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Items: 34

1.

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF.

Delacher M, Imbusch CD, Hotz-Wagenblatt A, Mallm JP, Bauer K, Simon M, Riegel D, Rendeiro AF, Bittner S, Sanderink L, Pant A, Schmidleithner L, Braband KL, Echtenachter B, Fischer A, Giunchiglia V, Hoffmann P, Edinger M, Bock C, Rehli M, Brors B, Schmidl C, Feuerer M.

Immunity. 2020 Jan 2. pii: S1074-7613(19)30498-4. doi: 10.1016/j.immuni.2019.12.002. [Epub ahead of print]

2.

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas.

Al-Ali R, Bauer K, Park JW, Al Abdulla R, Fermi V, von Deimling A, Herold-Mende C, Mallm JP, Herrmann C, Wick W, Turcan Ş.

Acta Neuropathol Commun. 2019 Dec 5;7(1):201. doi: 10.1186/s40478-019-0851-y.

3.

Haematopoietic stem cells in perisinusoidal niches are protected from ageing.

Saçma M, Pospiech J, Bogeska R, de Back W, Mallm JP, Sakk V, Soller K, Marka G, Vollmer A, Karns R, Cabezas-Wallscheid N, Trumpp A, Méndez-Ferrer S, Milsom MD, Mulaw MA, Geiger H, Florian MC.

Nat Cell Biol. 2019 Nov;21(11):1309-1320. doi: 10.1038/s41556-019-0418-y. Epub 2019 Nov 4.

PMID:
31685996
4.

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. 2020 Mar 1;146(5):1281-1292. doi: 10.1002/ijc.32649. Epub 2019 Oct 11.

PMID:
31456217
5.

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.

6.

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.

7.

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.

8.

Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain.

Kalamakis G, Brüne D, Ravichandran S, Bolz J, Fan W, Ziebell F, Stiehl T, Catalá-Martinez F, Kupke J, Zhao S, Llorens-Bobadilla E, Bauer K, Limpert S, Berger B, Christen U, Schmezer P, Mallm JP, Berninger B, Anders S, Del Sol A, Marciniak-Czochra A, Martin-Villalba A.

Cell. 2019 Mar 7;176(6):1407-1419.e14. doi: 10.1016/j.cell.2019.01.040. Epub 2019 Feb 28.

PMID:
30827680
9.

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation.

Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M.

Cancer Cell. 2019 Jan 14;35(1):95-110.e8. doi: 10.1016/j.ccell.2018.11.014. Epub 2018 Dec 27.

10.

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.

11.

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
12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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
20.

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.

21.

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
22.

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.

23.

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
24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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
30.

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
31.

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
32.

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
33.

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.

34.

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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