ArticleMethods (San Diego, Calif.)2021
SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics.
Article in Methods (San Diego, Calif.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 84 citations in OpenAlex.
- Multiple data set Bayesian analysis synergistically boosts ITC parameter precision.Biophysical journal · 2026Article
- Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication.Biophysical journal · 2026Article
- Review of Machine Learning for Single-Particle Tracking: Methods, Challenges, and Biophysical Insights.Chemical & biomedical imaging · 2026Review
- Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication.bioRxiv : the preprint server for biology · 2025Article
- Revealing plasma membrane protein dynamics in living plant cells with single-molecule tracking.Journal of experimental botany · 2025Article
- Improving parameter inference by resolving Bayesian prior ambiguity via multi-dataset analysis: Application to isothermal titration calorimetry.bioRxiv : the preprint server for biology · 2025Article
- Physics-Inspired Single-Particle Tracking Accelerated with Parallelism.bioRxiv : the preprint server for biology · 2025Article
- Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function.Nature methods · 2025Article
- Integrating Particle Motion Tracking into Thermal Gel Electrophoresis for Label-Free Sugar Sensing.ACS sensors · 2025Article
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions.Nucleic acids research · 2024Article
- Increasing the accuracy of single-molecule data analysis using tMAVEN.Biophysical journal · 2024Article
- BNP-Track: a framework for superresolved tracking.Nature methods · 2024Article
- Article
- Extracellular matrix rigidity modulates physical properties of subcapsular sinus macrophage-B cell immune synapses.Biophysical journal · 2024Article
- Robust Quantification of Live-Cell Single-Molecule Tracking Data for Fluorophores with Different Photophysical Properties.The journal of physical chemistry. B · 2024Article
- Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1.Nature communications · 2024Article
- The condensation of HP1α/Swi6 imparts nuclear stiffness.Cell reports · 2024Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Single-molecule fluorescence microscopy probes nanoscale, subcellular biology in real time. Existing methods for analyzing single-particle tracking data provide dynamical information, but can suffer from supervisory biases and high uncertainties. Here, we develop a method for the case of multiple interconverting species undergoing free diffusion and introduce a new approach to analyzing single-molecule trajectories: the Single-Molecule Analysis by Unsupervised Gibbs sampling (SMAUG) algorithm, which uses nonparametric Bayesian statistics to uncover the whole range of information contained within a single-particle trajectory dataset. Even in complex systems where multiple biological states lead to a number of observed mobility states, SMAUG provides the number of mobility states, the average diffusion coefficient of single molecules in that state, the fraction of single molecules in that state, the localization noise, and the probability of transitioning between two different states. In this paper, we provide the theoretical background for the SMAUG analysis and then we validate the method using realistic simulations of single-particle trajectory datasets as well as experiments on a controlled in vitro system. Finally, we demonstrate SMAUG on real experimental systems in both prokaryotes and eukaryotes to measure the motions of the regulatory protein TcpP in Vibrio cholerae and the dynamics of the B-cell receptor antigen response pathway in lymphocytes. Overall, SMAUG provides a mathematically rigorous approach to measuring the real-time dynamics of molecular interactions in living cells.
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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.