Zhang Lab

Plant Bioinformatics and Functional Epigenomics Group

Publication


2019-2016

2015-2010

Before 2010

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

[2019]

  • 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. doi: https://doi.org/10.1016/j.jgg.2019.03.001.
    https://doi.org/10.1186/s13059-018-1587-x 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. doi: https://doi.org/10.1111/pbi.13103.
    https://doi.org/10.1111/pbi.13103 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

[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. doi: https://doi.org/10.1186/s13059-018-1587-x
    https://doi.org/10.1186/s13059-018-1587-x PDF
  • Zhiye Wang#, Meiyue Wang#, Tian Wang, Yijing Zhang*, Xiuren Zhang*. (2018) Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis, Methods, doi: https://doi.org/10.1016/j.ymeth.2018.11.018
    https://doi.org/10.1016/j.ymeth.2018.11.018 PDF
  • Chunmei Liu#, Jingfei Cheng#, Yili Zhuang, Luhuan Ye, Zijuan Li, Yuejun Wang, Meifang Qi, Yijing Zhang* (2018) Polycomb repressive complex 2 attenuates ABA-induced senescence in Arabidopsis, Plant Journal, doi: 10.1111/tpj.14125
    https://doi.org/10.1111/tpj.14125 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

  • 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, 2018
    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

[2016]

  • Jia-Shi Peng#, Yue-Jun Wang#, Ge Ding, Hai-Ling Ma, Yi-Jing Zhang*, Ji-Ming Gong*. (2016) 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

  • 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.DOI: 10.1111/jipb.12485.
    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(4):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]