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Items: 1 to 20 of 232

1.

Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency.

Adachi K, Kopp W, Wu G, Heising S, Greber B, Stehling M, Araúzo-Bravo MJ, Boerno ST, Timmermann B, Vingron M, Schöler HR.

Cell Stem Cell. 2018 Jun 11. pii: S1934-5909(18)30238-8. doi: 10.1016/j.stem.2018.05.020. [Epub ahead of print]

PMID:
29910149
2.

Polymer physics predicts the effects of structural variants on chromatin architecture.

Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M.

Nat Genet. 2018 May;50(5):662-667. doi: 10.1038/s41588-018-0098-8. Epub 2018 Apr 16.

PMID:
29662163
3.

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.

George J, Walter V, Peifer M, Alexandrov LB, Seidel D, Leenders F, Maas L, Müller C, Dahmen I, Delhomme TM, Ardin M, Leblay N, Byrnes G, Sun R, De Reynies A, McLeer-Florin A, Bosco G, Malchers F, Menon R, Altmüller J, Becker C, Nürnberg P, Achter V, Lang U, Schneider PM, Bogus M, Soloway MG, Wilkerson MD, Cun Y, McKay JD, Moro-Sibilot D, Brambilla CG, Lantuejoul S, Lemaitre N, Soltermann A, Weder W, Tischler V, Brustugun OT, Lund-Iversen M, Helland Å, Solberg S, Ansén S, Wright G, Solomon B, Roz L, Pastorino U, Petersen I, Clement JH, Sänger J, Wolf J, Vingron M, Zander T, Perner S, Travis WD, Haas SA, Olivier M, Foll M, Büttner R, Hayes DN, Brambilla E, Fernandez-Cuesta L, Thomas RK.

Nat Commun. 2018 Mar 13;9(1):1048. doi: 10.1038/s41467-018-03099-x.

4.

Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts.

Thormann V, Rothkegel MC, Schöpflin R, Glaser LV, Djuric P, Li N, Chung HR, Schwahn K, Vingron M, Meijsing SH.

Nucleic Acids Res. 2018 Apr 6;46(6):3258. doi: 10.1093/nar/gky122. No abstract available.

5.

Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts.

Thormann V, Rothkegel MC, Schöpflin R, Glaser LV, Djuric P, Li N, Chung HR, Schwahn K, Vingron M, Meijsing SH.

Nucleic Acids Res. 2018 Apr 6;46(6):2868-2882. doi: 10.1093/nar/gky051.

6.

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.

Heller D, Krestel R, Ohler U, Vingron M, Marsico A.

Nucleic Acids Res. 2017 Nov 2;45(19):11004-11018. doi: 10.1093/nar/gkx756.

7.

An improved compound Poisson model for the number of motif hits in DNA sequences.

Kopp W, Vingron M.

Bioinformatics. 2017 Dec 15;33(24):3929-3937. doi: 10.1093/bioinformatics/btx539.

8.

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog).

Will AJ, Cova G, Osterwalder M, Chan WL, Wittler L, Brieske N, Heinrich V, de Villartay JP, Vingron M, Klopocki E, Visel A, Lupiáñez DG, Mundlos S.

Nat Genet. 2017 Oct;49(10):1539-1545. doi: 10.1038/ng.3939. Epub 2017 Aug 28.

9.

Haplotype-resolved sweet potato genome traces back its hexaploidization history.

Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, Haas S, Liu G, Zheng J, Sun Z, Fan W, Deng G, Wang H, Hu F, Zhao S, Fernie AR, Boerno S, Timmermann B, Zhang P, Vingron M.

Nat Plants. 2017 Sep;3(9):696-703. doi: 10.1038/s41477-017-0002-z. Epub 2017 Aug 21.

PMID:
28827752
10.

Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity.

Bhat J, Helmuth J, Chitadze G, Kouakanou L, Peters C, Vingron M, Ammerpohl O, Kabelitz D.

Scand J Immunol. 2017 Oct;86(4):184-195. doi: 10.1111/sji.12589. Epub 2017 Sep 12. Review.

PMID:
28799233
11.

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.

Huska M, Vingron M.

PLoS Comput Biol. 2016 Dec 16;12(12):e1005249. doi: 10.1371/journal.pcbi.1005249. eCollection 2016 Dec.

12.

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.

Andrey G, Schöpflin R, Jerković I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S.

Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6.

13.

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.

Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH.

Nucleic Acids Res. 2017 Feb 28;45(4):1805-1819. doi: 10.1093/nar/gkw1163.

14.

Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Vingron M, Thomas-Chollier M, Meijsing SH.

Nat Commun. 2016 Nov 22;7:13784. doi: 10.1038/ncomms13784. No abstract available.

15.

Formation of new chromatin domains determines pathogenicity of genomic duplications.

Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan WL, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S.

Nature. 2016 Oct 13;538(7624):265-269. doi: 10.1038/nature19800. Epub 2016 Oct 5.

PMID:
27706140
16.

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Vingron M, Thomas-Chollier M, Meijsing SH.

Nat Commun. 2016 Sep 1;7:12621. doi: 10.1038/ncomms12621.

17.

Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2.

Du Bois I, Marsico A, Bertrams W, Schweiger MR, Caffrey BE, Sittka-Stark A, Eberhardt M, Vera J, Vingron M, Schmeck BT.

J Infect Dis. 2016 Aug 1;214(3):454-63. doi: 10.1093/infdis/jiw171. Epub 2016 Apr 29.

PMID:
27130431
18.

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.

Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A.

Cell Rep. 2016 Feb 9;14(5):1246-1257. doi: 10.1016/j.celrep.2016.01.008. Epub 2016 Jan 28.

19.

Reconstruction of gene networks using prior knowledge.

Ghanbari M, Lasserre J, Vingron M.

BMC Syst Biol. 2015 Nov 20;9:84. doi: 10.1186/s12918-015-0233-4.

20.

Time-Dependent Gene Network Modelling by Sequential Monte Carlo.

Ancherbak S, Kuruoglu EE, Vingron M.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Nov-Dec;13(6):1183-1193. Epub 2015 Oct 30.

PMID:
26540693

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