ArticlePLoS computational biology2016
Stochastic Simulation of Biomolecular Networks in Dynamic Environments.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Simulation and inference methods for non-Markovian stochastic reaction networks.PLoS computational biology · 2026Article
- SIMPLICITY is an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution.Communications biology · 2026Article
- Quantifying and comparing causal patterns in stochastic chemical reaction networks.NPJ systems biology and applications · 2026Article
- Article
- Feedback between stochastic gene networks and population dynamics enables cellular decision-making.Science advances · 2024Article
- Review
- Studying stochastic systems biology of the cell with single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- Inference and uncertainty quantification of stochastic gene expression via synthetic models.Journal of the Royal Society, Interface · 2022Article
- Scalable and flexible inference framework for stochastic dynamic single-cell models.PLoS computational biology · 2022Article
- Single cell variability of CRISPR-Cas interference and adaptation.Molecular systems biology · 2022Article
- Evolution during primary HIV infection does not require adaptive immune selection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Exploiting Noise, Non-Linearity, and Feedback for Differential Control of Multiple Synthetic Cells with a Single Optogenetic Input.ACS synthetic biology · 2021Article
- Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes.PLoS computational biology · 2021Article
- Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations.Journal of the Royal Society, Interface · 2021Article
- The circadian oscillator analysed at the single-transcript level.Molecular systems biology · 2021Article
- Markovian approaches to modeling intracellular reaction processes with molecular memory.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics.PLoS computational biology · 2019Article
- Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art.Journal of the Royal Society, Interface · 2019Article
- Intrinsic and extrinsic noise of gene expression in lineage trees.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.
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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.