DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data.

Journal: Bioinformatics (Oxford, England)
Published Date: Oct 3, 2023

Abstract

MOTIVATION: Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA sequencing (scRNA-seq) technologies, it is of high importance to identify CCIs from the ever-increasing scRNA-seq data. However, limited by the algorithmic constraints, current computational methods based on statistical strategies ignore some key latent information contained in scRNA-seq data with high sparsity and heterogeneity.

Authors

  • Wenyi Yang
    School of Software, Central South University, Changsha, 410075, China.
  • Pingping Wang
    School of Electrical and Information Engineering, Tianjin University, 300072, Tianjin, China.
  • Meng Luo
    Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China.
  • Yideng Cai
    School of Computer Science and Engineering, Central South University, Changsha 410083, China.
  • Chang Xu
    Institute of Cardio-Cerebrovascular Medicine, Central Hospital of Dalian University of Technology, Dalian 116089, China.
  • Guangfu Xue
    School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China.
  • Xiyun Jin
    Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
  • Rui Cheng
    Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China.
  • Jinhao Que
    School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China.
  • Fenglan Pang
    School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China.
  • Yuexin Yang
    School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China.
  • Huan Nie
    Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China. nh1212@hit.edu.cn.
  • Qinghua Jiang
    School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
  • Zhigang Liu
    Cardiac Surgery, TEDA International Cardiovascular Hospital, Tianjin, China.
  • Zhaochun Xu
    Computer Department, Jingdezhen Ceramic University, Jingdezhen, China.

Keywords

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