ArticleNature methods2024
Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- scMOG: A graph neural network method for regulatory relationship-preserving single-cell multi-omics integration.Quantitative biology (Beijing, China) · 2026Article
- Targeted quantification assays for DNA repair and handling proteins and interactions in Huntington's disease models.bioRxiv : the preprint server for biology · 2026Article
- Omics-Level Approaches to Studying Gammaherpesvirus Infection.Pathogens (Basel, Switzerland) · 2026Review
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling.Cell systems · 2026Review
- Towards a phylogenetically informed approach to solving protein-protein interactions.Biochemical Society transactions · 2025Review
- MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages.Nature microbiology · 2025Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Sequestration of ribosome biogenesis factors in HSV-1 nuclear aggregates revealed by spatially resolved thermal profiling.Science advances · 2025Article
- Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.Bioinformatics (Oxford, England) · 2025Article
- Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures.Molecular systems biology · 2025Article
- Unraveling systemic responses to NQO1-activated IB-DNQ and Rucaparib single and dual agent therapy in triple-negative breast cancers.bioRxiv : the preprint server for biology · 2025Article
- Complete end-to-end learning from protein feature representation to protein interactome inference.GigaScience · 2025Article
- Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system.Journal of proteins and proteomics · 2024Article
- Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production.Journal of proteome research · 2024Article
- Community cohesion looseness in gene networks reveals individualized drug targets and resistance.Briefings in bioinformatics · 2024Article
- MGPPI: multiscale graph neural networks for explainable protein-protein interaction prediction.Frontiers in genetics · 2024Article
- Mapping protein-protein interactions by mass spectrometry.Mass spectrometry reviewsReview
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5 authors.
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Abstract
Protein-protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global PPIs in dynamic contexts. Tapioca predicts de novo interactions by integrating mass spectrometry interactome data from thermal/ion denaturation or cofractionation workflows with protein properties and tissue-specific functional networks. Focusing on the thermal proximity coaggregation method, we improved the experimental workflow. Finely tuned thermal denaturation afforded increased throughput, while cell lysis optimization enhanced protein detection from different subcellular compartments. The Tapioca workflow was next leveraged to investigate viral infection dynamics. Temporal PPIs were characterized during the reactivation from latency of the oncogenic Kaposi's sarcoma-associated herpesvirus. Together with functional assays, NUCKS was identified as a proviral hub protein, and a broader role was uncovered by integrating PPI networks from alpha- and betaherpesvirus infections. Altogether, Tapioca provides a web-accessible platform for predicting PPIs in dynamic contexts.
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