戚继

发布时间：2021-06-29浏览次数：5103

教师基本信息：

姓名：戚继

职称：研究员

职务：

电子邮箱：qij@fudan.edu.cn

办公地点：生科院E401

办公电话：021-31246533

个人网页/课题组主页：

研究方向：

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。

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）。

授课情况：本科生课程《生物信息学》

招生专业：生物信息学

科研项目：获得多项国家自然基金资助

代表性论文和论著：

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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.

9. 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

10. 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

11. 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

12. 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.

13. 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

Basic Information:

Name: Ji Qi

Title: Professor

Position:

Email: qij@fudan.edu.cn

Office Location: School of Life Sciences, E401

Office Phone: 021-31246533

Personal webpage/lab homepage:

Research intrested:

Development: Studying the construction process of plant floral organs based on spatial transcriptomics.

We use the spatial transcriptome technology to study the development of floral organs in model plants of monocots, eudicots and basal angiosperms. Through the analysis of high-resolution spatial expression patterns of thousands of key genes involved in flower development, various cell types in early orchid development were identified, including floral primordia, floral organ primordia, and various meristematic tissues. The meristematic cells at the base of floral organs were found to play a continuous role in multiple developmental stages after organ initiation. The study revealed detailed differentiation trajectories constructed by early organ primordia and various cell types during subsequent development, providing molecular-level information for understanding floral organogenesis and genomic and genetic studies of specific cell types.

Evolution: Plant genome variation and functional differentiation of repetitive genes.

By developing new bioinformatics methods and combining high-throughput sequencing of genomes and transcriptomes of various plants, it was discovered that genome duplication is widespread in different branches of angiosperms, and the retention of repetitive genes follows a consistent exponential decay pattern. The study found that these repetitive genes provide more materials for functional differentiation and the generation of new functions, contributing to increased environmental adaptability in plants.

Algorithms: Machine learning methods for spatial transcriptomics and molecular evolution.

We developed new methods for spatial transcriptomic analysis with single-cell precision, effectively identifying different cell types from sequencing data such as 10X Visium and Slide-seq, with higher accuracy than similar methods. By applying the method to the previously completed spatial transcriptomic analysis of Phalaenopsis orchid floral organs, the results showed high accuracy in predicting floral primordia, four types of floral organ primordia, and tissues undergoing morphogenesis. This is beneficial for precise analysis of key gene expression in different organs and further research into the complexity of cell type differentiation.

Personal Profile:

Ji Qi is a professor at the School of Life Sciences, Fudan University. Currently, his research focuses on plant development, molecular evolution, and bioinformatics methods. He holds a position as a faculty member and mentors doctoral students.He has published research papers in high-impact journals in the field of biology, including Nature Communications, PNAS, Nucleic Acids Research, Molecular Plant, and Molecular Biology and Evolution. His publications have collectively been cited over 10,000 times, with an h-index of 40 (source: Google Scholar).

Teaching: Ji Qi teaches the course Bioinformatics for undergraduate students.

Research Projects: Ji Qi has secured funding for multiple research projects from the National Natural Science Foundation of China (NSFC)

Selected publications:

5. 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

11. 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

doi: 10.1093/nar/gkz017.