ArticleNPJ systems biology and applications2018
Role of noise and parametric variation in the dynamics of gene regulatory circuits.
Article in NPJ systems biology and applications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Dissecting reversible and irreversible single cell state transitions from gene regulatory networks.Molecular systems biology · 2026Article
- Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype.NPJ systems biology and applications · 2026Article
- Gene Regulatory Networks for Enhanced Vision-Based Robot Control: A Bio-Inspired Approach.Sensors (Basel, Switzerland) · 2026Article
- sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation.Bioinformatics (Oxford, England) · 2026Article
- Building dynamical models of multi-step state transitions from single cell gene expression trajectories.bioRxiv : the preprint server for biology · 2025Article
- A computational approach for perturbation-induced EMT transitions.NPJ systems biology and applications · 2025Article
- Article
- Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells.Science advances · 2024Article
- Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.NPJ systems biology and applications · 2024Article
- Theoretical and computational tools to model multistable gene regulatory networks.Reports on progress in physics. Physical Society (Great Britain) · 2023Review
- Critical transition and reversion of tumorigenesis.Experimental & molecular medicine · 2023Review
- A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions.iScience · 2023Article
- Article
- NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity.Genome biology · 2022Article
- What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis.The journal of physical chemistry. B · 2022Article
- Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration.iScience · 2022Article
- Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.PLoS computational biology · 2022Article
- Data mining and mathematical models in cancer prognosis and prediction.Medical review (2021) · 2022Review
- Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro.American journal of physiology. Lung cellular and molecular physiology · 2022Article
- Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation.Molecular biology of the cell · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
Stochasticity in gene expression impacts the dynamics and functions of gene regulatory circuits. Intrinsic noises, including those that are caused by low copy number of molecules and transcriptional bursting, are usually studied by stochastic simulations. However, the role of extrinsic factors, such as cell-to-cell variability and heterogeneity in the microenvironment, is still elusive. To evaluate the effects of both the intrinsic and extrinsic noises, we develop a method, named sRACIPE, by integrating stochastic analysis with random circuit perturbation (RACIPE) method. RACIPE uniquely generates and analyzes an ensemble of models with random kinetic parameters. Previously, we have shown that the gene expression from random models form robust and functionally related clusters. In sRACIPE we further develop two stochastic simulation schemes, aiming to reduce the computational cost without sacrificing the convergence of statistics. One scheme uses constant noise to capture the basins of attraction, and the other one uses simulated annealing to detect the stability of states. By testing the methods on several synthetic gene regulatory circuits and an epithelial-mesenchymal transition network in squamous cell carcinoma, we demonstrate that sRACIPE can interpret the experimental observations from single-cell gene expression data. We observe that parametric variation (the spread of parameters around a median value) increases the spread of the gene expression clusters, whereas high noise merges the states. Our approach quantifies the robustness of a gene circuit in the presence of noise and sheds light on a new mechanism of noise-induced hybrid states. We have implemented sRACIPE as an R package.
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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.