教師基本信息：
姓名：張一婧
職稱：研究員
電子郵箱：zhangyijing@fudan.edu.cn
辦公地點：上海市楊浦區淞滬路2055號狗万外围充值 江灣校區生科院410
個人網頁/課題組主頁：//www.xahaidun.com/b1/cf/c28175a438735/page.htm
研究方向：噬菌體與轉座子生物信息學與合成生物學應用
噬菌體與轉座子，這些演化迅速的小型生物元件，是生命進化的重要推動者。它們在深入理解生命的核心問題和開發基因工程工具方麵發揮著關鍵作用。課題組結合生物信息學和合成生物學實驗，專注於噬菌體與轉座子的進化研究，並探索它們在醫藥領域的應用潛力。
我們是生物信息學與遺傳學實驗相結合的研究團隊，課題組設有幹濕結合的長期和短期項目，歡迎對邏輯思考和科學研究有熱情的同學聯係實習或攻讀研究生，也希望這一階段的學習能夠為同學未來的科研與職業生涯奠定良好的基礎。
1. 噬菌體的高通量篩選與合成：噬菌體是特異性攻擊細菌的病毒。麵對日益嚴峻的抗生素耐藥性問題，噬菌體的改造和應用展現出巨大潛力。我們利用高通量技術和生物信息學策略，設計新的篩選和合成方案，以改造天然噬菌體庫，針對人類和水產病原菌感染開展靶向治療。
2. 轉座子的機製與應用研究：以小麥和病原菌為研究模型，探究轉座子在進化中的作用，並開發基於轉座子的功能基因挖掘工具。小麥的基因組在多次雜交加倍和轉座子擴張事件中表現出高度的環境適應性。我們結合多種技術手段，揭示了轉座子在維持染色質穩定性、調控網絡的進化與分化中的作用。
3. 作物營養代謝研究：大眾飲食觀念正在從“吃得飽”向“吃得好”轉變，但傳統作物育種營養學研究滯後。我們通過與雜糧育種團隊合作，依托國家重點實驗室的代謝平台，結合基因組學技術開展新的營養物質挖掘與育種工作，旨在提高農作物的營養價值和健康效益。
個人簡介
2003年獲中國海洋大學學士；2008年獲中國科學院遺傳與發育生物學研究所博士；2008-2013先後在中國農業大學、波士頓大學和哈佛醫學院，從事博士後研究；2013-2021年在中科院上海植物生理生態研究所任研究員及課題組長；2021年任万博英超狼队网官方网 研究員。作為最後通訊作者在Nature Communications, Genome Research（期刊封麵），Plant Cell（亮點專評），Genome Biology和Nucleic Acids Research等國際學術期刊發表論文20餘篇。依托搭建的生物信息平台，合作發表Nature，Science，Nature Genetics等期刊論文。
獲獎情況
2021 國家自然科學基金委/優秀青年基金項目（終評“A”）
2015 上海市科技人才計劃項目/浦江人才計劃
2014 中國科學院上海生命科學院特殊（S類）人才計劃
招生專業：生物化學（表觀遺傳學）
代表性論文和論著：
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.
教師基本信息：
姓名：Yijing Zhang
職稱：Researcher
電子郵箱：zhangyijing@fudan.edu.cn
辦公地點：410, College of Life Sciences, Jiangwan campus, Fudan University, No. 2055, Songhu Road, Yangpu District, Shanghai
辦公電話：021-54924204
個人網頁/課題組主頁：//www.xahaidun.com/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.
個人簡介：
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.
招生專業：Biochemistry
代表性論文和論著：
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.