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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 …
prior knowledge resources, reducing the dimensionality for increased statistical power and …
[HTML][HTML] Recent advances in kinase signaling network profiling by mass spectrometry
Mass spectrometry-based phosphoproteomics is currently the leading methodology for the
study of global kinase signaling. The scientific community is continuously releasing …
study of global kinase signaling. The scientific community is continuously releasing …
[HTML][HTML] Truncated FGFR2 is a clinically actionable oncogene in multiple cancers
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 …
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
Despite producing a panoply of potential cancer-specific targets, the proteogenomic
characterization of human tumors has yet to demonstrate value for precision cancer …
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 …
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
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-
based phosphoproteomics for signaling pathway reconstitution is challenging, especially …
based phosphoproteomics for signaling pathway reconstitution is challenging, especially …
[HTML][HTML] BCAT1 redox function maintains mitotic fidelity
The metabolic enzyme branched-chain amino acid transaminase 1 (BCAT1) drives cell
proliferation in aggressive cancers such as glioblastoma. Here, we show that BCAT1 …
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
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 …
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
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 …
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
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 …
differentiation and is often dysregulated in human cancers. We combined genetic …