster; focus on practical and theoretical evolutionary biology, molecular cell biology, and bioinformatics.
- 2004-2005: study abroad year at the University of Auckland, New Zealand ; courses in microbiology, immunology, biochemistry, and ecology.
- 2006-2007: Diplom (MSc equivalent) thesis "The evolution of heterodimerising transcription factor networks." in the group of Evolutionary Bioinformatics in Muenster under the supervision of Amelie Veron and Erich Bornberg-Bauer.
- June 2010: research stay in Prof Hue Sun Chan's lab, University of Toronto
- 2008 - 2012: PhD project "The resolution of adaptive conflicts in protein evolution through shifts in thermodynamic stability and gene duplication"
- April 2012 -- March 2013: working with Juliette de Meaux at the IEB in Münster on miRNA in plants
Conferences and workshops attended
- 2008: Meeting of the Society for Molecular Biology and Evolution (SMBE), Barcelona, Spain
- 2009: Physical Principles of Protein Behavior in the Cell, Dresden, Germany
- list of participants (PDF)
- poster contribution: "Resolving adaptive conflicts by promiscuity and gene duplication "
- 2011: CamProEng - Protein evolution and engineering, Cambridge, UK
- talk: "Resolving adaptive conflicts by promiscuity and gene duplication"
- April 2012:Theoretical and Empirical Advances in Evolutionary Genomics, Roscoff, France
- poster contribution
- June 2012: Münster Graduate School in Evolution (MGSE) symposium, Münster, Gemany
- talk
- June 2012: Meeting of the Society for Molecular Biology and Evolution (SMBE), Dublin, Ireland
- talk
- July 2012: The Emerging Dynamic View of Proteins (DYPROT12), Dresden, Germany
- talk
- July 2012: Summer School on Protein Evolution, Fraunchiemsee, Germany
- workshop
- July 2012: Workshop on Protein Evolution, Munich, Germany
- talk
Technical skills:
- Programming: Java, Python, Linux bash
- Structural Bioinformatics: FoldX, Rosetta, PyMol, Chimera, PDB, CATH, python scripting
- Bioinformatics: BLAST, sequence alignment, database search, phylogeny
- Visualization/Illustration: Inkscape, Cinema 4D, Matplotlib (Python), Mayavi (Python), Prefuse (Java)
- Wetlab: basic molecular biology
Teaching/course co-ordination
- 2006-2010: teaching practicals "Bioinformatics 2 - sequence analysis" (since 2008 also course co-ordination); contents: sequence alignments, phylogenies, protein structure prediction
- 2009: project design and co-supervision of BSc thesis: "Testing a single-copy plasmid system for
Protein Evolution Experiments" by Dieter Weber - Jan 2010: BSc course "Modern Methods in Evolutiona
ry Biology" - lecture entitled: "Structural evolution and subfunctionalisation of proteins" - Dec 2010: MSc research project "A mutational path connecting two proteins"
- Feb 2011: BSc advanced project "Characterisation of the mutational energy landscape for the structural switch in Arc repressor"
Publications
- T. Sikosek, E. Bornberg-Bauer, and H.S. Chan
Evolutionary dynamics on bi-stability landscapes can potentially resolve adaptive conflicts.
PLoS Comput Biol (2012), 8(9): e1002659.
- T. Sikosek, H.S. Chan, and E. Bornberg-Bauer
Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness.
Proc Nat Acad Sci U S A (2012), 109(37):14888-14893.
- E. Bornberg-Bauer, A.-K. Huylmans, and T. Sikosek
How do new proteins arise?
Curr Opin Struct Biol (2010) 20(3):390-39.
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