Spatial transcriptomics data and analytical methods: an updated perspective

S Khan, JJ Kim - Drug Discovery Today, 2024 - Elsevier
Spatial transcriptomics (ST) is a newly emerging field that integrates high-resolution imaging
and transcriptomic data to enable the high-throughput analysis of the spatial localization of …

Deep learning in spatially resolved transcriptfomics: a comprehensive technical view

R Zahedi, R Ghamsari, A Argha… - Briefings in …, 2024 - academic.oup.com
Spatially resolved transcriptomics (SRT) is a pioneering method for simultaneously studying
morphological contexts and gene expression at single-cell precision. Data emerging from …

LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton …

L Peng, L Huang, Q Su, G Tian, M Chen… - Briefings in …, 2024 - academic.oup.com
Long noncoding RNAs (lncRNAs) participate in various biological processes and have close
linkages with diseases. In vivo and in vitro experiments have validated many associations …

BINDTI: a bi-directional intention network for drug-target interaction identification based on attention mechanisms

L Peng, X Liu, L Yang, L Liu, Z Bai… - IEEE Journal of …, 2024 - ieeexplore.ieee.org
The identification of drug-target interactions (DTIs) is an essential step in drug discovery. In
vitro experimental methods are expensive, laborious, and time-consuming. Deep learning …

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 …

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 …

Drug repositioning based on tripartite cross-network embedding and graph convolutional network

P Zeng, B Zhang, A Liu, Y Meng, X Tang, J Yang… - Expert Systems with …, 2024 - Elsevier
Drug-disease association prediction is an important part of drug discovery, which can help
researchers uncover potential drug candidates and disease targets more accurately to deal …

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks

F Xu, H Hu, H Lin, J Lu, F Cheng, J Zhang… - Briefings in …, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless …

SEnSCA: Identifying possible ligand‐receptor interactions and its application in cell–cell communication inference

L Zhou, X Wang, L Peng, M Chen… - Journal of Cellular and …, 2024 - Wiley Online Library
Multicellular organisms have dense affinity with the coordination of cellular activities, which
severely depend on communication across diverse cell types. Cell–cell communication …

Finding potential lncRNA–disease associations using a boosting-based ensemble learning model

L Zhou, X Peng, L Zeng, L Peng - Frontiers in Genetics, 2024 - frontiersin.org
Introduction: Long non-coding RNAs (lncRNAs) have been in the clinical use as potential
prognostic biomarkers of various types of cancer. Identifying associations between lncRNAs …