ArticleMultiscale modeling & simulation : a SIAM interdisciplinary journal2016
ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS.
Article in Multiscale modeling & simulation : a SIAM interdisciplinary journal, 2016. 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.
- Truncating the time-evolving discrete chemical master equation for stochastic biological networks.Biophysical journal · 2026Article
- Spatio-temporal multiscale cell modeling of skin wound healing.Biophysical journal · 2026Article
- Progenitor neighborhoods function as transient niches to sustain olfactory neurogenesis.Stem cell reports · 2025Article
- Distilling dynamical knowledge from stochastic reaction networks.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcriptional bursting dynamics in gene expression.Frontiers in genetics · 2024Review
- Network design principle for robust oscillatory behaviors with respect to biological noise.eLife · 2022Article
- Inferring initial state of the ancestral network of cellular fate decision: a case study of phage lambda.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2021Article
- Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality.Frontiers in genetics · 2021Article
- Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation.The Journal of chemical physics · 2020Article
- Discrete and continuous models of probability flux of switching dynamics: Uncovering stochastic oscillations in a toggle-switch system.The Journal of chemical physics · 2019Article
- Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.Bulletin of mathematical biology · 2019Article
- Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts.The Journal of chemical physics · 2019Article
- Sensitivities of Regulation Intensities in Feed-Forward Loops with Multistability.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2019Article
- Bayesian Estimation for Stochastic Gene Expression Using Multifidelity Models.The journal of physical chemistry. B · 2019Article
- Evolution of Coagulation-Fragmentation Stochastic Processes Using Accurate Chemical Master Equation Approach.Communications in information and systems · 2019Article
- Probabilistic control of HIV latency and transactivation by the Tat gene circuit.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Discrete flux and velocity fields of probability and their global maps in reaction systems.The Journal of chemical physics · 2018Article
- Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean.PLoS biology · 2017Article
- PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space.BMC bioinformatics · 2017Article
- Markov State Models of gene regulatory networks.BMC systems biology · 2017Article
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3 authors.
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Abstract
The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by
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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.