decoupleR: ensemble of computational methods to infer biological activities from omics data

P Badia-i-Mompel, J Vélez Santiago… - Bioinformatics …, 2022 - academic.oup.com
Many methods allow us to extract biological activities from omics data using information from
prior knowledge resources, reducing the dimensionality for increased statistical power and …

[HTML][HTML] Recent advances in kinase signaling network profiling by mass spectrometry

G Franciosa, M Locard-Paulet, LJ Jensen… - Current Opinion in …, 2023 - Elsevier
Mass spectrometry-based phosphoproteomics is currently the leading methodology for the
study of global kinase signaling. The scientific community is continuously releasing …

[HTML][HTML] Truncated FGFR2 is a clinically actionable oncogene in multiple cancers

D Zingg, J Bhin, J Yemelyanenko, SM Kas, F Rolfs… - Nature, 2022 - nature.com
Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast
growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer. However …

Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy

S Migliozzi, YT Oh, M Hasanain, L Garofano… - Nature cancer, 2023 - nature.com
Despite producing a panoply of potential cancer-specific targets, the proteogenomic
characterization of human tumors has yet to demonstrate value for precision cancer …

[HTML][HTML] Data-oriented protein kinase drug discovery

E Xerxa, J Bajorath - European Journal of Medicinal Chemistry, 2024 - Elsevier
The continued growth of data from biological screening and medicinal chemistry provides
opportunities for data-driven experimental design and decision making in early-phase drug …

Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

A Martínez-Val, K Fort, C Koenig… - Nature …, 2023 - nature.com
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-
based phosphoproteomics for signaling pathway reconstitution is challenging, especially …

[HTML][HTML] BCAT1 redox function maintains mitotic fidelity

L Francois, P Boskovic, J Knerr, W He, G Sigismondo… - Cell reports, 2022 - cell.com
The metabolic enzyme branched-chain amino acid transaminase 1 (BCAT1) drives cell
proliferation in aggressive cancers such as glioblastoma. Here, we show that BCAT1 …

Chemogenomic screening in a patient‐derived 3D fatty liver disease model reveals the CHRM1‐TRPM8 axis as a novel module for targeted intervention

S Youhanna, AM Kemas, SC Wright, Y Zhong… - Advanced …, 2025 - Wiley Online Library
Metabolic dysfunction‐associated steatohepatitis (MASH) is a leading cause of chronic liver
disease with few therapeutic options. To narrow the translational gap in the development of …

Microglial TNFα orchestrates protein phosphorylation in the cortex during the sleep period and controls homeostatic sleep

MJ Pinto, L Cottin, F Dingli, V Laigle, LF Ribeiro… - The EMBO …, 2023 - embopress.org
Sleep intensity is adjusted by the length of previous awake time, and under tight homeostatic
control by protein phosphorylation. Here, we establish microglia as a new cellular …

Characterization of TGF-β signaling in a human organotypic skin model reveals that loss of TGF-βRII induces invasive tissue growth

Z Ye, G Kilic, S Dabelsteen, IN Marinova… - Science …, 2022 - science.org
Transforming growth factor–β (TGF-β) signaling regulates various aspects of cell growth and
differentiation and is often dysregulated in human cancers. We combined genetic …