ArticleBiophysical journal2012
Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories.
Article in Biophysical journal, 2012. 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.
- Hidden Markov model analysis of fluorescence blinking in fluorescently labeled DNA.Scientific reports · 2026Article
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- Increasing the accuracy of single-molecule data analysis using tMAVEN.Biophysical journal · 2024Article
- Increasing the accuracy of single-molecule data analysis using tMAVEN.bioRxiv : the preprint server for biology · 2024Article
- Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology.Sensors (Basel, Switzerland) · 2023Review
- Gold Ion Beam Milled Gold Zero-Mode Waveguides.Nanomaterials (Basel, Switzerland) · 2022Article
- Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.Annual review of biophysics · 2021Review
- In-Cell Single-Molecule Analysis of Molecular State and Reaction Kinetics Coupling.Advances in experimental medicine and biology · 2021Article
- A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer.The journal of physical chemistry. B · 2019Article
- An automated Bayesian pipeline for rapid analysis of single-molecule binding data.Nature communications · 2019Article
- Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models.Biophysical journal · 2018Article
- Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories.Biophysical journal · 2018Article
- LinkingeLife · 2018Article
- Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems.Biophysical reviews · 2018Review
- Lipid-Protein Interplay in Dimerization of Juxtamembrane Domains of Epidermal Growth Factor Receptor.Biophysical journal · 2018Article
- Decoding Single Molecule Time Traces with Dynamic Disorder.PLoS computational biology · 2016Article
- smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding.FEBS letters · 2014Review
- Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.Biophysical journal · 2014Article
- Analyzing conformational dynamics of single P-glycoprotein transporters by Förster resonance energy transfer using hidden Markov models.Methods (San Diego, Calif.) · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) measurement is a powerful technique for investigating dynamics of biomolecules, for which various efforts have been made to overcome significant stochastic noise. Time stamp (TS) measurement has been employed experimentally to enrich information within the signals, while data analyses such as the hidden Markov model (HMM) have been successfully applied to recover the trajectories of molecular state transitions from time-binned photon counting signals or images. In this article, we introduce the HMM for TS-FRET signals, employing the variational Bayes (VB) inference to solve the model, and demonstrate the application of VB-HMM-TS-FRET to simulated TS-FRET data. The same analysis using VB-HMM is conducted for other models and the previously reported change point detection scheme. The performance is compared to other analysis methods or data types and we show that our VB-HMM-TS-FRET analysis can achieve the best performance and results in the highest time resolution. Finally, an smFRET experiment was conducted to observe spontaneous branch migration of Holliday-junction DNA. VB-HMM-TS-FRET was successfully applied to reconstruct the state transition trajectory with the number of states consistent with the nucleotide sequence. The results suggest that a single migration process frequently involves rearrangement of multiple basepairs.
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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.