ArticleBiophysical reports2023
Single-photon smFRET. I: Theory and conceptual basis.
Article in Biophysical reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 26 citations in OpenAlex.
- Resolving fluorescently labeled species using highly multiplexed spectral FLIM.Scientific reports · 2026Article
- Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome.Nature communications · 2026Article
- 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
- Bayesian Nonparametrics for FRET using Realistic Integrative Detectors.bioRxiv : the preprint server for biology · 2025Article
- Physics-Inspired Single-Particle Tracking Accelerated with Parallelism.bioRxiv : the preprint server for biology · 2025Article
- Single-molecule reaction-diffusion.Biophysical journal · 2025Article
- Bayesian Inference of Binding Kinetics from Fluorescence Time Series.The journal of physical chemistry. B · 2025Article
- Simultaneous particle tracking, phase retrieval and point spread function reconstruction.bioRxiv : the preprint server for biology · 2025Article
- Using Bayesian priors to overcome non-identifiablility issues in Hidden Markov models.bioRxiv : the preprint server for biology · 2025Article
- Avoiding matrix exponentials for large transition rate matrices.The Journal of chemical physics · 2024Article
- Building Fluorescence Lifetime Maps Photon-by-Photon by Leveraging Spatial Correlations.ACS photonics · 2023Article
- Article
- Time-resolved burst variance analysis.Biophysical reports · 2023Article
- Single-Molecule Reaction-Diffusion.bioRxiv : the preprint server for biology · 2023Article
- Single-photon smFRET: II. Application to continuous illumination.Biophysical reports · 2023Article
- Fluorescence lifetime: Beating the IRF and interpulse window.Biophysical journal · 2023Article
- Learning continuous potentials from smFRET.Biophysical journal · 2023Article
- Single-photon smFRET. III. Application to pulsed illumination.Biophysical reports · 2022Article
- Shelterin reduces the accessibility of telomeric overhangs.Nucleic acids research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.
Identifiers
What OpenQuestion holds
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.