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
本课题组立足于计算生物学、功能基因组学与合成生物学的交叉前沿，致力于打破传统农业与生物医药领域的进化与技术瓶颈。我们依托高通量遗传学实验和深度学习“干湿结合”范式，从源头解析复杂生命系统的代谢与防御网络。
欢迎对生命科学本质问题保持好奇、致力于将科研想法转化为算法与实验的同学加入。来自生物、农学、医学、计算机、数学或工程等相关专业的同学，均可在这里找到最适合自身背景的研究切入点。课题组不要求申请人同时具备计算与湿实验的双重基础。我们更看重的，是你的好奇心、自驱力、扎实的执行力以及开放包容的合作精神。有兴趣的同学，欢迎直接发邮件与我沟通。
1. 作物碳氮代谢重构与理性设计：高产高抗作物种质精准创制
“保供给”与“保生态”的农业绿色发展战略，需要协同实现作物的增产稳产与化肥农药减施。应对这一挑战的核心，在于打破植物氮肥利用与资源分配的底层症结：一方面，当前我国氮肥利用效率仅约40%，成为作物“减氮增产”的关键瓶颈；另一方面，植物在漫长演化中形成了固有的“产量-抗性权衡”，高产与抗病难以兼得，其本质是有限碳氮资源在生长与免疫网络间的分配竞争。本课题组从提升氮素利用效率这一核心切入点入手，运用计算生物学与高通量遗传学策略，重构作物底层代谢。我们以此为生化支点，在分子层面系统解耦生长与防御的资源分配冲突，为创制“减氮、少药、高产、多抗”的绿色作物提供理论范式与种源支撑。
2. 植物合成生物学与绿色医药创制：重塑高价值生物制品生产范式
合成生物学作为引领“第三次生物技术革命”的战略力量，正在深刻重塑生物医药的产业格局。尽管植物底盘具有成本低、易规模化的天然优势，但合成效率与标准化流程仍是核心瓶颈。本课题组将深度学习预测模型与高通量遗传筛选技术深度融合，对底盘植物进行功能模块的定向改造与底盘优化。我们致力于系统提升生物疫苗与高价值药物的合成效率，旨在构建具有自主知识产权、自主可控的绿色医药生产体系。
3. 工程化噬菌体的精准重构与定向合成：应对全球抗生素耐药性危机
面对全球持续升级的抗生素耐药性风险，噬菌体疗法展现出巨大的生物学优势与临床潜力。然而，噬菌体基因组的高度多样性、大量“暗物质”基因以及改造技术的匮乏，限制了其工程化应用。本课题组聚焦噬菌体基因组的功能精准解析与大片段基因组精准操控难题。通过人工智能辅助设计与高效遗传重构，实现对复杂噬菌体系统的程序化解码。我们致力于精准定制新型工程噬菌体，为后抗生素时代的公共卫生危机提供源头创新的解决方案。
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
授课与招生
招生专业：生物化学、生物医药与工程
代表性论文和论著
1. Wang M#, Li Z#, Wang H#, Zhao J, Zhang Y, Lin K, Zheng S, Feng Y, Zhang Y, Teng W, Tong Y, Zhang W, Xue Y, Mao H, Li H, Zhang B, Rasheed A, Bhavani S, Liu C, Ling HQ*, Hu YQ*, Zhang Y*. A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development. Molecular Biology and Evolution. 2024;41(9):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;14:7538.
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;14:7465.
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;16(2):318-321.
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*. 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;13:6940.
8. 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.
9. 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.
10.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;22:26.
11.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. The Plant Journal. 2020;101(1):237-248.
12.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;20:139.
13.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. The Plant Journal. 2019;97(2):368-377.
14.Zhou Y, Wang Y, Krause K, Yang T, Dongus JA, Zhang Y, Turck F*. Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. Nature Genetics. 2018;50(5):638-644.
15.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.
16.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.
17.Wang J#, Qi M#, Liu J#, Zhang Y*. CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data. The Plant Journal. 2015;83(2):359-374.
18.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.
# 共同第一作者；* 通讯作者。
Basic Information
Name: Yijing Zhang
Academic title: Research Professor
Position: Principal Investigator
Email: zhangyijing@fudan.edu.cn
Office: Room 410, School of Life Sciences, Fudan University, Jiangwan Campus, 2055 Songhu Road, Yangpu District, Shanghai 200438, China
Telephone: +86-21-54924204
Faculty profile / laboratory website:
https://life.fudan.edu.cn/b1/cf/c28175a438735/page.htm
Research Areas
Our laboratory works at the intersection of computational biology, functional genomics, and synthetic biology, addressing evolutionary constraints and technological challenges in sustainable agriculture and biomedicine. By integrating high-throughput genetic screening with deep learning in a tightly coupled computational–experimental framework, we seek to elucidate the metabolic and defense networks of complex biological systems and translate mechanistic insights into crop improvement and biotechnological innovation.
1: Rational redesign of crop carbon-nitrogen metabolism for high yield, disease resistance, and improved nitrogen-use efficiency
Meeting rising food demand while reducing fertilizer and pesticide inputs requires crops that combine high productivity, efficient resource use, and durable disease resistance. Two constraints are central: crop nitrogen-use efficiency remains suboptimal, and carbon and nitrogen allocation can impose a trade-off between growth and immune responses. We combine computational biology with high-throughput genetic screening to identify regulatory nodes governing nitrogen metabolism and resource allocation. By rewiring these nodes and testing their effects experimentally, we aim to decouple growth from defense and generate germplasm that maintains yield under reduced nitrogen input while providing enhanced resistance. This work seeks mechanistic principles and testable targets for sustainable crop improvement.
2: Plant synthetic biology for green biomanufacturing of high-value products
Plants offer a scalable and potentially cost-effective chassis for producing complex biological products, but low productivity, variable expression, and limited process standardization remain major obstacles. We integrate deep-learning-based prediction with high-throughput genetic screening to redesign functional modules and optimize plant chassis. Our goal is to improve the yield, stability, and reproducibility of vaccine antigens and high-value therapeutic molecules and to establish a modular plant biomanufacturing platform.
3: Functional dissection and programmable engineering of bacteriophages
The increasing burden of antimicrobial resistance has renewed interest in bacteriophages as host-specific antibacterial agents. Their engineering remains constrained by extensive genomic diversity, large fractions of uncharacterized genes, and limited methods for manipulating large phage genomes. We combine AI-assisted design, functional genomics, and high-efficiency genetic reconstruction to assign functions to phage genes and reconfigure large genomic regions. Our long-term objective is to enable predictable, programmable phage engineering and to develop candidate phages for combating drug-resistant bacterial pathogens.
Biography
Yijing Zhang received her BSc from Ocean University of China in 2003 and her PhD from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, in 2008. From 2008 to 2013, she conducted postdoctoral research at China Agricultural University, Boston University, and Harvard Medical School. She served as a principal investigator and group leader at the Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, from 2013 to 2021 and joined the School of Life Sciences, Fudan University, as a principal investigator in 2021. As a senior or corresponding author, she has published more than 20 papers in journals including Nature Communications, Genome Research, The Plant Cell, Genome Biology, and Nucleic Acids Research. Her collaborative work has also appeared in Nature, Science, and Nature Genetics.
Honors and Awards
2021 Excellent Young Scientists Fund, National Natural Science Foundation of China (final evaluation: A)
2015 Pujiang Talent Program, Shanghai Science and Technology Talent Program
2014 Special Talent Program (Class S), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Graduate Admissions
Program: Biochemistry
Selected Publications
1. Wang M#, Li Z#, Wang H#, Zhao J, Zhang Y, Lin K, Zheng S, Feng Y, Zhang Y, Teng W, Tong Y, Zhang W, Xue Y, Mao H, Li H, Zhang B, Rasheed A, Bhavani S, Liu C, Ling HQ*, Hu YQ*, Zhang Y*. A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development. Molecular Biology and Evolution. 2024;41(9):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;14:7538.
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;14:7465.
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;16(2):318-321.
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*. 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;13:6940.
8. 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.
9. 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.
10.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;22:26.
11.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. The Plant Journal. 2020;101(1):237-248.
12.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;20:139.
13.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. The Plant Journal. 2019;97(2):368-377.
14.Zhou Y, Wang Y, Krause K, Yang T, Dongus JA, Zhang Y, Turck F*. Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. Nature Genetics. 2018;50(5):638-644.
15.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.
16.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.
17.Wang J#, Qi M#, Liu J#, Zhang Y*. CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data. The Plant Journal. 2015;83(2):359-374.
18.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.
# Equal contribution; * Corresponding author.