Machine learning for synergistic network pharmacology: a comprehensive overview

F Noor, M Asif, UA Ashfaq, M Qasim… - Briefings in …, 2023 - academic.oup.com
Network pharmacology is an emerging area of systematic drug research that attempts to
understand drug actions and interactions with multiple targets. Network pharmacology has …

[HTML][HTML] Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

D Rosati, M Palmieri, G Brunelli, A Morrione… - Computational and …, 2024 - Elsevier
In recent years, the role of bioinformatics and computational biology together with omics
techniques and transcriptomics has gained tremendous importance in biomedicine and …

Differential co-expression network analysis reveals key hub-high traffic genes as potential therapeutic targets for COVID-19 pandemic

A Hasankhani, A Bahrami, N Sheybani, B Aria… - Frontiers in …, 2021 - frontiersin.org
Background The recent emergence of COVID-19, rapid worldwide spread, and incomplete
knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited …

siVAE: interpretable deep generative models for single-cell transcriptomes

Y Choi, R Li, G Quon - Genome biology, 2023 - Springer
Neural networks such as variational autoencoders (VAE) perform dimensionality reduction
for the visualization and analysis of genomic data, but are limited in their interpretability: it is …

Allelic variation in transcription factor PtoWRKY68 contributes to drought tolerance in Populus

Y Fang, D Wang, L Xiao, M Quan, W Qi, F Song… - Plant …, 2023 - academic.oup.com
Drought stress limits woody species productivity and influences tree distribution. However,
dissecting the molecular mechanisms that underpin drought responses in forest trees can be …

Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks

P Mignone, G Pio, S Džeroski, M Ceci - Scientific reports, 2020 - nature.com
Abstract The reconstruction of Gene Regulatory Networks (GRNs) from gene expression
data, supported by machine learning approaches, has received increasing attention in …

Transcriptomic profiling of early synucleinopathy in rats induced with preformed fibrils

JR Patterson, J Kochmanski, AC Stoll, M Kubik… - npj Parkinson's …, 2024 - nature.com
Examination of early phases of synucleinopathy when inclusions are present, but long
before neurodegeneration occurs, is critical to both understanding disease progression and …

Identification of key gene targets for sensitizing colorectal cancer to chemoradiation: an integrative network analysis on multiple transcriptomics data

H Manoochehri, A Jalali, H Tanzadehpanah… - Journal of …, 2022 - Springer
Purpose Colorectal cancer (CRC) is a main cause of morbidity and mortality in the world.
Chemoradioresistance is a major problem in CRC treatment. Identification of novel …

Coexistent ARID1A-PIK3CA mutations are associated with immune-related pathways in luminal breast cancer

L Anabel Sinberger, T Zahavi, A Sonnenblick… - Scientific Reports, 2023 - nature.com
Up to 40% of luminal breast cancer patients carry activating mutations in the PIK3CA gene.
PIK3CA mutations commonly co-occur with other mutations, but the implication of this co …

Integrative multiomics and regulatory network analyses uncovers the role of OAS3, TRAFD1, MiR-222-3p, and MiR-125b-5p in hepatitis E virus infection

S Gupta, P Singh, A Tasneem, A Almatroudi… - Genes, 2022 - mdpi.com
The hepatitis E virus (HEV) is a long-ignored virus that has spread globally with time. It
ranked 6 th among the top risk-ranking viruses with high zoonotic spillover potential; thus …