BIOQUANT

Publications

Current publications

Jäger, N., Schlesner, M., Jones, D. T. W., Raffel, S., Mallm, J.-P., Junge, K. M., Weichenhan, D., Bauer, T., Ishaque, N., Kool, M., Northcott, P. A., Korshunov, A., Drews, R. M., Koster, J., Versteeg, R., Richter, J., Hummel, M., Mack, S. C., Taylor, M. D., Witt, H., Swartman, B., Schulte-Bockholt, D., Sultan, M., Yaspo, M.-L., Lehrach, H., Hutter, B., Brors, B., Wolf, S., Plass, C., Siebert, R., Trumpp, A., Rippe, K., Lehmann, I., Lichter, P., Pfister, S. M., Eils, R. (2013). Hypermutation of the inactive X chromosome is a frequent event in cancer. Cell 155, 567-581. doi: 10.1016/j.cell.2013.09.042 | Abstract | Reprint (2.9 MB).

Erdel, F., Müller-Ott, K. & Rippe, K. (2013). Establishing epigenetic domains via chromatin-bound histone modifiers. Ann. N. Y. Acad. Sci. 1305, 29-43. doi: 10.1111/nyas.12262 | Abstract | Reprint (0.8 MB).

Eck, S., Rohr, K., Biesdorf, A., Müller-Ott, K., Rippe, K. & Wörz, S. (2013). A 3D intensity model based on spherical harmonics for automatic 3D segmentation of heterochromatin foci. Proc. IEEE Internat. Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2013), 1484-1487. doi: 10.1109/ISBI.2013.6556815 | Abstract | Reprint (1.3 MB).

Toiber, D., Erdel, F., Silberman, D. M., Zhong, L., Mulligan, P., Bouazoune, K., Sebastian, C., Cosentino, C., Martinez-Pastor, B., Giacosa, S., D'Urso, A., Naar, A., Kingston, R., Rippe, K. & Mostoslavsky, R. (2013). SIRT6 recruits SNF2H to sites of DNA breaks, preventing genomic instability through chromatin remodeling. Mol. Cell 51, 454-468. doi: 10.1016/j.molcel.2013.06.018 | Abstract | Reprint (6.2 MB).

Schöpflin, R., Teif, V. B., Müller, O., Weinberg, C., Rippe, K. & Wedemann, G. (2013). Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics 29, 2380-2386. doi: 10.1093/bioinformatics/btt404 | Abstract | Reprint (1.1 MB).

Walker, S. I., Callahan, B. J., Bhattacharya, T., Caporale, L. H., Grigoryev, S., Rippe, K. & Pellegrini, M. (2013). Evolutionary dynamics and information hierarchies in biological systems. Ann. N. Y. Acad. Sci. 1305, 1-17. doi: 10.1111/nyas.12140 | Abstract | Reprint (0.3 MB).

Eck, S., Wörz, S., Biesdorf, A., Müller-Ott, K., Rippe, K. & Rohr, K.(2013). Segmentation of heterochromatin foci using a 3D spherical harmonics intensity model (2013). In Bildverarbeitung für die Medizin 2013, Meinzer, H.-P., Deserno, T. M., Handels, H., Tolxdorff, T., eds., 308-313. Springer Berlin Heidelberg. doi: 10.1007/978-3-642-36480-8_54 | Abstract | Reprint (0.3 MB).

Hahn, M., Dambacher, S., Dulev, S., Kusnezova, A., Eck, S., Worz, S. , Sadic, D., Schulte, M., Mallm, J.-P., Schermelleh, L., Debs, P., Leonhardt, H., Rohr, K., Rippe, K., Storchova, Z. & Schotta, G. (2013). Chromatin compaction by Suv4-20h2 is essential for cohesion loading in heterochromatin. Genes & Dev. 27, 859-872. doi: 10.1101/gad.210377.112 | Abstract | Reprint (15.9 MB).

Garding, A., Bhattacharya, N., Claus, R., Ruppel, M., Tschuch, C., Filarsky, K., Idler, I., Zucknick, M., Caudron-Herger, M., Oakes, C., Fleig, V., Keklikoglou, I., Allegra, D., Serra, L., Thakurela, S., Tiwari, V.,  Weichenhan, D., Benner, A., Radlwimmer, B., Zentgraf, H., Wiemann, S., Rippe, K., Plass, C., Döhner, H., Lichter, P. Stilgenbauer, S., Mertens, D. (2013). Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the in cis downregulation of a gene cluster that targets NF-kB. PLoS Genetics 9, e1003373. doi: 10.1371/journal.pgen.1003373 | Abstract | Reprint (10.8 MB).

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 62, 26-38. doi: dx.doi.org/10.1016/j.ymeth.2013.03.011| Abstract | Reprint (1.0 MB)

Selected research articles

Erdel, F. & Rippe, K. (2012). Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis. Proc. Natl. Acad. Sci. USA 109, E3221-E3230. doi: 10.1073/pnas.1209579109 | Abstract | Reprint (3.4 MB)

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. doi: 10.1038/nsmb.2419 | Abstract | Reprint (7.4 MB)

Chung, I., Leonhardt, H. & Rippe, K. (2011). De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation. J. Cell Sci. 124, 3603-3618. doi: 10.1242/jcs.084681 | Abstract | Reprint (9.4 MB) | Comment

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. doi: 10.1016/j.bpj.2011.07.057 | Abstract | Reprint (5.8 MB)

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. doi: 10.4161/nucl.2.5.17736 | Abstract | Reprint (4.4 MB) | Comment

Erdel, F., Schubert, T., Marth, C., Längst, G. & Rippe, K. (2010). Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc. Natl. Acad. Sci. USA 107, 19873-19878. Abstract | Reprint (1.4 MB) | Commtent 1 | Comment 2

Müller, K. P., Erdel, F., Caudron, M., Marth, C., Fodor, B. D., Richter, M., Scaranaro, M., Beoudoin, J., Wachsmuth, M. & Rippe, K. (2009). A multi-scale analysis of dynamics and interactions of heterochromatin protein 1 in the nucleus by fluorescence fluctuation microscopy. Biophys. J. 97, 2876-2885. Abstract | Reprint (3.3 MB pdf file)

Jegou, T., Chung, I., Heuvelmann, G., Wachsmuth, M., Görisch, S. M., Greulich-Bode, K., Boukamp, P., Lichter, P. & Rippe, K. (2009). Dynamics of telomeres and promyelocytic leukemia nuclear bodies in a telomerase negative human cell line. Mol Biol Cell 20, 2070-2082. Abstract | Reprint (3.3 MB pdf file).

Kepper, N., Foethke, D., Stehr, R., Wedemann, G. & Rippe, K. (2008). Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation. Biophys. J. 95, 3692–3705. Abstract | Reprint (3.2 MB pdf file)

Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E. & Längst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc. Natl. Acad. Sci. USA 104, 15635-15640. Abstract | Reprint (1.4 MB pdf file) | Comment

Mazurkiewicz, J., Kepert, J. F. & Rippe, K. (2006). On the mechanism of nucleosome assembly by histone chaperone NAP1. J. Biol. Chem. 281, 16462-16472. Abstract | Reprint (2.4 MB pdf file)

Görisch, S. M., Wachsmuth, M., Fejes Tóth, K., Lichter, P. & Rippe, K. (2005). Histone acetylation increases chromatin accessibility. J. Cell Sci. 118, 5825-5834. Abstract | Reprint (0.7 MB pdf file) | Comment

Fejes Tóth, K., Knoch, T. A., Wachsmuth, M., Stöhr, M., Frank-Stöhr, M., Bacher, C. P., Müller, G. & Rippe, K. (2004). Trichostatin A induced histone acetylation causes decondensation of interphase chromatin. J. Cell Sci. 117, 4277-4287. Abstract | Reprint (0.4 MB pdf file)

Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. (2002). Capturing chromatin conformation. Science 295, 1306-1311. Abstract | Reprint (0.6 MB pdf file)***

Rippe, K. (2000). Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy. Biochemistry 39, 2131-2139. Abstract | Reprint (0.1 MB pdf file)

Rippe, K., Guthold, M., von Hippel, P. H. & Bustamante, C. (1997). Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase-sigma 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270, 125-138. Abstract | Reprint (4.6 MB pdf file)*

Rippe, K., Fritsch, V., Westhof, E. & Jovin, T. M. (1992). Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11, 3777-3786. Abstract | Reprint (2.2 MB pdf file)*

Selected reviews

Rippe, K., ed. (2012). Genome organization and function in the cell nucleus, 594 pages, Wiley-VCH, Weinheim. ISBN: 3527326987. Abstract | Comment 1 | Comment 2

Chung, I., Osterwald, S., Deeg, K. & Rippe, K. (2012). PML body meets telomere: The beginning of an ALTernate ending. Nucleus 3, 263-275. doi: 10.4161/nucl.20326 | Abstract | Reprint (2.3 MB)

Caudron-Herger, M. & Rippe, K. (2012). Nuclear architecture by RNA. Curr. Opin. Genet. Dev. 22, 187-197. doi: 10.1016/j.gde.2011.12.005 | Abstract | Reprint (1.9 MB)

Rippe, K. (2001). Making contacts on a nucleic acid polymer. Trends Biochem. Sci., 26, 733-740. Abstract | Reprint (0.1 MB pdf file)*

Rippe, K., von Hippel, P. H. & Langowski, J. (1995). Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20, 500-506. Abstract | Reprint (0.8 MB pdf file)**

* These papers have received more than 100 *, 200 ** or 600 *** citations. All publications h-index Karsten Rippe: 33

 

Research articles in peer reviewed journals 1989-2012 (68 articles)

Reviews and book chapters (peer reviewed) 1990-2012 (23 articles)

Other publications (5 items)

PhD theses (12), diploma/master theses (9) and patents (2)

Get a publication list of Karsten Rippe from Medline

 

 

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