ArticleBiophysical journal2022
Modeling bursty transcription and splicing with the chemical master equation.
Article in Biophysical journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 46 citations in OpenAlex.
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
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- From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.PLoS computational biology · 2026Article
- Intrinsic OASL expression governs heterogeneity in interferon induction during influenza A virus infection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data.Nature methods · 2025Article
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction.Mathematical biosciences · 2024Article
- Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions.Bulletin of mathematical biology · 2024Article
- Solving stochastic gene-expression models using queueing theory: A tutorial review.Biophysical journal · 2024Review
- Quantifying and correcting bias in transcriptional parameter inference from single-cell data.Biophysical journal · 2024Article
- Article
- Poisson representation: a bridge between discrete and continuous models of stochastic gene regulatory networks.Journal of the Royal Society, Interface · 2023Article
- Review
- Studying stochastic systems biology of the cell with single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Inferring transcriptional bursting kinetics from single-cell snapshot data using a generalized telegraph model.Royal Society open science · 2023Article
- Length biases in single-cell RNA sequencing of pre-mRNA.Biophysical reports · 2023Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
- Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination.Computational and structural biotechnology journal · 2023Review
- Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments.Nature communications · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Splicing cascades that alter gene products posttranscriptionally also affect expression dynamics. We study a class of processes and associated distributions that emerge from models of bursty promoters coupled to directed acyclic graphs of splicing. These solutions provide full time-dependent joint distributions for an arbitrary number of species with general noise behaviors and transient phenomena, offering qualitative and quantitative insights about how splicing can regulate expression dynamics. Finally, we derive a set of quantitative constraints on the minimum complexity necessary to reproduce gene coexpression patterns using synchronized burst models. We validate these findings by analyzing long-read sequencing data, where we find evidence of expression patterns largely consistent with these constraints.
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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.