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个人信息

博士生导师
研究员
 
Email: zhangyijing@sibs.ac.cn
个人网页: http://bioinfo.sibs.ac.cn/zhanglab/

研究方向

植物生物信息与功能表观组学

张一婧

个人简介

2011.10-2013.01 哈佛医学院附属麻省总医院和波士顿儿童医院 生物信息博士后和生物信息专家( Bioinformatics Post-doc Research Fellow 和 Bioinformatics Specialist)
2009.12-2011.09 波士顿大学 生物信息学博士后
2009.04-2009.10 哈佛医学院附属波士顿儿童医院,生物信息专家 (Bioinformatics expert)
2008.06-2009.03 中国农大 生物信息学博士后
2003.09-2008.06 中科院遗传与发育研究所 硕博
1999.09-2003.07 中国海洋大学

研究工作

本课题组致力于研究新一代高通量生物测序数据的挖掘,开发分析方法,并为研究所提供大规模生物数据分析服务。
如何使用各种统计方法和机器学习的方法挖掘数据中蕴含的信息,并提供数据分析网络服务是我们最关心的问题。
我们重点研究的生物学问题是通过大规模数据分析揭示植物表观遗传修饰复合体在控制微观和宏观生物学现象中的机制。

主要成果

 

    note: #Co-first author; *Corresponding author ; PI's name is shown in bold

    1. Zijuan Li#, Meiyue Wang#, Kande Lin#, Yilin Xie#, Jingyu Guo, Luhuan Ye, Yili Zhuang, Wan Teng, Xiaojuan Ran, Yiping Tong, Yongbiao Xue, Wenli Zhang* and Yijing Zhang*(2019) The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements, Genome Biology, 20(1):139

    2. Xiaojuan Ran#, Fei Zhao#, Yuejun Wang#, Jian Liu, Yili Zhuang, Luhuan Ye, Meifang Qi, Jingfei Cheng, Yijing Zhang*2019Plant Regulomics: A Data‐driven Interface for Retrieving Upstream Regulators from Plant Multi‐omics Data, The Plant Journal, doi: 10.1111/tpj.14526

    3. 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, The Plant Journal, 97(2):368-377

    4. 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

    5. Yuhao Liu, Kunpeng Liu, Liufan Yin, Yu Yu, Ji Qi, WenHui Shen, Jun Zhu, Yijing Zhang* and Aiwu Dong*2019H3K4me2 functions as a repressive epigenetic mark in plants, Epigenetics & Chromatin, 12(1):40

    6. 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

    7. Guifang Zhang#, Fei Zhao#, Lyuqin Chen#, Yu Pan, Lijun Sun, Ning Bao, Teng Zhang, Chun-Xiao Cui, Zaozao Qiu, Yijing Zhang, Li Yang and Lin Xu*2019Jasmonate-mediated wound signalling promotes plant regeneration, Nature Plants, 5(5):491-497

    8. 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

    9. 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*2019Ef-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

    10. 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, doi: 10.1038/s41421-019-0107-9

    11. 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

    12. Jie Yu, Yuyun Zhang, Wu Liu, Hua Wang, Shaoting Wen, Yijing Zhang, Lin Xu*2019Molecular evolution of auxin-mediated root initiation in plants, Molecular Biology and Evolution, doi: 10.1093/molbev/msz202

    13. Jingfei Cheng#, Qingfeng Niu#, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang* and Zhaobo Lang*(2018) Downregulation of RdDM during strawberry fruit ripening, Genome Biology, 19:212

    14. 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

    15. 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 Acids Research, 46(18):e107

    16. Wenbo Li, Haimin Li, Peng Xu, Zhi Xie, Yajin Ye, Lingting Li, Deqiang Li, Yijing Zhang, Laigeng Li, Yang Zhao2018Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway, Plant Molecular Biology, 98:275–287

    17. 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*2018Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly, GigaScience, 7(6)

    18. Yue Zhou, Yuejun Wang, Kristin Krause, Tingting Yang, Joram A. Dongus, Yijing Zhang and Franziska Turck* (2018) Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis, Nature Genetics, 50(5):638-644

    19. Xiaojuan Ran, Jian Liu, Meifang Qi, Yuejun Wang, Jingfei Cheng and Yijing Zhang*(2018).GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis,Frontiers in Plant Science,9:23

    20. Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K. Handab, and Jian-Kang Zhu(2017) Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proceedings of the National Academy of Sciences of the United States of America, 114(22):E4511-E4519

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

    22. Jiashi Peng#, Yuejun Wang#, Ge Ding, Hailing Ma, Yijing Zhang*, Jiming Gong*(2017) A Pivotal Role of Cell Wall in Cadmium Accumulation in the Crassulaceae hyperaccumulator Sedum plumbizincicola, Molecular Plant ,10(5): 771-774

    23. 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 with LHP1 to repress KNOX genes in Arabidopsis, Journal of Integrative Plant Biology,58(12):959-970

    24. 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

    25. 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, 5: p e11612

    26. 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

    27. 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, 1684):1417–1432

    28. Jiawei Wang#, Meifang Qi#, Jian Liu#, Yijing Zhang*(2015) CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data, The Plant Journal, 83(2):359-374

    29. 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)Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation, Human Molecular Genetics, 24( 9 ):2442–2457

    30. Guang Li#, Shujing Liu#, Jiawei Wang, Jianfeng He, Hai Huang, Yijing Zhang* and Lin Xu*(2014) ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis, The Plant Journal ,78(4):706–714

    31. 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 of the United States of America, 110(38):15395-15400

    32. 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

    33. 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

    34. 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

    35. 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

    36. Yijing Zhang, Kathrin Klein, Aarathi Sugathan, Najlla Nassery, Alan Dombkowski, Ulrich M. Zanger,David J. Waxman1*(2011) Transcriptional Profiling of Human Liver Identifies Sex-Biased Genes Associated with Polygenic Dyslipidemia and Coronary Artery Disease, PLos One, 6(8):e23506

    37. 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

    38. 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

    39. 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

    40. Yongbiao Xue#*, Yijing Zhang#, Qiuying Yang#, Qun Li,Zhukuan Cheng, Hugh G. Dickinson(2009) Genetic features of a pollen-part mutation suggest an inhibitory role for the Antirrhinum pollen self-incompatibility determinant, Plant Molecular Biology, 70(5): 499-509

    41. Yijing Zhang, Zhonghua Zhao, and Yongbiao Xue*(2009) Roles of Proteolysis in Plant Self-Incompatibility, Annual Review of Plant Biology, 60:21-42

    42. Zhang Y and Xue Y*. “Molecular Biology of S-RNase-based Self-Incompatibility” in Book “Self-Incompatibility in Flowering Plants”(2008) Berlin- Heidelberg-New York: Springer-Verlag, p193-215 

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