Danny Chi Yeu LEUNG
梁子宇
PhD in Medical Genetics
The University of British Columbia, 2012

Assistant Professor
Division of Life Science

Director of Center for Epigenomics Research

Associate Director of HKUST-BGI Joint Research Center



(852) 3469 2494
dcyleung@ust.hk
Room 5519
Personal Web

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ORCID
0000-0002-2472-894X

Scopus ID
36785209600




Research Interest Publications Projects Teaching Assignment RPG Supervision Space used




Research Interest

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Cancer genomics
Epigenomics
Epigenetics
Genome biology
Chromatin structure



Publications

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All Years 22 2022 0 2021 5 2020 2 2019 0 2018 1 2017 0 2016 14

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2021 5

DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response
Journal of Neuroscience, v. 41, (45), 10 November 2021, p. 9286-9307
Song, Xuan; Aw, Jacqueline Theeng Mei; Ma, Fulin; Cheung, Ming Fung; Leung, Danny Chi Yeu; Herrup, Karl Article
Epigenomic and transcriptomic analysis of chronic inflammatory diseases
Genes & Genomics, v. 43, (3), March 2021, article number 12, p. 227-236
Tam, Ka Man; Leung, Chi Yeu Danny Article
Humanizing the yeast origin recognition complex
Nature Communications, v. 12, (1), January 2021, article number 33
Lee, Clara S.K.; Cheung, Ming Fung; Li, Jinsen; Zhao, Yongqian; Lam, Wai Hei; Ho, Vincy Wing Sze; Rohs, Remo; Zhai, Yuanliang; Leung, Danny; Tye, Bik Kwoon Article
Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations
Nature Communications, v. 12, (1), 9 November 2021, article number 6462
Zhou, Xuemeng; Sam, Tsz Wing; Lee, Ah Young; Leung, Danny Chi Yeu Article
Replication timing maintains the global epigenetic state in human cells
Science, v. 372, (6540), April 2021, p. 371-378
Klein, Kyle N.; Zhao, Peiyao A.; Lyu, Xiaowen; Sasaki, Takayo; Bartlett, Daniel A,; Singh, Amar M.; Tasan, Ipek; Zhang, Meng; Watts, Lotte P.; Hiraga, Shin-ichiro; Natsume, Toyoaki; Zhou, Xuemeng; Baslan, Timour; Leung, Chi Yeu; Kanemaki, Masato T.; Donaldson, Anne D.; Zhao, Huimin; Dalton, Stephen; Corces, Victor G.; Gilbert, David M. Article

2020 2

A unified framework for integrative study of heterogeneous gene regulatory mechanisms
Nature Machine Intelligence, v. 2, (8), August 2020, p. 447-456
Cao, Qin; Zhang, Zhenghao; Fu, Alexander Xi; Wu, Qiong; Lee, Tin-Lap; Lo, Eric; Cheng, Alfred S.L.; Cheng, Chao; Leung, Danny Chi Yeu; Yip, Kevin Y. Article
G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping
Cell Reports, v. 33, (4), 27 October 2020, article number 108315
Jiang, Qinghong; Ang, Ying Jin Julie; Lee, Ah Young; Cao, Qin; Li, Kelly Y.; Yip, Kevin Y.; Leung, Chi Yeu Article

2018 1

Targeting Epigenetic Modifiers for Cancer Treatments
Current Pharmacology Reports, 5 March 2018, p. 1-9
Leung, Danny Chi Yeu; Chee, chin soon Article

2016 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development
Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei Article

2015 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation
Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R. Article
Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST
Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet Article
Integrative analysis of 111 reference human epigenomes
Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis Article
Integrative analysis of haplotype-resolved epigenomes across human tissues
Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing Article

2014 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing Article
The 3D genome in transcriptional regulation and pluripotency
Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing Article

2013 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells
Cell, v. 153, (5), May 2013, p. 1134-1148
Xie, Wei; Schultz, Matthew D.; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W.; Tian, Shulan; Hawkins, R. David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A.; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; Nery, Joseph R.; Urich, Mark A.; Kuan, Samantha; Yen, Chia-an; Klugman, Sarit; Yu, Pengzhi; Suknuntha, Kran; Propson, Nicholas E.; Chen, Huaming; Edsall, Lee E.; Wagner, Ulrich; Li, Yan; Ye, Zhen; Kulkarni, Ashwinikumar; Xuan, Zhenyu; Chung, Wen-Yu; Chi, Neil C.; Antosiewicz-Bourget, Jessica E.; Slukvin, Igor; Stewart, Ron; Zhang, Michael Q.; Wang, Wei; Thomson, James A.; Ecker, Joseph R.; Ren, Bing Article

2012 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression
Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F. Article
Silencing of endogenous retroviruses: When and why do histone marks predominate?
Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew Article

2011 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs
Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C. Article
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 of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C. Article

2010 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi Article

2008 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity
EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C. Article


Expand All Collapse All


Article 5

DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response
Journal of Neuroscience, v. 41, (45), 10 November 2021, p. 9286-9307
Song, Xuan; Aw, Jacqueline Theeng Mei; Ma, Fulin; Cheung, Ming Fung; Leung, Danny Chi Yeu; Herrup, Karl
Epigenomic and transcriptomic analysis of chronic inflammatory diseases
Genes & Genomics, v. 43, (3), March 2021, article number 12, p. 227-236
Tam, Ka Man; Leung, Chi Yeu Danny
Humanizing the yeast origin recognition complex
Nature Communications, v. 12, (1), January 2021, article number 33
Lee, Clara S.K.; Cheung, Ming Fung; Li, Jinsen; Zhao, Yongqian; Lam, Wai Hei; Ho, Vincy Wing Sze; Rohs, Remo; Zhai, Yuanliang; Leung, Danny; Tye, Bik Kwoon
Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations
Nature Communications, v. 12, (1), 9 November 2021, article number 6462
Zhou, Xuemeng; Sam, Tsz Wing; Lee, Ah Young; Leung, Danny Chi Yeu
Replication timing maintains the global epigenetic state in human cells
Science, v. 372, (6540), April 2021, p. 371-378
Klein, Kyle N.; Zhao, Peiyao A.; Lyu, Xiaowen; Sasaki, Takayo; Bartlett, Daniel A,; Singh, Amar M.; Tasan, Ipek; Zhang, Meng; Watts, Lotte P.; Hiraga, Shin-ichiro; Natsume, Toyoaki; Zhou, Xuemeng; Baslan, Timour; Leung, Chi Yeu; Kanemaki, Masato T.; Donaldson, Anne D.; Zhao, Huimin; Dalton, Stephen; Corces, Victor G.; Gilbert, David M.


Expand All Collapse All


Article 2

A unified framework for integrative study of heterogeneous gene regulatory mechanisms
Nature Machine Intelligence, v. 2, (8), August 2020, p. 447-456
Cao, Qin; Zhang, Zhenghao; Fu, Alexander Xi; Wu, Qiong; Lee, Tin-Lap; Lo, Eric; Cheng, Alfred S.L.; Cheng, Chao; Leung, Danny Chi Yeu; Yip, Kevin Y.
G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping
Cell Reports, v. 33, (4), 27 October 2020, article number 108315
Jiang, Qinghong; Ang, Ying Jin Julie; Lee, Ah Young; Cao, Qin; Li, Kelly Y.; Yip, Kevin Y.; Leung, Chi Yeu


Expand All Collapse All


Article 1

Targeting Epigenetic Modifiers for Cancer Treatments
Current Pharmacology Reports, 5 March 2018, p. 1-9
Leung, Danny Chi Yeu; Chee, chin soon


Expand All Collapse All


Article 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development
Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei


Expand All Collapse All


Article 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation
Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.
Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST
Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet
Integrative analysis of 111 reference human epigenomes
Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis
Integrative analysis of haplotype-resolved epigenomes across human tissues
Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing


Expand All Collapse All


Article 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing
The 3D genome in transcriptional regulation and pluripotency
Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing


Expand All Collapse All


Article 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells
Cell, v. 153, (5), May 2013, p. 1134-1148
Xie, Wei; Schultz, Matthew D.; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W.; Tian, Shulan; Hawkins, R. David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A.; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; Nery, Joseph R.; Urich, Mark A.; Kuan, Samantha; Yen, Chia-an; Klugman, Sarit; Yu, Pengzhi; Suknuntha, Kran; Propson, Nicholas E.; Chen, Huaming; Edsall, Lee E.; Wagner, Ulrich; Li, Yan; Ye, Zhen; Kulkarni, Ashwinikumar; Xuan, Zhenyu; Chung, Wen-Yu; Chi, Neil C.; Antosiewicz-Bourget, Jessica E.; Slukvin, Igor; Stewart, Ron; Zhang, Michael Q.; Wang, Wei; Thomson, James A.; Ecker, Joseph R.; Ren, Bing


Expand All Collapse All


Article 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression
Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F.
Silencing of endogenous retroviruses: When and why do histone marks predominate?
Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew


Expand All Collapse All


Article 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs
Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C.
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 of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C.


Expand All Collapse All


Article 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi


Expand All Collapse All


Article 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity
EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C.


Expand All Collapse All


2016 1

Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development
Molecular Cell, v. 64, (6), December 2016, p. 1062-1073
Zhang, Wenhao; Xia, Weikun; Wang, Qiujun; Towers, Aaron J.; Chen, Jiayu; Gao, Rui; Zhang, Yu; Yen, Chia-An; Lee, Ah Young; Li, Yuanyuan; Zhou, Chen; Liu, Kaili; Zhang, Jing; Gu, Tian-Peng; Chen, Xiuqi; Chang, Zai; Leung, Danny Chi Yeu; Gao, Shaorong; Jiang, Yong-Hui; Xie, Wei Article

2015 4

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation
Nature, v. 523, (7559), July 2015, p. 212-216
Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny Chi Yeu; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R. Article
Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST
Genome Biology, v. 16, (1), October 2015, article number 208
Kelsey, Angela D.; Yang, Christine; Leung, Danny Chi Yeu; Minks, Jakub; Dixon-McDougall, Thomas; Baldry, Sarah El L.; Bogutz, Aaron B.; Lefebvre, Louis; Brown, Carolyn Janet Article
Integrative analysis of 111 reference human epigenomes
Nature, v. 518, (7539), February 2015, p. 319-329
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R. David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J.; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K.; Hansen, R. Scott; Kaul, Rajinder; Sabo, Peter J.; Bansal, Mukul S.; Carles, Annaick; Dixon, Jesse R.; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R.; Neph, Shane J.; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C.; Siebenthall, Kyle T.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Thurman, Robert E.; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E.; Boyer, Laurie A.; De Jager, Philip L.; Farnham, Peggy J.; Fisher, Susan J.; Haussler, David; Jones, Steven J.M.; Li, Wei; Marra, Marco A.; McManus, Michael T.; Sunyaev, Shamil; Thomson, James A.; Tlsty, Thea D.; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A.; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Costello, Joseph F.; Ecker, Joseph R.; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A.; Wang, Ting; Kellis, Manolis Article
Integrative analysis of haplotype-resolved epigenomes across human tissues
Nature, v. 518, (7539), February 2015, p. 350-354
Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C.; Zhang, Michael Q.; Ecker, Joseph R.; Ren, Bing Article

2014 2

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (18), May 2014, p. 6690-6695
Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E.; Jin, Peng; Lorincz, Matthew C.; Ren, Bing Article
The 3D genome in transcriptional regulation and pluripotency
Cell Stem Cell, v. 14, (6), June 2014, p. 771-775
Gorkin, David U.; Leung, Danny; Ren, Bing Article

2013 1

Epigenomic analysis of multilineage differentiation of human embryonic stem cells
Cell, v. 153, (5), May 2013, p. 1134-1148
Xie, Wei; Schultz, Matthew D.; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W.; Tian, Shulan; Hawkins, R. David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A.; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; Nery, Joseph R.; Urich, Mark A.; Kuan, Samantha; Yen, Chia-an; Klugman, Sarit; Yu, Pengzhi; Suknuntha, Kran; Propson, Nicholas E.; Chen, Huaming; Edsall, Lee E.; Wagner, Ulrich; Li, Yan; Ye, Zhen; Kulkarni, Ashwinikumar; Xuan, Zhenyu; Chung, Wen-Yu; Chi, Neil C.; Antosiewicz-Bourget, Jessica E.; Slukvin, Igor; Stewart, Ron; Zhang, Michael Q.; Wang, Wei; Thomson, James A.; Ecker, Joseph R.; Ren, Bing Article

2012 2

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression
Human Molecular Genetics, v. 21, (11), 2012, June, Article number dds083, p. 2572-2587
Baradaran-Heravi, Alireza; Cho, Kyoung Sang; Tolhuis, Bas; Sanyal, Mrinmoy; Morozova, Olena; Morimoto, Marie; Elizondo, Leah I.; Bridgewater, Darren; Lubieniecka, Joanna; Beirnes, Kimberly; Myung, Clara; Leung, Danny; Fam, Hok Khim; Choi, Kunho; Huang, Yan; Dionis, Kira Y.; Zonana, Jonathan; Keller, Kory; Stenzel, Peter; Mayfield, Christy; Luecke, Thomas; Bokenkamp, Arend; Marra, Marco A.; van Lohuizen, Maarten; Lewis, David B.; Shaw, Chad; Boerkoel, Cornelius F. Article
Silencing of endogenous retroviruses: When and why do histone marks predominate?
Trends in Biochemical Sciences, v. 37, (4), 2012, April, p. 127-133
Leung, Danny; Lorincz, Matthew Article

2011 2

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs
Cell Stem Cell, v.8, (6), 2011, June, p. 676-687
Karimi, Mohammad M.; Goyal, Preeti; Maksakova, Irina A.; Bilenky, Misha; Leung, Danny; Tang, Jie Xin; Shinkai, Yoichi; Mager, Dixie L.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C. Article
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 of the United States of America, v. 108, (14), 2011, April, p. 5718-5723
Leung, Danny; Dong, Kevin B.; Maksakova, I.A.; Goyal, P.; Appanah, R.; Lee, S.; Tachibana, M.; Shinkai, Y.; Lehnertz, B.; Mager, D.L.; Rossi, F.; Lorincz, M.C. Article

2010 1

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
Nature, v. 464, (7290), 2010, April, p. 927-931
Matsui, Toshiyuki; Leung, Danny; Miyashita, Hiroki; Maksakova, Irina A.; Miyachi, Hitoshi; Kimura, Hiroshi; Tachibana, Makoto; Lorincz, Matthew C.; Shinkai, Yoichi Article

2008 1

DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity
EMBO Journal, v. 27, (20), 2008, Oct, p. 2691-2701
Dong, K.B.; Maksakova, I.A.; Mohn, F.; Leung, Danny; Appanah, R.; Lee, S.; Yang, H.W.; Lam, L.L.; Mager, D.L.; Schübeler, D.; Tachibana, M.; Shinkai, Y.; Lorincz, M.C. Article


No Publications


No Publications


No Publications






Teaching Assignment

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2021-22 Winter 0 2021-22 Fall 3 2020-21 Summer 2 2020-21 Spring 8 2020-21 Winter 0 2020-21 Fall 5

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LIFS3140 General Genetics
LIFS4961 Biochemistry and Cell Biology Capstone Project
LIFS4971 Biochemistry and Cell Biology Project Research I


LIFS3510 Junior Research Project I
UROP1100D Undergraduate Research Opportunities Series 1


LIFS3580 Bioinformatics
LIFS4960 Biological Science Capstone Project
LIFS4963 Biotechnology Capstone Project
LIFS4981 Biochemistry and Cell Biology Project Research II
LIFS4983 Biotechnology Project Research II
LIFS5001 Responsible Conduct of Biomedical and Biotechnology Research
LIFS6116D Current Topics in Genomics and Bioinformatics
LIFS6800 Frontiers in Nucleic Acid Research


LIFS3140 General Genetics
LIFS4963 Biotechnology Capstone Project
LIFS4971 Biochemistry and Cell Biology Project Research I
LIFS4973 Biotechnology Project Research I
SCIE4500 IRE Research Project II


No Teaching Assignments


No Teaching Assignments






Research Postgraduate (RPG) Supervision From January 2019 to December 2022 (As of 30 January 2022)

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All Supervisions Current RPGs Graduated RPGs

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Current RPGs

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Doctor of Philosophy JIANG, Qinghong
Life Science( 2021 - )

LIU, Kwok Yu
Life Science( 2021 - )

WAI, Geena
Life Science( 2021 - )

CHENG, Cheuk Yin
Life Science( 2020 - )

GAO, Lin
Life Science( 2020 - )

AW, Jacqueline Theeng Mei
Life Science( 2019 - )

TAM, Ka Man
Life Science( 2019 - )

TAM, Lut Fei
Life Science( 2019 - )

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Master of Philosophy KAN, Ying Hei
Life Science( 2021 - )

MATHUR, Vrinda
Life Science( 2020 - )

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Graduated RPGs

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Doctor of Philosophy ZHOU, Xuemeng
Life Science( Completed in 2021 )

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Master of Philosophy JIANG, Qinghong
Life Science( Completed in 2021 )

LIU, Kwok Yu
Life Science( Completed in 2021 )

WAI, Geena
Life Science( Completed in 2021 )

CHENG, Cheuk Yin
Life Science( Completed in 2020 )

GAO, Lin
Life Science( Completed in 2020 )

XU, Heming
Life Science( Completed in 2020 )

AW, Jacqueline Theeng Mei
Life Science( Completed in 2019 )

TAM, Ka Man
Life Science( Completed in 2019 )

TAM, Lut Fei
Life Science( Completed in 2019 )









ProjectsFrom January 2020 to December 2022

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All Projects 9 Leading Projects 6 Participating Projects 3

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Stem cell-niche interactions in tissue maintenance and engineering


干细胞与微环境互作在组织维持和组织工程中的应用 Participating


RGC - Theme-based Research Scheme


Project Team (HKUST)
XIE Ting (Lead)
CHEUNG Tom
GUO Yusong
LEUNG Danny Chi Yeu
LIU Kai
MAK Ho Yi
SUN Fei
WEN Zilong
WU Angela Ruohao
WU Zhenguo
YAN Yan


2022 -




Delineating the role of retrotransposons in placenta development and disease


反转录转座子与胎盘发育和疾病 Leading


RGC - General Research Fund


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2022 -




The Center for Neurodegenerative Diseases


N/A Participating


Innovation and Technology Fund


Project Team (HKUST)
IP Nancy Yuk-Yu (Lead)
CHEUNG Tom
FU Amy Kit Yu
LEUNG Danny Chi Yeu
LIU Kai
WANG Jiguang
WONG Yung Hou
WU Zhenguo


2020 -




Molecular regulation of quiescence and early activation in muscle stem cells


骨骼肌干细胞静息态及早期活化的分子调控 Participating


RGC - Collaborative Research Fund


Project Team (HKUST)
WU Zhenguo (Lead)
CHEUNG Tom
LEUNG Danny Chi Yeu


2020 -




Epigenetic dysregulation of human endogenous retroviruses in chronic inflammatory diseases


慢性炎症疾病的内源性逆转录病毒表观遗传失调 Leading


Germany / Hong Kong Joint Research Scheme


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2020 - 2020




Hong Kong Epigenomics Project Leading


Lo Ka Chung Charitable Foundation Limited


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2018 -




Deciphering the epigenome of melanomas Leading


Croucher Foundation


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2017 -




Determining the role of histone methyltransferase G9a in regulating the epigenome and chromatin organization


测定组蛋白转甲基酶G9a对於调控表观基因组及染色质构型的作用 Leading


RGC - General Research Fund


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2017 - 2021




Deciphering the non-coding elements of mammalian genomes


拆解基因组中的非编码序列 Leading


RGC - Early Career Scheme


Project Team (HKUST)
LEUNG Danny Chi Yeu (Lead)


2016 - 2020