ArticleGenome biology2017
BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 64 citations in OpenAlex.
- Transcriptional Bursting in Pluripotent Stem Cells.Biology · 2026Review
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- Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.PLoS computational biology · 2026Article
- Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.Bioinformatics (Oxford, England) · 2025Article
- Incorporating spatial diffusion into models of bursty stochastic transcription.Journal of the Royal Society, Interface · 2025Article
- Sequential design of single-cell experiments to identify discrete stochastic models for gene expression.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2024Article
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 2024Article
- Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions.Bulletin of mathematical biology · 2024Article
- Article
- Stochastic modeling of the mRNA life process: A generalized master equation.Biophysical journal · 2023Article
- Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- Gene expression model inference from snapshot RNA data using Bayesian non-parametrics.Nature computational science · 2023Article
- Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise.Frontiers in cell and developmental biology · 2023Article
- Variability of the innate immune response is globally constrained by transcriptional bursting.Frontiers in molecular biosciences · 2023Article
- Scalable inference of transcriptional kinetic parameters from MS2 time series data.Bioinformatics (Oxford, England) · 2022Article
- Inferring kinetic parameters of oscillatory gene regulation from single cell time-series data.Journal of the Royal Society, Interface · 2021Article
- Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage.PLoS computational biology · 2021Article
- The circadian oscillator analysed at the single-transcript level.Molecular systems biology · 2021Article
- BAYESIAN INFERENCE OF STOCHASTIC REACTION NETWORKS USING MULTIFIDELITY SEQUENTIAL TEMPERED MARKOV CHAIN MONTE CARLO.International journal for uncertainty quantification · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data. We tested BayFish on synthetic data and smFISH measurements of the neuronal activity-inducible gene Npas4 in primary neurons.
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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.