Publications

Jiejun Shi, Jianfeng Xu, Yiling Elaine Chen, Jason Sheng Li, Ya Cui, Lanlan Shen, Jingyi Jessica Li, Wei Li. The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nature Communications, 2021.
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Carolina M. Greco, Kevin B. Koronowski, Jacob G. Smith, Jiejun Shi, Paolo Kunderfranco, Roberta Carriero, Siwei Chen, Muntaha Samad, Patrick-Simon Welz, Valentina M. Zinna, Thomas Mortimer, Sung Kook Chun, Kohei Shimaji, Tomoki Sato, Paul Petrus, Arun Kumar, Mireia Vaca-Dempere, Oleg Deryagin, Cassandra Van, José Manuel Monroy Kuhn, Dominik Lutter, Marcus M. Seldin, Selma Masri, Wei Li, Pierre Baldi, Kenneth A. Dyar, Pura Muñoz-Cánoves, Salvador Aznar Benitah, Paolo Sassone-Corsi. Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms. Science Advances, 2021.
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Jianfeng Xu, Jiejun Shi, Xiaodong Cui, Ya Cui, Jingyi Jessica Li, Ajay Goel, Xi Chen, Jean-Pierre Issa, Jianzhong Su, Wei Li. Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression. Nature Communications, 2021.
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Carolina Magdalen Greco, Marlene Cervantes, Jean-Michel Fustin, Kakeru Ito, Nicholas Ceglia, Muntaha Samad, Jiejun Shi, Kevin Brian Koronowski, Ignasi Forne, Suman Ranjit, Jonathan Gaucher, Kenichiro Kinouchi, Rika Kojima, Enrico Gratton, Wei Li, Pierre Baldi, Axel Imhof, Hitoshi Okamura, Paolo Sassone-Corsi. S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling. Science Advances, 2020.
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Ya Cui, Zhe Cui, Jianfeng Xu, Dapeng Hao, Jiejun Shi, Dan Wang, Hui Xiao, Xiaohong Duan, Runsheng Chen, Wei Li. NG-Circos: next-generation Circos for data visualization and interpretation. NAR genomics and bioinformatics, 2020.
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Li-Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailovic, Thalia A. Farazi, Thomas Tuschl, Samuel Singer. Statistical Assessment of Depth Normalization for Small RNA Sequencing. JCO clinical cancer informatics, 2020.
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Yilei Zhang, Jiejun Shi, Xiaoguang Liu, Zhenna Xiao, Guang Lei, Hyemin Lee, Pranavi Koppula, Weijie Cheng, Chao Mao, Li Zhuang, Li Ma, Wei Li, Boyi Gan. H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death. Cancer Research, 2020.
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Xiaoguang Liu, Kellen Olszewski, Yilei Zhang, Esther W. Lim, Jiejun Shi, Xiaoshan Zhang, Jie Zhang, Hyemin Lee, Pranavi Koppula, Guang Lei, Li Zhuang, M. James You, Bingliang Fang, Wei Li, Christian M. Metallo, Masha V. Poyurovsky, Boyi Gan. Cystine transporter regulation of pentose phosphate pathway dependency and disulfide stress exposes a targetable metabolic vulnerability in cancer. Nature Cell Biology, 2020.
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Ze-Yi Zheng, Meenakshi Anurag, Jonathan T. Lei, Jin Cao, Purba Singh, Jianheng Peng, Hilda Kennedy, Nhu-Chau Nguyen, Yue Chen, Philip Lavere, Jing Li, Xin-Hui Du, Burcu Cakar, Wei Song, Beom-Jun Kim, Jiejun Shi, Sinem Seker, Doug W. Chan, Guo-Qiang Zhao, Xi Chen, Kimberly C. Banks, Richard B. Lanman, Maryam Nemati Shafaee, Xiang H.-F. Zhang, Suhas Vasaikar, Bing Zhang, Susan G. Hilsenbeck, Wei Li, Charles E. Foulds, Matthew J. Ellis, Eric C. Chang. Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer. Cancer Cell, 2020.
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Yu Chen, Haiping Zhang, Zhu Xu, Huanyin Tang, Anke Geng, Bailian Cai, Tao Su, Jiejun Shi, Cizhong Jiang, Xiao Tian, Andrei Seluanov, Jun Huang, Xiaoping Wan, Ying Jiang, Vera Gorbunova, Zhiyong Mao. A PARP1-BRG1-SIRT1 axis promotes HR repair by reducing nucleosome density at DNA damage sites. Nucleic Acids Research, 2019.
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Kevin B. Koronowski, Kenichiro Kinouchi, Patrick-Simon Welz, Jacob G. Smith, Valentina M. Zinna, Jiejun Shi, Muntaha Samad, Siwei Chen, Christophe N. Magnan, Jason M. Kinchen, Wei Li, Pierre Baldi, Salvador Aznar Benitah, Paolo Sassone-Corsi. Defining the Independence of the Liver Circadian Clock. Cell, 2019.
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Yilei Zhang, Jiejun Shi, Xiaoguang Liu, Li Feng, Zihua Gong, Pranavi Koppula, Kapil Sirohi, Xu Li, Yongkun Wei, Hyemin Lee, Li Zhuang, Gang Chen, Zhen-Dong Xiao, Mien-Chie Hung, Junjie Chen, Peng Huang, Wei Li, Boyi Gan. BAP1 links metabolic regulation of ferroptosis to tumour suppression. Nature Cell Biology, 2018.
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Yi Zhang, Yongming Xue, Jiejun Shi, JaeWoo Ahn, Wenyi Mi, Muzaffar Ali, Xiaolu Wang, Brianna J. Klein, Hong Wen, Wei Li, Xiaobing Shi, Tatiana G. Kutateladze. The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3. Nature Structural & Molecular Biology, 2018.
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Leilei Shi, Jiejun Shi, Xiaobing Shi, Wei Li, Hong Wen. Histone H3.3 G34 Mutations Alter Histone H3K36 and H3K27 Methylation In Cis. Journal of Molecular Biology, 2018.
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Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y. R. Dent. Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC genomics, 2018.
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Chih-Chao Hsu, Jiejun Shi, Chao Yuan, Dan Zhao, Shiming Jiang, Jie Lyu, Xiaolu Wang, Haitao Li, Hong Wen, Wei Li, Xiaobing Shi. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes & Development, 2018.
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Chih-Chao Hsu, Dan Zhao, Jiejun Shi, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li, Xiaobing Shi. Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. Cell Discovery, 2018.
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Leah A. Gates, Jiejun Shi, Aarti D. Rohira, Qin Feng, Bokai Zhu, Mark T. Bedford, Cari A. Sagum, Sung Yun Jung, Jun Qin, Ming-Jer Tsai, Sophia Y. Tsai, Wei Li, Charles E. Foulds, Bert W. O'Malley. Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation. The Journal of Biological Chemistry, 2017.
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Pranavi Koppula, Yilei Zhang, Jiejun Shi, Wei Li, Boyi Gan. The glutamate/cystine antiporter SLC7A11/xCT enhances cancer cell dependency on glucose by exporting glutamate. The Journal of Biological Chemistry, 2017.
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Youqiong Ye, Min Li, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang. Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death and Differentiation, 2017.
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Youqiong Ye, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang. Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos. Scientific Reports, 2016.
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Jiejun Shi, Jiangtu He, Jing Lin, Xin Sun, Fenyong Sun, Chao Ou, Cizhong Jiang. Distinct response of the hepatic transcriptome to Aflatoxin B1 induced hepatocellular carcinogenesis and resistance in rats. Scientific Reports, 2016.
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Dong Li, Jiejun Shi, Yanhua Du, Kaiming Chen, Zhenping Liu, Bing Li, Jie Li, Fei Tao, Hua Gu, Cizhong Jiang, Jianmin Fang. Profiling Analysis of Histone Modifications and Gene Expression in Lewis Lung Carcinoma Murine Cells Resistant to Anti-VEGF Treatment. PloS One, 2016.
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Kaimeng Huang, Xiaobai Zhang, Jiejun Shi, Mingze Yao, Jiannan Lin, Jiao Li, He Liu, Huanhuan Li, Guang Shi, Zhibin Wang, Biliang Zhang, Jiekai Chen, Guangjin Pan, Cizhong Jiang, Duanqing Pei, Hongjie Yao. Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells. Scientific Reports, 2015.
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Jiejun Shi, Meizhu Zheng, Youqiong Ye, Min Li, Xiaolong Chen, Xinjie Hu, Jin Sun, Xiaobai Zhang, Cizhong Jiang. Drosophila Brahma complex remodels nucleosome organizations in multiple aspects. Nucleic Acids Research, 2014.
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Jiejun Shi, Li-Xuan Qin. CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering. Cancer Informatics, 2014.
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Jiejun Shi, Jian Hu, Qing Zhou, Yanhua Du, Cizhong Jiang. PEpiD: a prostate epigenetic database in mammals. PloS One, 2013.
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Xiaojing Wang, Jiejun Shi, JF Yang, Y Liang, YF Wang, ML Wu, SY Li, XD Guo, ZG Wang, DJ Liu. Molecular Characterization and Expression Pattern of Gene IGFBP-5 in the Cashmere Goat (Capra hircus). Asian-Australasian journal of animal sciences, 2012.
Xu Zheng, Jiao-fu YANG, Xiao-jing WANG, Yan Liang, Manlin WU, Jiejun Shi, Tao Zhang, QIN Yin, Shuyu LI, Xiyan HAO, others. Molecular characterization and expression pattern of rheb gene in inner mongolia cashmere goat (Capra hircus). Agricultural Sciences in China, 2011.
JiaoFu Yang, Jiejun Shi, Yan Liang, Xu Zheng, Tao Zhang, Yi Qin, ZhiGang Wang, DongJun Liu, others. Cloning and expression pattern of protein kinase B/AKT gene in Inner Mongolia Cashmere Goat.. Scientia Agricultura Sinica, 2011.
Tao Zhang, ZhiGang Wang, Bin Li, Jiejun Shi, Yi Qin, DongJun Liu. Molecular cloning and characterization analysis of LEF-1 gene from Inner Mongolia Cashmere Goat. 2010 3rd International Conference on Biomedical Engineering and Informatics, 2010.