Identifying potential ligand–receptor interactions based on gradient boosted neural network and interpretable boosting machine for intercellular communication …

L Peng, P Gao, W Xiong, Z Li, X Chen - Computers in Biology and Medicine, 2024 - Elsevier
Cell–cell communication is essential to many key biological processes. Intercellular
communication is generally mediated by ligand–receptor interactions (LRIs). Thus, building …

Deciphering ligand–receptor-mediated intercellular communication based on ensemble deep learning and the joint scoring strategy from single-cell transcriptomic …

L Peng, J Tan, W Xiong, L Zhang, Z Wang… - Computers in Biology …, 2023 - Elsevier
Background: Cell–cell communication in a tumor microenvironment is vital to tumorigenesis,
tumor progression and therapy. Intercellular communication inference helps understand …

CellDialog: A Computational Framework for Ligand-receptor-mediated Cell-cell Communication Analysis III

L Peng, W Xiong, C Han, Z Li… - IEEE Journal of …, 2023 - ieeexplore.ieee.org
Intercellularcommunication significantly influences tumor progression, metastasis, and
therapy resistance. An intercellular communication inference method includes two main …

Cellenboost: a boosting-based ligand-receptor interaction identification model for cell-to-cell communication inference

L Peng, R Yuan, C Han, G Han, J Tan… - IEEE Transactions …, 2023 - ieeexplore.ieee.org
Cell-to-cell communication (CCC) plays important roles in multicellular organisms. The
identification of communication between cancer cells themselves and one between cancer …

Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis

Y Zhang, T Liu, J Wang, B Zou, L Li, L Yao… - …, 2021 - academic.oup.com
Abstract Motivation Ligand–receptor (L–R) interactions mediate cell adhesion, recognition
and communication and play essential roles in physiological and pathological signaling …

A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference

S Wang, H Zheng, JS Choi, JK Lee… - Briefings in functional …, 2022 - academic.oup.com
Cell–cell interactions (CCIs) are essential for multicellular organisms to coordinate
biological processes and functions. One classical type of CCI interaction is between …

LR hunting: A random forest based cell–cell interaction discovery method for single-cell gene expression data

M Lu, Y Sha, TC Silva, A Colaprico, X Sun, Y Ban… - Frontiers in …, 2021 - frontiersin.org
Cell–cell interactions (CCIs) and cell–cell communication (CCC) are critical for maintaining
complex biological systems. The availability of single-cell RNA sequencing (scRNA-seq) …

CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication

Y Zhang, T Liu, X Hu, M Wang, J Wang… - Nucleic acids …, 2021 - academic.oup.com
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies,
the systematic decoding of cell-cell communication has received great research interest. To …

Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

L Peng, F Wang, Z Wang, J Tan, L Huang… - Briefings in …, 2022 - academic.oup.com
Carcinomas are complex ecosystems composed of cancer, stromal and immune cells.
Communication between these cells and their microenvironments induces cancer …

scTenifoldXct: a semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

Y Yang, G Li, Y Zhong, Q Xu, YT Lin… - Cell systems, 2023 - cell.com
We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-
receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs …