Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Exploring protein-protein interactions at the proteome level

H Elhabashy, F Merino, V Alva, O Kohlbacher… - Structure, 2022 - cell.com
Proteins are central to all of the processes of life. For their activity, they almost invariably
need to interact with other macromolecules, be they nucleic acids, membranes, glycans, or …

ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components

T Obayashi, H Hibara, Y Kagaya, Y Aoki… - Plant and Cell …, 2022 - academic.oup.com
Abstract ATTED-II (https://atted. jp) is a gene coexpression database for nine plant species
based on publicly available RNAseq and microarray data. One of the challenges in …

[HTML][HTML] Protection against COVID-19 injury by qingfei paidu decoction via anti-viral, anti-inflammatory activity and metabolic programming

J Chen, Y Wang, Y Gao, LS Hu, J Yang, J Wang… - Biomedicine & …, 2020 - Elsevier
Qingfei Paidu decoction (QFPD), a multi-component herbal formula, has been widely used
to treat COVID-19 in China. However, its active compounds and mechanisms of action are …

Correlation AnalyzeR: functional predictions from gene co-expression correlations

HE Miller, AJR Bishop - BMC bioinformatics, 2021 - Springer
Background Co-expression correlations provide the ability to predict gene functionality
within specific biological contexts, such as different tissue and disease conditions. However …

GeneFriends: gene co-expression databases and tools for humans and model organisms

P Raina, R Guinea, K Chatsirisupachai… - Nucleic Acids …, 2023 - academic.oup.com
Gene co-expression analysis has emerged as a powerful method to provide insights into
gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA …

Matrix reconstruction with reliable neighbors for predicting potential MiRNA–disease associations

H Feng, D Jin, J Li, Y Li, Q Zou… - Briefings in Bioinformatics, 2023 - academic.oup.com
Numerous experimental studies have indicated that alteration and dysregulation in
mircroRNAs (miRNAs) are associated with serious diseases. Identifying disease-related …

A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE

JA Watts, C Grunseich, Y Rodriguez, Y Liu… - Nucleic Acids …, 2022 - academic.oup.com
RNA is modified by hundreds of chemical reactions and folds into innumerable shapes.
However, the regulatory role of RNA sequence and structure and how dysregulation leads to …

COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations

T Obayashi, S Kodate, H Hibara, Y Kagaya… - Nucleic Acids …, 2023 - academic.oup.com
Gene coexpression is synchronization of gene expression across many cellular and
environmental conditions and is widely used to infer the biological function of genes. Gene …

Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson's disease

K Mihajlović, G Ceddia, N Malod-Dognin, G Novak… - Scientific Reports, 2024 - nature.com
Parkinson's disease (PD) is a complex neurodegenerative disorder without a cure. The
onset of PD symptoms corresponds to 50% loss of midbrain dopaminergic (mDA) neurons …