ArticleThe journal of physical chemistry. B2009
Extracting kinetics information from single-molecule fluorescence resonance energy transfer data using hidden markov models.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Single-molecule dissection of CFTR folding defects and pharmacological rescue.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hidden Markov model analysis of fluorescence blinking in fluorescently labeled DNA.Scientific reports · 2026Article
- Single Molecule Tracking: Visualizing Transcription of Endogenous Loci in Living Cells.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Bayesian analysis and efficient algorithms for single-molecule fluorescence data and step counting.Biophysical journal · 2025Article
- Single-molecule tweezers decode hidden dimerization patterns of membrane proteins within lipid bilayers.Nature communications · 2025Article
- Bayesian analysis and efficient algorithms for single-molecule fluorescence data and step counting.bioRxiv : the preprint server for biology · 2025Article
- Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens.Molecular cell · 2025Article
- Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary balance between foldability and functionality of a glucose transporter.Nature chemical biology · 2022Article
- DOT1L activity in leukemia cells requires interaction with ubiquitylated H2B that promotes productive nucleosome binding.Cell reports · 2022Article
- MYC amplifies gene expression through global changes in transcription factor dynamics.Cell reports · 2022Article
- Theory and Analysis of Single-Molecule FRET Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes.Biophysical journal · 2021Article
- Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy.Frontiers in molecular biosciences · 2021Review
- Article
- Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway.Science (New York, N.Y.) · 2019Article
- Physical Chemistry of Epigenetics: Single-Molecule Investigations.The journal of physical chemistry. B · 2019Review
- Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II.Methods (San Diego, Calif.) · 2019Article
- How Protein Binding Sensitizes the Nucleosome to Histone H3K56 Acetylation.ACS chemical biology · 2019Article
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Abstract
Hidden Markov models (HMM) have been proposed as a method of analysis for noisy single-molecule fluorescence resonance energy transfer (SM FRET) data. However, there are practical and fundamental limits in applying HMM to SM FRET data due to the short photobleaching lifetimes of fluorophores and the limited time resolution of detection devices. The fast photobleaching fluorophores yield short SM FRET time traces, and the limited detection time resolution generates abnormal FRET values, which result in systematic underestimation of kinetic rates. In this work, a HMM algorithm is implemented to optimize one set of HMM parameters with multiple short SM FRET traces. The FRET efficiency distribution function for the HMM optimization was modified to accommodate the abnormal FRET values resulting from limited detection time resolution. Computer simulations reveal that one set of HMM parameters is optimized successfully using multiple short SM FRET traces and that the degree of the kinetic rate underestimation is reduced by using the proposed modified FRET efficiency distribution. In conclusion, it is demonstrated that HMM can be used to reproducibly analyze short SM FRET time traces.
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