Publications 2018

Gao Q, Eck S, Matthias J, Chung I, Engelhardt J, Rippe K & Rohr K (2018). Bayesian joint super-resolution, deconvolution, and denoising of images with Poisson-Gaussian noise. ISBI 2018, in press.

Wollmann T, Ivanova J, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2018). Multi-channel deep transfer learning for nuclei segmentation in glioblastoma cell tissue images. In Bildverarbeitung für die Medizin 2018, Springer Berlin Heidelberg, in press.

Chudasama P, Mughal S, Sanders M, Hübschmann D, Chung I, Deeg KI, Wong SH, Rabe S, Hlevnjak M, Zapatka M, Ernst A, Kleinheinz K, Schlesner M, Sieverling L, Klink B, Schröck E, Hoogenboezem R, Kasper B, Heilig C, Egerer G, Wolf S, von Kalle C, Eils R, Stenzinger A, Weichert W, Glimm H, Gröschel S, Kopp H-G, Omlor G, Lehner B, Bauer S, Schimmack S, Ulrich A, Mechtersheimer G, Rippe K, Brors B, Hutter B, Renner M, Hohenberger P, Scholl C & Fröhling S (2018). Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nat Commun 9, 144. doi: 10.1038/s41467-017-02602-0 | Abstract | Reprint (3.1 MB) | Article metrics

Publications 2017

Rademacher A, Erdel F, Trojanowski J, Schumacher S & Rippe K (2017). Real-time observation of light-controlled transcription in living cells. J Cell Sci 130, 4213-4224. doi: 10.1242/jcs.205534 | Abstract | Reprint (12.9 MB) | JCS First person | Article metrics

Erdel F (2017). How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications. Bioessays 39, 1700053. doi: 10.1002/bies.201700053 | Abstract | Article metrics

Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, RippeK & Längst G (2017). CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 45, 10534-10554. doi: 10.1093/nar/gkx711 | Abstract | Reprint (7.3 MB) | Article metrics

Delacher M, Imbusch CD, Weichenhan D, Breiling A, Hotz-Wagenblatt A, Trager U, Hofer AC, Kagebein D, Wang Q, Frauhammer F, Mallm JP, Bauer K, Herrmann C, Lang PA, Brors B, Plass C & Feuerer M (2017). Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. Nat Immunol 18, 1160-1172. doi: 10.1038/ni.3799 | Abstract | Article metrics

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T & Plass C (2017). DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 49, 1052-106. doi: 10.1038/ng.3889 | Abstract | Reprint (8.7 MB) | Article metrics

Chaturvedi A, Herbst L, Pusch S, Klett L, Goparaju R, Stichel D, Kaulfuss S, Panknin O, Zimmermann K, Toschi L, Neuhaus R, Haegebarth, A, Rehwinkel H, Hess-Stumpp H, Bauser M, Bochtler T, Struys EA, Sharma A, Bakkali A, Geffers R, Araujo-Cruz MM, Thol F, Gabdoulline R, Ganser A, Ho AD, von Deimling A, Rippe K, Heuser M & Kraemer A (2017). Pan-mutant IDH1 inhibitor BAY1436032 is highly effective against human IDH1 mutant acute myeloid leukemia in vivo. Leukemia 31, 2020-2028. doi: 10.1038/leu.2017.46 | Abstract | Reprint (2.2 MB) | Article metrics

Teif VB, Mallm JP, Sharma T, Welch DBM, Rippe K, Eils R, Langowski J, Olins AL & Olins DE (2017). Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus 8, 188-204. doi: 10.1080/19491034.2017.1295201 | Abstract | Reprint (1.8 MB) | Article metrics

Pankert T, Jegou T, Caudron-Herger M & Rippe K (2017). Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 123, 98-101. doi: 10.1016/j.ymeth.2017.01.010 | Abstract | Reprint (4.2 MB) | Article metrics

Vainshtein Y, Rippe K & Teif VB (2017). NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 18, 158. doi: 10.1186/s12864-017-3580-2 | Abstract | Reprint (9.7 MB) | Article metrics.

Molitor J, Mallm JP, Rippe K & Erdel F (2017). Retrieving chromatin patterns from deep sequencing data with correlation functions. Biophys J 112, 473-490. doi: 10.1016/j.bpj.2017.01.001 | Abstract | Reprint (10.3 MB) | Software | Article metrics

Gunkel M, Chung I, Wörz S, Deeg KI, Simon R, Sauter G, Jones DT, Korshunov A, Rohr K, Erfle H & Rippe K (2017). Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Methods 114, 60-73. doi: 10.1016/j.ymeth.2016.09.014 | Abstract | Reprint (7.3 MB) | Article metrics

Current preprints

Sieverling L, Chen Hong, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortes-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Rippe K, Jones DTW, Brors B & Feuerbach L (2017). Genomic footprints of activated telomere maintenance mechanisms in cancer. biorxiv 157560. doi: 10.1101/157560

Braun DM, Chung I, Kepper N & Rippe K (2017). TelNet - a database for human and yeast genes involved in telomere maintenance. biorxiv 130153. doi: 10.1101/130153

Deeg KI, Chung I, Poos AM, Braun DM, Korshunov A, Oswald M, Kepper, N, Bender S, Castel D, Lichter P, Grill J, Pfister SM, König R, Jones DT & Rippe K (2017). Dissecting telomere maintenance mechanisms in pediatric glioblastoma. biorxiv 129106. doi: 10.1101/129106

Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brant L, Becker C, Altmuelle, J, Franzen J, Koke, M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Nuernberg P, Rippe K & Papantonis A (2017). Topological demarcation by HMGB2 is disrupted early upon senescence entry across cell types and induces CTCF clustering. biorxiv 127522. doi: 10.1101/127522

Feuerbach L, Sieverling L Deeg, KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Lichter P, Pfister SM, Jones DT, Rippe K & Brors, B (2016). TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. bioRxiv 065532. doi: 10.1101/065532

Selected publications 2011-2017 (more selected publications)

Rademacher A, Erdel F, Trojanowski J, Schumacher S & Rippe K (2017). Real-time observation of light-controlled transcription in living cells. J Cell Sci 130, 4213-4224. doi: 10.1242/jcs.205534 | Abstract | Reprint (12.9 MB) | JCS First person | Article metrics

Wachsmuth M, Knoch TA & Rippe K (2016). Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 9, 57. doi: 10.1186/s13072-016-0093-1 | Abstract | Reprint (5.1 MB) | Article metrics.

Caudron-Herger M, Pankert T, Seiler J, Nemeth A, Voit R, Grummt I & Rippe K (2015). Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 34, 2758-2771. doi: 10.15252/embj.201591458 | Abstract | Reprint (4.6 MB) | Comment | Cover | Article metrics

Mallm JP & Rippe K (2015). Aurora kinase B regulates telomerase activity via a centromeric RNA in stem cells. Cell Rep 11, 1667-1678. doi: 10.1016/j.celrep.2015.05.015 | Abstract | Reprint (5.9 MB) | Article metrics

Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, Erfle H & Rippe K (2015). PML induces compaction, partial TRF2 depletion and DNA damage signaling at telomeres and promotes alternative lengthening of telomeres. J Cell Sci 128, 1887-1900. doi: 10.1242/jcs.148296 | Abstract | Reprint (4.3 MB) | Article metrics

Müller-Ott K, Erdel F, Matveeva A, Hahn M, Mallm, JP, Rademacher A, Marth C, Zhang Q, Kaltofen S, Schotta G, Höfer T & Rippe K (2014). Specificity, propagation and memory of pericentric heterochromatin. Mol Syst Biol 10, 746. doi: 10.15252/msb.20145377 | Abstract | Reprint (7.4 MB) | Article metrics

Baum M, Wachsmuth M, Erdel F & Rippe K (2014). Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat Commun 5, 4494. doi: 10.1038/ncomms5494 | Abstract | Reprint (6.4 MB) | Article metrics

Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T & Rippe K (2014). Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res 24, 1285-1295. doi: 10.1101/gr.164418.113 | Abstract | Reprint (3.3 MB) | Article metrics

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) | Article metrics

Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, 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) | Article metrics

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, 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 | Article metrics

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) | Article metrics

All publications 1989-2017

All publications h-index Karsten Rippe: 50 (Google Scholar), 44 (Researcher ID)

Publications and bibliometric data of Karsten Rippe from databases

Yearly citation numbers from 2003 to 2017. Total number of citations: 8475, h-index: 50, i10 index: 109. Bibliometric data are taken from Google Scholar.

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