ArticleThe journal of physical chemistry. B2006
Hidden Markov model analysis of multichromophore photobleaching.
Article in The journal of physical chemistry. B, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- Hidden Markov model analysis of fluorescence blinking in fluorescently labeled DNA.Scientific reports · 2026Article
- FluoroTensor: Identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning.Computational and structural biotechnology journal · 2024Article
- Unlicensed origin DNA melting by MCV and SV40 polyomavirus LT proteins is independent of ATP-dependent helicase activity.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier.PLoS computational biology · 2023Article
- Deep learning in single-molecule imaging and analysis: recent advances and prospects.Chemical science · 2022Review
- Gold Ion Beam Milled Gold Zero-Mode Waveguides.Nanomaterials (Basel, Switzerland) · 2022Article
- Article
- Toward high-throughput oligomer detection and classification for early-stage aggregation of amyloidogenic protein.Frontiers in chemistry · 2022Article
- Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching.Methods (San Diego, Calif.) · 2021Article
- Analyzing protein dynamics from fluorescence intensity traces using unsupervised deep learning network.Communications biology · 2020Article
- Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models.Biophysical journal · 2018Article
- Enzyme-Mediated Directional Transport of a Small-Molecule Walker With Chemically Identical Feet.Journal of the American Chemical Society · 2017Article
- Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.Chemical reviews · 2017Article
- State aggregation for fast likelihood computations in molecular evolution.Bioinformatics (Oxford, England) · 2017Article
- A novel method to accurately locate and count large numbers of steps by photobleaching.Molecular biology of the cell · 2016Article
- Counting tagged molecules one by one: Quantitative photoactivation and bleaching of photoactivatable fluorophores.The Journal of chemical physics · 2015Article
- Analyzing conformational dynamics of single P-glycoprotein transporters by Förster resonance energy transfer using hidden Markov models.Methods (San Diego, Calif.) · 2014Article
- Long-lived intracellular single-molecule fluorescence using electroporated molecules.Biophysical journal · 2013Article
- Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories.Biophysical journal · 2012Article
- Hidden markov analysis of short single molecule intensity trajectories.The journal of physical chemistry. B · 2009Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The interpretation of single-molecule measurements is greatly complicated by the presence of multiple fluorescent labels. However, many molecular systems of interest consist of multiple interacting components. We investigate this issue using multiply labeled dextran polymers that we intentionally photobleach to the background on a single-molecule basis. Hidden Markov models allow for unsupervised analysis of the data to determine the number of fluorescent subunits involved in the fluorescence intermittency of the 6-carboxy-tetramethylrhodamine labels by counting the discrete steps in fluorescence intensity. The Bayes information criterion allows us to distinguish between hidden Markov models that differ by the number of states, that is, the number of fluorescent molecules. We determine information-theoretical limits and show via Monte Carlo simulations that the hidden Markov model analysis approaches these theoretical limits. This technique has resolving power of one fluorescing unit up to as many as 30 fluorescent dyes with the appropriate choice of dye and adequate detection capability. We discuss the general utility of this method for determining aggregation-state distributions as could appear in many biologically important systems and its adaptability to general photometric experiments.
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Registered trials
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.