ArticleCell reports2018
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.
Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages.International journal of molecular sciences · 2020Pooled it
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- Scalable phosphotyrosine enrichment with SH2 superbinder enables deep profiling of EGF responses.The EMBO journal · 2026Article
- 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
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Comprehensive evaluation of phosphoproteomic-based kinase activity inference.Nature communications · 2025Article
- Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.NPJ systems biology and applications · 2024Article
- Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.bioRxiv : the preprint server for biology · 2024Article
- SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.NPJ systems biology and applications · 2024Article
- A Causal Regulation Modeling Algorithm for Temporal Events with Application toInternational journal of molecular sciences · 2024Article
- HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B.PLoS pathogens · 2023Article
- Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer.PLoS computational biology · 2023Article
- Phosphoproteomics data-driven signalling network inference: Does it work?Computational and structural biotechnology journal · 2023Article
- Graph algorithms for predicting subcellular localization at the pathway levelPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2023Article
- Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE.Nature communications · 2022Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.Patterns (New York, N.Y.) · 2021Article
- Automating parameter selection to avoid implausible biological pathway models.NPJ systems biology and applications · 2021Article
- ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses.PLoS pathogens · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
We present a method for automatically discovering signaling pathways from time-resolved phosphoproteomic data. The Temporal Pathway Synthesizer (TPS) algorithm uses constraint-solving techniques first developed in the context of formal verification to explore paths in an interaction network. It systematically eliminates all candidate structures for a signaling pathway where a protein is activated or inactivated before its upstream regulators. The algorithm can model more than one hundred thousand dynamic phosphosites and can discover pathway members that are not differentially phosphorylated. By analyzing temporal data, TPS defines signaling cascades without needing to experimentally perturb individual proteins. It recovers known pathways and proposes pathway connections when applied to the human epidermal growth factor and yeast osmotic stress responses. Independent kinase mutant studies validate predicted substrates in the TPS osmotic stress pathway.
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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.