BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.
Publication
, Journal Article
Gómez-Schiavon, M; Chen, L-F; West, AE; Buchler, NE
Published in: Genome Biol
September 4, 2017
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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Published In
Genome Biol
DOI
EISSN
1474-760X
Publication Date
September 4, 2017
Volume
18
Issue
1
Start / End Page
164
Location
England
Related Subject Headings
- Transcription, Genetic
- Stochastic Processes
- Software
- RNA
- Probability
- Neurons
- Models, Genetic
- Mice
- Male
- In Situ Hybridization, Fluorescence
Citation
APA
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MLA
NLM
Gómez-Schiavon, M., Chen, L.-F., West, A. E., & Buchler, N. E. (2017). BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. Genome Biol, 18(1), 164. https://doi.org/10.1186/s13059-017-1297-9
Gómez-Schiavon, Mariana, Liang-Fu Chen, Anne E. West, and Nicolas E. Buchler. “BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.” Genome Biol 18, no. 1 (September 4, 2017): 164. https://doi.org/10.1186/s13059-017-1297-9.
Gómez-Schiavon M, Chen L-F, West AE, Buchler NE. BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. Genome Biol. 2017 Sep 4;18(1):164.
Gómez-Schiavon, Mariana, et al. “BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.” Genome Biol, vol. 18, no. 1, Sept. 2017, p. 164. Pubmed, doi:10.1186/s13059-017-1297-9.
Gómez-Schiavon M, Chen L-F, West AE, Buchler NE. BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. Genome Biol. 2017 Sep 4;18(1):164.
Published In
Genome Biol
DOI
EISSN
1474-760X
Publication Date
September 4, 2017
Volume
18
Issue
1
Start / End Page
164
Location
England
Related Subject Headings
- Transcription, Genetic
- Stochastic Processes
- Software
- RNA
- Probability
- Neurons
- Models, Genetic
- Mice
- Male
- In Situ Hybridization, Fluorescence