Deep learning for drug repurposing: Methods, databases, and applications

X Pan, X Lin, D Cao, X Zeng, PS Yu… - Wiley …, 2022 - Wiley Online Library
Drug development is time‐consuming and expensive. Repurposing existing drugs for new
therapies is an attractive solution that accelerates drug development at reduced …

Graph neural network approaches for drug-target interactions

Z Zhang, L Chen, F Zhong, D Wang, J Jiang… - Current Opinion in …, 2022 - Elsevier
Developing new drugs remains prohibitively expensive, time-consuming, and often involves
safety issues. Accurate prediction of drug-target interactions (DTIs) can guide the drug …

Graph neural networks: foundation, frontiers and applications

L Wu, P Cui, J Pei, L Zhao, X Guo - … of the 28th ACM SIGKDD Conference …, 2022 - dl.acm.org
The field of graph neural networks (GNNs) has seen rapid and incredible strides over the
recent years. Graph neural networks, also known as deep learning on graphs, graph …

Comparative toxicogenomics database (CTD): update 2021

AP Davis, CJ Grondin, RJ Johnson… - Nucleic acids …, 2021 - academic.oup.com
Abstract The public Comparative Toxicogenomics Database (CTD; http://ctdbase. org/) is an
innovative digital ecosystem that relates toxicological information for chemicals, genes …

Open graph benchmark: Datasets for machine learning on graphs

W Hu, M Fey, M Zitnik, Y Dong, H Ren… - Advances in neural …, 2020 - proceedings.neurips.cc
Abstract We present the Open Graph Benchmark (OGB), a diverse set of challenging and
realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine …

Molecular and network-level mechanisms explaining individual differences in autism spectrum disorder

AM Buch, PE Vértes, J Seidlitz, SH Kim… - Nature …, 2023 - nature.com
The mechanisms underlying phenotypic heterogeneity in autism spectrum disorder (ASD)
are not well understood. Using a large neuroimaging dataset, we identified three latent …

Self-alignment pretraining for biomedical entity representations

F Liu, E Shareghi, Z Meng, M Basaldella… - arXiv preprint arXiv …, 2020 - arxiv.org
Despite the widespread success of self-supervised learning via masked language models
(MLM), accurately capturing fine-grained semantic relationships in the biomedical domain …

High-depth African genomes inform human migration and health

A Choudhury, S Aron, LR Botigué, D Sengupta… - Nature, 2020 - nature.com
The African continent is regarded as the cradle of modern humans and African genomes
contain more genetic variation than those from any other continent, yet only a fraction of the …

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

G Zhou, O Soufan, J Ewald, REW Hancock… - Nucleic acids …, 2019 - academic.oup.com
The growing application of gene expression profiling demands powerful yet user-friendly
bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first …

Computational approaches in preclinical studies on drug discovery and development

F Wu, Y Zhou, L Li, X Shen, G Chen, X Wang… - Frontiers in …, 2020 - frontiersin.org
Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of
drug development in the costly late stage, it has been widely recognized that drug ADMET …