ArticleBMC bioinformatics2016
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Boolean modelling as a logic-based dynamic approach in systems medicine.Computational and structural biotechnology journal · 2022Review
- RMut: R package for a Boolean sensitivity analysis against various types of mutations.PloS one · 2019Article
- ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming.Scientific reports · 2018Article
- Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks.BMC systems biology · 2017Article
- CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer.Cancer informatics · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and functional characterization of real GRNs is often still partial and an exhaustive picture of their functioning is missing.
resultsWe here introduce CABERNET, a Cytoscape app for the generation, simulation and analysis of Boolean models of GRNs, specifically focused on their augmentation when a only partial topological and functional characterization of the network is available. By generating large ensembles of networks in which user-defined entities and relations are added to the original core, CABERNET allows to formulate hypotheses on the missing portions of real networks, as well to investigate their generic properties, in the spirit of complexity science.
conclusionsCABERNET offers a series of innovative simulation and modeling functions and tools, including (but not being limited to) the dynamical characterization of the gene activation patterns ruling cell types and differentiation fates, and sophisticated robustness assessments, as in the case of gene knockouts. The integration within the widely used Cytoscape framework for the visualization and analysis of biological networks, makes CABERNET a new essential instrument for both the bioinformatician and the computational biologist, as well as a computational support for the experimentalist. An example application concerning the analysis of an augmented T-helper cell GRN is provided.
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