ArticleNature communications2022
Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Dissecting autonomous enzymatic variability in single cells.Nature communications · 2026Article
- Masters of perception: phosphorylation-dependent signaling in plants.The New phytologist · 2026Review
- Spatial distribution of isoprenoid enzymes and MpABCG1 transporter influences sesquiterpene accumulation in Marchantia polymorpha oil bodies.Communications biology · 2026Article
- Dynamic subcellular proteomics identifies regulators of adipocyte insulin action.Nature communications · 2026Article
- C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels.Nature methods · 2026Article
- An updated Bioconductor workflow for correlation profiling subcellular proteomics.F1000Research · 2025Article
- Multimodal knowledge expansion widget powered by plant protein phosphorylation database and ChatGPT.Frontiers in bioinformatics · 2025Article
- Global Proteomics Indicates Subcellular-Specific Anti-Ferroptotic Responses to Ionizing Radiation.Molecular & cellular proteomics : MCP · 2025Article
- Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology.Journal of proteome research · 2024Review
- Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions.Nature communications · 2024Article
- TransGCN: a semi-supervised graph convolution network-based framework to infer protein translocations in spatio-temporal proteomics.Briefings in bioinformatics · 2024Article
- Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions.bioRxiv : the preprint server for biology · 2024Article
- System-wide analysis of RNA and protein subcellular localization dynamics.Nature methods · 2024Article
- Challenges and Opportunities for Bayesian Statistics in Proteomics.Journal of proteome research · 2022Review
- Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression.Molecular & cellular proteomics : MCP · 2022Article
- Subcellular Transcriptomics and Proteomics: A Comparative Methods Review.Molecular & cellular proteomics : MCP · 2022Review
- Subcellular proteomics.Nature reviews. Methods primers · 2021Article
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7 authors.
Funding
Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different subcellular niches upon perturbation of the subcellular environment. Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to several datasets recovers well-studied translocations. In an application to cytomegalovirus infection, we obtain insights into the rewiring of the host proteome. Integration of other high-throughput datasets allows us to provide the functional context of these data.
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