ArticleNature communications2019
Topological scoring of protein interaction networks.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 45 citations in OpenAlex.
- Revolutionizing Stem Cell Sorting with Machine Learning: A Review of Trends, Tools, and Future Directions.Iranian journal of medical sciences · 2026Review
- Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex.bioRxiv : the preprint server for biology · 2026Article
- Improving protein interaction prediction in GenPPi: a novel interaction sampling approach preserving network topology.BMC bioinformatics · 2025Article
- Metabolic control of glycosylation forms for establishing glycan-dependent protein interaction networks.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrative approaches for predicting protein network perturbations through machine learning and structural characterization.Journal of proteomics · 2025Article
- Distinct Regions within SAP25 Recruit O-Linked Glycosylation, DNA Demethylation, and Ubiquitin Ligase and Hydrolase Activities to the Sin3/HDAC Complex.Journal of proteome research · 2024Article
- Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach.Proteomics · 2023Article
- PerSEveML: A Web-Based Tool to Identify Persistent Biomarker Structure for Rare Events Using Integrative Machine Learning Approach.bioRxiv : the preprint server for biology · 2023Article
- Graph 'texture' features as novel metrics that can summarize complex biological graphs.Physics in medicine and biology · 2023Article
- NeuMapper: A scalable computational framework for multiscale exploration of the brain's dynamical organization.Network neuroscience (Cambridge, Mass.) · 2022Article
- A proximity labeling method for protein-protein interactions on cell membrane.Chemical science · 2022Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- Identification of stem cells from large cell populations with topological scoring.Molecular omics · 2021Article
- Article
- Driving integrative structural modeling with serial capture affinity purification.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Generating topological protein interaction scores and data visualization with TopS.Methods (San Diego, Calif.) · 2020Article
- Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics.Genetics · 2020Article
- A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks.Cell chemical biology · 2020Article
- The chromatin bound proteome of the human malaria parasite.Microbial genomics · 2020Article
- Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome.Journal of proteome research · 2019Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic datasets from affinity purifications. Data is analyzed in a parallel fashion where a prey protein is scored in an individual affinity purification by aggregating information from the entire dataset. Topological scores span a broad range of values indicating the enrichment of an individual protein in every bait protein purification. TopS is applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS highlights potential direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides important insights into protein interaction networks.
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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.