ArticleScience (New York, N.Y.)2021
Interpretation of cancer mutations using a multiscale map of protein systems.
Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Identifying multigenic modules under selection in the tumor genome.Bioinformatics (Oxford, England) · 2026Article
- An embedding-based framework enables statistical testing of gene-set function hypotheses inferred by large language models.Nature communications · 2026Article
- Human genetics across levels of biological organization.Nature reviews. Genetics · 2026Review
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- A framework for the exploration of subcellular compartmentalization of RNA-binding proteins.Nature communications · 2026Article
- OncoBERT: Context-Aware Modeling of Somatic Mutations for Precision Oncology.bioRxiv : the preprint server for biology · 2026Article
- Mutation-informed gene pairs to predict melanoma metastasis.Cell communication and signaling : CCS · 2026Article
- Using Biological Networks to Guide Biomedical Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- Article
- AdaSemb: an adaptive knowledge-driven deep learning framework integrating cancer protein assemblies for predicting PI3Kα inhibitor response and resistance.Briefings in bioinformatics · 2025Article
- Article
- Network-based approach identifies key genes associated with tumor heterogeneity in HPV positive and negative head and neck cancer patients.Scientific reports · 2025Article
- The coming era of proteomics-driven precision medicine.National science review · 2025Review
- GeneAgent: self-verification language agent for gene-set analysis using domain databases.Nature methods · 2025Article
- Learning Universal Representations of Intermolecular Interactions with ATOMICA.bioRxiv : the preprint server for biology · 2025Article
- Cytoscape Web: bringing network biology to the browser.Nucleic acids research · 2025Article
- A genotype-to-drug diffusion model for generation of tailored anti-cancer small molecules.Nature communications · 2025Article
- Article
Corrections and comments
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Authors and funding
32 authors.
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Abstract
A major goal of cancer research is to understand how mutations distributed across diverse genes affect common cellular systems, including multiprotein complexes and assemblies. Two challenges—how to comprehensively map such systems and how to identify which are under mutational selection—have hindered this understanding. Accordingly, we created a comprehensive map of cancer protein systems integrating both new and published multi-omic interaction data at multiple scales of analysis. We then developed a unified statistical model that pinpoints 395 specific systems under mutational selection across 13 cancer types. This map, called NeST (Nested Systems in Tumors), incorporates canonical processes and notable discoveries, including a PIK3CA-actomyosin complex that inhibits phosphatidylinositol 3-kinase signaling and recurrent mutations in collagen complexes that promote tumor proliferation. These systems can be used as clinical biomarkers and implicate a total of 548 genes in cancer evolution and progression. This work shows how disparate tumor mutations converge on protein assemblies at different scales.
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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.