ArticleBMC systems biology2018
RACIPE: a computational tool for modeling gene regulatory circuits using randomization.
Article in BMC systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Article
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- Design principles for robust multistability in coupled feedforward-feedback regulatory circuits.NPJ systems biology and applications · 2026Article
- Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype.NPJ systems biology and applications · 2026Article
- Bidirectional coupling among EMT, AXL-RB1 signaling and lineage switch drives resistance to osimertinib and worse clinical outcomes in NSCLC.bioRxiv : the preprint server for biology · 2026Article
- Network hypermotifs in biological systems: structure, dynamics, and functional implications.NPJ systems biology and applications · 2026Review
- 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
- GRiNS: a python library for simulating gene regulatory network dynamics.BMC bioinformatics · 2025Article
- Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor.PLoS computational biology · 2025Article
- Gene regulatory network inference during cell fate decisions by perturbation strategies.NPJ systems biology and applications · 2025Article
- The switch-liker's guide to plant synthetic gene circuits.The Plant journal : for cell and molecular biology · 2025Review
- Operating principles of interconnected feedback loops driving cell fate transitions.NPJ systems biology and applications · 2025Article
- Article
- Endothelial Dysfunction in the Tubule Area Accelerates the Progression of Early Diabetic Kidney Disease.Physiological research · 2024Article
- OneSC: a computational platform for recapitulating cell state transitions.Bioinformatics (Oxford, England) · 2024Article
- Distinct melanocyte subpopulations defined by stochastic expression of proliferation or maturation programs enable a rapid and sustainable pigmentation response.PLoS biology · 2024Article
- Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells.Science advances · 2024Article
- OneSC: A computational platform for recapitulating cell state transitions.bioRxiv : the preprint server for biology · 2024Article
- A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets.Mathematical biosciences · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundOne of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental data and/or educated guesses, which can be time-consuming and error-prone, especially for large networks.
resultsWe present a user-friendly computational tool for the community to use our newly developed method named random circuit perturbation (RACIPE), to explore the robust dynamical features of gene regulatory circuits without the requirement of detailed kinetic parameters. Taking the network topology as the only input, RACIPE generates an ensemble of circuit models with distinct randomized parameters and uniquely identifies robust dynamical properties by statistical analysis. Here, we discuss the implementation of the software and the statistical analysis methods of RACIPE-generated data to identify robust gene expression patterns and the functions of genes and regulatory links. Finally, we apply the tool on coupled toggle-switch circuits and a published circuit of B-lymphopoiesis.
conclusionsWe expect our new computational tool to contribute to a more comprehensive and unbiased understanding of mechanisms underlying gene regulatory networks. RACIPE is a free open source software distributed under (Apache 2.0) license and can be downloaded from GitHub ( https://github.com/simonhb1990/RACIPE-1.0 ).
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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.