ArticlePLoS computational biology2019
Computational design and interpretation of single-RNA translation experiments.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Real-time single-molecule imaging in zebrafish embryos uncovers noncanonical translation.Science advances · 2026Article
- UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.Research square · 2026Article
- UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.bioRxiv : the preprint server for biology · 2026Article
- Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.eLife · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- All Probes Plasmids (APPs) for multicolor and long-term tracking of single-mRNA translation dynamics.Molecular biology of the cell · 2025Article
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.PLoS computational biology · 2024Article
- Translation Dynamics of Single mRNAs in Live Cells.Annual review of biophysics · 2024Review
- Bursting translation on single mRNAs in live cells.Molecular cell · 2023Article
- Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments.bioRxiv : the preprint server for biology · 2023Article
- Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments.Frontiers in cell and developmental biology · 2023Article
- Imaging translational control by Argonaute with single-molecule resolution in live cells.Nature communications · 2022Article
- Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene.Nature communications · 2021Article
- What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis.Open biology · 2020Review
- Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells.Nature structural & molecular biology · 2020Article
- Lighting up single-mRNA translation dynamics in living cells.Current opinion in genetics & development · 2020Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Advances in fluorescence microscopy have introduced new assays to quantify live-cell translation dynamics at single-RNA resolution. We introduce a detailed, yet efficient sequence-based stochastic model that generates realistic synthetic data for several such assays, including Fluorescence Correlation Spectroscopy (FCS), ribosome Run-Off Assays (ROA) after Harringtonine application, and Fluorescence Recovery After Photobleaching (FRAP). We simulate these experiments under multiple imaging conditions and for thousands of human genes, and we evaluate through simulations which experiments are most likely to provide accurate estimates of elongation kinetics. Finding that FCS analyses are optimal for both short and long length genes, we integrate our model with experimental FCS data to capture the nascent protein statistics and temporal dynamics for three human genes: KDM5B, β-actin, and H2B. Finally, we introduce a new open-source software package, RNA Sequence to NAscent Protein Simulator (rSNAPsim), to easily simulate the single-molecule translation dynamics of any gene sequence for any of these assays and for different assumptions regarding synonymous codon usage, tRNA level modifications, or ribosome pauses. rSNAPsim is implemented in Python and is available at: https://github.com/MunskyGroup/rSNAPsim.git.
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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.