Publications of Ho-Ryun Chung

Sahu, A.; Li, N.; Dunkel, I.; Chung, H.-R.: EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications. Epigenetics & Chromatin 13 (1), Article 20 (2020)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Perner, J.; Chung, H. R.: Chromatin signaling and transcription initiation. Frontiers in Life Science 7 (1-2), pp. 22 - 30 (2013)

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)

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)

Heise, F.; Chung, H.-R.; Weber, J. M.; Xu, Z.; Klein-Hitpass, L.; Steinmetz, L. M.; Vingron, M.; Ehrenhofer-Murray, A. E.: Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange. Nucleic Acids Research (London) 40 (1), pp. 65 - 74 (2012)

Sun, R.; Love, M.; Zemojtel, T.; Emde, A.-K.; Chung, H.-R.; Vingron, M.; Haas, S.: Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics 28 (7), pp. 1024 - 1025 (2012)

Chung, H.-R.; Dunkel, I.; Heise, F.; Linke, C.; Krobitsch, S.; Ehrenhofer-Murray, A. E.; Sperling, S. R.; Vingron, M.: The effect of MNase on nucleosome positioning data. PLoS ONE 5 (12), p. e15754 - e15754 (2010)

Löhr, U.; Chung, H. R.; Beller, M.; Jäckle, H.: Bicoid: Morphogen function revisited. Fly (Austin) 4 (3), pp. 236 - 240 (2010)