2022
- Yiming Yu+, Hong Zhang+,
Yanping Long, Yi Shu, Jixian Zhai✉.
Plant Public
RNA-seq Database: a comprehensive online database for expression analysis
of ~45 000 plant public RNA-Seq libraries. Plant Biotechnology Journal, 2022 (+ co-first author)
- Zhuowen Li+, Yanping Long+, Yiming Yu,
Fei Zhang, Hong Zhang, Zhijian Liu, Jinbu Jia, Weipeng Mo, Simon Zhongyuan Tian, Meizhen Zheng,
Jixian Zhai✉.
Pore-C simultaneously captures genome-wide
multi-way chromatin interaction and associated DNA methylation status in Arabidopsis.
Plant Biotechnology Journal, 2022 (+ co-first author)
- Jinbu Jia+, Wenqin Lu+, Bo Liu, HuiHui Fang, Yiming Yu,
Weipeng Mo, Hong Zhang, Xianhao Jin, Yi Shu, Yangping Long, Yanxi Pei,
Jixian Zhai✉.
An atlas of plant full-length RNA reveals tissue-specific and monocots-dicots conserved
regulation of poly(A) tail length. Nature plants, 2022 (+ co-first author)
2021
- Sylvain Bischof✉.
Which factors shape the rice DNA methylome?. The Plant Cell, 2021 (SPOTLIGHT for our work)
- Daoheng Hu+, Yiming Yu+, Chun Wang+,
Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong,
Lei Gong, Kejian Wang✉, Jixian Zhai✉.
Multiplex CRISPR-Cas9 editing of DNA
methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich
regions. The Plant Cell, 2021 (+ co-first author)
- Weipeng Mo+, Bo Liu+, Hong Zhang, Xianhao Jin, Dongdong Lu, Yiming Yu,
Yuelin Liu, Jinbu Jia, Yanping Long, Xian Deng, Xiaofeng Cao, Hongwei Guo, Jixian Zhai✉.
Landscape of transcription termination
in Arabidopsis revealed by single-molecule nascent RNA sequencing.
Genome Biology, 2021 (+ co-first author)
2020
- Yiming Yu and Jixian Zhai✉.
The chromatin will never forget.
Nature Plants, 2020
- Hong Zhang+, Fei Zhang+, Yiming Yu+, Li Feng, Jinbu Jia,
Bo Liu, Bosheng Li, Hongwei Guo, Jixian Zhai✉.
A comprehensive online database
for exploring ∼20,000 public Arabidopsis RNA-Seq libraries.
Molecular Plant, 2020 (+ co-first author)
- Jinbu Jia+, Ronghuan Jin+, Zhuowen Li, Yiming Yu, Mayumi Nakano,
Yanping Long, Li Feng, Chao Qin, Dongdong Lu, Junpeng Zhan, Rui Xia, Blake C Meyers, Bin Liu✉,
Jixian Zhai✉.
Soybean DICER-LIKE2 regulates seed coat
color via production of primary 22-nucleotide small interfering RNAs from Long Inverted Repeats.
The Plant Cell, 2020 (+ co-first author)
2019
- Yiming Yu+, Wen Yao+,✉, Yuping Wang, Fangfang Huang.
shinyChromosome:
An R/Shiny Application for Interactive Creation of Non-circular Plots of
Whole Genomes. Genomics, Proteomics &
Bioinformatics, 2019 (+ co-first author)
- Wen Yao+, Guangwei Li+, Yanru Cui, Yiming Yu, Qifa Zhang✉, Shizhong Xu✉,
Wen Yao✉.
Mapping quantitative trait loci using
binned genotypes. Journal of Genetics and Genomics, 2019 (+ co-first author)
2018
- Yiming Yu, Yidan Ouyang✉, Wen Yao✉.
shinyCircos:
an R/Shiny application for interactive creation of Circos plot.
Bioinformatics, 2018
- Wen Yao✉, Guangwei Li, Yiming Yu, Yidan Ouyang✉.
funRiceGenes
dataset for comprehensive understanding and application of rice
functional genes. GigaScience, 2018
- Chunmei Zhu+, Qiang Peng, Debao Fu, Dongxia Zhuang, Yiming Yu, Min Duan, Weibo Xie, Yaohui Cai, Yidang Ouyang,
Xingming Lian, Changyin Wu✉.
The E3 ubiquitin ligase HAF1 modulates circadian accumulation of EARLY FLOWERING3 to control heading date in rice under long-day
conditions. The Plant Cell, 2018
2017
- Yanfen Zhu+, Yiming Yu, Ke Cheng, Yidan Ouyang, Jia Wang, Liang Gong, Qinghua Zhang, Xianghua Li, Jinghua Xiao, Qifa Zhang✉.
Processes underlying a reproductive barrier in
indica-japonica rice hybrids revealed by transcriptome analysis. Plant Physiology, 2017