ArticleNature communications2018
Quantitative diffusion measurements using the open-source software PyFRAP.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- Development of a deep neural network model for simultaneous analysis of extracellular analyte gradients for a population of cells.Artificial intelligence in the life sciences · 2026Article
- Measuring morphogen transport over multiple spatial scales in live zebrafish embryos.Nature communications · 2026Article
- Compartmentalization and Aggregation of Biomolecular Condensates in Crowded Hydrogels for Enhanced Nucleic Acid Diagnosis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Protocol for characterizing biomolecular condensates through live-cell imaging and analysis.STAR protocols · 2025Article
- Inferring diffusion, reaction, and exchange parameters from imperfect FRAP.Biophysical journal · 2025Article
- Programming-Assisted Imaging of Cellular Nitric Oxide Efflux Gradients and Directionality via Carbon Nanotube Sensors.Small science · 2025Article
- Receptor binding and tortuosity explain morphogen local-to-global diffusion coefficient transition.Biophysical journal · 2025Article
- Exploring focal adhesion data: dynamic parameter extraction from FRAP and FLAP experiments using chemical master equation.Frontiers in molecular biosciences · 2025Article
- Dried Blood Matrix as a New Material for the Detection of DNA Viruses.Advanced healthcare materials · 2024Article
- Brain clearance is reduced during sleep and anesthesia.Nature neuroscience · 2024Article
- Diffusion-Based 3D Bioprinting Strategies.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Probing Microscale Structuring-Induced Phase Separation with Fluorescence Recovery Diffusion Dynamics in Poly(ethylene glycol) Solutions.ACS omega · 2023Article
- Beyond analytic solution: Analysis of FRAP experiments by spatial simulation of the forward problem.Biophysical journal · 2023Article
- What's past is prologue: FRAP keeps delivering 50 years later.Biophysical journal · 2023Review
- Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model.Nature communications · 2022Article
- Regulation of Nodal signaling propagation by receptor interactions and positive feedback.eLife · 2022Article
- Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion.Journal of mathematical biology · 2021Article
- Generation of extracellular morphogen gradients: the case for diffusion.Nature reviews. Genetics · 2021Review
- A noninvasive fluorescence imaging-based platform measures 3D anisotropic extracellular diffusion.Nature communications · 2021Article
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Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorescence Recovery After Photobleaching (FRAP) and inverse FRAP (iFRAP) assays can be used to assess the mobility of fluorescent molecules. These assays measure diffusion by monitoring the return of fluorescence in bleached regions (FRAP), or the dissipation of fluorescence from photoconverted regions (iFRAP). However, current FRAP/iFRAP analysis methods suffer from simplified assumptions about sample geometry, bleaching/photoconversion inhomogeneities, and the underlying reaction-diffusion kinetics. To address these shortcomings, we developed the software PyFRAP, which fits numerical simulations of three-dimensional models to FRAP/iFRAP data and accounts for bleaching/photoconversion inhomogeneities. Using PyFRAP we determined the diffusivities of fluorescent molecules spanning two orders of magnitude in molecular weight. We measured the tortuous effects that cell-like obstacles exert on effective diffusivity and show that reaction kinetics can be accounted for by model selection. These applications demonstrate the utility of PyFRAP, which can be widely adapted as a new extensible standard for FRAP analysis.
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.