Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Phosphosignaling networks control cellular processes. We built kinase-mediated regulatory networks elicited by thrombin stimulation of brain endothelial cells using two computational strategies: Temporal Pathway Synthesizer (TPS), which uses phosphoproteomics data as input, and Temporally REsolved KInase Network Generation (TREKING), which uses kinase inhibitor screens. TPS and TREKING predicted overlapping barrier-regulatory kinases connected with unique network topology. Each strategy effectively describes regulatory signaling networks and is broadly applicable across biological systems.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568298 | PMC |
| http://dx.doi.org/10.1038/s41540-024-00468-9 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Nigericin-Triggered Phosphodynamics in Inflammasome Formation and Pyroptosis.
Proteomics
September 2025
Functional Cellular Networks Section, Laboratory of Immune System Biology, NIAID, Bethesda, Maryland, USA.
Innate immune signaling relies heavily on phosphorylation cascades to mount effective immune responses. Although traditional innate immune signaling cascades following TLR4 stimulation have been investigated through a temporally quantitative phosphoproteomic lens, far fewer studies have applied these methods to distinct signaling following the inflammasome trigger leading to IL-1β release. Here, we conducted time-resolved phosphoproteomic profiling to investigate kinase signaling downstream of the inflammasome trigger nigericin.
View Article and Find Full Text PDFPhosphoproteomic insights into GFPT2-Associated cellular phospho-signaling networks.
Biochem Biophys Rep
September 2025
Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India.
The GFPT2 protein, also known as glutamine-fructose-6-phosphate aminotransferase 2, regulates glucose flux through the hexosamine biosynthesis pathway (HBP). It is primarily expressed in the spinal cord and central nervous system and is notably abundant in various cancers while being dysregulated in diabetes. Despite its significant role in critical diseases, the phospho-regulatory mechanisms governing GFPT2 function remain largely unexplored.
View Article and Find Full Text PDFIntegration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates.
Cell Rep
August 2025
Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, UAB, Birmingham, AL, USA. Electronic address:
Single-cell RNA sequencing (scRNA-seq) provides the resolution and scale necessary to identify transcriptional programs but fails to capture post-transcriptional information critical to decipher signaling networks and cellular states. We present Vivo-seq, an innovative platform that integrates scRNA-seq and intracellular cellular indexing of transcriptomes and epitopes by sequencing following cellular fixation with a deep eutectic solvent, which preserves multiple domains of biological information beyond RNA transcripts alone. Vivo-seq enables simultaneous capture of both transcriptional and phospho-signaling states in single cells.
View Article and Find Full Text PDFA Methanolic Urea-Enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource.
Mol Cell Proteomics
June 2025
Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan. Electronic address:
Mass spectrometry (MS)-based phosphoproteomics analysis is a powerful approach for elucidating the regulatory roles of protein phosphorylation across all domains of life. However, bacterial phosphoproteomics still faces significant technical challenges due to the extremely low substoichiometry of phosphorylation evens and the structural complexity of bacterial cell envelopes, which impede efficient cell lysis, protein recovery, and purity. To address these obstacles, we developed Methanolic Urea-enhanced Protein Extraction (MUPE), a streamlined, detergent-free, solvent-based method that leverages the amphiphilic nature of methanol and the chaotropic properties of urea to enhance protein yield and lysis efficiency.
View Article and Find Full Text PDFMapping Cophosphoregulation Networks Linked to Transcriptional Regulator Bromodomain-Containing Protein 4.
DNA Cell Biol
August 2025
Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India.
Bromodomain-containing protein 4 (BRD4) is a pivotal transcriptional regulator implicated in cancer, fibrosis, and inflammation, yet its phospho-regulatory network remains underexplored. This study leverages an extensive analysis of 1000 qualitative and 225 quantitative global phosphoproteome datasets to decode the BRD4 phosphorylation landscape. We identified S601 and S1117 as predominant phosphorylation sites, driving the majority of BRD4 phospho-signaling.
View Article and Find Full Text PDF