Publications
Peer-reviewed Articles
- Tilo Zülske, Aymen Attou, Laurens Groß, David Hörl, Hartmann Harz, Gero Wedemann: Nucleosome spacing controls chromatin spatial structure and accessibility. Biophysical Journal, 2024, Volume 123, Isssue 7, 847-857.
- Aymen Attou, Tilo Zülske, Gero Wedemann: Cohesin and CTCF complexes mediate contacts in
chromatin loops depending on nucleosome positions. Biophysical Journal, 2022, Volume 121, Issue 24, 4788-4799.
- Katharina Brandstetter, Tilo Zülske, Tobias Ragoczy, David Hörl, Miguel Guirao-Ortiz, Clemens Steinek, Toby Barnes, Gabriela Stumberger, Jonathan Schwach, Eric Haugen, Eric Rynes, Philipp Korber, John A. Stamatoyannopoulos, Heinrich Leonhardt, Gero Wedemann, Hartmann Harz: Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophysical Journal, 2022, Vol 121(6), 977-990.
- Bertin Hoffmann, Udo Schumacher, Gero Wedemann: Absence of convection in solid tumors caused by raised interstitial fluid pressure severely limits success of chemotherapy - a numerical study in cancers. Mathematical Biosciences and Engineering, 2020, 17(5): 6128-6148.
- Bertin Hoffmann, Tobias Lange, Vera Labitzky, Kristoffer Riecken, Andreas Wree, Udo Schumacher, Gero Wedemann: The initial engraftment of tumor cells is critical for the future growth pattern: A mathematical study based on simulations and animal experiments. BMC Cancer 20, 524, 2020.
- Michael-Christian Mörl, Tilo Zülske, Robert Schöpflin, Gero Wedemann: Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes. AIMS Biophysics, 6(3), 83–98, 2019
- Thorsten Frenzel, Bertin Hoffmann, Rüdiger Schmitz, Anja Bethge, Udo Schumacher, Gero Wedemann: Radiotherapy and chemotherapy change vessel tree geometry and metastatic spread in a small cell lung cancer xenograft mouse tumor model. PLoS ONE 12(11), e0187144, 2017.
- Bertin Hoffmann, Anja Bethge, Udo Schumacher, Gero Wedemann: Computer Simulation of the Metastatic Progression and Treatment Intervention. Simulation Notes Europe SNE 25(3-4), p. 123-131, 2015.
- 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. VRML-models
- 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.
Posters
- Aymen Attou, Tilo Zülske, Gero Wedemann: The effect of chromatin properties on cohesin mediated loops. 4DGenomics. IFOM, Milan (IT), 09-11.05.2023.
- Tilo Zülske, Aymen Attou, Gero Wedemann: Chromatin in interphase nuclei is more ordered then presumed. 4DGenomics. IFOM, Milan (IT), 09-11.05.2023.
- Aymen Attou, Tilo Zülske, Gero Wedemann: The effect of chromatin properties on cohesin mediated loops. Chromosome Dynamics (GRS), Lucca (IT), 25.-30.06.2023.
- Gero Wedemann, Tilo Zülske, Aymen Attou: Effect of nucleosome density, nucleosome positions and cohesin on the structure of chromatin studied with Monte Carlo simulations.
2023 Annual Biophysical Society Meeting, 17.-22.2.2023.
- Tilo Zülske, Aymen Attou, Gero Wedemann: Enabling computer simulations of chromatin at physiological density with a resolution of individual nucleosomes.
Nuclear architecture & Functions,
Toulouse (France), 28.06.–01.07.2022.
- Aymen Attou, Tilo Zülske, Gero Wedemann: Effects of CTCF and Cohesin complexes on chromatin architecture and genome topology.
Biophysics at the Dawn of Exascale Computers,
Hamburg (Germany), 16.–20.05.2022.
- Tilo Zülske, Aymen Attou, Gero Wedemann: Enabling computer simulations of chromatin at physiological density with a resolution of individual nucleosomes.
Biophysics at the Dawn of Exascale Computers,
Hamburg (Germany), 16.–20.05.2022.
- Bertin Hoffmann, Tobias Lange, Vera Labitzky, Kristoffer Riecken, Andreas Wree, Udo Schumacher, Gero Wedemann: The initial engraftment of tumor cells is critical for the future growth pattern. eSMB 2020 - Society of Mathematical Biology Annual Meeting, virtual meeting, 17.08.-20.08.2020.
- Bertin Hoffmann, Tobias Lange, Vera Labitzky, Kristoffer Riecken, Andreas Wree, Udo Schumacher, Gero Wedemann: The initial engraftment of tumor cells is critical for the future growth pattern. ECMTB 2020 - 12th European Conference on Mathematical and Theoretical Biology, Heidelberg, 31.08.-04.09.2020. conference cancelled due to COVID-19
- Tilo Zülske, Michael Mörl, Robert Schöpflin, Gero Wedemann: Modelling spatial structure of chromatin based on experimental positions of nucleosomes. Multiscale Modeling of Chromatin: Bridging Experiment with Theory, Les Houches, France, 31.03.-05.04.2019.
- Gero Wedemann: Modeling Effects of Nucleosome Positioning in Chromatin. Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes, Santa Cruz, California, 19–24.08.2018.
- 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.
