GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data

被引:0
|
作者
Kai Wang [1 ]
Yulong Li [1 ]
Fei Liu [1 ]
Xiaoli Luan [1 ]
Xinglong Wang [2 ]
Jingwen Zhou [3 ]
机构
[1] Jiangnan University,Key Laboratory of Advanced Process Control for Light Industry (Ministry of Education), School of Internet of Things Engineering
[2] Jiangnan University,Science Center for Future Foods
[3] Jiangnan University,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology
[4] Jiangnan University,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology
[5] Jiangnan University,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology
关键词
Gene regulatory network; Gene expression data; Graph representation learning; Implicit links;
D O I
10.1186/s12859-025-06116-1
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 50 条
  • [1] Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data
    Stock, Marco
    Popp, Niclas
    Fiorentino, Jonathan
    Scialdone, Antonio
    BIOINFORMATICS, 2024, 40 (05)
  • [2] Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
    Mao, Guo
    Pang, Zhengbin
    Zuo, Ke
    Wang, Qinglin
    Pei, Xiangdong
    Chen, Xinhai
    Liu, Jie
    BRIEFINGS IN BIOINFORMATICS, 2023, 24 (06)
  • [3] A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data
    Zhao, Mengyuan
    Li, Jiawei
    Liu, Xiaoyi
    Ma, Ke
    Tang, Jijun
    Guo, Fei
    GENOME RESEARCH, 2024, 34 (07) : 1036 - 1051
  • [4] Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
    Li, Yang
    Ma, Anjun
    Wang, Yizhong
    Guo, Qi
    Wang, Cankun
    Fu, Hongjun
    Liu, Bingqiang
    Ma, Qin
    BRIEFINGS IN BIOINFORMATICS, 2024, 25 (05)
  • [5] Single-cell RNA-seq data analysis using graph autoencoders and graph attention networks
    Feng, Xiang
    Fang, Fang
    Long, Haixia
    Zeng, Rao
    Yao, Yuhua
    FRONTIERS IN GENETICS, 2022, 13
  • [6] Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data
    Bin Yang
    Bao, Wenzheng
    Chen, Baitong
    Song, Dan
    BIODATA MINING, 2022, 15 (01)
  • [7] Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data
    Bin Yang
    Wenzheng Bao
    Baitong Chen
    Dan Song
    BioData Mining, 15
  • [8] Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning
    Lee, Junseok
    Kim, Sungwon
    Hyun, Dongmin
    Lee, Namkyeong
    Kim, Yejin
    Park, Chanyoung
    BIOINFORMATICS, 2023, 39 (06)
  • [9] Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data
    Yanhong Wu
    Qifan Hu
    Shicheng Wang
    Changyi Liu
    Yiran Shan
    Wenbo Guo
    Rui Jiang
    Xiaowo Wang
    Jin Gu
    Journal of Genetics and Genomics, 2022, 49 (09) : 891 - 899
  • [10] Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data
    Wu, Yanhong
    Hu, Qifan
    Wang, Shicheng
    Liu, Changyi
    Shan, Yiran
    Guo, Wenbo
    Jiang, Rui
    Wang, Xiaowo
    Gu, Jin
    JOURNAL OF GENETICS AND GENOMICS, 2022, 49 (09) : 891 - 899