ReviewEssays in biochemistry2018
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.
Review in Essays in biochemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Review
- Biologically informed neural network models are robust to spurious interactions via self-pruning.Bioinformatics (Oxford, England) · 2026Article
- Scalable phosphotyrosine enrichment with SH2 superbinder enables deep profiling of EGF responses.The EMBO journal · 2026Article
- Protein Methylation as a Regulatory Logic Layer in Cancer Signaling: Interplay with Phosphorylation and Network Plasticity.Cancers · 2026Review
- Biologically informed neural network models are robust to spurious interactions via self-pruning.bioRxiv : the preprint server for biology · 2025Article
- R2HaPpY: Rapid-robust phosphotyrosine peptide enrichment using HaloTag-Src SH2 pY superbinder.bioRxiv : the preprint server for biology · 2025Article
- CoPPIs algorithm: a tool to unravel protein cooperative strategies in pathophysiological conditions.Briefings in bioinformatics · 2025Article
- The fitness cost of spurious phosphorylation.The EMBO journal · 2024Article
- The fitness cost of spurious phosphorylation.bioRxiv : the preprint server for biology · 2023Article
- CDK6 activity in a recurring convergent kinase network motif.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2023Article
- Phosphoproteomics data-driven signalling network inference: Does it work?Computational and structural biotechnology journal · 2023Article
- Artificial neural networks enable genome-scale simulations of intracellular signaling.Nature communications · 2022Article
- Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data.PLoS computational biology · 2022Article
- A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.BMC plant biology · 2021Article
- Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.PLoS computational biology · 2021Article
- Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions.PLoS computational biology · 2021Article
- Phosphoproteome Response to Dithiothreitol Reveals UniqueJournal of proteome research · 2020Article
- Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring.Nature biotechnology · 2020Article
- TopoFilter: a MATLAB package for mechanistic model identification in systems biology.BMC bioinformatics · 2020Article
- Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction.Frontiers in physiology · 2020Article
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2 authors.
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Abstract
Cascades of phosphorylation between protein kinases comprise a core mechanism in the integration and propagation of intracellular signals. Although we have accumulated a wealth of knowledge around some such pathways, this is subject to study biases and much remains to be uncovered. Phosphoproteomics, the identification and quantification of phosphorylated proteins on a proteomic scale, provides a high-throughput means of interrogating the state of intracellular phosphorylation, both at the pathway level and at the whole-cell level. In this review, we discuss methods for using human quantitative phosphoproteomic data to reconstruct the underlying signalling networks that generated it. We address several challenges imposed by the data on such analyses and we consider promising advances towards reconstructing unbiased, kinome-scale signalling networks.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.