Validating small molecule chemical probes for biological discovery

V Vu, MM Szewczyk, DY Nie… - Annual review of …, 2022 - annualreviews.org
Small molecule chemical probes are valuable tools for interrogating protein biological
functions and relevance as a therapeutic target. Rigorous validation of chemical probe …

Connecting omics signatures and revealing biological mechanisms with iLINCS

M Pilarczyk, M Fazel-Najafabadi, M Kouril… - Nature …, 2022 - nature.com
There are only a few platforms that integrate multiple omics data types, bioinformatics tools,
and interfaces for integrative analyses and visualization that do not require programming …

[HTML][HTML] Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing

TH Pham, Y Qiu, J Liu, S Zimmer, E O'Neill, L Xie… - Patterns, 2022 - cell.com
Chemical-induced gene expression profiles provide critical information of chemicals in a
biological system, thus offering new opportunities for drug discovery. Despite their success …

Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding

G Jang, S Park, S Lee, S Kim, S Park, J Kang - Bioinformatics, 2021 - academic.oup.com
Motivation Identifying mechanism of actions (MoA) of novel compounds is crucial in drug
discovery. Careful understanding of MoA can avoid potential side effects of drug candidates …

Guiding drug repositioning for cancers based on drug similarity networks

S Qin, W Li, H Yu, M Xu, C Li, L Fu, S Sun, Y He… - International Journal of …, 2023 - mdpi.com
Drug repositioning aims to discover novel clinical benefits of existing drugs, is an effective
way to develop drugs for complex diseases such as cancer and may facilitate the process of …

Integrative signatures of signaling pathway response increase robustness and accuracy of pathway predictions

NA Clark, Y Ren, DR Plas, S Sivaganesan… - bioRxiv, 2022 - biorxiv.org
Motivation Aberrant cell signaling is known to drive progression of cancer and many other
diseases. The study of signaling pathways within cells is central to identifying drugs that …

A Novel Ensemble Method using Signed and Unsigned Graph Convolutional Networks for Predicting Mechanisms of Action of Small Molecules from Gene Expression …

RS Karim - 2022 - search.proquest.com
Identification of the mechanism of action (MoA) of a small molecule which causes
pharmacological effects on cellular networks governing gene expression levels is an …

Targeting Drug-Induced Transcriptional Mechanisms to Guide Effective Cancer Therapy

CT Huang, CH Hsieh, KJ Chang, JY Liu… - Available at SSRN … - papers.ssrn.com
Resistance to cancer therapy seems to be inevitable in many clinical settings. Increasing
evidence has suggested that treatment-elicited molecular responses may play a role in …

Creating integrative signatures of signaling pathway activity from diverse cell lines

NA Clark - 2021 - search.proquest.com
Studying changes in gene expression caused by genetic and chemical perturbations in cells
can allow scientists to learn more about genetic diseases, such as cancer, and the cellular …