System Biological Determination of the Epigenomic Structure – Function Relation

– EpiGenSys –

Publications

 

Research articles

Pham, T.-H., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Längst, G., Benner, C. & Rehli, M. (2013). Mechanisms of in-vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. in press.

Larkin, J. D., Papantonis, A., & Cook, P. R. (2013). Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J. Cell Sci. published online 26 Feb 2013.

Larkin, J. D., Papantonis, A., Cook, P. R., & Marenduzzo, D. (2013). Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res. 41, 2216-2227.

Teif, V. B., Erdel, F., Beshnova, D. A., Vainshtein, Y., Mallm, J. P. & Rippe, K. (2013). Taking into account nucleosomes for predicting gene expression. Methods, published online 23 March 2013

Papantonis. A., Kohro, T., Baboo, S., Larkin, J., Deng, B., Short, P., Tsutsumi, T., Taylor, S., Kanki, Y., Kobayashi, M., Li, G., Poh, H.-M., Ruan, X., Aburatani, H., Ruan, Y., Kodama, T., Wada, Y., & Cook, P.R. (2012). TNFa signals through specialized factories where responsive coding and micro-RNA genes are transcribed.  EMBO J. 31, 4404-4414.

Teif, V. B., Vainshtein, Y., Caudron-Herger, M., Mallm, J.-P., Marth, C., Höfer, T. & Rippe, K. (2012). Genome-wide nucleosome positioning during embryonic stem cell development. Nat. Struct. Mol. Biol. 19, 1185-1191.

Larkin, J. D., Cook, P. R., & Papantonis, A. (2012). Dynamic reconfiguration of long human genes during one transcription cycle. Mol. Cell. Biol. 32, 2738-2747.

Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R., & Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 5, 1.

Ettig, R., Kepper, N., Stehr, R., Wedemann, G. & Rippe, K. (2011). Dissecting DNA-histone interactions by molecular dynamics simulations of unwrapping DNA from the nucleosome, Biophys. J. 101, 1999-2008.

Caudron-Herger, M., Müller-Ott, K., Mallm, J.-P., Marth, C., Schmidt, U., Fejes-Tóth, K. & Rippe, K. (2011). Coding RNAs with a non-coding function: maintenance of open chromatin structure, Nucleus 2, 410-424.

Felle, M., Hofmeister, H., Rothammer, J., Fuchs, A., Exler, J. & Längst, G. (2011). Nucleosomes protect DNA from DNA methylation in vivo and in vitro. Nucleic Acids Res. 39, 6956-6969.

Melnik, S., Deng, B., Papantonis, A., Babbo, S., Carr, I.M. & Cook, P.R. (2011). The proteomes of transcription factories containing polymerases I, II, or III. Nat. Methods 25, 963-968.

Teif, V. & Rippe, K. (2011). Nucleosome mediated cross-talk between transcription factors, Phys. Biol. 8, 044001.

Kepper, N., Ettig, R., Stehr, R., Wedemann, G. & Rippe, K. (2011). Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations. Biopolymers 95, 435-447.

Skrowny, D., Dickmann, F., Löhnhardt, B., Knoch, T. A. & Sax, U. (2010). Development of an information platform for new grid users in the biomedical field. Stud. Health Techno. Inform. 159, 277-282.

Kepper, N., Ettig, R., Dickmann, F., Stehr, R., Grosveld, F. G., Wedemann, G. & Knoch, T. A. (2010). Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency. Stud. Health Techno. Inform. 159, 264-271.

Kepper, N., Schmitt, E., Lesnussa, M., Weiland, Y., Eussen, H. B., Grosveld, F. G., Hausmann, M. & Knoch, T. A. (2010). Visualization, analysis, and design of COMBO-FISH probes in the grid-based GLOBE 3D genome platform. Stud. Health Techno. Inform. 159, 159-171.

 

Reviews

Papantonis, A., & Cook, P. R. (2013). Transcription factories. Chem. Rev. published online 18 Apr 2013.

Teif, V. & Rippe, K. (2012). Calculating transcription factor binding maps for chromatin. Briefings Bioinf. 13, 187-201.

Rippe, K., Stehr, R. & Wedemann, G. (2012). Monte Carlo simulations of nucleosome chains to identify factors that control DNA compaction and access. In Innovations in Biomolecular Modeling and Simulation, Schlick, T., ed., pp. 198-235, RSC Publishing, Cambridge.

Papantonis, A. & Cook, P.R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription, 2, 41-44.