Zhang Lab

Plant Bioinformatics and Functional Epigenomics Group

Publication


2020-2016

2015-2010

Before 2010

note: #, Co-first author;  *, Corresponding author;  Lab members' name are in bold.

[2020]

  • Kun Wu#, Shuansuo Wang#, Wenzhen Song, Jianqing Zhang, Yun Wang, Qian Liu, Jianping Wang, Yafeng Ye, Shan Li, Jianfeng Chen, Ying Zhao, Jing Wang, Xiaokang Wu, Meiyue Wang, Yijing Zhang, Binmei Liu, Yuejun Wu, Nicholas P. Harberd*, Xiangdong Fu*(2020) Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice, Science, DOI: 10.1126/science.aaz2046
    http://dx.doi.org/10.1126/science.aaz2046 PDF
  • Bo Yu#, Yuejun Wang#,Hua Zhou, Ping Li, Chunmei Liu, Sunlu Chen, Yu Peng, Yijing Zhang*, Sheng Teng*(2020) Genome‐wide binding analysis reveals that ANAC060 directly represses sugar‐induced ABI5 transcription in Arabidopsis, The Plant Journal
    https://doi.org/10.1111/tpj.14777 PDF
  • Xiaojuan Ran#, Fei Zhao#, Yuejun Wang#, Jian Liu, Yili Zhuang, Luhuan Ye, Meifang Qi, Jingfei Cheng, Yijing Zhang* (2020) Plant Regulomics: A Data-driven Interface for Retrieving Upstream Regulators from Plant Multi-omics Data, The Plant Journal, 101(1):237-248
    https://doi.org/10.1111/tpj.14526 PDF

[2019]

  • Zijuan Li#, Meiyue Wang#,Kande Lin#, Yilin Xie#, Jingyu Guo, Luhuan Ye, Yili Zhuang, Wan Teng, Xiaojuan Ran, Yiping Tong, Yongbiao Xue, Wenli Zhang*, Yijing Zhang* (2019) The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements, Genome Biology, 20(1):139
    https://doi.org/10.1186/s13059-019-1746-8 PDF
  • Chunmei Liu#, Jingfei Cheng#, Yili Zhuang, Luhuan Ye, Zijuan Li, Yuejun Wang, Meifang Qi, Yijing Zhang* (2019) Polycomb repressive complex 2 attenuates ABA-induced senescence in Arabidopsis, Plant Journal, 97(2):368-377
    https://doi.org/10.1111/tpj.14125 PDF
  • Jing Pan#, Fei Zhao#, Guifang Zhang#, Yu Pan, Lijun Sun, Ning Bao, Peng Qin, Lyuqin Chen, Jie Yu*, Yijing Zhang*, Lin Xu*. (2019) Control of de novo root regeneration efficiency by developmental status of Arabidopsis leaf explants, Journal of Genetics and Genomics. 46(3):133-140
    https://doi.org/10.1186/s13059-018-1587-x PDF
  • Yuhao Liu, Kunpeng Liu, Liufan Yin, Yu Yu, Ji Qi, Wen‑Hui Shen, Jun Zhu, Yijing Zhang* and Aiwu Dong* (2019) H3K4me2 functions as a repressive epigenetic mark in plants, Epigenetics and Chromatin, 12(1):40
    https://doi.org/10.1186/s13072-019-0285-6 PDF
  • Zhiye Wang#, Meiyue Wang#, Tian Wang, Yijing Zhang*, Xiuren Zhang*. (2019) Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis, Methods, 155:30-40
    https://doi.org/10.1016/j.ymeth.2018.11.018 PDF
  • Guifang Zhang#, Fei Zhao#, Lyuqin Chen#, Yu Pan, Lijun Sun, Ning Bao, Teng Zhang, Chun-Xiao Cui, Zaozao Qiu, Yijing Zhang and Lin Xu*. (2019) Jasmonate-mediated wound signalling promotes plant regeneration, Nature Plants. 5(5):491-497
    https://doi.org/10.1038/s41477-019-0408-x PDF
  • Miaomiao Li, Dongfen Zhang, Qiang Gao, Yingfeng Luo, Hui Zhang, Bin Ma, Chunhai Chen, Annabel Whibley, Yu'e Zhang, Yinghao Cao, Qun Li, Han Guo, Junhui Li,Yanzhai Song, Yue Zhang, Lucy Copsey, Yan Li, Xiuxiu Li, Ming Qi, Jiawei Wang, Yan Chen, Dan Wang, Jinyang Zhao, Guocheng Liu, Bin Wu, Lili Yu, Chunyan Xu, Jiang Li, Shancen Zhao, Yijing Zhang, Songnian Hu, Chengzhi Liang*, Ye Yin*, Enrico Coen* and Yongbiao Xue*. (2019) Genome structure and evolution of Antirrhinum majus L, Nature Plants, 5(2):174-183
    https://www.nature.com/articles/s41477-018-0349-9 PDF
  • Jun Fang#*, Fantao Zhang#, Hongru Wang, Wei Wang, Fei Zhao, Zijuan Li, Changhui Sun, Faming Chen,Fan Xu, Shuoqi Chang, Liang Wu, Qingyun Bu, Pingrong Wang, Jiankun Xie, Fan Chena, Xuehui Huang, Yijing Zhang, Xinguang Zhu, Bin Han, Xiaojian Deng*, and Chengcai Chu* (2019) Ef-Cd Locus Shortens Rice Maturity Duration without Yield Penalty, Proceedings of the National Academy of Sciences of the United States of America,116(37):18717-18722
    https://doi.org/10.1073/pnas.1815030116 PDF
  • Mushan Li, Shiqi Tu, Zijia Li, Fengxiang Tan, Jian Liu, Qian Wang, Yuannyu Zhang, Jian Xu, Yijing Zhang, Feng Zhou, Zhen Shao (2019) MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes, Cell Discovery, 5:40
    https://doi.org/10.1038/s41421-019-0107-9 PDF
  • Junbo Yang, Meiyue Wang, Wenjing Li, Xue He, Wan Teng, Wenying Ma, Xueqiang Zhao, Mengyun Hu, Hui Li, Yijing Zhang, Yiping Tong*. (2019) Reducing expression of a nitrate-responsive bZIP transcription factor increases grain yield and N use in wheat, Plant Biotechnology Journal. 17(9):1823-1833
    https://doi.org/10.1111/pbi.13103 PDF
  • Jie Yu, Yuyun Zhang, Wu Liu, Hua Wang, Shaoting Wen, Yijing Zhang, Lin Xu* (2019) Molecular evolution of auxin-mediated root initiation in plants, Molecular Biology and Evolution, pii: msz202
    https://doi.org/10.1093/molbev/msz202 PDF

[2018]

  • Jingfei Cheng#, Qingfeng Niu#, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang*, Zhaobo Lang*. (2018) Downregulation of RdDM during strawberry fruit ripening, Genome Biology. 19:212
    https://doi.org/10.1186/s13059-018-1587-x PDF
  • Hongduo Sun, Jiawei Wang, Zhaohui Gong, Jiaying Yao, Yuangao Wang, Jian Xu, Guo-cheng Yuan, Yijing Zhang* and Zhen Shao* (2018) Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters, Cell Discovery, 4:38
    https://doi.org/10.1038/s41421-018-0045-y PDF
  • Meifang Qi#, Zijuan Li#, Chunmei Liu#, Wenyan Hu, Luhuan Ye, Yilin Xie, Yili Zhuang, Fei Zhao, Wan Teng, Qi Zheng, Zhenjun Fan, Lin Xu, Zhaobo Lang, Yiping Tong*, and Yijing Zhang*. (2018) CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome, Nucleic Acid Research, gky522.
    https://doi.org/10.1093/nar/gky522 PDF

  • Wenbo Li, Haimin Li, Peng Xu, Zhi Xie, Yajin Ye, Lingting Li, Deqiang Li, Yijing Zhang, Laigeng Li, Yang Zhao (2018) Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway, Plant Molecular Biology, 98:275-287
    https://doi.org/10.1007/s11103-018-0779-9 PDF
  • Dongmei Yin*#,Changmian Ji#, Xingli Ma#, Hang Li, Wanke Zhang, Song Li, Fuyan Liu, unkun Zhao, Fapeng Li, Ke Li, Longlong Ning, Jialin He, Yuejun Wang, Fei Zhao, Yilin Xie, Hongkun Zheng, Xingguo Zhang, Yijing Zhang and Jinsong Zhang* (2018) Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly, GigaScience, 7(6)
    https://doi.org/10.1093/gigascience/giy066 PDF

  • Yue Zhou, Yuejun Wang, Kristin Krause, Tingting Yang, Joram A. Dongus, Yijing Zhang and Franziska Turck*. Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. Nature Genetics, 50(5):638-644
    10.1038/s41588-018-0109-9 PDF

  • Xiaojuan Ran, Jian Liu, Meifang Qi, Yuejun Wang, Jingfei Cheng and Yijing Zhang*. GSHR, a Web-based Platform Provides Gene Set-level Analyses of Hormone Responses in Arabidopsis[J]. Frontiers in Plant Science, 2018, 9: 23
    https://doi.org/10.3389/fpls.2018.00023 PDF

[2017]

  • Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K. Handab, and Jian-Kang Zhu. Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit[J]. Proceedings of the National Academy of Sciences, 2017: 201705233.
    https://doi.org/10.1073/pnas.1705233114 PDF

  • Bo Hu#, Guifang Zhang#, Wu Liu#, Jianmin Shi#, Hua Wang#, Meifang Qi, Jiqin Li, Peng Qin, Ying Ruan, Hai Huang, Yijing Zhang, Lin Xu*. (2017) Divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms, Regeneration, 4(3):132-139.
    https://doi.org/10.1002/reg2.82 PDF

  • Jia-Shi Peng#, Yue-Jun Wang#, Ge Ding, Hai-Ling Ma, Yi-Jing Zhang*, Ji-Ming Gong*. (2017) A Pivotal Role of Cell Wall in Cadmium Accumulation in the Crassulaceae hyperaccumulator Sedum plumbizincicola. Molecular Plant, Volume 10 , Issue 5 , 771 - 774
    https://doi.org/10.1016/j.molp.2016.12.007 PDF

[2016]

  • Zhongfei Li#, Bin Li#, Jian Liu, Zhihao Guo, Yuhao Liu, Yan Li, Wen-Hui Shen, Ying Huang, Hai Huang, Yijing Zhang* and Aiwu Dong*. (2016) Transcription factors AS1 and AS2 interact withLHP1 to repress KNOX genes in Arabidopsis. Journal of Integrative Plant Biology. 58(12):959-970
    http://onlinelibrary.wiley.com/doi/10.1111/jipb.12485/abstract PDF

  • Xiaodong Chen, Jingfei Cheng, Lyuqin Chen, Guifang Zhang, Hai Huang, Yijing Zhang and Lin Xu*. (2016) Auxin-Independent NAC Pathway Acts in Response to Explant-Specific Wounding and Promotes Root Tip Emergence during de Novo Root Organogenesis in Arabidopsis, Plant Physiology,170(4):2136-2145.
    https://doi.org/10.1104/pp.15.01733 PDF

  • Anthony J Covarrubias#, Halil Ibrahim Aksoylar, Jiujiu Yu, Nathaniel W Snyder, Andrew J Worth, Shankar S Iyer, Jiawei Wang, Issam Ben-Sahra, Vanessa Byles, Tiffany Polynne-Stapornkul, Erika C Espinosa, Dudley Lamming, Brendan D Manning, Yijing Zhang, Ian A Blair, Tiffany Horng*. (2016) Akt-mTORC1signaling regulates Acly to integrate metabolic input to control of macrophage activation. eLIFE.2016,5: p e11612.
    https://elifesciences.org/content/5/e11612 PDF

  • Hua Wang#, Chunmei Liu#, Jingfei Cheng#, Jian Liu, Lei Zhang, Chongsheng He, Wen-Hui Shen, Hong Jin*, Lin Xu*, Yijing Zhang*. (2016) Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements, PLoS Genetics, 12(1): e1005771.
    http://www.plosgenetics.org/article/comments/info:doi/10.1371/journal.pgen.1005771 PDF Data Browse

[2015]

  • Meiqing Xing#, Yijing Zhang#, Shirong Zhou#, Wenyan Hu#, Xueting Wu, Yajin Ye, Xiaoxia Wu, Yunping Xiao, Xuan Li, and Hongwei Xue*. (2015) Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development, Plant Physiology, 168, pp, 1417-1432.
    https://doi.org/10.1104/pp.15.00414 PDF

  • Jiawei Wang#, Meifang Qi#, Jian Liu#, Yijing Zhang*. (2015) CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data, Plant Journal, 83(2):359-374.
    http://bioinfo.sibs.ac.cn/carmo PDF

  • Marta Biagioli#, Francesco Ferrari#, Eric M. Mendenhall, Yijing Zhang, Serkan Erdin, Ravi Vijayvargia, Sonia M. Vallabh, Nicole Solomos,Poornima Manavalan, Ashok Ragavendran, Fatih Ozsolak, Jong Min Lee,Michael E. Talkowski, James F. Gusella, Marcy E. Macdonald,Peter J. Park and Ihn Sik Seong*. (2015)HttCAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation, Human Molecular Genetics, 24( 9 ):2442-2457.
    https://doi.org/10.1093/hmg/ddv006 PDF

[2014]

[2013]

  • Pingzhu Zhou, Yijing Zhang, Qing Maa, Fei Gu, Daniel S. Dayb,c, Aibin He, Bin Zhou, Jing Li, Sean M. Stevens, Daniel Romo, and William T. Pu*. (2013) Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification, Proceedings of the National Academy of Sciences, 110(38):15395-15400.
    http://www.pnas.org/content/110/38/15395.long PDF

[2012]

  • Gaihua Zhang#, Yijing Zhang# and Zhen Su*. (2012) CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana, BMC Bioinformatics, 13: 332 .
    http://www.biomedcentral.com/1471-2105/13/332 PDF

  • Tara L. Conforto, Yijing Zhang, Jennifer Sherman, and David J. Waxman*. (2012) Impact of CUX2 on the Female Mouse Liver Transcriptome: Activation of Female-Biased Genes and Repression of Male-Biased Genes, Molecular and Cellular Biology, 32(22): 4611-4627.
    http://mcb.asm.org/content/32/22/4611.long PDF

  • Zhen Shao#, Yijing Zhang#, Guo-Cheng Yuan, Stuart H Orkin* and David J Waxman*. (2012) MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets, Genome Biology, 13(3):R16.
    http://genomebiology.com/content/13/3/R16 PDF

[2011]

  • Yijing Zhang, Ekaterina V. Laz, and David J. Waxman*. (2011) Dynamic, Sex-Differential STAT5 and BCL6 Binding to Sex-Biased, Growth Hormone-Regulated Genes in Adult Mouse Liver, Molecular and Cellular Biology,32(4): 880-896.
    http://mcb.asm.org/content/32/4/880.lon PDF

  • Yijing Zhang, Kathrin Klein, Aarathi Sugathan, Najlla Nassery, Alan Dombkowski, Ulrich M. Zanger,David J. Waxman*. (2011) Transcriptional Profiling of Human Liver Identifies Sex-Biased Genes Associated with Polygenic Dyslipidemia and Coronary Artery Disease, PLos One, 6(8):e23506.
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023506 PDF

  • Gargi Bagchi#, Yijing Zhang#, Kerri A Stanley and David J Waxman*. (2011) Complex modulation of androgen responsive gene expression by methoxyacetic acid, Reproductive Biology and Endocrinology, 9(1):42
    http://www.rbej.com/content/9/1/42g PDF

[2010]

  • Gargi Bagchi, Yijing Zhang and David J Waxman*. (2010) Impact of methoxyacetic acid on mouse Leydig cell gene expression, Reproductive Biology and Endocrinology, 2010, 8:65.
    http://www.rbej.com/content/8/1/65 PDF

  • Evelyn Dixit, Steeve Boulant, Yijing Zhang, Amy S. Lee, Charlotte Odendall, Bennett Shum, Nir Hacohen, Zhijian J. Chen, Sean P. Whelan, Marc Fransen, Max L. Nibert,Giulio Superti-Furga, and Jonathan C. Kagan*. (2010) Peroxisomes are signaling platforms for antiviral innate immunity, Cell, 141(4): 668-681.
    http://www.sciencedirect.com/science/article/pii/S0092867410004356 PDF

[2009]

[2008]