Professor | Ji Qi | Asia Growth Partners

Name	Ji Qi
Contact Information	qij@fudan.edu.cn
Language ability	English, Chinese
Province	Shanghai

Name

Ji Qi

Contact Information

qij@fudan.edu.cn

Language ability

English, Chinese

Province

Shanghai

University/Lab Affiliation and Title	Fudan University
Faculty	Life Sciences

University/Lab Affiliation and Title

Fudan University

Faculty

Life Sciences

Areas of Focus	Development: Studying the construction process of plant floral organs based on spatial transcriptomics. Evolution: Plant genome variation and functional differentiation of repetitive genes. Algorithms: Machine learning methods for spatial transcriptomics and molecular evolution.
Publications	STEEL enables high-resolution delineation of spatiotemporal transcriptomic data., Yamao Chen†, Shengyu Zhou†, Ming Li, Fangqing Zhao* and Ji Qi, 2023 TransMCL enables the assembly of full-length coding genes for collecting complete hierarchical orthogroups., Jingting Shen1†, Shengyu Zhou1†, Yamao Chen and Ji Qi, 2023 A spatiotemporal atlas of organogenesis in the development of orchid flowers., Chang Liu, Jing Leng, Yonglong Li, Tingting Ge, Jinglong Li, Yamao Chen, Chunce Guo* and Ji Qi, 2022 The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution., Jinglong Li, Jingting Shen, Rui Wang, Yamao Chen, Taikui Zhang, Haifeng Wang, Chunce Guo, Ji Qi, 2022 Tree2GD: a phylogenomic method to detect large-scale gene duplication events., Duoyuan Chen#, Taikui Zhang#, Yamao Chen, Hong Ma and Ji Qi, 2022 Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations., Ying Zhao#, Duoyuan Chen#, Jianping Tang, Yufang Zheng, Ji Qi, Hongyan Wang, 2022 Histone demethylase IBM1-mediated meiocyte gene expression ensures meiotic chromosome synapsis and recombination., Chengpeng He#; Zhiyu Chen#; Yiyong Zhao; Yue Yu; Hongkuan Wang; Cong Wang; Gregory P. Copenhaver; Ji Qi; Yingxiang Wang, 2022 inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities., Q. Lian, Y. Chen, F. Chang, Y. Fu and J. Qi, 2021 Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications., 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 PhyloMCL: accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events., S. Zhou, Y. Chen, C. Guo, J. Qi, 2020 Meeting the Challenges of Detecting Polyploidy Events from Transcriptomic Data., H. Wang, C. Guo, H. Ma, J. Qi, 2019 Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads., J. Liu, Q. Lian, Y. Chen, J. Qi, 2019 Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms., Ren Ren#, Haifeng Wang#, Chunce Guo#, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi, 2018

Areas of Focus

Development: Studying the construction process of plant floral organs based on spatial transcriptomics.
Evolution: Plant genome variation and functional differentiation of repetitive genes.
Algorithms: Machine learning methods for spatial transcriptomics and molecular evolution.

Publications

STEEL enables high-resolution delineation of spatiotemporal transcriptomic data., Yamao Chen†, Shengyu Zhou†, Ming Li, Fangqing Zhao* and Ji Qi*, 2023
TransMCL enables the assembly of full-length coding genes for collecting complete hierarchical orthogroups., Jingting Shen1†, Shengyu Zhou1†, Yamao Chen and Ji Qi*, 2023
A spatiotemporal atlas of organogenesis in the development of orchid flowers., Chang Liu, Jing Leng, Yonglong Li, Tingting Ge, Jinglong Li, Yamao Chen, Chunce Guo* and Ji Qi*, 2022
The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution., Jinglong Li, Jingting Shen, Rui Wang, Yamao Chen, Taikui Zhang, Haifeng Wang, Chunce Guo, Ji Qi*, 2022
Tree2GD: a phylogenomic method to detect large-scale gene duplication events., Duoyuan Chen#, Taikui Zhang#, Yamao Chen, Hong Ma and Ji Qi*, 2022
Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations., Ying Zhao#, Duoyuan Chen#, Jianping Tang, Yufang Zheng*, Ji Qi*, Hongyan Wang*, 2022
Histone demethylase IBM1-mediated meiocyte gene expression ensures meiotic chromosome synapsis and recombination., Chengpeng He#; Zhiyu Chen#; Yiyong Zhao; Yue Yu; Hongkuan Wang; Cong Wang; Gregory P. Copenhaver; Ji Qi*; Yingxiang Wang*, 2022
inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities., Q. Lian, Y. Chen, F. Chang, Y. Fu and J. Qi*, 2021
Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications., 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
PhyloMCL: accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events., S. Zhou, Y. Chen, C. Guo*, J. Qi*, 2020
Meeting the Challenges of Detecting Polyploidy Events from Transcriptomic Data., H. Wang, C. Guo, H. Ma, J. Qi*, 2019
Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads., J. Liu, Q. Lian, Y. Chen, J. Qi*, 2019
Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms., Ren Ren#, Haifeng Wang#, Chunce Guo#, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma*, Ji Qi*, 2018

Spatial Transcriptomics Plant Development Floral Organs Genome Variation Gene Duplication Bioinformatics Machine Learning High-Throughput Sequencing Cell Differentiation Gene Expression

Qi Liu - Tongji University

Lu Dongdong - Tongji University

Song Lei - Shanghai Normal University

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