戚继 - 复旦大学 - 生命科学学院

个人简介

复旦大学生命科学学院，研究员，博士生导师。目前在植物发育、分子进化、生物信息学方法等研究方向上开展研究工作。在Nature Communications、PNAS、Nucleic Acids Research、Molecular Plant、Molecular Biology and Evolution等在生物学领域有较高影响力的期刊上发表多篇SCI科研论文，合计被引用超过10,000次，h-index为40（来源：Google Scholar）。

研究领域

发育：基于空间转录组研究植物花器官的建成过程利用10X Visium技术研究兰科植物蝴蝶兰的花器官发生与发育过程。通过分析数以千计的花发育关键基因的高分辨率空间表达模式，发现了兰花早期发育的多种细胞类型，包括花原基、花器官原基和多种分生组织。其中花器官基部的分生组织细胞在器官起始后的多个发育阶段持续发挥功能。发现早期器官原基与后续发育时期多种细胞类型联合构建了详细的分化轨迹，为理解花器官发生以及特定细胞类型的基因组学和遗传学研究提供了分子层面的信息。进化：植物基因组变异和重复基因功能分化通过开发生物信息学新方法并结合多种植物的基因组、转录组高通量测序，发现被子植物不同分支上普遍存在基因组多倍化，重复基因的保留程度符合一致的指数衰减规律。研究发现这些重复基因为基因功能分化和新功能的产生提供了更多的材料，有利于增加植物的环境适应性。算法：空间转录组和分子进化的机器学习方法开发了可以用于单细胞精度的空间转录组分析新方法，可以从10X Visium、Slide-seq等测序数据中有效识别不同类型的细胞，准确性远高于同类方法。通过将方法应用于本项目前期已完成的蝴蝶兰花器官空间转录组分析中，结果表明预测的花原基、四类花器官原基、形态建成中的组织等具有高度的准确性，有利于精确分析不同器官的起始状态差异和关键基因表达，同时还可进一步研究同类器官在不同发育时期的细胞类型分化和基因表达调控复杂性。

近期论文

查看导师新发文章（温馨提示：请注意重名现象，建议点开原文通过作者单位确认）

Yamao Chen†, Shengyu Zhou†, Ming Li, Fangqing Zhao* and Ji Qi* (2023) STEEL enables high-resolution delineation of spatiotemporal transcriptomic data. Briefings in Bioinformatics. DOI:10.1093/bib/bbad068 Jingting Shen1†, Shengyu Zhou1†, Yamao Chen and Ji Qi* (2023) TransMCL enables the assembly of full-length coding genes for collecting complete hierarchical orthogroups. Methods in Ecology & Evolution.DOI:10.1111/2041-210X.14179 Chang Liu, Jing Leng, Yonglong Li, Tingting Ge, Jinglong Li, Yamao Chen, Chunce Guo* and Ji Qi* (2022) A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Research. 50(17):9724-9737 Jinglong Li, Jingting Shen, Rui Wang, Yamao Chen, Taikui Zhang, Haifeng Wang, Chunce Guo, Ji Qi* (2022) The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. Plant Communications. 4(1):100422 Duoyuan Chen#, Taikui Zhang#, Yamao Chen, Hong Ma and Ji Qi* (2022) Tree2GD: a phylogenomic method to detect large-scale gene duplication events. Bioinformatics. 38(23):5317-5321 Ying Zhao#, Duoyuan Chen#, Jianping Tang, Yufang Zheng*, Ji Qi*, Hongyan Wang* (2022) Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations. Cell Discovery. 8:18 Chengpeng He#; Zhiyu Chen#; Yiyong Zhao; Yue Yu; Hongkuan Wang; Cong Wang; Gregory P. Cop enhaver; Ji Qi*; Yingxiang Wang* (2022) Histone demethylase IBM1-mediated meiocyte gene expression ensur es meiotic chromosome synapsis and recombination. PLoS Genetics. 18(2):e1010041 Q. Lian, Y. Chen, F. Chang, Y. Fu and J. Qi* (2021) inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities. Genomics, Protoemics & Bioinformatics https://doi.org/10.1016/j.gpb.2019.11.014. Caifei Zhang#, Taikui Zhang#, Federico Luebert# Yezi Xiang, Chien-Hsun Huang, Yi Hu, Mathew Rees, Michael W. Frohlich, Ji Qi*, Maximilian Weigend*, Hong Ma*. (2020) Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications. Mol. Biol. Evol. 37:3188-3210 S. Zhou, Y. Chen, C. Guo*, J. Qi* (2020) PhyloMCL: accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events. Methods in Ecology & Evolution. 11: 943-954 https://doi.org/10.1111/2041-210X.13401 H. Wang, C. Guo, H. Ma, J. Qi* (2019) Meeting the Challenges of Detecting Polyploidy Events from Transcriptomic Data. Mol. Plant 12(2):137-140 J. Liu, Q. Lian, Y. Chen, J. Qi* (2019) Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads. Nucleic Acids Res. 47: e30 doi: 10.1093/nar/gkz017. Ren Ren#, Haifeng Wang#, Chunce Guo#, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma*, Ji Qi* (2018) Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol. Plant 11: 414-428. DOI: https://doi.org/10.1016/j.molp.2018.01.002