ArticleNature computational science2022
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics.
Article in Nature computational science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Avoiding subtraction and division of stochastic signals using normalizing flows: NFdeconvolve.iScience · 2025Article
- Single-Photon Single-Particle Tracking.bioRxiv : the preprint server for biology · 2025Article
- Bayesian analysis and efficient algorithms for single-molecule fluorescence data and step counting.Biophysical journal · 2025Article
- Mamba time series forecasting with uncertainty quantification.Machine learning: science and technology · 2025Article
- Bayesian analysis and efficient algorithms for single-molecule fluorescence data and step counting.bioRxiv : the preprint server for biology · 2025Article
- Physics-Inspired Single-Particle Tracking Accelerated with Parallelism.bioRxiv : the preprint server for biology · 2025Article
- Single-molecule reaction-diffusion.Biophysical journal · 2025Article
- Bayesian Inference of Binding Kinetics from Fluorescence Time Series.The journal of physical chemistry. B · 2025Article
- Simultaneous particle tracking, phase retrieval and point spread function reconstruction.bioRxiv : the preprint server for biology · 2025Article
- Cholesterol inhibits assembly and oncogenic activation of the EphA2 receptor.Communications biology · 2025Article
- An accurate probabilistic step finder for time-series analysis.Biophysical journal · 2024Article
- BNP-Track: a framework for superresolved tracking.Nature methods · 2024Article
- Cholesterol inhibits assembly and activation of the EphA2 receptor.bioRxiv : the preprint server for biology · 2024Article
- Avoiding matrix exponentials for large transition rate matrices.The Journal of chemical physics · 2024Article
- Building Fluorescence Lifetime Maps Photon-by-Photon by Leveraging Spatial Correlations.ACS photonics · 2023Article
- Article
- An accurate probabilistic step finder for time-series analysis.bioRxiv : the preprint server for biology · 2023Article
- Single-photon smFRET. I: Theory and conceptual basis.Biophysical reports · 2023Article
- Fluorescence lifetime: Beating the IRF and interpulse window.Biophysical journal · 2023Article
- Gene expression model inference from snapshot RNA data using Bayesian non-parametrics.Nature computational science · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Life's fundamental processes involve multiple molecules operating in close proximity within cells. To probe the composition and kinetics of molecular clusters confined within small (diffraction-limited) regions, experiments often report on the total fluorescence intensity simultaneously emitted from labeled molecules confined to such regions. Methods exist to enumerate total fluorophore numbers (e.g., step counting by photobleaching). However, methods aimed at step counting by photobleaching cannot treat photophysical dynamics in counting nor learn their associated kinetic rates. Here we propose a method to simultaneously enumerate fluorophores and determine their individual photophysical state trajectories. As the number of active (fluorescent) molecules at any given time is unknown, we rely on Bayesian nonparametrics and use specialized Monte Carlo algorithms to derive our estimates. Our formulation is benchmarked on synthetic and real data sets. While our focus here is on photophysical dynamics (in which labels transition between active and inactive states), such dynamics can also serve as a proxy for other types of dynamics such as assembly and disassembly kinetics of clusters. Similarly, while we focus on the case where all labels are initially fluorescent, other regimes, more appropriate to photoactivated localization microscopy, where fluorophores are instantiated in a non-fluorescent state, fall within the scope of the framework. As such, we provide a complete and versatile framework for the interpretation of complex time traces arising from the simultaneous activity of up to 100 fluorophores.
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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 Socratic graph.