ArticleNature communications2021
Robust inference of kinase activity using functional networks.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Trial
- Integrated Analysis of Posttranslational Modifications and Total Proteome: Methods for Distinguishing Abundance from Usage Changes.Methods in molecular biology (Clifton, N.J.) · 2027Article
- A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.Nature structural & molecular biology · 2026Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- Mesoscale proximity labeling at chromatin leads to identification of small molecule mechanism of action.Nature communications · 2026Article
- Phosphoproteomics of WHO-Priority Fungal Pathogens: Conserved Signaling Architecture, Pathogen-Specific Outputs, and Therapeutic Vulnerabilities.Pathogens (Basel, Switzerland) · 2026Review
- Identifying ROCK2 as an intervention target for bilirubin encephalopathy.Fundamental research · 2026Article
- The proteomics and phosphoproteomics landscape of melanoma under T cell attack.Cell reports. Medicine · 2026Article
- Glucocorticoid-Induced Proteome and Phosphoproteome Changes in Breast Cancer Cell Lines.Journal of proteome research · 2026Article
- Phosphoproteome Remodeling upon CDK1 Inhibition Restricts HSV-1 IE Gene Transcription and Replication.Cells · 2026Article
- Quantitative proteomics and phosphoproteomics reveal glucocorticoid stimulation of TLR and Rho GTPase signaling in neutrophil-like cells.Genome biology · 2026Article
- Dual FAK and EPHA2 targeting by brigatinib tackles PARP inhibitor adaptive survival response in high-grade serous ovarian cancer.Science translational medicine · 2026Article
- Proteogenomic profiling of soft tissue leiomyosarcoma reveals distinct molecular subtypes with divergent outcomes and therapeutic vulnerabilities.bioRxiv : the preprint server for biology · 2025Article
- A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Bias-aware training and evaluation of link prediction algorithms in network biology.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrating gene expression, genomic, and phosphoproteomic data to infer transcription factor activity in lung cancer.NAR genomics and bioinformatics · 2025Article
- Acid ceramidase controls proteasome inhibitor resistance and is a novel therapeutic target for the treatment of relapsed/refractory multiple myeloma.Haematologica · 2025Article
- Comprehensive evaluation of phosphoproteomic-based kinase activity inference.Nature communications · 2025Article
- KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics.Bioinformatics (Oxford, England) · 2025Article
- Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells.Molecular & cellular proteomics : MCP · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Mass spectrometry enables high-throughput screening of phosphoproteins across a broad range of biological contexts. When complemented by computational algorithms, phospho-proteomic data allows the inference of kinase activity, facilitating the identification of dysregulated kinases in various diseases including cancer, Alzheimer's disease and Parkinson's disease. To enhance the reliability of kinase activity inference, we present a network-based framework, RoKAI, that integrates various sources of functional information to capture coordinated changes in signaling. Through computational experiments, we show that phosphorylation of sites in the functional neighborhood of a kinase are significantly predictive of its activity. The incorporation of this knowledge in RoKAI consistently enhances the accuracy of kinase activity inference methods while making them more robust to missing annotations and quantifications. This enables the identification of understudied kinases and will likely lead to the development of novel kinase inhibitors for targeted therapy of many diseases. RoKAI is available as web-based tool at http://rokai.io .
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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.