教师基本信息：
姓名：张一婧
职称：研究员
电子邮箱：zhangyijing@fudan.edu.cn
办公地点：上海市杨浦区淞沪路2055号复旦大学江湾校区生科院410
个人网页/课题组主页：
https://faculty.fudan.edu.cn/zhangyijing/zh_CN/index.htm
研究方向：植物生物信息与合成生物学
我们是生物信息学与遗传学实验相结合的研究团队，课题组设有干湿结合的长期和短期项目，欢迎对逻辑思考和科学研究有热情的同学联系实习或攻读研究生，也希望这一阶段的学习能够为同学未来的科研与职业生涯奠定良好的基础。
1. 以小麦为模式，研究转座子在多倍体进化中的作用。小麦起源于东亚新月沃地，其进化过程中经历多次基因组杂交加倍与转座子扩张事件，具备高度的环境适应性，成为全球分布最广的主粮作物。 McClintock在诺贝尔奖获奖致辞中推测，小麦族物种杂交后转座子爆发可能迅速推动新性状的获得。当转座子扩张遇到多倍化事件，会给基因组带来怎样的变化？不同时期不同类型的扩张，在选择压力下选取了怎样的进化路径？我们结合表观组、染色质高级结构刻画及调控组技术，在揭示转座子维持染色质稳定性、调控网络进化与分化等方面取得一系列有趣的进展。
2. 开发生物学技术挖掘和利用基因资源库。自然界存在大量基因资源，可以应用于作物改良和合成生物学。我们通过结合生物信息学策略，设计新的基因挖掘方案，充分利用天然存在的基因资源库。
3.以衣藻为底盘开展人类营养健康相关的合成生物学。莱茵衣藻是单细胞模式生物，在诱变、育种、高通量筛选方面操作方便，与传统微生物合成底盘相比，其蛋白修饰、代谢与动物更加接近。利用课题组的多学科优势，我们正在搭建体系，高效合成人类营养与健康相关的蛋白与化合物，也希望与志同道合的同学老师及创业团队有深入的交流合作。
个人简介:
2003年获中国海洋大学学士；2008年获中国科学院遗传与发育生物学研究所博士；2008-2013先后在中国农业大学、波士顿大学和哈佛医学院，从事博士后研究；2013-2021年在中科院上海植物生理生态研究所任研究员及课题组长；2021年任复旦大学生命科学学院研究员。作为通讯作者在Nature Communications, Genome Research（期刊封面），Plant Cell（亮点专评），Genome Biology和Nucleic Acids Research等国际学术期刊发表论文20余篇。
获奖情况:
2021 国家自然科学基金委/优秀青年基金项目资助
2015 上海市科技人才计划项目/浦江人才计划
2014 中国科学院上海生命科学院特殊（S类）人才计划
招生专业：生物化学（表观遗传学）
代表性论文和论著：
1. Zhang Y#, Li Z#, Liu J#, Zhang Y#, Ye L#, Peng Y, Wang H, Diao H, Ma Y, Wang M, Xie Y, Tang T, Zhuang Y, Teng W, Tong Y, Zhang W, Lang Z*, Xue Y*, Zhang Y*: Transposable elements orchestrate subgenome convergent and -divergent transcription in common wheat, Nature Communications, 2022, 13(1):6940
2. Tang T#, Tian S#, Wang H#, Lv X#, Xie Y, Liu J, Wang M, Zhao F, Zhang W*, Li H*, Zhang Y*: Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory networks, Molecular Plant 2022, S1674-2052(22)00453-1.
3. Zhang Y#, Li Z#, Zhang Y#, Lin K#, Peng Y, Ye L,Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W*, Xue Y*, Lang Z*, Zhang Y*: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Research 2021, 31(12):2276-2289.
4. Wang M#, Li Z#, Zhang Y#, Zhang Y#, Xie Y, Ye L, Zhuang Y, Lin K, Zhao F, Guo J, Teng W, Zhang W, Tong Y, Xue Y*, Zhang Y*: An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses. The Plant Cell 2021, 33(4):865-881.
5. Jia J#, Xie Y#, Cheng J#, Kong C#, Wang M, Gao L, Zhao F, Guo J, Wang K, Li G, Cui D, Hu T, Zhao G*, Wang D*, Ru Z*, Zhang Y*: Homology-mediated Inter-chromosomal Interactions in Hexaploid Wheat Lead to Specific Subgenome Territories Following Polyploidization and Introgression. Genome Biology 2021, 22(1):26.
6. Ran X#, Zhao F#, Wang Y#, Liu J, Zhuang Y, Ye L, Qi M, Cheng J, Zhang Y*: Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data. Plant Journal 2020. 101(1):237-248.
7. Li Z#, Wang M#, Lin K#, Xie Y#, Guo J, Ye L, Zhuang Y, Teng W, Ran X, Tong Y, Xue Y, Zhang W*, Zhang Y*: The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements. Genome Biology 2019, 20(1):139.
8. Liu C#, Cheng J#, Zhuang Y, Ye L, Li Z, Wang Y, Qi M, Xu L, Zhang Y*: Polycomb repressive complex 2 attenuates ABA-induced senescence in Arabidopsis. Plant Journal 2019, 97(2):368-377.
9. 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. Qi M#, Li Z#, Liu C#, Hu W, Ye L, Xie Y, Zhuang Y, Zhao F, Teng W, Zheng Q, Fan Z, Xu L, Lang Z, Tong Y*, Zhang Y*: CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome. Nucleic Acids Research 2018, 46(18):e107.
11. Wang H#, Liu C#, Cheng J#, Liu J, Zhang L, He C, Shen W, Jin H*, Xu L*, Zhang Y*: 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 2016, 12(1):e1005771.
12. Wang J#, Qi M#, Liu J#, Zhang Y*: CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data. Plant Journal 2015, 83(2):359-374.
13. Shao Z,#Zhang Y#, Yuan G, Orkin S*, Waxman D*: MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology 2012, 13(3):R16.
Personal Information:
Name：Yijing Zhang
Title：Researcher
E-mail：zhangyijing@fudan.edu.cn
Office Address：410, College of Life Sciences, Jiangwan campus, Fudan University, No. 2055, Songhu Road, Yangpu District, Shanghai
Office-Tel：021-54924204
Website：
https://faculty.fudan.edu.cn/zhangyijing/zh_CN/index.htm
Research direction: plant bioinformatics and synthetic biology
We are a research group combining molecular experiments and bioinformatics strategies to decode and exploit epigenetic mechanisms to improve agronomic traits of crops or synthesize proteins and chemicals to serve human nutrition and health. We welcome students who are passionate about logical thinking and scientific research to contact us for internships or graduate studies. We also hope that this stage of the study can lay a good foundation for students' future scientific research and career.
Current research foci:
1. Using wheat as a model to study the role of transposons in polyploid evolution. Wheat originated in the Fertile Crescent of East Asia. During its evolution, wheat has experienced multiple rounds of genome hybrid，doubling, and transposon expansion events, making it highly adaptable to the environments and becoming the most widely distributed staple food crop in the world. McClintock speculated that bursts of transposons following hybridization of Triticeae species could rapidly drive the acquisition of new traits in her Nobel Prize Acceptance Speech. When transposon expansion encounters polyploidy events, what changes will it bring to the genome? What evolutionary trajectories were selected by different types of expansions in different periods under selection pressure? Combining epigenomics, chromatin 3D structures and phylogenetic technologies, we have made a series of interesting progress in revealing that transposons maintain chromatin stability and regulate network evolution and innovation.
2. Development of biological technologies to utilize the rich genetic resources in nature. The abundant genetic resources in nature have a great potential for crop improvement and synthetic biology. By combining bioinformatics and molecular strategies, we design new gene mining solutions to make full use of natural gene resources.
3. Using algae as the cell factory to carry out synthetic biology related to human nutrition and health. Chlamydomonas reinhardtii is a single-cell green algae, which is easy to manipulate in terms of mutagenesis, breeding, and high-throughput screening. Compared with traditional microbial synthesis chassis, its protein modification and metabolism are closer to animals. Taking advantage of the multidisciplinary background of the research group, we are building systems to efficiently synthesize proteins and compounds related to human nutrition and health. We also hope to have in-depth exchanges and cooperation with like-minded classmates, researchers and entrepreneurial teams.
Personal Profile：
2003, bachelor degree from Ocean University of China in 2003;
2008 Ph.D. degree from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences;
2008- 2013, postdoctoral research at China Agricultural University, Boston University and Harvard Medical School;
2013-2021, group leader in Institute of Physiological Ecology;
2021- , group leader at the School of Life Sciences, Fudan University.
Admissions Major ：Biochemistry (Epigenetics)
Selected Publications：
1. Zhang Y#, Li Z#, Liu J#, Zhang Y#, Ye L#, Peng Y, Wang H, Diao H, Ma Y, Wang M, Xie Y, Tang T, Zhuang Y, Teng W, Tong Y, Zhang W, Lang Z*, Xue Y*, Zhang Y*: Transposable elements orchestrate subgenome convergent and -divergent transcription in common wheat, Nature Communications, 2022, 13(1):6940
2. Tang T#, Tian S#, Wang H#, Lv X#, Xie Y, Liu J, Wang M, Zhao F, Zhang W*, Li H*, Zhang Y*: Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory networks, Molecular Plant 2022, S1674-2052(22)00453-1.
3. Zhang Y#, Li Z#, Zhang Y#, Lin K#, Peng Y, Ye L,Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W*, Xue Y*, Lang Z*, Zhang Y*: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Research 2021, 31(12):2276-2289.
4. Wang M#, Li Z#, Zhang Y#, Zhang Y#, Xie Y, Ye L, Zhuang Y, Lin K, Zhao F, Guo J, Teng W, Zhang W, Tong Y, Xue Y*, Zhang Y*: An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses. The Plant Cell 2021, 33(4):865-881.
5. Jia J#, Xie Y#, Cheng J#, Kong C#, Wang M, Gao L, Zhao F, Guo J, Wang K, Li G, Cui D, Hu T, Zhao G*, Wang D*, Ru Z*, Zhang Y*: Homology-mediated Inter-chromosomal Interactions in Hexaploid Wheat Lead to Specific Subgenome Territories Following Polyploidization and Introgression. Genome Biology 2021, 22(1):26.
6. Ran X#, Zhao F#, Wang Y#, Liu J, Zhuang Y, Ye L, Qi M, Cheng J, Zhang Y*: Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data. Plant Journal 2020. 101(1):237-248.
7. Li Z#, Wang M#, Lin K#, Xie Y#, Guo J, Ye L, Zhuang Y, Teng W, Ran X, Tong Y, Xue Y, Zhang W*, Zhang Y*: The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements. Genome Biology 2019, 20(1):139.
8. Liu C#, Cheng J#, Zhuang Y, Ye L, Li Z, Wang Y, Qi M, Xu L, Zhang Y*: Polycomb repressive complex 2 attenuates ABA-induced senescence in Arabidopsis. Plant Journal 2019, 97(2):368-377.
9. 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. Qi M#, Li Z#, Liu C#, Hu W, Ye L, Xie Y, Zhuang Y, Zhao F, Teng W, Zheng Q, Fan Z, Xu L, Lang Z, Tong Y*, Zhang Y*: CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome. Nucleic Acids Research 2018, 46(18):e107.
11. Wang H#, Liu C#, Cheng J#, Liu J, Zhang L, He C, Shen W, Jin H*, Xu L*, Zhang Y*: 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 2016, 12(1):e1005771.
12. Wang J#, Qi M#, Liu J#, Zhang Y*: CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data. Plant Journal 2015, 83(2):359-374.
13. Shao Z,#Zhang Y#, Yuan G, Orkin S*, Waxman D*: MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology 2012, 13(3):R16.