ReviewCell systems2023
Studying stochastic systems biology of the cell with single-cell genomics data.
Review in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 39 citations in OpenAlex.
- Efficiency, accuracy and robustness of probability generating function based parameter inference method for stochastic biochemical reactions.PLoS computational biology · 2026Article
- Article
- Predicting Cardiovascular Events with Time-Lagged Inflammatory Dynamics: Stochastic Delay Modeling.Computational and structural biotechnology journal · 2026Article
- Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances.bioRxiv : the preprint server for biology · 2025Article
- 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
- Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data.Nucleic acids research · 2025Article
- Incorporating spatial diffusion into models of bursty stochastic transcription.Journal of the Royal Society, Interface · 2025Article
- Fokker-Planck diffusion maps of microglial transcriptomes reveal radial differentiation into substates associated with Alzheimer's pathology.Communications biology · 2025Article
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Trajectory inference from single-cell genomics data with a process time model.PLoS computational biology · 2025Article
- Studying RNA dynamics from single-cell RNA sequencing snapshots.Nature methods · 2024Article
- Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer's pathology.bioRxiv : the preprint server for biology · 2024Article
- Solving stochastic gene-expression models using queueing theory: A tutorial review.Biophysical journal · 2024Review
- The impact of package selection and versioning on single-cell RNA-seq analysis.bioRxiv : the preprint server for biology · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- New and notable: Revisiting the "two cultures" through extrinsic noise.Biophysical journal · 2024Article
- Quantifying and correcting bias in transcriptional parameter inference from single-cell data.Biophysical journal · 2024Article
- Stochastic modeling of the mRNA life process: A generalized master equation.Biophysical journal · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
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What OpenQuestion holds
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.