Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models

L Huang, L Zhang, X Chen - Briefings in bioinformatics, 2022 - academic.oup.com
Since the problem proposed in late 2000s, microRNA–disease association (MDA)
predictions have been implemented based on the data fusion paradigm. Integrating diverse …

Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models

L Huang, L Zhang, X Chen - Briefings in bioinformatics, 2022 - academic.oup.com
Currently, there exist no generally accepted strategies of evaluating computational models
for microRNA-disease associations (MDAs). Though K-fold cross validations and case …

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data

F Yang, W Wang, F Wang, Y Fang, D Tang… - Nature Machine …, 2022 - nature.com
Annotating cell types on the basis of single-cell RNA-seq data is a prerequisite for research
on disease progress and tumour microenvironments. Here we show that existing annotation …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion

L Huang, L Zhang, X Chen - Briefings in bioinformatics, 2022 - academic.oup.com
MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex
diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic …

HumanNet v3: an improved database of human gene networks for disease research

CY Kim, S Baek, J Cha, S Yang, E Kim… - Nucleic acids …, 2022 - academic.oup.com
Network medicine has proven useful for dissecting genetic organization of complex human
diseases. We have previously published HumanNet, an integrated network of human genes …

Large-scale meta-analysis across East Asian and European populations updated genetic architecture and variant-driven biology of rheumatoid arthritis, identifying 11 …

E Ha, SC Bae, K Kim - Annals of the rheumatic diseases, 2021 - Elsevier
Objectives Nearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes
have been identified by population-based genetic association studies, suggesting a large …

Multi-view multichannel attention graph convolutional network for miRNA–disease association prediction

X Tang, J Luo, C Shen, Z Lai - Briefings in bioinformatics, 2021 - academic.oup.com
Motivation: In recent years, a growing number of studies have proved that microRNAs
(miRNAs) play significant roles in the development of human complex diseases. Discovering …

A review of biomedical datasets relating to drug discovery: a knowledge graph perspective

S Bonner, IP Barrett, C Ye, R Swiers… - Briefings in …, 2022 - academic.oup.com
Drug discovery and development is a complex and costly process. Machine learning
approaches are being investigated to help improve the effectiveness and speed of multiple …

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

PC Havugimana, RK Goel, S Phanse, A Youssef… - Nature …, 2022 - nature.com
Co-fractionation/mass spectrometry (CF/MS) enables the map** of endogenous
macromolecular networks on a proteome scale, but current methods are experimentally …