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Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE
He, Jiangping, Babarinde, Isaac A., Sun, Li, Xu, Shuyang, Chen, Ruhai, Shi, Junjie, Wei, Yuanjie, Li, Yuhao, Ma, Gang, Zhuang, Qiang, Hutchins, Andrew P., Chen, Jiekai
Published in Nature communications (05.03.2021)
Published in Nature communications (05.03.2021)
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Chromatin Accessibility Dynamics during iPSC Reprogramming
Li, Dongwei, Liu, Jing, Yang, Xuejie, Zhou, Chunhua, Guo, Jing, Wu, Chuman, Qin, Yue, Guo, Lin, He, Jiangping, Yu, Shenyong, Liu, He, Wang, Xiaoshan, Wu, Fang, Kuang, Junqi, Hutchins, Andrew P., Chen, Jiekai, Pei, Duanqing
Published in Cell stem cell (07.12.2017)
Published in Cell stem cell (07.12.2017)
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A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes
Li, Qiuhong, Hutchins, Andrew P., Chen, Yong, Li, Shengbiao, Shan, Yongli, Liao, Baojian, Zheng, Dejin, Shi, Xi, Li, Yinxiong, Chan, Wai-Yee, Pan, Guangjin, Wei, Shicheng, Shu, Xiaodong, Pei, Duanqing
Published in Nature communications (03.05.2017)
Published in Nature communications (03.05.2017)
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c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells
Zhang, Ran, Li, Guihuan, Zhang, Qi, Wang, Zhenhua, Xiang, Dan, Zhang, Xiaofei, Chen, Jiekai, Hutchins, Andrew P, Qin, Dajiang, Su, Huanxing, Pei, Duanqing, Li, Dongwei
Published in Nucleic acids research (24.01.2025)
Published in Nucleic acids research (24.01.2025)
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The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters
Bao, Xichen, Wu, Haitao, Zhu, Xihua, Guo, Xiangpeng, Hutchins, Andrew P, Luo, Zhiwei, Song, Hong, Chen, Yongqiang, Lai, Keyu, Yin, Menghui, Xu, Lingxiao, Zhou, Liang, Chen, Jiekai, Wang, Dongye, Qin, Baoming, Frampton, Jon, Tse, Hung-Fat, Pei, Duanqing, Wang, Huating, Zhang, Biliang, Esteban, Miguel A
Published in Cell research (01.01.2015)
Published in Cell research (01.01.2015)
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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells
He, Jiangping, Fu, Xiuling, Zhang, Meng, He, Fangfang, Li, Wenjuan, Abdul, Mazid Md, Zhou, Jianguo, Sun, Li, Chang, Chen, Li, Yuhao, Liu, He, Wu, Kaixin, Babarinde, Isaac A., Zhuang, Qiang, Loh, Yuin-Han, Chen, Jiekai, Esteban, Miguel A., Hutchins, Andrew P.
Published in Nature communications (03.01.2019)
Published in Nature communications (03.01.2019)
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Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq
Guo, Lin, Lin, Lihui, Wang, Xiaoshan, Gao, Mingwei, Cao, Shangtao, Mai, Yuanbang, Wu, Fang, Kuang, Junqi, Liu, He, Yang, Jiaqi, Chu, Shilong, Song, Hong, Li, Dongwei, Liu, Yujian, Wu, Kaixin, Liu, Jiadong, Wang, Jinyong, Pan, Guangjin, Hutchins, Andrew P., Liu, Jing, Pei, Duanqing, Chen, Jiekai
Published in Molecular cell (21.02.2019)
Published in Molecular cell (21.02.2019)
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PCGF5 is required for neural differentiation of embryonic stem cells
Yao, Mingze, Zhou, Xueke, Zhou, Jiajian, Gong, Shixin, Hu, Gongcheng, Li, Jiao, Huang, Kaimeng, Lai, Ping, Shi, Guang, Hutchins, Andrew P., Sun, Hao, Wang, Huating, Yao, Hongjie
Published in Nature communications (15.05.2018)
Published in Nature communications (15.05.2018)
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Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells
Babarinde, Isaac A, Ma, Gang, Li, Yuhao, Deng, Boping, Luo, Zhiwei, Liu, Hao, Abdul, Mazid Md, Ward, Carl, Chen, Minchun, Fu, Xiuling, Shi, Liyang, Duttlinger, Martha, He, Jiangping, Sun, Li, Li, Wenjuan, Zhuang, Qiang, Tong, Guoqing, Frampton, Jon, Cazier, Jean-Baptiste, Chen, Jiekai, Jauch, Ralf, Esteban, Miguel A, Hutchins, Andrew P
Published in Nucleic acids research (20.09.2021)
Published in Nucleic acids research (20.09.2021)
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Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2
Malik, Vikas, Glaser, Laura V., Zimmer, Dennis, Velychko, Sergiy, Weng, Mingxi, Holzner, Markus, Arend, Marius, Chen, Yanpu, Srivastava, Yogesh, Veerapandian, Veeramohan, Shah, Zahir, Esteban, Miguel A., Wang, Huating, Chen, Jiekai, Schöler, Hans R., Hutchins, Andrew P., Meijsing, Sebastiaan H., Pott, Sebastian, Jauch, Ralf
Published in Nature communications (02.08.2019)
Published in Nature communications (02.08.2019)
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Metabolic and epigenetic dysfunctions underlie the arrest of in vitro fertilized human embryos in a senescent-like state
Yang, Yang, Shi, Liyang, Fu, Xiuling, Ma, Gang, Yang, Zhongzhou, Li, Yuhao, Zhou, Yibin, Yuan, Lihua, Xia, Ye, Zhong, Xiufang, Yin, Ping, Sun, Li, Zhang, Wuwen, Babarinde, Isaac A., Wang, Yongjun, Zhao, Xiaoyang, Hutchins, Andrew P., Tong, Guoqing
Published in PLoS biology (30.06.2022)
Published in PLoS biology (30.06.2022)
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Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages
Babarinde, Isaac A., Fu, Xiuling, Ma, Gang, Li, Yuhao, Liang, Zhangting, Xu, Jianfei, Xiao, Zhen, Qiao, Yu, Lin, Zheng, Oleynikova, Katerina, Akinwole, Mobolaji T., Zhou, Xuemeng, Ruzov, Alexey, Hutchins, Andrew P.
Published in Nature communications (18.08.2025)
Published in Nature communications (18.08.2025)
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Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm
Aksoy, Irene, Jauch, Ralf, Chen, Jiaxuan, Dyla, Mateusz, Divakar, Ushashree, Bogu, Gireesh K, Teo, Roy, Leng Ng, Calista Keow, Herath, Wishva, Lili, Sun, Hutchins, Andrew P, Robson, Paul, Kolatkar, Prasanna R, Stanton, Lawrence W
Published in The EMBO journal (03.04.2013)
Published in The EMBO journal (03.04.2013)
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RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions
Li, Huanhuan, Lai, Ping, Jia, Jinping, Song, Yawei, Xia, Qing, Huang, Kaimeng, He, Na, Ping, Wangfang, Chen, Jiayu, Yang, Zhongzhou, Li, Jiao, Yao, Mingze, Dong, Xiaotao, Zhao, Jicheng, Hou, Chunhui, Esteban, Miguel A., Gao, Shaorong, Pei, Duanqing, Hutchins, Andrew P., Yao, Hongjie
Published in Cell stem cell (06.04.2017)
Published in Cell stem cell (06.04.2017)
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Author Correction: VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification
Yang, Yueli, Jia, Wenqi, Luo, Zhiwei, Li, Yunpan, Liu, Hao, Fu, Lixin, Li, Jinxiu, Jiang, Yu, Lai, Junjian, Li, Haiwei, Saeed, Babangida Jabir, Zou, Yi, Lv, Yuan, Wu, Liang, Zhou, Ting, Shan, Yongli, Liu, Chuanyu, Lai, Yiwei, Liu, Longqi, Hutchins, Andrew P., Esteban, Miguel A., Mazid, Md. Abdul, Li, Wenjuan
Published in Nature communications (18.03.2025)
Published in Nature communications (18.03.2025)
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An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis
Li, Jiao, Huang, Kaimeng, Hu, Gongcheng, Babarinde, Isaac A., Li, Yaoyi, Dong, Xiaotao, Chen, Yu-Sheng, Shang, Liping, Guo, Wenjing, Wang, Junwei, Chen, Zhaoming, Hutchins, Andrew P., Yang, Yun-Gui, Yao, Hongjie
Published in Nature communications (04.04.2019)
Published in Nature communications (04.04.2019)
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VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification
Yang, Yueli, Jia, Wenqi, Luo, Zhiwei, Li, Yunpan, Liu, Hao, Fu, Lixin, Li, Jinxiu, Jiang, Yu, Lai, Junjian, Li, Haiwei, Saeed, Babangida Jabir, Zou, Yi, Lv, Yuan, Wu, Liang, Zhou, Ting, Shan, Yongli, Liu, Chuanyu, Lai, Yiwei, Liu, Longqi, Hutchins, Andrew P., Esteban, Miguel A., Mazid, Md. Abdul, Li, Wenjuan
Published in Nature communications (17.01.2024)
Published in Nature communications (17.01.2024)
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CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming
Song, Yawei, Liang, Zhengyu, Zhang, Jie, Hu, Gongcheng, Wang, Juehan, Li, Yaoyi, Guo, Rong, Dong, Xiaotao, Babarinde, Isaac A., Ping, Wangfang, Sheng, Ying-Liang, Li, Huanhuan, Chen, Zhaoming, Gao, Minghui, Chen, Yang, Shan, Ge, Zhang, Michael Q., Hutchins, Andrew P., Fu, Xiang-Dong, Yao, Hongjie
Published in Cell reports (Cambridge) (05.04.2022)
Published in Cell reports (Cambridge) (05.04.2022)
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Transposable Elements in Pluripotent Stem Cells and Human Disease
Ma, Gang, Babarinde, Isaac A., Zhou, Xuemeng, Hutchins, Andrew P.
Published in Frontiers in genetics (02.06.2022)
Published in Frontiers in genetics (02.06.2022)
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