Researcher Portfolio
Chung, Ho-Ryun
Epigenomics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society
Researcher Profile
Position: Epigenomics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society
Researcher ID: https://pure.mpg.de/cone/persons/resource/persons50124
Research Fields: Epigenomics
Publications
: Lam, K. C., Chung, H.-R., Semplicio, G., Iyer, S. S., Gaub, A., Bhardwaj, V., Holz, H., Georgiev, P., & Akhtar, A. (2019). The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise. Genes and Development, 33(7-8), 452-465. doi:10.1101/gad.321489.118. [PubMan] : van Bömmel, A., Love, M. I., Chung, H.-R., & Vingron, M. (2018). coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Computational Biology, 14(8): e1006372. doi:10.1371/journal.pcbi.1006372. [PubMan] : Thormann, V., Rothkegel, M. C., Schöpflin, R., Glaser, L. V., Djuric, P., Li, N., Chung, H.-R., Schwahn, K., Vingron, M., & Meijsing, S. (2018). Genomic dissection of enhancers uncovers principles of combinatorial regulation and dynamic wiring of enhancer-promoter contacts. Nucleic Acids Research (London), 46(6), 2868-2882. doi:10.1093/nar/gky051. [PubMan] : Kinkley, S., Helmuth, J., Polansky, J. K., Dunkel, I., Gasparoni, G., Fröhler, S., Chen, W., Walter, J., Hamann, A., & Chung, H.-R. (2016). reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells. Nature Communications, 7: 7:12514. doi:10.1038/ncomms12514. [PubMan] : Chung, H.-R., Xu, C., Fuchs, A., Mund, A., Lange, M., Staege, H., Schubert, T., Bian, C., Dunkel, I., Eberharter, A., Regnard, C., Klinker, H., Meierhofer, D., Cozzuto, L., Winterpracht, A., Di Croce, L., Min, J., Will, H., & Kinkley, S. (2016). PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. eLife, 5: 5:e10607. doi:10.7554/eLife.10607. [PubMan] : Juan, D., Perner, J., Carrillo de Santa Pau, E., Marsili, S., Ochoa, D., Chung, H. R., Vingron, M., Rico, D., & Valencia, A. (2016). 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), 1246-1257. doi:10.1016/j.celrep.2016.01.008. [PubMan] : Reiter, C., Heise, F., Chung, H.-R., & Ehrenhofer-Murray, A. E. (2015). 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. doi:10.1093/femsyr/fov073. [PubMan] : 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., Dekker, J., Manke, T., & Akhtar, A. (2015). High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Molecular Cell, 60(1), 146-162. doi:10.1016/j.molcel.2015.08.024. [PubMan] : Starick, S. R., Ibn-Salem, J., Jurk, M., Hernandez, C., Love, M. I., Chung, H.-R., Vingron, M., Thomas-Chollier, M., & Meijsing, S. H. (2015). 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), 825-835. doi:10.1101/gr.185157.114. [PubMan] : Mammana, A., & Chung, H.-R. (2015). Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biology, 16: 16:151. doi:10.1186/s13059-015-0708-z. [PubMan] : Perner, J., Lasserre, J., Kinkley, S., Vingron, M., & Chung, H.-R. (2014). Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Research (London), 42(22), 13689-13695. doi:10.1093/nar/gku1234. [PubMan] : 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., Lewis, S. E., Ott, C. E., Bauer, S., Schofield, P. N., Mundlos, S., Spielmann, M., & Robinson, P. N. (2014). Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biology: Biology for the Post-Genomic Era, 15: 15:423. doi:10.1186/s13059-014-0423-1. [PubMan] : Perner, J., & Chung, H. R. (2013). Chromatin signaling and transcription initiation. Frontiers in Life Science, 7(1-2), 22-30. doi:10.1080/21553769.2013.856038. [PubMan] : Mammana, A., Vingron, M., & Chung, H.-R. (2013). Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics, 29(20), 2547-2554. doi:10.1093/bioinformatics/btt449. [PubMan] : Lasserre, J., Chung, H.-R., & Vingron, M. (2013). Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks. PLoS Computational Biology, 9(9), e1003168-e1003168. doi:10.1371/journal.pcbi.1003168. [PubMan] : Heise, F., Chung, H.-R., Weber, J. M., Xu, Z., Klein-Hitpass, L., Steinmetz, L. M., Vingron, M., & Ehrenhofer-Murray, A. E. (2012). Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange. Nucleic Acids Research (London), 40(1), 65-74. doi:10.1093/nar/gkr649. [PubMan] : Sun, R., Love, M., Zemojtel, T., Emde, A.-K., Chung, H.-R., Vingron, M., & Haas, S. (2012). Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics, 28(7), 1024-1025. doi:10.1093/bioinformatics/bts064. [PubMan] : Chung, H.-R., Dunkel, I., Heise, F., Linke, C., Krobitsch, S., Ehrenhofer-Murray, A. E., Sperling, S. R., & Vingron, M. (2010). The effect of MNase on nucleosome positioning data. PLoS ONE, 5(12), e15754-e15754. doi:10.1371/journal.pone.0015754. [PubMan] : Löhr, U., Chung, H. R., Beller, M., & Jäckle, H. (2010). Bicoid: Morphogen function revisited. Fly (Austin), 4(3), 236-240. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20404518. [PubMan] : Karlic, R., Chung, H. R., Lasserre, J., Vlahovicek, K., & Vingron, M. (2010). Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences USA, 107(7), 2926-2931. doi:10.073/pnas.0909344107. [PubMan] : Löhr, U., Chung, H.-R., Beller, M., & Jäckle, H. (2009). Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains. Proceedings of the National Academy of Sciences of the United States of America, 106(51), 21695-21700. doi:10.1073/pnas.0910225106. [PubMan] : Chung, H.-R., & Vingron, M. (2009). Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics, 10, 204-204. doi:10.1186/1471-2105-10-204. [PubMan] : Chung, H.-R., & Vingron, M. (2009). Sequence-dependent Nucleosome Positioning. Journal of Molecular Biology, 386(5), 1411-1422. doi:10.1016/j.physletb.2003.10.071. [PubMan] : Zemojtel, T., Kielbasa, S. M., Arndt, P. F., Chung, H.-R., & Vingron, M. (2009). Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends in Genetics, 25(2), 63-66. doi:10.1016/j.tig.2008.11.005. [PubMan] : Chung, H.-R., Kostka, D., & Vingron, M. (2007). A physical model for tiling array analysis. Bioinformatics, 23(13), i80-i86. doi:10.1093/bioinformatics/btm167. [PubMan]