A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype

D He, L Xie - Bioinformatics, 2022 - academic.oup.com
Motivation An unsolved fundamental problem in biology is to predict phenotypes from a new
genotype under environmental perturbations. The emergence of multiple omics data …

A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease

JA Timmons, A Anighoro, RJ Brogan, J Stahl… - Elife, 2022 - elifesciences.org
Insulin resistance (IR) contributes to the pathophysiology of diabetes, dementia, viral
infection, and cardiovascular disease. Drug repurposing (DR) may identify treatments for IR; …

A novel network based linear model for prioritization of synergistic drug combinations

J Li, H Xu, RA McIndoe - PloS one, 2022 - journals.plos.org
Drug combination therapies can improve drug efficacy, reduce drug dosage, and overcome
drug resistance in cancer treatments. Current research strategies to determine which drug …

Precision combination therapies based on recurrent oncogenic coalterations

X Li, EK Dowling, G Yan, Z Dereli, B Bozorgui… - Cancer discovery, 2022 - AACR
Cancer cells depend on multiple driver alterations whose oncogenic effects can be
suppressed by drug combinations. Here, we provide a comprehensive resource of precision …

Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry

X Lu, GL Hackman, A Saha, AS Rathore, M Collins… - Iscience, 2022 - cell.com
Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent
drug resistance. While conventional high-throughput screens that rely on univariate data are …

A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction

Y Shim, M Lee, PJ Kim, HG Kim - BMC bioinformatics, 2022 - Springer
Background To reduce drug side effects and enhance their therapeutic effect compared with
single drugs, drug combination research, combining two or more drugs, is highly important …

Recover: sequential model optimization platform for combination drug repurposing identifies novel synergistic compounds in vitro

P Bertin, J Rector-Brooks, D Sharma… - arXiv preprint arXiv …, 2022 - arxiv.org
For large libraries of small molecules, exhaustive combinatorial chemical screens become
infeasible to perform when considering a range of disease models, assay conditions, and …

Bioinformatics roadmap for therapy selection in cancer genomics

MJ Jiménez‐Santos, S García‐Martín… - Molecular …, 2022 - Wiley Online Library
Tumour heterogeneity is one of the main characteristics of cancer and can be categorised
into inter‐or intratumour heterogeneity. This heterogeneity has been revealed as one of the …

Artificial Intelligence Approaches in Drug Discovery: Towards the Laboratory of the Future

L Frusciante, A Visibelli, M Geminiani… - Current Topics in …, 2022 - ingentaconnect.com
The role of computational tools in the drug discovery and development process is becoming
central, thanks to the possibility to analyze large amounts of data. The high throughput and …

Functional stratification of cancer drugs through integrated network similarity

S Unsal-Beyge, N Tuncbag - NPJ Systems Biology and Applications, 2022 - nature.com
Drugs not only perturb their immediate protein targets but also modulate multiple signaling
pathways. In this study, we explored networks modulated by several drugs across multiple …