ArticleBiophysical journal2010
Denoising single-molecule FRET trajectories with wavelets and Bayesian inference.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Dynamic positioning of Rpc34 winged helix in RNA polymerase III elongation complex for its stability with implications for reinitiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- JNJ-55511118 Stabilizes a Desensitized-like Conformation of γ8-Containing AMPA Receptors through Long-Range Allosteric Modulation.bioRxiv : the preprint server for biology · 2025Article
- Time-Frequency Analysis of Two-Dimensional Electron Spin Resonance Signals.The journal of physical chemistry. A · 2023Article
- Extraction of Weak Spectroscopic Signals with High Fidelity: Examples from ESR.The journal of physical chemistry. A · 2021Article
- Single molecule FRET methodology for investigating glutamate receptors.Methods in enzymology · 2021Article
- Mechanism of modulation of AMPA receptors by TARP-γ8.The Journal of general physiology · 2020Article
- Mechanistic Understanding of the Phosphorylation-Induced Conformational Rigidity at the AMPA Receptor C-terminal Domain.ACS omega · 2019Article
- Phosphorylation Induces Conformational Rigidity at the C-Terminal Domain of AMPA Receptors.The journal of physical chemistry. B · 2019Article
- Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models.Biophysical journal · 2018Article
- The structure-energy landscape of NMDA receptor gating.Nature chemical biology · 2017Article
- Conformational transitions in the glycine-bound GluN1 NMDA receptor LBD via single-molecule FRET.Biophysical journal · 2015Article
- Error-based extraction of states and energy landscapes from experimental single-molecule time-series.Scientific reports · 2015Article
- Analyzing single-molecule time series via nonparametric Bayesian inference.Biophysical journal · 2015Article
- Structural dynamics of the glycine-binding domain of the N-methyl-D-aspartate receptor.The Journal of biological chemistry · 2015Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding.FEBS letters · 2014Review
- Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis.The journal of physical chemistry letters · 2014Article
- Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.Chemical physics · 2013Article
- Article
- Role of conformational dynamics in α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor partial agonism.The Journal of biological chemistry · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A method to denoise single-molecule fluorescence resonance energy (smFRET) trajectories using wavelet detail thresholding and Bayesian inference is presented. Bayesian methods are developed to identify fluorophore photoblinks in the time trajectories. Simulated data are used to quantify the improvement in static and dynamic data analysis. Application of the method to experimental smFRET data shows that it distinguishes photoblinks from large shifts in smFRET efficiency while maintaining the important advantage of an unbiased approach. Known sources of experimental noise are examined and quantified as a means to remove their contributions via soft thresholding of wavelet coefficients. A wavelet decomposition algorithm is described, and thresholds are produced through the knowledge of noise parameters in the discrete-time photon signals. Reconstruction of the signals from thresholded coefficients produces signals that contain noise arising only from unquantifiable parameters. The method is applied to simulated and observed smFRET data, and it is found that the denoised data retain their underlying dynamic properties, but with increased resolution.
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