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Items: 1 to 50 of 144

1.

Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer.

Höflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Büscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, König R, Schroeder C.

Mol Oncol. 2019 Nov 17. doi: 10.1002/1878-0261.12597. [Epub ahead of print]

2.

Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to epigenetic deregulation.

Mallm JP, Windisch P, Biran A, Gal Z, Schumacher S, Glass R, Herold-Mende C, Meshorer E, Barbus M, Rippe K.

Int J Cancer. 2019 Aug 28. doi: 10.1002/ijc.32649. [Epub ahead of print]

PMID:
31456217
3.

Pheno-seq - linking visual features and gene expression in 3D cell culture systems.

Tirier SM, Park J, Preußer F, Amrhein L, Gu Z, Steiger S, Mallm JP, Krieger T, Waschow M, Eismann B, Gut M, Gut IG, Rippe K, Schlesner M, Theis F, Fuchs C, Ball CR, Glimm H, Eils R, Conrad C.

Sci Rep. 2019 Aug 26;9(1):12367. doi: 10.1038/s41598-019-48771-4.

4.

Light-Induced Transcription Activation for Time-Lapse Microscopy Experiments in Living Cells.

Trojanowski J, Rademacher A, Erdel F, Rippe K.

Methods Mol Biol. 2019;2038:251-270. doi: 10.1007/978-1-4939-9674-2_17.

PMID:
31407290
5.

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation.

Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K, Rohr K.

Med Image Anal. 2019 Aug;56:68-79. doi: 10.1016/j.media.2019.04.011. Epub 2019 May 31.

PMID:
31200289
6.

Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells.

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.

Int J Comput Assist Radiol Surg. 2019 Nov;14(11):1847-1857. doi: 10.1007/s11548-019-02010-3. Epub 2019 Jun 8.

PMID:
31177423
7.

TelomereHunter - in silico estimation of telomere content and composition from cancer genomes.

Feuerbach L, Sieverling L, Deeg KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Lichter P, Fröhling S, Pfister SM, Jones DTW, Rippe K, Brors B.

BMC Bioinformatics. 2019 May 28;20(1):272. doi: 10.1186/s12859-019-2851-0.

8.

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks.

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.

Mol Syst Biol. 2019 May 22;15(5):e8339. doi: 10.15252/msb.20188339.

9.

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries.

Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB.

Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4.

10.

Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia.

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.

Blood Adv. 2019 Mar 12;3(5):761-765. doi: 10.1182/bloodadvances.2018023879. No abstract available.

11.

The Idea of Precaution: Ethical Requirements for the Regulation of New Biotechnologies in the Environmental Field.

Rippe KP, Willemsen A.

Front Plant Sci. 2018 Dec 21;9:1868. doi: 10.3389/fpls.2018.01868. eCollection 2018. Review.

12.

Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers.

Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Höflmayer D, Burandt E, Tsourlakis MC, Sauter G, Büscheck 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, König R, Schroeder C.

Prostate. 2019 Feb;79(3):302-311. doi: 10.1002/pros.23736. Epub 2018 Nov 14.

PMID:
30430607
13.

TelNet - a database for human and yeast genes involved in telomere maintenance.

Braun DM, Chung I, Kepper N, Deeg KI, Rippe K.

BMC Genet. 2018 May 18;19(1):32. doi: 10.1186/s12863-018-0617-8.

14.

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmüller J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nürnberg P, Marenduzzo D, Rippe K, Papantonis A.

Mol Cell. 2018 May 17;70(4):730-744.e6. doi: 10.1016/j.molcel.2018.03.030. Epub 2018 Apr 26.

15.

Formation of Chromatin Subcompartments by Phase Separation.

Erdel F, Rippe K.

Biophys J. 2018 May 22;114(10):2262-2270. doi: 10.1016/j.bpj.2018.03.011. Epub 2018 Apr 6. Review.

16.

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

Chudasama P, Mughal SS, Sanders MA, 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 RM, Kasper B, Heilig CE, Egerer G, Wolf S, von Kalle C, Eils R, Stenzinger A, Weichert W, Glimm H, Gröschel S, Kopp HG, 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.

Nat Commun. 2018 Jan 10;9(1):144. doi: 10.1038/s41467-017-02602-0.

17.

Real-time observation of light-controlled transcription in living cells.

Rademacher A, Erdel F, Trojanowski J, Schumacher S, Rippe K.

J Cell Sci. 2017 Dec 15;130(24):4213-4224. doi: 10.1242/jcs.205534. Epub 2017 Nov 9.

18.

Erratum: DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

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.

Nat Genet. 2017 Oct 27;49(11):1661. doi: 10.1038/ng1117-1661c.

PMID:
29074949
19.

CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality.

Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, Rippe K, Längst G.

Nucleic Acids Res. 2017 Oct 13;45(18):10534-10554. doi: 10.1093/nar/gkx711.

20.

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

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.

Nat Genet. 2017 Jul;49(7):1052-1060. doi: 10.1038/ng.3889. Epub 2017 Jun 12. Erratum in: Nat Genet. 2017 Oct 27;49(11):1661.

21.

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line.

Teif VB, Mallm JP, Sharma T, Mark Welch DB, Rippe K, Eils R, Langowski J, Olins AL, Olins DE.

Nucleus. 2017 Mar 4;8(2):188-204. doi: 10.1080/19491034.2017.1295201.

22.

Pan-mutant-IDH1 inhibitor BAY1436032 is highly effective against human IDH1 mutant acute myeloid leukemia in vivo.

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, Krämer A.

Leukemia. 2017 Oct;31(10):2020-2028. doi: 10.1038/leu.2017.46. Epub 2017 Jan 31.

23.

Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization.

Pankert T, Jegou T, Caudron-Herger M, Rippe K.

Methods. 2017 Jul 1;123:89-101. doi: 10.1016/j.ymeth.2017.01.010. Epub 2017 Feb 14.

PMID:
28213279
24.

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.

Vainshtein Y, Rippe K, Teif VB.

BMC Genomics. 2017 Feb 14;18(1):158. doi: 10.1186/s12864-017-3580-2.

25.

Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.

Molitor J, Mallm JP, Rippe K, Erdel F.

Biophys J. 2017 Feb 7;112(3):473-490. doi: 10.1016/j.bpj.2017.01.001. Epub 2017 Jan 26.

26.

Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells.

Wachsmuth M, Knoch TA, Rippe K.

Epigenetics Chromatin. 2016 Dec 24;9:57. doi: 10.1186/s13072-016-0093-1. eCollection 2016.

27.

Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow.

Gunkel M, Chung I, Wörz S, Deeg KI, Simon R, Sauter G, Jones DTW, Korshunov A, Rohr K, Erfle H, Rippe K.

Methods. 2017 Feb 1;114:60-73. doi: 10.1016/j.ymeth.2016.09.014. Epub 2016 Oct 7.

PMID:
27725304
28.

Cancer Cells with Alternative Lengthening of Telomeres Do Not Display a General Hypersensitivity to ATR Inhibition.

Deeg KI, Chung I, Bauer C, Rippe K.

Front Oncol. 2016 Aug 23;6:186. doi: 10.3389/fonc.2016.00186. eCollection 2016.

29.

Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts.

Caudron-Herger M, Pankert T, Rippe K.

Nucleus. 2016 May 3;7(3):308-18. doi: 10.1080/19491034.2016.1190890. Review.

30.

A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

Eck S, Wörz S, Müller-Ott K, Hahn M, Biesdorf A, Schotta G, Rippe K, Rohr K.

Med Image Anal. 2016 Aug;32:18-31. doi: 10.1016/j.media.2016.03.001. Epub 2016 Mar 17.

PMID:
27037463
31.

Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children.

Bauer T, Trump S, Ishaque N, Thürmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm JP, Röder S, Herberth G, Takada E, Mücke O, Winter M, Junge KM, Grützmann K, Rolle-Kampczyk U, Wang Q, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Geörg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C, Eils R, Lehmann I.

Mol Syst Biol. 2016 Mar 24;12(3):861. doi: 10.15252/msb.20156520.

32.

Isolation of the protein and RNA content of active sites of transcription from mammalian cells.

Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook PR, Papantonis A.

Nat Protoc. 2016 Mar;11(3):553-65. doi: 10.1038/nprot.2016.032. Epub 2016 Feb 25.

33.

Telomere dysfunction and chromothripsis.

Ernst A, Jones DT, Maass KK, Rode A, Deeg KI, Jebaraj BM, Korshunov A, Hovestadt V, Tainsky MA, Pajtler KW, Bender S, Brabetz S, Gröbner S, Kool M, Devens F, Edelmann J, Zhang C, Castelo-Branco P, Tabori U, Malkin D, Rippe K, Stilgenbauer S, Pfister SM, Zapatka M, Lichter P.

Int J Cancer. 2016 Jun 15;138(12):2905-14. doi: 10.1002/ijc.30033. Epub 2016 Feb 29.

34.

TERRA and the state of the telomere.

Rippe K, Luke B.

Nat Struct Mol Biol. 2015 Nov;22(11):853-8. doi: 10.1038/nsmb.3078.

PMID:
26581519
35.

Alu element-containing RNAs maintain nucleolar structure and function.

Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K.

EMBO J. 2015 Nov 12;34(22):2758-74. doi: 10.15252/embj.201591458. Epub 2015 Oct 13.

36.

Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells.

Mattout A, Aaronson Y, Sailaja BS, Raghu Ram EV, Harikumar A, Mallm JP, Sim KH, Nissim-Rafinia M, Supper E, Singh PB, Sze SK, Gasser SM, Rippe K, Meshorer E.

Genome Biol. 2015 Sep 28;16:213. doi: 10.1186/s13059-015-0760-8.

37.

Increased vitamin D levels at birth and in early infancy increase offspring allergy risk-evidence for involvement of epigenetic mechanisms.

Junge KM, Bauer T, Geissler S, Hirche F, Thürmann L, Bauer M, Trump S, Bieg M, Weichenhan D, Gu L, Mallm JP, Ishaque N, Mücke O, Röder S, Herberth G, Diez U, Borte M, Rippe K, Plass C, Hermann C, Stangl GI, Eils R, Lehmann I.

J Allergy Clin Immunol. 2016 Feb;137(2):610-3. doi: 10.1016/j.jaci.2015.06.040. Epub 2015 Aug 15. No abstract available.

PMID:
26282283
38.

Aurora Kinase B Regulates Telomerase Activity via a Centromeric RNA in Stem Cells.

Mallm JP, Rippe K.

Cell Rep. 2015 Jun 16;11(10):1667-78. doi: 10.1016/j.celrep.2015.05.015. Epub 2015 Jun 4.

39.

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments.

Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2931-43. doi: 10.1016/j.febslet.2015.05.037. Epub 2015 May 28. Review.

40.

PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening.

Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, Erfle H, Rippe K.

J Cell Sci. 2015 May 15;128(10):1887-900. doi: 10.1242/jcs.148296. Epub 2015 Apr 23.

41.

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.

Caudron-Herger M, Cook PR, Rippe K, Papantonis A.

Nucleic Acids Res. 2015 Aug 18;43(14):e95. doi: 10.1093/nar/gkv390. Epub 2015 Apr 20.

42.

HP1 is involved in regulating the global impact of DNA methylation on alternative splicing.

Yearim A, Gelfman S, Shayevitch R, Melcer S, Glaich O, Mallm JP, Nissim-Rafinia M, Cohen AH, Rippe K, Meshorer E, Ast G.

Cell Rep. 2015 Feb 24;10(7):1122-34. doi: 10.1016/j.celrep.2015.01.038. Epub 2015 Feb 19.

43.

Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays.

Teif VB, Kepper N, Yserentant K, Wedemann G, Rippe K.

J Phys Condens Matter. 2015 Feb 18;27(6):064110. doi: 10.1088/0953-8984/27/6/064110. Epub 2015 Jan 7.

PMID:
25563825
44.

The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility.

Erdel F, Baum M, Rippe K.

J Phys Condens Matter. 2015 Feb 18;27(6):064115. doi: 10.1088/0953-8984/27/6/064115. Epub 2015 Jan 7.

PMID:
25563347
45.

Changing chromatin fiber conformation by nucleosome repositioning.

Müller O, Kepper N, Schöpflin R, Ettig R, Rippe K, Wedemann G.

Biophys J. 2014 Nov 4;107(9):2141-50. doi: 10.1016/j.bpj.2014.09.026.

46.

Specificity, propagation, and memory of pericentric heterochromatin.

Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K.

Mol Syst Biol. 2014 Aug 18;10:746. doi: 10.15252/msb.20145377.

47.

Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells.

Baum M, Erdel F, Wachsmuth M, Rippe K.

Nat Commun. 2014 Jul 24;5:4494. doi: 10.1038/ncomms5494.

48.

Loss of cooperativity of secreted CD40L and increased dose-response to IL4 on CLL cell viability correlates with enhanced activation of NF-kB and STAT6.

Bhattacharya N, Reichenzeller M, Caudron-Herger M, Haebe S, Brady N, Diener S, Nothing M, Döhner H, Stilgenbauer S, Rippe K, Mertens D.

Int J Cancer. 2015 Jan 1;136(1):65-73. doi: 10.1002/ijc.28974. Epub 2014 May 27.

49.

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.

Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T, Rippe K.

Genome Res. 2014 Aug;24(8):1285-95. doi: 10.1101/gr.164418.113. Epub 2014 May 8.

50.

Hypermutation of the inactive X chromosome is a frequent event in cancer.

Jäger N, Schlesner M, Jones DT, Raffel S, Mallm JP, Junge KM, Weichenhan D, Bauer T, Ishaque N, Kool M, Northcott PA, Korshunov A, Drews RM, Koster J, Versteeg R, Richter J, Hummel M, Mack SC, Taylor MD, Witt H, Swartman B, Schulte-Bockholt D, Sultan M, Yaspo ML, Lehrach H, Hutter B, Brors B, Wolf S, Plass C, Siebert R, Trumpp A, Rippe K, Lehmann I, Lichter P, Pfister SM, Eils R.

Cell. 2013 Oct 24;155(3):567-81. doi: 10.1016/j.cell.2013.09.042. Epub 2013 Oct 17.

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