ArticleeLife2021
Pathway dynamics can delineate the sources of transcriptional noise in gene expression.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Molecular noise modulates transitions in the cell-fate differentiation landscape.NPJ systems biology and applications · 2026Article
- MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.Journal of translational medicine · 2026Article
- From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.PLoS computational biology · 2026Article
- Article
- Relationships between gene expression variability, expression levels, and Protein-Protein interactions in mouse and yeast.PloS one · 2026Article
- Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data.Nature methods · 2025Article
- Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.Bioinformatics (Oxford, England) · 2025Article
- Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression.Nature communications · 2025Article
- A stochastic vs deterministic perspective on the timing of cellular events.Nature communications · 2024Article
- Cis-regulatory control of transcriptional timing and noise in response to estrogen.Cell genomics · 2024Article
- Article
- Quantifying and correcting bias in transcriptional parameter inference from single-cell data.Biophysical journal · 2024Article
- Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics.Bioinformatics (Oxford, England) · 2023Article
- Long-Term Transcriptomic Changes and Cardiomyocyte Hyperpolyploidy after Lactose Intolerance in Neonatal Rats.International journal of molecular sciences · 2023Article
- Article
- Article
- Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks.Cell systems · 2022Article
- Transcriptional noise adjusted for expression levels reveals genes with high transcriptional noise that are highly expressed, functionally related, and co-regulated in yeast.Current genetics · 2022Article
- Scalable and flexible inference framework for stochastic dynamic single-cell models.PLoS computational biology · 2022Article
- Identifying cell-to-cell variability in internalization using flow cytometry.Journal of the Royal Society, Interface · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell expression profiling opens up new vistas on cellular processes. Extensive cell-to-cell variability at the transcriptomic and proteomic level has been one of the stand-out observations. Because most experimental analyses are destructive we only have access to snapshot data of cellular states. This loss of temporal information presents significant challenges for inferring dynamics, as well as causes of cell-to-cell variability. In particular, we typically cannot separate dynamic variability from within cells ('intrinsic noise') from variability across the population ('extrinsic noise'). Here, we make this non-identifiability mathematically precise, allowing us to identify new experimental set-ups that can assist in resolving this non-identifiability. We show that multiple generic reporters from the same biochemical pathways (e.g. mRNA and protein) can infer magnitudes of intrinsic and extrinsic transcriptional noise, identifying sources of heterogeneity. Stochastic simulations support our theory, and demonstrate that 'pathway-reporters' compare favourably to the well-known, but often difficult to implement, dual-reporter method.
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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.