Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks
Signal transduction governs cellular behavior, and its dysregulation often leads to human
disease. To understand this process, we can use network models based on prior …
disease. To understand this process, we can use network models based on prior …
[PDF][PDF] A community challenge for a pancancer drug mechanism of action inference from perturbational profile data
Summary The Columbia Cancer Target Discovery and Development (CTD2) Center is
developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA …
developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA …
Gene regulatory networks in disease and ageing
P Unger Avila, T Padvitski, AC Leote, H Chen… - Nature Reviews …, 2024 - nature.com
The precise control of gene expression is required for the maintenance of cellular
homeostasis and proper cellular function, and the declining control of gene expression with …
homeostasis and proper cellular function, and the declining control of gene expression with …
Positive correlation between transcriptomic stemness and PI3K/AKT/mTOR signaling scores in breast cancer, and a counterintuitive relationship with PIK3CA …
A PI3Kα-selective inhibitor has recently been approved for use in breast tumors harboring
mutations in PIK3CA, the gene encoding p110α. Preclinical studies have suggested that the …
mutations in PIK3CA, the gene encoding p110α. Preclinical studies have suggested that the …
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding
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 …
discovery. Careful understanding of MoA can avoid potential side effects of drug candidates …
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis
Background Elucidating compound mechanism of action (MoA) is beneficial to drug
discovery, but in practice often represents a significant challenge. Causal Reasoning …
discovery, but in practice often represents a significant challenge. Causal Reasoning …
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition
ML Burtscher, S Gade… - Molecular Systems …, 2024 - embopress.org
Complex disease phenotypes often span multiple molecular processes. Functional
characterization of these processes can shed light on disease mechanisms and drug effects …
characterization of these processes can shed light on disease mechanisms and drug effects …
Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity
Comparing SARS-CoV-2 infection-induced gene expression signatures to drug treatment-
induced gene expression signatures is a promising bioinformatic tool to repurpose existing …
induced gene expression signatures is a promising bioinformatic tool to repurpose existing …
Characterization of type 1 angiotensin II receptor activation induced dual-specificity MAPK phosphatase gene expression changes in rat vascular smooth muscle cells
JB Gém, KB Kovács, L Szalai, G Szakadáti, E Porkoláb… - Cells, 2021 - mdpi.com
Activation of the type I angiotensin receptor (AT1-R) in vascular smooth muscle cells
(VSMCs) plays a crucial role in the regulation of blood pressure; however, it is also …
(VSMCs) plays a crucial role in the regulation of blood pressure; however, it is also …
[HTML][HTML] Signatures of discriminative copy number aberrations in 31 cancer subtypes
B Gao, M Baudis - Frontiers in genetics, 2021 - frontiersin.org
Copy number aberrations (CNA) are one of the most important classes of genomic mutations
related to oncogenetic effects. In the past three decades, a vast amount of CNA data has …
related to oncogenetic effects. In the past three decades, a vast amount of CNA data has …