Academic
Publications
Publications
ARTICLES
2023
Lin Gao, Vrinda Mathur, Sabrina Ka Man Tam, Xuemeng Zhou, Ming Fung Cheung, Lu Yan Chan, Guadalupe Estrada-Gutiérrez, Bo Wah Leung, Sakita Moungmaithong, Chi Chiu Wang, Liona C. Poon, Danny Leung. Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal–fetal interface following SARS-CoV-2 infection. Nature Cell Biology, vol. , 2023, doi: 10.1038/s41556-023-01169-x2022
Can Alkan, Lucia Carbone, Megan Dennis, Jason Ernst, Gilad Evrony, Santhosh Girirajan, Danny Leung, Cheuk Yin Cheng, David MacAlpine, Ting Ni, Michèle Ramsay, Rowe Helen, Poppy Gould, Rocio Enriquez-Gasca, Beth Sullivan. Implications of the first complete human genome assembly. Genome Research, vol. 32, 2022, pp. 595--598, doi: 10.1101/gr.276723.1222021
Xuemeng Zhou, Tsz Wing Sam, Ah Young Lee, Danny Leung. Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations. Nature Communications, vol. 12, 2021, doi: 10.1038/s41467-021-26630-z
Xuan Song, Jacqueline T. M. Aw, Fulin Ma, Ming Fung Cheung, Danny Leung, Karl Herrup. DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response. Journal of Neuroscience, vol. 41, 2021, pp. 9286-9307, doi: 10.1523/jneurosci.0845-21.2021
Kyle N. Klein, Peiyao A. Zhao, Xiaowen Lyu, Takayo Sasaki, Daniel A. Bartlett, Amar M. Singh, Ipek Tasan, Meng Zhang, Lotte P. Watts, Shin-ichiro Hiraga, Toyoaki Natsume, Xuemeng Zhou, Timour Baslan, Danny Leung, Masato T. Kanemaki, Anne D. Donaldson, Huimin Zhao, Stephen Dalton, Victor G. Corces, David M. Gilbert. Replication timing maintains the global epigenetic state in human cells. Science, vol. 372, 2021, pp. 371-378, doi: 10.1126/science.aba5545
Sabrina Ka Man Tam, Danny Chi Yeu Leung. Epigenomic and transcriptomic analysis of chronic inflammatory diseases. Genes Genomics, vol. 43, 2021, pp. 227-236, doi: 10.1007/s13258-021-01045-8
Clare S. K. Lee, Ming Fung Cheung, Jinsen Li, Yongqian Zhao, Wai Hei Lam, Vincy Ho, Remo Rohs, Yuanliang Zhai, Danny Leung, Bik-Kwoon Tye. Humanizing the yeast origin recognition complex. Nature Communications, vol. 12, 2021, doi: 10.1038/s41467-020-20277-y2020
Qinghong Jiang, Julie Y.J. Ang, Ah Young Lee, Qin Cao, Kelly Y. Li, Kevin Y. Yip, Danny C.Y. Leung. G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping. Cell Reports, vol. 33, 2020, pp. 108315, doi: 10.1016/j.celrep.2020.108315
Qin Cao, Zhenghao Zhang, Alexander Xi Fu, Qiong Wu, Tin-Lap Lee, Eric Lo, Alfred S. L. Cheng, Chao Cheng, Danny Leung, Kevin Y. Yip. A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Nature Machine Intelligence, vol. 2, 2020, pp. 447-456, doi: 10.1038/s42256-020-0205-22018
Chin Soon Chee, Danny Leung. Targeting Epigenetic Modifiers for Cancer Treatments. Current Pharmacology Reports, vol. 4, 2018, pp. 193-201, doi: 10.1007/s40495-018-0130-92016
Wenhao Zhang, Weikun Xia, Qiujun Wang, Aaron J Towers, Jiayu Chen, Rui Gao, Yu Zhang, Chia-an Yen, Ah Young Lee, Yuanyuan Li, Chen Zhou, Kaili Liu, Jing Zhang, Tian-Peng Gu, Xiuqi Chen, Zai Chang, Danny Leung, Shaorong Gao, Yong-hui Jiang, Wei Xie. Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development. Molecular Cell, vol. 64, 2016, pp. 1062-1073, doi: 10.1016/j.molcel.2016.10.0302015
Angela D. Kelsey, Christine Yang, Danny Leung, Jakub Minks, Thomas Dixon-McDougall, Sarah E.L. Baldry, Aaron B. Bogutz, Louis Lefebvre, Carolyn J. Brown. Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST. Genome Biology, vol. 16, 2015, doi: 10.1186/s13059-015-0774-2
Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature, vol. 523, 2015, pp. 212-216, doi: 10.1038/nature14465
Anshul Kundaje, , Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning. Integrative analysis of 111 reference human epigenomes. Nature, vol. 518, 2015, pp. 317-330, doi: 10.1038/nature14248
Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Shin Lin, Yiing Lin, Yunjiang Qiu, Wei Xie, Feng Yue, Manoj Hariharan, Pradipta Ray, Samantha Kuan, Lee Edsall, Hongbo Yang, Neil C. Chi, Michael Q. Zhang, Joseph R. Ecker, Bing Ren. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, vol. 518, 2015, pp. 350-354, doi: 10.1038/nature142172014
David U. Gorkin, Danny Leung, Bing Ren. The 3D Genome in Transcriptional Regulation and Pluripotency. Cell Stem Cell, vol. 14, 2014, pp. 762-775, doi: 10.1016/j.stem.2014.05.017
D. Leung, T. Du, U. Wagner, W. Xie, A. Y. Lee, P. Goyal, Y. Li, K. E. Szulwach, P. Jin, M. C. Lorincz, B. Ren. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proceedings of the National Academy of Sciences, vol. 111, 2014, pp. 6690-6695, doi: 10.1073/pnas.13222731112013
Wei Xie, Matthew D. Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W. Whitaker, Shulan Tian, R.~David Hawkins, Danny Leung, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph~R. Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen. Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells. Cell, vol. 153, 2013, pp. 1134-1148, doi: 10.1016/j.cell.2013.04.0222012
Alireza Baradaran-Heravi, Kyoung Sang Cho, Bas Tolhuis, Mrinmoy Sanyal, Olena Morozova, Marie Morimoto, Leah I. Elizondo, Darren Bridgewater, Joanna Lubieniecka, Kimberly Beirnes, Clara Myung, Danny Leung, Hok Khim Fam, Kunho Choi, Yan Huang, Kira Y. Dionis, Jonathan Zonana, Kory Keller, Peter Stenzel, Christy Mayfield, Thomas Lücke. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. Human Molecular Genetics, vol. 21, 2012, pp. 2572-2587, doi: 10.1093/hmg/dds083
Danny C. Leung, Matthew C. Lorincz. Silencing of endogenous retroviruses: when and why do histone marks predominate?. Trends in Biochemical Sciences, vol. 37, 2012, pp. 127-133, doi: 10.1016/j.tibs.2011.11.0062011
Mohammad M. Karimi, Preeti Goyal, Irina A. Maksakova, Misha Bilenky, Danny Leung, Jie Xin Tang, Yoichi Shinkai, Dixie L. Mager, Steven Jones, Martin Hirst, Matthew C. Lorincz. DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell, vol. 8, 2011, pp. 676-687, doi: 10.1016/j.stem.2011.04.004
D. C. Leung, K. B. Dong, I. A. Maksakova, P. Goyal, R. Appanah, S. Lee, M. Tachibana, Y. Shinkai, B. Lehnertz, D. L. Mager, F. Rossi, M. C. Lorincz. Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing. Proceedings of the National Academy of Sciences, vol. 108, 2011, pp. 5718-5723, doi: 10.1073/pnas.10146601082010
Toshiyuki Matsui, Danny Leung, Hiroki Miyashita, Irina A. Maksakova, Hitoshi Miyachi, Hiroshi Kimura, Makoto Tachibana, Matthew C. Lorincz, Yoichi Shinkai. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature, vol. 464, 2010, pp. 927-931, doi: 10.1038/nature088582008
Kevin B Dong, Irina A Maksakova, Fabio Mohn, Danny Leung, Ruth Appanah, Sandra Lee, Hao W Yang, Lucia L Lam, Dixie L Mager, Dirk Schübeler, Makoto Tachibana, Yoichi Shinkai, Matthew C Lorincz. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. The EMBO Journal, vol. 27, 2008, pp. 2691-2701, doi: 10.1038/emboj.2008.193