Publications of the Chung lab

Journal Article (41)

1.
Journal Article
Lam, K. C.; Chung, H.-R.; Semplicio, G.; Iyer, S. S.; Gaub, A.; Bhardwaj, V.; Holz, H.; Georgiev, P.; Akhtar, A.: The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise. Genes and Development 33 (7-8), pp. 452 - 465 (2019)
2.
Journal Article
van Bömmel, A.; Love, M. I.; Chung, H.-R.; Vingron, M.: coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Computational Biology 14 (8), e1006372 (2018)
3.
Journal Article
Thormann, V.; Rothkegel, M. C.; Schöpflin, R.; Glaser, L. V.; Djuric, P.; Li, N.; Chung, H.-R.; Schwahn, K.; Vingron, M.; Meijsing, S.: Genomic dissection of enhancers uncovers principles of combinatorial regulation and dynamic wiring of enhancer-promoter contacts. Nucleic Acids Research (London) 46 (6), pp. 2868 - 2882 (2018)
4.
Journal Article
Bhat, J.; Helmuth, J.; Chitadze, G.; Kouakanou, L.; Peters, C.; Vingron, M.; Ammerpohl, O.; Kabelitz, D.: Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity. Scand J Immunol 86 (4), pp. 184 - 195 (2017)
5.
Journal Article
Yang, J.; Moeinzadeh, M. H.; Kuhl, H.; Helmuth, J.; Xiao, P.; Haas, S.; Liu, G.; Zheng, J.; Sun, Z.; Fan, W. et al.; Deng, G.; Wang, H.; Hu, F.; Zhao, S.; Fernie, A. R.; Börno, S. T.; Timmermann, B.; Zhang, P.; Vingron, M.: Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants 2017 (3), pp. 696 - 703 (2017)
6.
Journal Article
Kinkley, S.; Helmuth, J.; Polansky, J. K.; Dunkel, I.; Gasparoni, G.; Fröhler, S.; Chen, W.; Walter, J.; Hamann, A.; Chung, H.-R.: reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells. Nature Communications 7, 7:12514 (2016)
7.
Journal Article
Chung, H.-R.; Xu, C.; Fuchs, A.; Mund, A.; Lange, M.; Staege, H.; Schubert, T.; Bian, C.; Dunkel, I.; Eberharter, A. et al.; Regnard, C.; Klinker, H.; Meierhofer, D.; Cozzuto, L.; Winterpracht, A.; Di Croce, L.; Min, J.; Will, H.; Kinkley, S.: PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. eLife 5, 5:e10607 (2016)
8.
Journal Article
Juan, D.; Perner, J.; Carrillo de Santa Pau, E.; Marsili, S.; Ochoa, D.; Chung, H. R.; Vingron, M.; Rico, D.; Valencia, A.: Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. Cell Reports 14 (5), pp. 1246 - 1257 (2016)
9.
Journal Article
Reiter, C.; Heise, F.; Chung, H.-R.; Ehrenhofer-Murray, A. E.: A link between Sas2-mediated H4 K16 acetylation, chromatin assembly in S-phase by CAF-I and Asf1, and nucleosome assembly by Spt6 during transcription. FEMS Yeast Research 15 (7), fov073 (2015)
10.
Journal Article
Ramirez, F.; Lingg, T.; Toscano, S.; Lam, K. C.; Georgiev, P.; Chung, H. R.; Lajoie, B. R.; de Wit, E.; Zhan, Y.; de Laat, W. et al.; Dekker, J.; Manke, T.; Akhtar, A.: High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Molecular Cell 60 (1), pp. 146 - 162 (2015)
11.
Journal Article
Eduati, F.; Mangravite, L. M.; Wang, T.; Tang, H.; Bare, J. C.; Huang, R.; Norman, T.; Kellen, M.; Menden, M. P.; Yang, J. et al.; Zhan, X.; Zhong, R.; Xiao, G.; Xia, M.; Abdo, N.; Kosyk, O.; Collaboration, N.-N.-U. D. T.; van Bömmel, A.; Caffrey, B.; Heinig, M.; Huska, M.; Mammana, A.; Perner, J.; Vingron, M.; Friend, S.; Dearry, A.; Simeonov, A.; Tice, R. R.; Rusyn, I.; Wright, F. A.; Stolovitzky, G.; Xie, Y.; Saez-Rodriguez, J.: Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol 33 (9), pp. 933 - 940 (2015)
12.
Journal Article
Starick, S. R.; Ibn-Salem, J.; Jurk, M.; Hernandez, C.; Love, M. I.; Chung, H.-R.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Res 25 (6), pp. 825 - 835 (2015)
13.
Journal Article
Mammana, A.; Chung, H.-R.: Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biology 16, 16:151 (2015)
14.
Journal Article
Perner, J.; Lasserre, J.; Kinkley, S.; Vingron, M.; Chung, H.-R.: Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Research (London) 42 (22), pp. 13689 - 13695 (2014)
15.
Journal Article
Ibn-Salem, J.; Köhler, S.; Love, M. I.; Chung, H.-R.; Huang, N.; Hurles, M. E.; Haendel, M.; Washington, N. L.; Smedley, D.; Mungall, C. J. et al.; Lewis, S. E.; Ott, C. E.; Bauer, S.; Schofield, P. N.; Mundlos, S.; Spielmann, M.; Robinson, P. N.: Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biology: Biology for the Post-Genomic Era 15, 15:423 (2014)
16.
Journal Article
Cui, H.; Schlesinger, J.; Bansal, V.; Dunkel, I.; Meierhofer, D.; Rickert-Sperling, S.: 5Regulation of myogenesis via kinase driven activation of DPF3a, a BAF complex member and its interaction with transcription repressor HEY1. Cardiovascular Research 103 (Suppl 1), S 1 (2014)
17.
Journal Article
Grunert, M.; Dorn, C.; Schueler, M.; Dunkel, I.; Schlesinger, J.; Mebus, S.; Alexi-Meskishvili, V.; Perrot, A.; Wassilew, K.; Timmermann, B. et al.; Hetzer, R.; Berger, F.; Sperling, S. R.: Rare and Private Variations in Neural Crest, Apoptosis and Sarcomere Genes Define the Polygenic Background of Isolated Tetralogy of Fallot. Human Molecular Genetics 23 (12), pp. 3115 - 3128 (2014)
18.
Journal Article
Perner, J.; Chung, H. R.: Chromatin signaling and transcription initiation. Frontiers in Life Science 7 (1-2), pp. 22 - 30 (2013)
19.
Journal Article
Mammana, A.; Vingron, M.; Chung, H.-R.: Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics 29 (20), pp. 2547 - 2554 (2013)
20.
Journal Article
Lasserre, J.; Chung, H.-R.; Vingron, M.: Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks. PLoS Computational Biology 9 (9), p. e1003168 - e1003168 (2013)
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