ArticleThe journal of physical chemistry. B2019
A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- A cautious user's guide in applying HMMs to physical systems.The Journal of chemical physics · 2025Article
- Unmasking complex kinetics in viral entry by inferring hypoexponential models.Biophysical journal · 2025Article
- Bayesian Nonparametrics for FRET using Realistic Integrative Detectors.bioRxiv : the preprint server for biology · 2025Article
- Single-molecule reaction-diffusion.Biophysical journal · 2025Article
- Article
- Model-free idealization: Adaptive integrated approach for idealization of ion-channel currents.Biophysical journal · 2023Article
- Single-Molecule Reaction-Diffusion.bioRxiv : the preprint server for biology · 2023Article
- Monte Carlo samplers for efficient network inference.PLoS computational biology · 2023Article
- Single-photon smFRET. I: Theory and conceptual basis.Biophysical reports · 2023Article
- Single-photon smFRET: II. Application to continuous illumination.Biophysical reports · 2023Article
- Resolving Molecular Heterogeneity with Single-Molecule Centrifugation.Journal of the American Chemical Society · 2023Article
- Learning continuous potentials from smFRET.Biophysical journal · 2023Article
- Single-photon smFRET. III. Application to pulsed illumination.Biophysical reports · 2022Article
- Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap.iScience · 2022Article
- Heterogeneous migration routes of DNA triplet repeat slip-outs.Biophysical reports · 2022Article
- A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories.Nature communications · 2022Article
- Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores.The journal of physical chemistry. B · 2022Article
- Extraction of rapid kinetics from smFRET measurements using integrative detectors.Cell reports. Physical science · 2021Article
- Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.Annual review of biophysics · 2021Review
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6 authors.
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Abstract
We develop a Bayesian nonparametric framework to analyze single molecule FRET (smFRET) data. This framework, a variation on infinite hidden Markov models, goes beyond traditional hidden Markov analysis, which already treats photon shot noise, in three critical ways: (1) it learns the number of molecular states present in a smFRET time trace (a hallmark of nonparametric approaches), (2) it accounts, simultaneously and self-consistently, for photophysical features of donor and acceptor fluorophores (blinking kinetics, spectral cross-talk, detector quantum efficiency), and (3) it treats background photons. Point 2 is essential in reducing the tendency of nonparametric approaches to overinterpret noisy single molecule time traces and so to estimate states and transition kinetics robust to photophysical artifacts. As a result, with the proposed framework, we obtain accurate estimates of single molecule properties even when the supplied traces are excessively noisy, subject to photoartifacts, and of short duration. We validate our method using synthetic data sets and demonstrate its applicability to real data sets from single molecule experiments on Holliday junctions labeled with conventional fluorescent dyes.
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