Research
PUBLICATIONS
通讯及第一作者论文（含共同）：
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[2024-04-10][PDF]
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Jun Sun, Jiale Qu*, Jun Sun*, Cai Zhao*, et al. Yong Yuan#, Lili Fan#, Haopeng Yu#, Junjun Ding# (Corresponding author). Precise prediction of phase-separation key residues by machine learning. Nature Communications. 2024. https://doi.org/10.1038/s41467-024-46901-9. (IF:16.6)
[2024-04-01][PDF]
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Jiale Qu*, Jun Sun*, Cai Zhao, Xinyi liu, Shaoshuai Jiang, Chao Wei, Haopeng Yu, Xiaoxi Zeng#, Lili Fan#, Junjun Ding# (Corresponding author). Simultaneous profiling of chromatin architecture and transcription in single cells. Nature Structural & Molecular Biology. 2023. https://doi.org/10.1038/s41594-023-01066-9. (IF:16.8)
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Xiaoru Ling*, Xinyi liu*, Shaoshuai Jiang, Lili Fan#, Junjun Ding# (Corresponding author). The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. Cell Regeneration. 2022 dec 21;11(1):42. doi: 10.1186/s13619-022-00145-4.
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Chao Wei*, Lumeng Jia*, Xiaona Huang*, Jin Tan*, Mulan Wang, Jing Niu, Yingping Hou, Jun Sun, Pengguihang Zeng, Jia Wang, Li Qing, Lin Ma, Xinyi Liu, Xiuxiao Tang, Fenjie Li, Shaoshuai Jiang, Jingxin Liu, Tingting Li, Lili Fan, Yujie Sun, Juntao Gao, Cheng Li, Junjun Ding# (Corresponding author). CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation. Cell Research. 2022 Aug;32(8):744-760. doi: 10.1038/s41422-022-00676-0. (IF:46.297)
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Jiahao Chen*, Jingxin Liu*, Pengguihang Zeng*, Cai Zhao, Xinyi Liu, Jun Sun, Jia Wang, Peihang Fang, Wenjie Chen, Junjun Ding# (Corresponding author). Estrogen and BRCA1 deficiency synergistically induce breast cancer mutation-related DNA damage. Biochemical and Biophysical Research Communications. 2022 Jul 12;613:140-145. doi: 10.1016/j.bbrc.2022.04.142. (IF:3.322)
[2022-08-29][PDF]
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Qian Ma*, Jia Wang*, Haopeng Yu, Junyi Sun, Jun Sun, Jiahao Chen, Yangyinhui Yu, Peihang Fang, Qi Tian, Junjun Ding# (Corresponding author). Protocol to alter a protein’s phase separation capacity to control cell fate transitions. STAR protocols. 2021 Oct 14;2(4):100887. doi: 10.1016/j.xpro.2021.100887.
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Jia Wang*, Qian Ma*, Peihang Fang, Qi Tian, Haopeng Yu, Junyi Sun, Junjun Ding# (Corresponding author). Manipulation of TAD reorganization by chemical-dependent genome linking. STAR protocols. 2021 Sep 8;2(3):100799. doi: 10.1016/j.xpro.2021.100799.
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Xinyi Liu*, Shaoshuai Jiang*, Lin Ma, Jiale Qu, Longying Zhao, Xing Zhu, Junjun Ding* (Corresponding author). Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization. Genome Biol. 2021 Aug 17;22(1):230. (IF: 13.580)
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Jia Wang*, Haopeng Yu*, Qian Ma*, Pengguihang Zeng, Danya Wu, Yingping Hou, Xinyi Liu, Lumeng Jia, Jun Sun, Yilong Chen, D. Guallar, M. Fidalgo, Jiahao Chen, Yangyinhui Yu, S. Jiang, F. Li, C. Zhao, X. Huang, J. Wang, C. Li, Y. Sun, X. Zeng, W. Zhang, Y. Miao, Junjun Ding# (Corresponding author). Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions. Cell Stem Cell. 2021 May 25.（IF: 23.394, Cover article)
11Xiaona Huang* Chao Wei* Fenjie Li* Lumeng Jia, Pengguihang Zeng, Jiahe Li, Jin Tan, Tuanfeng Sun, Shaoshuai Jiang, Jia Wang, Xiuxiao Tang, Qingquan Zhao, Bin Liu, Limin Rong, Cheng Li, and Junjun Ding# (Corresponding author). PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions. Protein & Cell. 2019 Oct;10(10):709-725. （IF: 15.328）
12Li Fenjie, Junjun Ding# (Corresponding author). Sialylation is involved in cell fate decision during development, reprogramming and cancer progression. Protein & Cell. 2019 Aug;10(8):550-565. Review.（IF: 15.328）
13Jia Wang*, Xingui Wu*, Chao Wei*, Xin Huang, Qian Ma, Xiaona Huang, Francesco Faiola, Diana Guallar, Miguel Fidalgo, Tingyuan Huang, Di Peng, Li Chen, Haopeng Yu, Xingyu Li, Junyi Sun, Xinyi Liu, Xiaoxia Cai, Xiao Chen, Ling Wang, Jian Ren, Jianlong Wang#, Junjun Ding# (Corresponding author). YY1 Positively Regulates Transcription by Targeting Promoters and Super-Enhancers through the BAF Complex in Embryonic Stem Cells, Stem Cell Reports. 2018 March 1; doi: 10.1016/j.stemcr.2018.02.004.（IF: 7.294）
14Junjun Ding, Xin Huang, Ningyi Shao, Hongwei Zhou, Dung-Fang Lee, Francesco Faiola, Miguel Fidalgo, Diana Guallar, Arven Saunders, Pavel V. Shliaha, Hailong Wang, Avinash Waghray, Dmitri Papatsenko, Carlos Sánchez-Priego, Dan Li, Ye Yuan, Ihor R. Lemischka, Li Shen, Kevin Kelley, Haiteng Deng, Xiaohua Shen, and Jianlong Wang. Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming, Cell Stem Cell. 2015 Jun 4;16(6):653-68.（IF: 25.269）
15Yael Costa*, Junjun Ding* (co-first author), Thorold W. Theunissen*, Francesco Faiola*, Timothy A. Hore, Pavel V. Shliaha, Miguel Fidalgo, Arven Saunders, Moyra Lawrence, Sabine Dietmann, Satyabrata Das, Dana N. Levasseur, Zhe Li, Mingjiang Xu, Wolf Reik, Jose´ C. R. Silva & Jianlong Wang. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature. 2013 Mar 21;495(7441):370-4.（IF: 69.504）
16Junjun Ding, Huilei Xu, Francesco Faiola, Avi Ma'ayan, Jianlong Wang. Oct4 links multiple epigenetic pathways to the pluripotency network, Cell Research. 2012 Jan;22(1):155-67.（IF: 46.297）
17Junjun Ding*, Yuanbiao Guo*, Sheng Liu, Yujuan Yan, Gang Chang, Zhaohui Kou, Yu Zhang, Ying Jiang, Fuchu He, Shaorong Gao and Jianli Sang. ES Cells Derived from Somatic Cloned and Fertilized Blastocysts are Post- transcriptionally Indistinguishable: a MicroRNA and Protein Profiles Comparison, Proteomics. 2009 May; 9(10):2711-21.（IF: 5.393）
18Ding Jun-Jun*, Guo Chen-Ying*, Cai Qi-Liang, Lin Ya-Hui, Wang Heng. In vivo expression of green fluorescent protein gene and immunogenicity of ES312 vaccine both mediated by starburst polyamidoamine dendrimers, Acta Academiae Medicinae Sinicae, 2005 March; Vol.27 (4): 499-503
合作论文：
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Guang Shi, Yaofu Bai, Xiya Zhang, Junfeng Su, Junjie Pang, Quanyuan He, Pengguihang Zeng, Junjun Ding, Yuanyan Xiong, Jingran Zhang, Jingwen Wang, Dan Liu, Wenbin Ma, Junjiu Huang, Zhou Songyang. Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation. Protein & Cell. 2022 Oct;13(10):721-741. doi: 10.1007/s13238-021-00884-1. (IF:15.328)
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Mingsen Li, Huaxing Huang, Bofeng Wang, Shaoshuai Jiang, Huizhen Guo, Liqiong Zhu, Siqi Wu, Jiafeng Liu, Li Wang, Xihong Lan, Wang Zhang, Jin Zhu, Fuxi Li, Jieying Tan, Zhen Mao, Chunqiao Liu, Jianping Ji, Junjun Ding, Kang Zhang, Jin Yuan, Yizhi Liu, Hong Ouyang. Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity. Nature Communications. 2022 Mar 11;13(1):1293. doi: 10.1038/s41467-022-28966-6. (IF:17.694)
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Xin Huang, Kyoung-Mi Park, Paul Gontarz, Bo Zhang, Joshua Pan, Zachary McKenzie, Laura A Fischer, Chen Dong, Sabine Dietmann, Xiaoyun Xing, Pavel V Shliaha, Jihong Yang, Dan Li, Junjun Ding, Tenzin Lungjangwa, Maya Mitalipova, Shafqat A Khan, Sumeth Imsoonthornruksa, Nick Jensen, Ting Wang, Cigall Kadoch, Rudolf Jaenisch, Jianlong Wang, Thorold W Theunissen. OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nature Communications. 2021 Aug 26;12(1):5123. doi: 10.1038/s41467-021-25107-3. (IF:17.694)
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Mingsen Li, Huaxing Huang, Lingyu Li, Chenxi He, Liqiong Zhu, Huizhen Guo, Li Wang, Jiafeng Liu, Siqi Wu, Jingxin Liu, Tao Xu, Zhen Mao, Nan Cao, Kang Zhang, Fei Lan, Junjun Ding, Jin Yuan, Yizhi Liu, Hong Ouyang. Core transcription regulatory circuitry orchestrates corneal epithelial homeostasis. Nature Communicaitons. 2021 Jan 18;12(1):420. doi: 10.1038/s41467-020-20713-z.（IF: 17.694）
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Xiang Sun, Zhijun Ren, Yixian Cun, Cai Zhao, Xianglin Huang, Jiajian Zhou, Rong Hu, Xiaoxi Su, Lu Ji, Peng Li, King Lun Kingston Mak, Feng Gao, Yi Yang, He Xu, Junjun Ding, Nan Cao, Shuo Li, Wensheng Zhang, Ping Lan, Hao Sun, Jinkai Wang, Ping Yuan. Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers. Nucleic acids research. 2020 Jul 27;48(13):7182-7196. doi: 10.1093/nar/gkaa482. (IF:19.160)
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Fuxi Li, Yang Yi, Yanyan Miao, Wenyong Long, Teng Long, Siyun Chen, Weisheng Cheng, Changye Zou, Yueyuan Zheng, Xingui Wu, Junjun Ding, Kaiyu Zhu, Delin Chen, Qiongcong Xu, Jinkai Wang, Qing Liu, Feng Zhi, Jian Ren, Qi Cao and Wei Zhao. N6-Methyladenosine Modulates Nonsense-Mediated mRNA Decay in Human Glioblastoma. Cancer Research. 2019 Nov 15;79(22):5785-5798. （IF: 13.312）
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Kun-Yong Kim, Yoshiaki Tanaka, Juan Su, Bilal Cakir, Yangfei Xiang, Benjamin Patterson, Junjun Ding, Yong-Wook Jung, Ji-Hyun Kim, Eriona Hysolli, Haelim Lee, Rana Dajani, Jonghwan Kim, Mei Zhong, Jeong-Heon Lee, David Skalnik, Jeong Mook Lim, Gareth J. Sullivan, Jianlong Wang & In-Hyun Park. Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a, Nature Communicaitons. 2018 Jul 3;9(1):2583. doi: 10.1038/s41467-018-04818-0. （IF: 17.694）
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Songyan Han, Christopher Tan, Junjun Ding, Jianlong Wang, Avi Ma'ayan, Valerie Gouon-Evans. Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications, Stem Cell Research. 2018 Jul;30:163-170. doi: 10.1016/j.scr.2018.06.004. （IF: 1.587）
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Diana Guallar, Xianju Bi, Jose Angel Pardavila, Xin Huang, Carmen Saenz, Xianle Shi, Hongwei Zhou, Francesco Faiola, Junjun Ding, Phensinee Haruehanroengra, Fan Yang, Dan Li, Carlos Sanchez-Priego, Arven Saunders, Feng Pan, Victor Julian Valdes, Kevin Kelley, Miguel G. Blanco, Lingyi Chen, Huayan Wang, Jia Sheng, Mingjiang Xu, Miguel Fidalgo, Xiaohua Shen & Jianlong Wang. RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells, Nature Genetics. 2018 Feb 26. doi: 10.1038/s41588-018-0060-9. （IF: 41.307）
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Chunliu Huang Junjie Shi Yibin Guo Weijun Huang Shanshan Huang Siqi Ming Xingui Wu Rui Zhang Junjun Ding Wei Zhao Jie Jia Xi Huang Andy Peng Xiang Yongsheng Shi Chengguo Yao. A snoRNA modulates mRNA 3' end processing and regulates the expression of a subset of mRNAs, Nucleic Acids Research. 2017 Sep 6;45(15):8647-8660. （IF: 19.160）
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Francesco Faiola, Nuoya Yin, Miguel Fidalgo, Xin Huang, Arven Saunders, Junjun Ding, DianaGuallar, BaoyenDang, JianlongWang. NAC1 Regulates Somatic Cell Reprogramming by Controlling Zeb1 and E-cadherin Expression, Stem Cell Reports. 2017 Sep 12;9(3):913-926. （IF: 7.294）
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Arven Saunders, Dan Li, Francesco Faiola, Xin Huang, Miguel Fidalgo, Diana Guallar, Junjun Ding, Fan Yang, Yang Xu, Hongwei Zhou, Jianlong Wang. Context-Dependent Functions of NANOG Phosphorylation in Pluripotency and Reprogramming, Stem Cell Reports. 2017 May 9;8(5):1115-1123. （IF: 7.294）
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Bo Yang, Yi Qiu, Niu Zhou, Hong Ouyang, Junjun Ding, Bin Cheng, Jianbo Sun. Application of Stem Cells in Oral Disease Therapy: Progresses and Perspectives. Frontiers in Physiology. 2017 Apr 3;8:197. Review. （IF: 4.755）
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Arven Saunders, Xin Huang, Miguel Fidalgo, Michael H. Reimer Jr., Francesco Faiola, Junjun Ding, Carlos Sánchez-Priego, Diana Guallar, Carmen Sáenz, Dan Li, Jianlong Wang. The SIN3A/HDAC Corepressor Complex Functionally Cooperates with NANOG to Promote Pluripotency, Cell Reports. 2017 Feb 14;18(7):1713-1726. （IF: 9.995）
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Miguel Fidalgo, Xin Huang, Diana Guallar, Carlos Sanchez-Priego, Victor Julian Valdes, Arven Saunders, Junjun Ding, Wen-Shu Wu, Carlos Clave, Jianlong Wang. Zfp281 Coordinates Opposing Functions of Tet1 and Tet2 in Pluripotent States, Cell Stem Cell. 2016 Jun 21. （IF: 25.269）
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Jiao Yang, Renpeng Guo, Hua Wang, Xiaoying Ye, Zhongcheng Zhou, Jiameng Dan, Haiying Wang, Peng Gong, Wei Deng, Yu Yin, ShiQing Mao, Lingbo Wang, Junjun Ding, Jinsong Li, David L. Keefe, Meelad M. Dawlaty, Jianlong Wang, GuoLiang Xu, Lin Liu. Tet Enzymes Regulate Telomere Maintenance and Chromosomal Stability of Mouse ESCs, Cell Reports. 2016 May 24;15(8):1809-21. （IF: 9.995）
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Miguel Fidalgo, Francesco Faiola, Carlos-Filipe Pereira, Junjun Ding, Arven Saunders, Julian Gingold, Christoph Schaniel, Ihor R. Lemischka, José C. R. Silva, and Jianlong Wang. Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming, Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16202-7. （IF: 12.779）
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Yen-Sin Ang, Su-Yi Tsai, Dung-Fang Lee, Jonathan Monk, Jie Su, Kajan Ratnakumar, Junjun Ding, Yongchao Ge, Henia Darr, Betty Chang, Jianlong Wang, Michael Rendl, Emily Bernstein, Christoph Schaniel and Ihor R. Lemischkar. Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network, Cell. 2011, Volume 145, Issue 2, 15 April 2011, Pages 183-197. （IF: 66.850）
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Gang Chang, Yi-Liang Miao, Yu Zhang, Sheng Liu, Zhaohui Kou, Junjun Ding, Da-Yuan Chen, Qing-Yuan Sun, Shaorong Gao. Linking incomplete reprogramming to the improved pluripotency of murine embryonal carcinoma cell-derived pluripotent stem cells, PLoS One. 2010 Apr 26;5(4):e10320. （IF: 3.752）