A review of recent advances and research on drug target identification methods

Y Hu, T Zhao, N Zhang, Y Zhang… - Current drug …, 2019 - benthamdirect.com
Background: From a therapeutic viewpoint, understanding how drugs bind and regulate the
functions of their target proteins to protect against disease is crucial. The identification of …

Identifying diseases-related metabolites using random walk

Y Hu, T Zhao, N Zhang, T Zang, J Zhang, L Cheng - BMC bioinformatics, 2018 - Springer
Background Metabolites disrupted by abnormal state of human body are deemed as the
effect of diseases. In comparison with the cause of diseases like genes, these markers are …

Study on the multitarget mechanism and key active ingredients of herba siegesbeckiae and volatile oil against rheumatoid arthritis based on network pharmacology

X Yang, Y Li, R Lv, H Qian, X Chen… - Evidence‐Based …, 2019 - Wiley Online Library
Background. Herba Siegesbeckiae (HS, **xiancao in Chinese) is widely used to treat
inflammatory joint diseases such as rheumatoid arthritis (RA) and arthritis, and its molecular …

Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data

J Peng, X Wang, X Shang - BMC bioinformatics, 2019 - Springer
Background Single cell RNA sequencing (scRNA-seq) is applied to assay the individual
transcriptomes of large numbers of cells. The gene expression at single-cell level provides …

OAHG: an integrated resource for annotating human genes with multi-level ontologies

L Cheng, J Sun, W Xu, L Dong, Y Hu, M Zhou - Scientific reports, 2016 - nature.com
OAHG, an integrated resource, aims to establish a comprehensive functional annotation
resource for human protein-coding genes (PCGs), miRNAs, and lncRNAs by multi-level …

Identifying term relations cross different gene ontology categories

J Peng, H Wang, J Lu, W Hui, Y Wang, X Shang - BMC bioinformatics, 2017 - Springer
Abstract Background The Gene Ontology (GO) is a community-based bioinformatics
resource that employs ontologies to represent biological knowledge and describes …

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach

J Peng, X Zhang, W Hui, J Lu, Q Li, S Liu, X Shang - BMC systems biology, 2018 - Springer
Abstract Background Gene Ontology (GO) is one of the most popular bioinformatics
resources. In the past decade, Gene Ontology-based gene semantic similarity has been …

Measuring disease similarity and predicting disease-related ncRNAs by a novel method

Y Hu, M Zhou, H Shi, H Ju, Q Jiang, L Cheng - BMC medical genomics, 2017 - Springer
Background Similar diseases are always caused by similar molecular origins, such as
diasease-related protein-coding genes (PCGs). And the molecular associations reflect their …

Predicting disease-related genes using integrated biomedical networks

J Peng, K Bai, X Shang, G Wang, H Xue, S **… - BMC genomics, 2017 - Springer
Background Identifying the genes associated to human diseases is crucial for disease
diagnosis and drug design. Computational approaches, esp. the network-based …

A novel method to measure the semantic similarity of HPO terms

J Peng, H Xue, Y Shao, X Shang… - … Journal of Data …, 2017 - inderscienceonline.com
It is critical yet remains to be challenging to make precise disease diagnosis from complex
clinical features and highly heterogeneous genetic background. Recently, phenotype …