Network pharmacology: curing causal mechanisms instead of treating symptoms

C Nogales, ZM Mamdouh, M List, C Kiel… - Trends in …, 2022 - cell.com
For complex diseases, most drugs are highly ineffective, and the success rate of drug
discovery is in constant decline. While low quality, reproducibility issues, and translational …

The emerging role of mass spectrometry-based proteomics in drug discovery

F Meissner, J Geddes-McAlister, M Mann… - Nature Reviews Drug …, 2022 - nature.com
Proteins are the main targets of most drugs; however, system-wide methods to monitor
protein activity and function are still underused in drug discovery. Novel biochemical …

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 …

Large-scale deep multi-layer analysis of Alzheimer's disease brain reveals strong proteomic disease-related changes not observed at the RNA level

ECB Johnson, EK Carter, EB Dammer, DM Duong… - Nature …, 2022 - nature.com
The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain
incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain …

More is different in real-world multilayer networks

M De Domenico - Nature Physics, 2023 - nature.com
The constituents of many complex systems are characterized by non-trivial connectivity
patterns and dynamical processes that are well captured by network models. However, most …

Artificial intelligence in cancer target identification and drug discovery

Y You, X Lai, Y Pan, H Zheng, J Vera, S Liu… - … and Targeted Therapy, 2022 - nature.com
Artificial intelligence is an advanced method to identify novel anticancer targets and discover
novel drugs from biology networks because the networks can effectively preserve and …

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials

Y Zheng, Y Liu, J Yang, L Dong, R Zhang, S Tian… - Nature …, 2024 - nature.com
Abstract Characterization and integration of the genome, epigenome, transcriptome,
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …

Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy

K Kiryluk, E Sanchez-Rodriguez, XJ Zhou, F Zanoni… - Nature …, 2023 - nature.com
IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular
deposition of IgA. Here we performed a genome-wide association study of 10,146 kidney …

Systems biology in cardiovascular disease: a multiomics approach

A Joshi, M Rienks, K Theofilatos, M Mayr - Nature Reviews Cardiology, 2021 - nature.com
Omics techniques generate large, multidimensional data that are amenable to analysis by
new informatics approaches alongside conventional statistical methods. Systems theories …

Metabolomics in diabetes and diabetic complications: insights from epidemiological studies

Q **, RCW Ma - Cells, 2021 - mdpi.com
The increasing prevalence of diabetes and its complications, such as cardiovascular and
kidney disease, remains a huge burden globally. Identification of biomarkers for the …