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Items: 1 to 50 of 132

1.

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.

2.

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.

PMID:
29706538
3.

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.

PMID:
29628210
4.

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.

5.

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.

6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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
32.

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
33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

Establishing epigenetic domains via chromatin-bound histone modifiers.

Erdel F, Müller-Ott K, Rippe K.

Ann N Y Acad Sci. 2013 Dec;1305:29-43. doi: 10.1111/nyas.12262. Epub 2013 Sep 13. Review.

PMID:
24033539
40.

SIRT6 recruits SNF2H to DNA break sites, preventing genomic instability through chromatin remodeling.

Toiber D, Erdel F, Bouazoune K, Silberman DM, Zhong L, Mulligan P, Sebastian C, Cosentino C, Martinez-Pastor B, Giacosa S, D'Urso A, Näär AM, Kingston R, Rippe K, Mostoslavsky R.

Mol Cell. 2013 Aug 22;51(4):454-68. doi: 10.1016/j.molcel.2013.06.018. Epub 2013 Aug 1.

41.

Modeling nucleosome position distributions from experimental nucleosome positioning maps.

Schöpflin R, Teif VB, Müller O, Weinberg C, Rippe K, Wedemann G.

Bioinformatics. 2013 Oct 1;29(19):2380-6. doi: 10.1093/bioinformatics/btt404. Epub 2013 Jul 11.

PMID:
23846748
42.

Evolutionary dynamics and information hierarchies in biological systems.

Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM.

Ann N Y Acad Sci. 2013 Dec;1305:1-17. doi: 10.1111/nyas.12140. Epub 2013 May 20. Review.

PMID:
23691975
43.

Suv4-20h2 mediates chromatin compaction and is important for cohesin recruitment to heterochromatin.

Hahn M, Dambacher S, Dulev S, Kuznetsova AY, Eck S, Wörz S, Sadic D, Schulte M, Mallm JP, Maiser A, Debs P, von Melchner H, Leonhardt H, Schermelleh L, Rohr K, Rippe K, Storchova Z, Schotta G.

Genes Dev. 2013 Apr 15;27(8):859-72. doi: 10.1101/gad.210377.112. Epub 2013 Apr 18.

44.

Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB.

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.

PLoS Genet. 2013 Apr;9(4):e1003373. doi: 10.1371/journal.pgen.1003373. Epub 2013 Apr 4.

45.

Taking into account nucleosomes for predicting gene expression.

Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K.

Methods. 2013 Jul 15;62(1):26-38. doi: 10.1016/j.ymeth.2013.03.011. Epub 2013 Mar 21. Review.

PMID:
23523656
46.

Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis.

Erdel F, Rippe K.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):E3221-30. doi: 10.1073/pnas.1209579109. Epub 2012 Nov 5.

47.

Genome-wide nucleosome positioning during embryonic stem cell development.

Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K.

Nat Struct Mol Biol. 2012 Nov;19(11):1185-92. doi: 10.1038/nsmb.2419. Epub 2012 Oct 21.

PMID:
23085715
48.

Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development.

Eißmann M, Gutschner T, Hämmerle M, Günther S, Caudron-Herger M, Groß M, Schirmacher P, Rippe K, Braun T, Zörnig M, Diederichs S.

RNA Biol. 2012 Aug;9(8):1076-87. doi: 10.4161/rna.21089. Epub 2012 Aug 1.

49.

PML body meets telomere: the beginning of an ALTernate ending?

Chung I, Osterwald S, Deeg KI, Rippe K.

Nucleus. 2012 May-Jun;3(3):263-75. doi: 10.4161/nucl.20326. Epub 2012 May 1. Review.

50.

Nuclear architecture by RNA.

Caudron-Herger M, Rippe K.

Curr Opin Genet Dev. 2012 Apr;22(2):179-87. doi: 10.1016/j.gde.2011.12.005. Epub 2012 Jan 24. Review.

PMID:
22281031

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