500 Papers
2.3K Citations
Jie Deng is an academic researcher from Northwestern Polytechnical University. The author has contributed to research in topics: Medicine & Population. The author has an hindex of 54, co-authored 423 publications. Previous affiliations of Jie Deng include University of Pennsylvania & Chongqing University.
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Papers
The genome of the mesopolyploid crop species Brassica rapa
Xiaowu Wang,Hanzhong Wang,Jun Wang,Jun Wang,Jun Wang,Rifei Sun,Jian Wu,Shengyi Liu,Yinqi Bai,Jeong-Hwan Mun,Ian Bancroft,Feng Cheng,Sanwen Huang,Xixiang Li,Wei Hua,Junyi Wang,Xiyin Wang,Xiyin Wang,Michael Freeling,J. Chris Pires,Andrew H. Paterson,Boulos Chalhoub,Bo Wang,Alice Hayward,Alice Hayward,Andrew G. Sharpe,Beom-Seok Park,Bernd Weisshaar,Binghang Liu,Bo Li,Bo Liu,Chaobo Tong,Chi Song,Chris Duran,Chris Duran,Chunfang Peng,Geng Chunyu,Chushin Koh,Chuyu Lin,David Edwards,David Edwards,Desheng Mu,Di Shen,Eleni Soumpourou,Fei Li,Fiona Fraser,Gavin C. Conant,Gilles Lassalle,Graham J.W. King,Guusje Bonnema,Haibao Tang,Haiping Wang,Harry Belcram,Heling Zhou,Hideki Hirakawa,Hiroshi Abe,Hui Guo,Hui Wang,Huizhe Jin,Isobel A. P. Parkin,Jacqueline Batley,Jacqueline Batley,Jeong-Sun Kim,Jérémy Just,Jianwen Li,Jiaohui Xu,Jie Deng,Jin A Kim,Jingping Li,Jingyin Yu,Jinling Meng,Jinpeng Wang,Jiumeng Min,Julie Poulain,Katsunori Hatakeyama,Kui Wu,Li Wang,Lu Fang,Martin Trick,Matthew G. Links,Meixia Zhao,Mina Jin,Nirala Ramchiary,Nizar Drou,Paul J. Berkman,Paul J. Berkman,Qingle Cai,Quanfei Huang,Ruiqiang Li,Satoshi Tabata,Shifeng Cheng,Shu Zhang,Shujiang Zhang,Shunmou Huang,Shusei Sato,Silong Sun,Soo-Jin Kwon,Su-Ryun Choi,Tae-Ho Lee,Wei Fan,Xiang Zhao,Xu Tan,Xun Xu,Yan Wang,Yang Qiu,Ye Yin,Yingrui Li,Yongchen Du,Yongcui Liao,Yong Pyo Lim,Yoshihiro Narusaka,Yupeng Wang,Zhenyi Wang,Zhenyu Li,Zhiwen Wang,Zhiyong Xiong,Zhonghua Zhang +116 more
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells
Yufei Xu,Feizhen Wu,Li Tan,Lingchun Kong,Lijun Xiong,Jie Deng,Andrew J. Barbera,Lijuan Zheng,Haikuo Zhang,Stephen A. Huang,Jinrong Min,Thomas B. Nicholson,Taiping Chen,Guoliang Xu,Yang Shi,Yang Shi,Kun Zhang,Yujiang Geno Shi,Yujiang Geno Shi +18 more
TL;DR: The data suggest that Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting 5mC to 5hmC through hydroxylase activity.
671
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
Jie Deng,Robert Shoemaker,Bin Xie,Athurva Gore,Emily M LeProust,Jessica Antosiewicz-Bourget,Dieter Egli,Nimet Maherali,In-Hyun Park,Junying Yu,George Q. Daley,Kevin Eggan,Konrad Hochedlinger,James A. Thomson,Wei Li Wang,Yuan Gao,Kun Zhang +16 more
TL;DR: A method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution is reported.
573
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
TL;DR: A chromosome-wide survey of ASM was carried out across 16 human pluripotent and adult cell lines using Illumina bisulfite sequencing and a potential role for CpG-SNP is suggested in connecting genetic variation with the epigenome.
Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea
Feng Cheng,Rifei Sun,Xilin Hou,Hongkun Zheng,Fenglan Zhang,Yangyong Zhang,Bo Liu,Jianli Liang,Mu Zhuang,Yunxia Liu,Dongyuan Liu,Xiaobo Wang,Pingxia Li,Yumei Liu,Ke Lin,Johan Bucher,Ningwen Zhang,Yan Wang,Hui Wang,Jie Deng,Yongcui Liao,Keyun Wei,Xueming Zhang,Lixia Fu,Yunyan Hu,Jisheng Liu,Chengcheng Cai,Shujiang Zhang,Shifan Zhang,Fei Li,Hui Zhang,Jifang Zhang,Ning Guo,Zhiyuan Liu,Jin Liu,Chao Sun,Yuan Ma,Haijiao Zhang,Yang Cui,M Freeling,Theo Borm,Guusje Bonnema,Jian Wu,Xiaowu Wang +43 more
TL;DR: It is demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.
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