Network propagation: a universal amplifier of genetic associations

L Cowen, T Ideker, BJ Raphael, R Sharan - Nature Reviews Genetics, 2017 - nature.com
Biological networks are powerful resources for the discovery of genes and genetic modules
that drive disease. Fundamental to network analysis is the concept that genes underlying the …

Recent advances in network-based methods for disease gene prediction

SK Ata, M Wu, Y Fang, L Ou-Yang… - Briefings in …, 2021 - academic.oup.com
Disease–gene association through genome-wide association study (GWAS) is an arduous
task for researchers. Investigating single nucleotide polymorphisms that correlate with …

deepDR: a network-based deep learning approach to in silico drug repositioning

X Zeng, S Zhu, X Liu, Y Zhou, R Nussinov… - …, 2019 - academic.oup.com
Motivation Traditional drug discovery and development are often time-consuming and high
risk. Repurposing/repositioning of approved drugs offers a relatively low-cost and high …

Predicting miRNA–disease association based on inductive matrix completion

X Chen, L Wang, J Qu, NN Guan, JQ Li - Bioinformatics, 2018 - academic.oup.com
Motivation It has been shown that microRNAs (miRNAs) play key roles in variety of
biological processes associated with human diseases. In Consideration of the cost and …

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

Y Luo, X Zhao, J Zhou, J Yang, Y Zhang… - Nature …, 2017 - nature.com
The emergence of large-scale genomic, chemical and pharmacological data provides new
opportunities for drug discovery and repositioning. In this work, we develop a computational …

Uncovering disease-disease relationships through the incomplete interactome

J Menche, A Sharma, M Kitsak, SD Ghiassian, M Vidal… - Science, 2015 - science.org
INTRODUCTION A disease is rarely a straightforward consequence of an abnormality in a
single gene, but rather reflects the interplay of multiple molecular processes. The …

Inductive matrix completion for predicting gene–disease associations

N Natarajan, IS Dhillon - Bioinformatics, 2014 - academic.oup.com
Motivation: Most existing methods for predicting causal disease genes rely on specific type
of evidence, and are therefore limited in terms of applicability. More often than not, the type …

GCN-MF: disease-gene association identification by graph convolutional networks and matrix factorization

P Han, P Yang, P Zhao, S Shang, Y Liu… - Proceedings of the 25th …, 2019 - dl.acm.org
Discovering disease-gene association is a fundamental and critical biomedical task, which
assists biologists and physicians to discover pathogenic mechanism of syndromes. With …

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods

X Zeng, Y Zhong, W Lin, Q Zou - Briefings in bioinformatics, 2020 - academic.oup.com
Identification of disease-associated circular RNAs (circRNAs) is of critical importance,
especially with the dramatic increase in the amount of circRNAs. However, the availability of …

Prediction and validation of disease genes using HeteSim Scores

X Zeng, Y Liao, Y Liu, Q Zou - IEEE/ACM transactions on …, 2016 - ieeexplore.ieee.org
Deciphering the gene disease association is an important goal in biomedical research. In
this paper, we use a novel relevance measure, called HeteSim, to prioritize candidate …