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Nina M. Fischer
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Nina M. Fischer

Eberhard Karls University Tübingen
Dept. of Computer Science
Center for Bioinformatics Tübingen
Applied Bioinformatics
Room C323, Sand 14, D-72076 Tübingen

Work: +49-7071-29-70462

Biography:

  • Since 2007 PhD student in Oliver Kohlbacher's group (Applied Bioinformatics), Dept. of Computer Science, Eberhard Karls University Tübingen, Germany.
  • October - December 2006 Visitor in Boris Lenhard' group at CBU, which is part of the Bergen Center for Computational Science at the University of Bergen, Norway.
  • 2006 Diploma Thesis - Structure-based prediction of transcription factor-DNA binding free energies using MM/GBSA - in Oliver Kohlbacher's group.
  • 2003-2006 Eberhard Karls University Tübingen, Computational Biology (Diploma in Computer Science / Computational Biology).
  • 2002-2003 Western Michigan University, Kalamazoo, USA, Computer Science/Biochemistry.
  • 2000-2002 Eberhard Karls University Tübingen, Computational Biology.
  • In 2000 High school graduation.


Research Interests:

  • Protein-DNA complexes: Structural modeling of protein-DNA complexes for exploring protein-DNA interactions at the binding interface using molecular dynamics (MD) simulations.

  • Flexible proteins and protein-ligand complexes: Studying protein-ligand interactions using flexible receptor docking and clustering approaches as well as molecular dynamics (MD) simulations and PCA.


Selected Publications and Posters:

  • Fischer, N.M., Kohlbacher, O., The Analysis of Cis-elements: Current developments, knowledge and application to gene networking, Chapter 13: Structural insights into physical interactions of transcription factor-DNA complexes at an atomic level. (submitted in 2011) [e-book chapter]

  • Wanke, D., Brand, L.H., Fischer, N.M., Peschke, F., Kilian, J., and Berendzen K.W., Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding. In: WSPC – Proceedings (submitted in 2011) [book chapter]

  • Fischer, N.M., Wanke, D., Kohlbacher, O., Shedding light on transcription factor binding sites using MD. Hünfeld 2009 Workshop on Computer Simulation and Theory of Macromolecules [poster]

  • Fischer, N.M., Schneider, W.M, Kohlbacher, O., Rescoring of docking poses using force field based methods. J Cheminform. 2010; 2(Suppl 1):P52, published online May 2010. GCC 2009 [poster]

  • Fischer, N.M., Höglund A., Kohlbacher, O., Structure-based prediction of transcription factor-DNA binding free energies using MM/GBSA. ISMB/ECCB 2007 [poster]