BIOQUANT

Publications

Publications 2019-2020

Rademacher A, Erdel F Trojanowski J & Rippe K (2020) Tracing reversible light-induced chromatin binding with near-infrared fluorescent proteins. In Photoswitching Proteins: Methods and Protocols, Methods in Molecular Biology, D Niopek, ed., Springer Nature, New York.

Tirier SM, Park J, Preusser F, Amrhein L, Gu Z, Steiger S, Mallm JP, Waschow M, Eismann B, Gut M, Gut IG, Rippe K, Schlesner M, Theis F, Fuchs C, Ball CR, Glimm H, Eils R & Conrad C (2019) Pheno-seq - linking 3D phenotypes of clonal tumor spheroids to gene expression. Sci Rep, accepted for publication. bioRxiv 311472. doi: 10.1101/311472

Mallm JP, Windisch P, Biran A, Schumacher S, Glass R, Herold-Mende C, Meshorer E, Barbus M & Rippe K (2019) Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to loss of DNA repair capacity. Intl J Cancer, accepted for publication.

Trojanowski J, Rademacher A, Erdel F & Rippe K (2019) Light-induced transcription activation for time-lapse microscopy experiments in living cells. In Imaging Gene Expression: Methods and Protocols, Methods in Molecular Biology, vol. 2028, Y Shav-Tal, ed., Springer Nature, New York, 251-270. doi: 10.1007/978-1-4939-9674-2_17 | Abstract

Ritter C, Wollmann T, Bernhard P, Gunkel M, Braun DM, Lee JY, Meiners J, Simon R, Sauter G, Erfle H, Rippe K, Bartenschlager R & Rohr K (2019) Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells. Int J Comput Assist Radiol Surg, published online 8 June 2019. doi: 10.1007/s11548-019-02010-3 | Abstract | Reprint (1.8 MB).

Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2019) GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation. Med. Image Anal. 56,68-79. doi: 10.1016/j.media.2019.04.011 | Abstract | Reprint (2.1 MB).

Feuerbach L, Sieverling L Deeg, KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Peter Lichter P, Fröhling S, Pfister SM, Jones DT, Rippe K & Brors B (2019). TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. BMC Bioinformatics 20, 272. doi: 10.1186/s12859-019-2851-0 | Abstract | Reprint (1.4 MB) | Article metrics.

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D & Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: 10.15252/msb.20188339 | Abstract | Reprint (7.1 MB) | Appendix (6.8 MB) | Additional data | Article metrics

Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A & Teif VB (2019). DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res, published online 4 April 2019. doi: 10.1101/gr.239707.118 | Abstract | Reprint (8.8 MB) | Article metrics.

Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary, ML, Schüler J, Rippe K, Ogawa S & Lübbert M (2019) Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 3, 761-765. doi: 10.1182/bloodadvances.2018023879 | Abstract | Reprint (1.7 MB) | Article metrics.

Wollmann T, Bernhard P, Gunkel M, Braun DM, Erfle H, Rippe K & Rohr K (2019) Black-box hyperparameter optimization for nuclei segmentation in prostate tissue images. In Bildverarbeitung für die Medizin 2019 (BVM 2019), Handels H, Deserno T, Maier A, Maier-Hein K, Palm C & Tolxdorff T, eds., Springer Vieweg, Wiesbaden, 345-350. doi: 10.1007/978-3-658-25326-4_75 | Reprint (0.7 MB) | Article metrics.

Sieverling L, Hong C, 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 (2019). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun, accepted for publication. Preprint: biorxiv 157560. doi: 10.1101/157560

Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Hoflmayer D, Burandt E, Tsourlakis MC, Sauter G, Buscheck F, Wilczak W, Steurer S, Schlomm T, Huland H, Graefen M, Haese A, Heinzer H, Jacobsen F, Hinsch A, Poos A, Oswald M, Rippe K, Konig R, Schroeder C (2019) Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers. Prostate 79, 302-311. doi: 10.1002/pros.23736 | Abstract | Reprint (1.4 MB) | Article metrics.

Current preprints

Solé-Boldo, L., Raddatz, G., Schütz, S., Mallm, J.-P., Rippe, K., Lonsdorf, A.S., Rodríguez-Paredes, M., and Lyko, F. (2019). Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming. bioRxiv 633131. doi: 10.1101/633131

Poos, AM, Kordaß, T, Kolte, A, Ast, V, Oswald, M, Rippe, K, König, R (2019) Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. bioRxiv 513259. doi: 10.1101/513259

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

Selected recent publications since 2014 (more selected publications)

Braun DM, Chung I, Kepper N & Rippe K (2018). TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet 19, 32. doi: 10.1186/s12863-018-0617-8 | Abstract | Reprint (2.4 MB) | Article metrics.

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

All publications 1989-2018

All publications h-index Karsten Rippe: 54 (Google Scholar), 46 (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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