Comprehensive evaluation of deep and graph learning on drug–drug interactions prediction
Recent advances and achievements of artificial intelligence (AI) as well as deep and graph
learning models have established their usefulness in biomedical applications, especially in …
learning models have established their usefulness in biomedical applications, especially in …
Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism
T Wang, J Sun, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
Human ether-a-go-go-related gene (hERG) channel blockade by small molecules is a big
concern during drug development in the pharmaceutical industry. Failure or inhibition of …
concern during drug development in the pharmaceutical industry. Failure or inhibition of …
scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention
R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …
Structural basis for T cell recognition of cancer neoantigens and implications for predicting neoepitope immunogenicity
Adoptive cell therapy (ACT) with tumor-specific T cells has been shown to mediate durable
cancer regression. Tumor-specific T cells are also the basis of other therapies, notably …
cancer regression. Tumor-specific T cells are also the basis of other therapies, notably …
Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity
Identifying neoepitopes that elicit an adaptive immune response is a major bottleneck to
developing personalized cancer vaccines. Experimental validation of candidate …
developing personalized cancer vaccines. Experimental validation of candidate …
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data
J Xu, A Zhang, F Liu, X Zhang - Bioinformatics, 2023 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) technologies provide an opportunity to
infer cell-specific gene regulatory networks (GRNs), which is an important challenge in …
infer cell-specific gene regulatory networks (GRNs), which is an important challenge in …
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning
S Lin, W Chen, G Chen, S Zhou, DQ Wei… - Journal of …, 2022 - Springer
The joint use of multiple drugs may cause unintended drug-drug interactions (DDIs) and
result in adverse consequence to the patients. Accurate identification of DDI types can not …
result in adverse consequence to the patients. Accurate identification of DDI types can not …
PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction
S Zhai, Y Tan, C Zhang, CJ Hipolito… - Journal of Medicinal …, 2023 - ACS Publications
The combination of library-based screening and artificial intelligence (AI) has been
accelerating the discovery and optimization of hit ligands. However, the potential of AI to …
accelerating the discovery and optimization of hit ligands. However, the potential of AI to …
Multitask joint strategies of self-supervised representation learning on biomedical networks for drug discovery
Self-supervised representation learning (SSL) on biomedical networks provides new
opportunities for drug discovery; however, effectively combining multiple SSL models is still …
opportunities for drug discovery; however, effectively combining multiple SSL models is still …
[HTML][HTML] Drug discovery by targeting the protein‒protein interactions involved in autophagy
H Xiang, M Zhou, Y Li, L Zhou, R Wang - Acta Pharmaceutica Sinica B, 2023 - Elsevier
Autophagy is a cellular process in which proteins and organelles are engulfed in
autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein …
autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein …