Computational systems biology in disease modeling and control, review and perspectives

• Published in: NPJ systems biology and applications Vol. 8; no. 1; pp. 37 - 16
• Main Authors: Yue, Rongting, Dutta, Abhishek
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.10.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/553/1833; 631/553/2702; 631/553/2711; 631/553/2712; Bioinformatics; Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer applications; Disease; Life Sciences; Mathematical models; Proteomics; Review; Review Article; Systems Biology; Toxicity
• ISSN: 2056-7189; 2056-7189
• DOI: 10.1038/s41540-022-00247-4

Omics-based approaches have become increasingly influential in identifying disease mechanisms and drug responses. Considering that diseases and drug responses are co-expressed and regulated in the relevant omics data interactions, the traditional way of grabbing omics data from single isolated layers cannot always obtain valuable inference. Also, drugs have adverse effects that may impair patients, and launching new medicines for diseases is costly. To resolve the above difficulties, systems biology is applied to predict potential molecular interactions by integrating omics data from genomic, proteomic, transcriptional, and metabolic layers. Combined with known drug reactions, the resulting models improve medicines’ therapeutical performance by re-purposing the existing drugs and combining drug molecules without off-target effects. Based on the identified computational models, drug administration control laws are designed to balance toxicity and efficacy. This review introduces biomedical applications and analyses of interactions among gene, protein and drug molecules for modeling disease mechanisms and drug responses. The therapeutical performance can be improved by combining the predictive and computational models with drug administration designed by control laws. The challenges are also discussed for its clinical uses in this work.