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://life.fudan.edu.cn/b1/cf/c28175a438735/page.htm
研究方向：噬菌体与转座子生物信息学与合成生物学应用
噬菌体与转座子，这些演化迅速的小型生物元件，是生命进化的重要推动者。它们在深入理解生命的核心问题和开发基因工程工具方面发挥着关键作用。课题组结合生物信息学和合成生物学实验，专注于噬菌体与转座子的进化研究，并探索它们在医药领域的应用潜力。
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. 噬菌体的高通量筛选与合成：噬菌体是特异性攻击细菌的病毒。面对日益严峻的抗生素耐药性问题，噬菌体的改造和应用展现出巨大潜力。我们利用高通量技术和生物信息学策略，设计新的筛选和合成方案，以改造天然噬菌体库，针对人类和水产病原菌感染开展靶向治疗。
2. 转座子的机制与应用研究：以小麦和病原菌为研究模型，探究转座子在进化中的作用，并开发基于转座子的功能基因挖掘工具。小麦的基因组在多次杂交加倍和转座子扩张事件中表现出高度的环境适应性。我们结合多种技术手段，揭示了转座子在维持染色质稳定性、调控网络的进化与分化中的作用。
3. 作物营养代谢研究：大众饮食观念正在从“吃得饱”向“吃得好”转变，但传统作物育种营养学研究滞后。我们通过与杂粮育种团队合作，依托国家重点实验室的代谢平台，结合基因组学技术开展新的营养物质挖掘与育种工作，旨在提高农作物的营养价值和健康效益。
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。作为最后通讯作者在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。依托搭建的生物信息平台，合作发表Nature，Science，Nature Genetics等期刊论文。
获奖情况
2021 国家自然科学基金委/优秀青年基金项目（终评“A”）
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. Wang M#, Li Z#, Wang H#, Lin K, Zheng S, Feng Y, Teng W, Tong Y, Zhang W, Liu C, Ling HQ, Hu YQ, Zhang Y: A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development. Mol Biol Evol. 2024 doi: 10.1093/molbev/msae178.
2. Li Z#, Zhang Y#, Ding C#, Chen Y#, Wang H#, Zhang J, Ying S, Wang M, Zhang R, Liu J, Xie Y, Tang T, Diao H, Ye L, Zhuang Y, Teng W, Huang L, Tong Y, Zhang W, Li G, Benhamed M*, Dong Z*, Gou J*, Zhang Y*: LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat, Nature Communications 2023, https://doi.org/10.1038/s41467-023-43178-2
3. Xie Y#, Ying S#, Li Z#, Zhang Y#, Zhu J#, Zhang J, Wang M, Diao H, Wang H, Zhang Y, Ye L, Zhuang Y, Zhao F, Teng W, Zhang W, Tong Y, Cho J*, Dong Z*, Xue Y*, Zhang Y*: Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat, Nature Communications 2023, https://doi.org/10.1038/s41467-023-42771-9.
4. Li M#, Wang H#, Tian S, Zhu Y*, Zhang Y*: Triticeae-BGC: a web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae, Journal of Genetics and Genomics 2023, 50(11):921-923.
5. 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 2023, S1674-2052(22)00453-1.
6. Ye R, Wang M, Du H, Chhajed S, Koh J, Liu K, Shin J, Wu Y, Shi L, Xu L, Chen S, Zhang Y, Sheen J* (2022) Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature 2022, 609(7929):986-993.
7. 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
8. 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.
9. 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.
10.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.
11.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.
12.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.
13.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.
14.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.
15.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
16.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.,
17.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.
18.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.
19.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.
教师基本信息：
姓名：Yijing Zhang
职称：Researcher
电子邮箱：zhangyijing@fudan.edu.cn
办公地点：410, College of Life Sciences, Jiangwan campus, Fudan University, No. 2055, Songhu Road, Yangpu District, Shanghai
办公电话：021-54924204
个人网页/课题组主页：https://life.fudan.edu.cn/b1/cf/c28175a438735/page.htm
Research Direction: Bioinformatics and Synthetic BiologyApplications of Transposons and Phages
Transposons and phages, these rapidly evolving small biological elements, are important drivers of the evolution of life. They play a key role in deeply understanding the core issues of life and developing genetic engineering tools. Our research group combines bioinformatics and synthetic biology experiments to focus on the evolutionary study of transposons and phages, and to explore their potential applications in the medical field.
We welcome students who are passionate about logical thinking and scientific research to intern or pursue graduate studies, and we hope that this stage of learning will lay a solid foundation for students' future scientific research and career.
1. High-throughput Screening and Synthesis of Phages: Phages are viruses that specifically attack bacteria. Faced with the increasingly severe problem of antibiotic resistance, the modification and application of phages show great potential. We use high-throughput technology and bioinformatics strategies to design new screening and synthesis schemes to modify the natural phage library, and carry out targeted treatment for human and aquaculture pathogen infections.
2. Mechanism and Application Research of Transposons: Using wheat and pathogens as research models, we explore the role of transposons in evolution and develop functional gene mining tools based on transposons. The genome of wheat has shown a high degree of environmental adaptability in multiple hybridization and transposon expansion events. We combine various technical means to reveal the role of transposons in maintaining polyploid chromatin stability, the evolution and differentiation of regulatory networks.
3. Crop Nutrition Metabolism Research: Public dietary concepts are shifting from eating enough to eating well, but traditional crop breeding nutrition research is lagging behind. We cooperate with the grain breeding team, relying on the metabolic platform of the national key laboratory, and combining genomics technology to carry out new nutritional substance mining and breeding work, aiming to improve the nutritional value and health benefits of crops.
个人简介：
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.
招生专业：Biochemistry
代表性论文和论著：
1. Wang M#, Li Z#, Wang H#, Lin K, Zheng S, Feng Y, Teng W, Tong Y, Zhang W, Liu C, Ling HQ, Hu YQ, Zhang Y: A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development. Mol Biol Evol. 2024 doi: 10.1093/molbev/msae178.
2. Li Z#, Zhang Y#, Ding C#, Chen Y#, Wang H#, Zhang J, Ying S, Wang M, Zhang R, Liu J, Xie Y, Tang T, Diao H, Ye L, Zhuang Y, Teng W, Huang L, Tong Y, Zhang W, Li G, Benhamed M*, Dong Z*, Gou J*, Zhang Y*: LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat, Nature Communications 2023, https://doi.org/10.1038/s41467-023-43178-2
3. Xie Y#, Ying S#, Li Z#, Zhang Y#, Zhu J#, Zhang J, Wang M, Diao H, Wang H, Zhang Y, Ye L, Zhuang Y, Zhao F, Teng W, Zhang W, Tong Y, Cho J*, Dong Z*, Xue Y*, Zhang Y*: Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat, Nature Communications 2023, https://doi.org/10.1038/s41467-023-42771-9.
4. Li M#, Wang H#, Tian S, Zhu Y*, Zhang Y*: Triticeae-BGC: a web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae, Journal of Genetics and Genomics 2023, 50(11):921-923.
5. 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 2023, S1674-2052(22)00453-1.
6. Ye R, Wang M, Du H, Chhajed S, Koh J, Liu K, Shin J, Wu Y, Shi L, Xu L, Chen S, Zhang Y, Sheen J* (2022) Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature 2022, 609(7929):986-993.
7. 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
8. 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.
9. 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.
10.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.
11.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.
12.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.
13.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.
14.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.
15.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
16.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.,
17.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.
18.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.
19.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.