ArticleNature communications2015
Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Monocyte Migration Emerges from a Divergent Chemokine Signaling Network.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions.Nature communications · 2026Article
- MAP2 phosphorylation: mechanisms, functional consequences, and emerging insights.Frontiers in cellular neuroscience · 2025Review
- DecipheringmSystems · 2024Article
- A perfectly imperfect engine: Utilizing the digital twin paradigm in pulmonary hypertension.Pulmonary circulation · 2024Review
- Altered CELF4 splicing factor enhances pancreatic neuroendocrine tumors aggressiveness influencing mTOR and everolimus response.Molecular therapy. Nucleic acids · 2024Article
- A comprehensive mechanistic model of adipocyte signaling with layers of confidence.NPJ systems biology and applications · 2023Article
- Community detection in empirical kinase networks identifies new potential members of signalling pathways.PLoS computational biology · 2023Article
- Principles of phosphoproteomics and applications in cancer research.The Biochemical journal · 2023Article
- Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.Clinical and translational medicine · 2023Article
- Pharmacological approaches to understanding protein kinase signaling networks.Frontiers in pharmacology · 2023Review
- Systematic identification of biochemical networks in cancer cells by functional pathway inference analysis.Bioinformatics (Oxford, England) · 2023Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.PLoS computational biology · 2021Article
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis.Genome medicine · 2021Article
- Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.Patterns (New York, N.Y.) · 2021Article
- Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Briefings in bioinformatics · 2021Review
- The tissue proteome in the multi-omic landscape of kidney disease.Nature reviews. Nephrology · 2021Review
- Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring.Nature biotechnology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Mass spectrometry is widely used to probe the proteome and its modifications in an untargeted manner, with unrivalled coverage. Applied to phosphoproteomics, it has tremendous potential to interrogate phospho-signalling and its therapeutic implications. However, this task is complicated by issues of undersampling of the phosphoproteome and challenges stemming from its high-content but low-sample-throughput nature. Hence, methods using such data to reconstruct signalling networks have been limited to restricted data sets and insights (for example, groups of kinases likely to be active in a sample). We propose a new method to handle high-content discovery phosphoproteomics data on perturbation by putting it in the context of kinase/phosphatase-substrate knowledge, from which we derive and train logic models. We show, on a data set obtained through perturbations of cancer cells with small-molecule inhibitors, that this method can study the targets and effects of kinase inhibitors, and reconcile insights obtained from multiple data sets, a common issue with these data.
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Registered trials
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.