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Items: 25

1.

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
2.

Corrigendum: Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues.

Delacher M, Imbusch CD, Weichenhan D, Breiling A, Hotz-Wagenblatt A, Träger U, Hofer AC, Kägebein D, Wang Q, Frauhammer F, Mallm JP, Bauer K, Herrmann C, Lang PA, Brors B, Plass C, Feuerer M.

Nat Immunol. 2017 Nov 16;18(12):1361. doi: 10.1038/ni1217-1361b.

PMID:
29144491
3.

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
4.

Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues.

Delacher M, Imbusch CD, Weichenhan D, Breiling A, Hotz-Wagenblatt A, Träger U, Hofer AC, Kägebein D, Wang Q, Frauhammer F, Mallm JP, Bauer K, Herrmann C, Lang PA, Brors B, Plass C, Feuerer M.

Nat Immunol. 2017 Oct;18(10):1160-1172. doi: 10.1038/ni.3799. Epub 2017 Aug 7. Erratum in: Nat Immunol. 2017 Nov 16;18(12 ):1361.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

Retinoid resistance and multifaceted impairment of retinoic acid synthesis in glioblastoma.

Campos B, Weisang S, Osswald F, Ali R, Sedlmeier G, Bageritz J, Mallm JP, Hartmann C, von Deimling A, Popanda O, Goidts V, Plass C, Unterberg A, Schmezer P, Burhenne J, Herold-Mende C.

Glia. 2015 Oct;63(10):1850-9. doi: 10.1002/glia.22849. Epub 2015 May 6.

PMID:
25944104
13.

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.

14.

Erratum to: Acute function of secreted amyloid precursor protein fragment APPsα in synaptic plasticity.

Hick M, Herrmann U, Weyer SW, Mallm JP, Tschäpe JA, Borgers M, Mercken M, Roth FC, Draguhn A, Slomianka L, Wolfer DP, Korte M, Müller UC.

Acta Neuropathol. 2015 Jan;129(1):161-2. doi: 10.1007/s00401-014-1374-z. No abstract available.

PMID:
25527084
15.

Acute function of secreted amyloid precursor protein fragment APPsα in synaptic plasticity.

Hick M, Herrmann U, Weyer SW, Mallm JP, Tschäpe JA, Borgers M, Mercken M, Roth FC, Draguhn A, Slomianka L, Wolfer DP, Korte M, Müller UC.

Acta Neuropathol. 2015 Jan;129(1):21-37. doi: 10.1007/s00401-014-1368-x. Epub 2014 Nov 29. Erratum in: Acta Neuropathol. 2015 Jan;129(1):161-2.

PMID:
25432317
16.

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.

17.

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.

18.

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.

19.

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.

20.

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
21.

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
22.

Coding RNAs with a non-coding function: maintenance of open chromatin structure.

Caudron-Herger M, Müller-Ott K, Mallm JP, Marth C, Schmidt U, Fejes-Tóth K, Rippe K.

Nucleus. 2011 Sep-Oct;2(5):410-24. doi: 10.4161/nucl.2.5.17736. Epub 2011 Sep 1.

PMID:
21983088
23.

Generation of conditional null alleles for APP and APLP2.

Mallm JP, Tschäpe JA, Hick M, Filippov MA, Müller UC.

Genesis. 2010 Mar;48(3):200-6. doi: 10.1002/dvg.20601.

PMID:
20140888
24.

Machine learning based analyses on metabolic networks supports high-throughput knockout screens.

Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R.

BMC Syst Biol. 2008 Jul 24;2:67. doi: 10.1186/1752-0509-2-67.

25.

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico.

Fatumo S, Plaimas K, Mallm JP, Schramm G, Adebiyi E, Oswald M, Eils R, König R.

Infect Genet Evol. 2009 May;9(3):351-8. doi: 10.1016/j.meegid.2008.01.007. Epub 2008 Jan 20.

PMID:
18313365

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