Competence Center Bioinformatics

Publications

Papers

Bertin Hoffmann, Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression and Treatment Intervention. Simulation Notes Europe SNE 25(3-4), 2015, 123-131.

Anja Bethge, Udo Schumacher, Gero Wedemann: Simulation of Metastatic Progression Using a Computer Model Including Chemotherapy and Radiation Therapy. Journal of Biomedical Informatics, 57, p. 74–87, 2015.

Vladimir Teif, Nick Kepper, Gero Wedemann, Karsten Rippe: Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. Journal of Physics: Condensed Matter 27, 064110, 2015.

Sarah Diermeier,Petros Kolovos,Leonhard Heizinger, Uwe Schwartz, Theodore Georgomanolis, Anne Zirkel, Gero Wedemann, Frank Grosveld, Tobias A Knoch, Rainer Merkl, Peter R Cook, Gernot Längst and Argyris Papantonis: TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biology, 15:536, 2014.

Tobias Brodbeck, Nina Nehmann, Anja Bethge, Gero Wedemann, Udo Schumacher: Perforin-dependent direct cytotoxicity in Natural killer cells induces considerable knockdown of spontaneous lung metastases and computer modelling-proven tumor cell dormancy in a HT29 human colon cancer xenograft mouse model. Molecular Cancer, 13:244, 2014.

Oliver Müller, Nick Kepper, Robert Schöpflin, Ramona Ettig, Karsten Rippe, Gero Wedemann: Changing chromatin fiber conformation by nucleosome repositioning. Biophysical Journal, 107 (9), 2141-2150, 2014.

Robert Schöpflin, Vladimir B. Teif, Oliver Müller, Christin Weinberg, Karsten Rippe, Gero Wedemann: Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics 29 (19), 2380-2386, 2013.

Robert Schöpflin, Hergen Brutzer, Oliver Müller, Ralf Seidel, Gero Wedemann: Probing the Elasticity of DNA on Short Length Scales by Modeling Supercoiling under Tension. Biophys. J., 103(2), 323-330, 2012.

Anja Bethge, Udo Schumacher, Andreas Wree, Gero Wedemann: Are Metastases from Metastases Clinically Relevant? Computer Modelling of Cancer Spread in a Case of Hepatocellular Carcinoma. PLoS ONE 7(4), e35689, 2012.

Ramona Ettig, Nick Kepper, René Stehr, Gero Wedemann, Karsten Rippe: Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping. Biophys. J., 101(8), 1999-2008, 2011.

Nick Kepper, Ramona Ettig, René Stehr, Sven Marnach, Gero Wedemann, Karsten Rippe: Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations. Biopolymers, 95 (7), 435-447, 2011.

Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Gero Wedemann, Aleksei Aksimentiev, Ralf Seidel: DNA-DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density. Phys. Rev. Lett. 105(15), 158101, 2010.

René Stehr, Robert Schöpflin, Ramona Ettig, Nick Kepper, Karsten Rippe, Gero Wedemann: Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams. Biophys. J., 98(6), 1028-1037, 2010.

Norbert Busch, Gero Wedemann. Modeling genomic data with type attributes, balancing stability and maintainability. BMC Bioinformatics, 10:97, 2009.

René Stehr, Nick Kepper, Karsten Rippe, Gero Wedemann. The effect of the internucleosomal interaction on the folding of the chromatin fiber. Biophys. J., 95(8), 3677-3691, 2008.

Nick Kepper, Dietrich Foethke, René Stehr, Gero Wedemann, Karsten Rippe. Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation. Biophys. J. 95(8), 3692-3705, 2008.

Chapters in Books

Bertin Hoffmann, Thorsten Frenzel, Rüdiger Schmitz, Udo Schumacher, Gero Wedemann: Modelling growth of tumours and its spreading behaviour using mathematical functions. In Cancer Bioinformatics, Methods in Molecular, Springer, in press.

Wedemann, Gero, Anja Bethge, Volker Haustein, und Udo Schumacher: "Computer Simulation of the Metastatic Progression". In Metastasis Research Protocols, 2nd Edition. Methods in Molecular Biology 1070, p. 107-116. Springer, New York, 2014.

Karsten Rippe, René Stehr, Gero Wedemann: Monte Carlo simulations of nucleosome chains to identify factors that control DNA compaction and access. In Innovations in Biomolecular Modeling and Simulation ed. T. Schlick, Vol. 2, 198-235, RSC Publishing, Cambridge, 2012.

Papers in Conference Proceedings

Gero Wedemann: Requirements Engineering an der Hochschule in einer Blockwoche – Best Practices und Lessons Learned. INFORMATIK 2015. 45. Jahrestagung der Gesellschaft für Informatik. September, 28 - October 2, 2015. Cottbus, Germany, Lecture Notes in Informatics (LNI) - Proceedings, Gesellschaft für Informatik, Volume P-246, p. 621-622.

Bertin Hoffmann, Anja Bethge, Udo Schumacher, Gero Wedemann: Computer-Simulation der Ausbreitung von Metastasen und ihrer Behandlung. Workshop der ASIM/GI-Fachgruppen Simulation technischer Systeme, Grundlagen und Methoden in Modellbildung und Simulation. June 18-19, 2015. Stralsund, Germany. Argesim Report AR 50, ARGE Simulation News, p. 5-14.

Gero Wedemann: Scrum Essentials in der Lehre. INFORMATIK 2013. 43. Jahrestagung der Gesellschaft für Informatik. September 16-20, 2013. Koblenz, Germany, Lecture Notes in Informatics (LNI) - Proceedings, Gesellschaft für Informatik, Volume P-220, p. 240-241.

Peer-reviewed Books

Gero Wedemann: Grundlagen der Softwaretechnik und Requirements Engineering. Zentralstelle für Fernstudien an Fachhochschulen, Koblenz, 2009. Table of contents.

Gero Wedemann: Objektorientierte Analyse und Entwurf. Zentralstelle für Fernstudien an Fachhochschulen, Koblenz, 2009. Table of contents.

Gero Wedemann: Softwarequalitätssicherung. Zentralstelle für Fernstudien an Fachhochschulen, Koblenz, 2009. Table of contents.

Popular Science Articles

Karsten Rippe, Gero Wedemann: Das Nukleosom – Zugangskontrolle zum Genom? systembiologie.de, 8, 67-71, 2014

Gero Wedemann. Simulation: Auf der Suche nach der Struktur: Modellierung von Chromatin. Laborpraxis 07/08, 20, 2007.

Talks

Gero Wedemann: Effects of changes of nucleosome positioning and internucleosomal interactions on small and large chromatin chains. Minisymposium "The interplay of chromatin conformation and function" at ECMTB/SMB 2016, Nottingham, UK, 11.-15.07.2016.

Robert Schöpflin, Oliver Müller, Vladimir Teif, Karsten Rippe, Gero Wedemann: Modeling effects of nucleosome positioning in short and long chromatin fibers. GenPhysChrom - Integrating genomics with hierarchical physical models of DNA and chromosomes, Lyon, 25.06.2015

Anja Bethge, Bertin Hoffmann, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression and Treatment Interventions. Workshop of the ASIM/GI-Team, Stralsund, 18.06.2015

Robert Schöpflin, Oliver Müller, Vladimir B. Teif, Karsten Rippe, Gero Wedemann: Modeling effects of nucleosome positioning in short and long chromatin fibers. The 4D Nucleome 2014, Hiroshima, Japan, 17.-20.12.2014.

Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression and Treatment Interventions. 9th European Conference on Mathematical and Theoretical Biology, Gothenburg, Sweden, 17.06.2014.

Robert Schöpflin, Oliver Müller, Christin Weinberg, Vladimir B. Teif, Karsten Rippe, Gero Wedemann: Effects of nucleosome positioning on condensation of short and long chromatin fibers. DPG conference, Dresden, 03.04.2014. Verhandl. DPG (VI) 49, 4/2014, p. 139.

Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression and Treatment Interventions. DPG conference, Dresden, 02.04.2014. Verhandl. DPG (VI) 49, 4/2014, p. 109.

Gero Wedemann: Scrum Essentials in der Lehre. Studentische AusbildunG und berufliche Weiterbildung in Agiler Softwareentwicklung, GI-Jahrestagung INFORMATIK 2013, Koblenz, 19.09.2013.

Gero Wedemann, Robert Schöpflin, Vladimir B. Teif, Oliver Müller, Christin Weinberg, Karsten Rippe: Modeling Chromatin with Monte Carlo Simulations - From the Test-Tube to the Nucleus. 6. Monte Carlo Workshop, Heidelberg, 12./13.04.2013.

Oliver Müller, Robert Schöpflin, Nick Kepper, Ramona Ettig, Karsten Rippe, Gero Wedemann: Computer simulation of chromatin: Effects of nucleosome positioning on chromatin structure. DPG conference, Berlin, 29.04.2012. Verhandl. DPG (VI) 47, 4/2012, p. 95.

Robert Schöpflin, Hergen Brutzer, Oliver Müller, Ralf Seidel, Gero Wedemann: Probing the elasticity of DNA on short length scales by modeling supercoiled DNA under tension. DPG conference, Dresden, 14.03.2011. Verhandl. DPG (VI) 46, 1/2011, p. 229.

Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Cascade. Dresden, International Society for Cellular Oncology Meeting, 19.03.2010. Cellular Oncology, 32(3), p. 188, 2010.

Robert Schöpflin, Hergen Brutzer, René Stehr, Ralf Seidel, Gero Wedemann. Integrative investigation of DNA supercoiling under tension. DPG conference, Regensburg, 22.03.2010. Verhandl. DPG (VI) 45, 3/2010, p. 69.

René Stehr, Robert Schöpflin, Nick Kepper, Ramona Ettig, Karsten Rippe, Gero Wedemann. Computer simulations of chromatin fibers. VolkswagenStiftung Statussymposium 2009, Mainz, 22.09.2009.

René Stehr, Nick Kepper, Ramona Ettig, Karsten Rippe, Gero Wedemann. The Investigation of the three-dimensional structure of chromatin. DPG conference, Dresden, 26.03.2009. Verhandl. DPG (VI) 44, 5/2009, p. 54.

René Stehr, Robert Schöpflin, Nick Kepper, Ramona Ettig, Karsten Rippe, Gero Wedemann. Dynamic numerical phase diagrams of chromatin. Biophysics of Chromatin Workshop, EML, Heidelberg, 06.02.2009.

René Stehr, Nick Kepper, Karsten Rippe, Gero Wedemann. The Influence of internucleosomal interaction and local structure on the geometry of large chromatin fibers. DPG conference, Regensburg, 26.03.2007. Verhandl. DPG (VI) 42, 4/2007, p. 78.

Nick Kepper, René Stehr, Evrim Ilden, Dietrich Foethke, Gero Wedemann, Karsten Rippe. Monte Carlo simulations of chromatin fibers I: Effect of local nucleosome geometry. Workshop on computer simulations of soft matter and biosystems, 14.03.2007, Bioquant, Heidelberg.

René Stehr, Nick Kepper, Karsten Rippe, Gero Wedemann. Monte Carlo simulations of chromatin fibers II: effects of interactions between nucleosomes. Workshop on computer simulations of soft matter and biosystems, 14.03.2007, Bioquant, Heidelberg.

Posters

Bertin Hoffmann, Thorsten Frenzel, Rüdiger Schmitz, Udo Schumacher, Gero Wedemann: Analysis of primary tumour growth and metastasis formation of human small cell lung cancer cells xenografted into immunodeficient mice using computer simulation. ECMTB/SMB 2016, Nottingham, UK, 11.-15.07.2016.

Gero Wedemann: Requirements Engineering an der Hochschule in einer Blockwoche - Best Practices und Lessons Learned. GI-Jahrestagung INFORMATIK 2015, Cottbus, Germany, October 1, 2015.

Robert Schöpflin, Oliver Müller, Christin Weinberg, Vladimir B. Teif, Karsten Rippe, Gero Wedemann: Modeling effects of nucleosome positioning in short and long chromatin fibers. Biophysical Society 58th Annual Meeting, San Francisco, February 15 - 19, 2014.

Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression. 17th International AEK Cancer Congress, Heidelberg, 20.-22.03.2013.

Robert Schöpflin, Vladimir B. Teif, Oliver Müller, Christin Weinberg, Karsten Rippe, Gero Wedemann: Modeling Long Chromatin Fibers based on In-Vivo Nucleosome Positioning Maps. Biophysical Society 57th Annual Meeting, Philadelphia, February 2-6, 2013.

Robert Schöpflin, Hergen Brutzer, Oliver Müller, Ralf Seidel, Gero Wedemann: Testing models for DNA elasticity on short length scales by simulating DNA supercoiling under tension. Biophysical Society 56th Annual Meeting, San Diego, California, February 25-29, 2012.

Oliver Müller, Nick Kepper, Robert Schöpflin, Ramona Ettig, Karsten Rippe, Gero Wedemann: Computer simulation of chromatin: Interdependency between nucleosome positions and chromatin structure. Biophysical Society 56th Annual Meeting, San Diego, California, February 25-29, 2012.

Gero Wedemann, Robert Schöpflin, Oliver Müller, Nick Kepper, Karsten Rippe: Computer simulation of chromatin: Modeling the influence of global and local modifications. EMBO Conference Series on Nuclear Structure and Dynamics, 9/2011, L'Isle sur la Sorgue, France.

Robert Schöpflin, Hergen Brutzer, Nicholas Luzzietti, Oliver Müller, Ralf Seidel, Gero Wedemann: Simulations of DNA and chromatin under tension and twist. EMBO Conference Series on Nuclear Structure and Dynamics, 9/2011, L'Isle sur la Sorgue, France.

Gero Wedemann, René Stehr, Robert Schöpflin, Oliver Müller, Nick Kepper, Ramona Ettig, Karsten Rippe: Computer Simulation of Chromatin: Modeling the Influence of Global and Local Modifications. Biophysical Society - Dynamic DNA Packaging Across Kingdoms: Chromatin & Beyond. Asilomar, Pacific Grove, CA, 05.-08.07.2011.

Anja Bethge, Udo Schumacher, Gero Wedemann: Are metastases from metastases clinically relevant? A novel computer model helps understanding the metastatic progression. 8th European Conference on Mathematical and Theoretical Biology, and Annual Meeting of The Society for Mathematical Biology, Kraków, 28.06.-02.07.2011.

Oliver Müller, René Stehr, Robert Schöpflin, Ramona Ettig, Nick Kepper, Karsten Rippe, Gero Wedemann: Computer simulation of chromatin: Modeling the influence of nucleosome repositioning. DPG conference, Dresden, 14.03.2011. Verhandl. DPG(VI) 46, 1/2011, p. 231.

Robert Schöpflin, Hergen Brutzer, Rene Stehr, Ralf Seidel, Gero Wedemann: Monte Carlo simulation of supercoiled DNA at buckling transition. Biophysical Society 54th Annual Meeting, San Francisco, California, February 20-24, 2010. Biophysical J. 98(3) pp. 470a.

Hergen Brutzer, Robert Schöpflin, René Stehr, Gero Wedemann, Ralf Seidel: A theoretical description of DNA plectonemes under tension. Biophysical Society 54th Annual Meeting, San Francisco, California, February 20-24, 2010. Biophysical J. 98(3) p. 470a.

René Stehr, Nick Kepper, Ramona Ettig, Karsten Rippe, Gero Wedemann: Computer simulations of chromatin fibers. Biophysical Society 53rd Annual Meeting, Boston, 2009. Biophysical Journal, 96 (3), p. 55a, 2009

Norbert Busch, Gero Wedemann: Towards the End User - A modular platform for the implementation of algorithms. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, 2007.

Norbert Busch, Gero Wedemann: Molecule Computation Kit (MCK), an extensible kit for molecular biologists. German Conference on Bioinformatics (GCB), Tübingen, 2006.

Older Publications

Gero Wedemann, Jörg Langowski. Computer Simulation of the 30-Nanometer Chromatin Fiber. Biophys J 82(6), 2847-2859, 2002.

Jörg Langowski, Carsten Mehring, Markus Hammermann, Konstantin Klenin, Christian Münkel, Katalin Tóth, Gero Wedemann: The genome as a flexible polymer chain: recent results from simulations and experiments. In: Genomics and Proteomics - functional and computational aspects, ed. S. Suhai (2000) Plenum Press, New York, 121-131.

Christian Münkel, Roland Eils, S. Dietzel, D. Zink, Carsten Mehring, Gero Wedemann, Thomas Cremer, Jörg Langowski. Compartmentalization of Interphase Chromosomes Observed in Simulation and Experiment. Journal of Molecular Biology 285 (3), 1053-1065, 1999.

Gero Wedemann, Christian Münkel, Gunther Schöppe, Jörg Langowski. Kinetics of structural changes in superhelical DNA. Phys. Rev. E 58, 3537 - 3546, 1998.

Jörg Langowski, Lutz Ehrlich, Markus Hammermann, Christian Münkel, Gero Wedemann. Polymer dynamics of DNA, chromatin and chromosomes, pp. 57-72, in: Theoretical and computational methods in genome research, ed. S. Suhai, 1997 Plenum Press, New York