ArticleBioinformatics (Oxford, England)2017
FALCON: a toolbox for the fast contextualization of logical networks.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Reconstructing and comparing signal transduction networks from single-cell protein quantification data.Bioinformatics (Oxford, England) · 2026Article
- Transcriptomic Evidence Reveals the Dysfunctional Mechanism of Synaptic Plasticity Control in ASD.Genes · 2024Article
- L-plastin Ser5 phosphorylation is modulated by the PI3K/SGK pathway and promotes breast cancer cell invasiveness.Cell communication and signaling : CCS · 2021Article
- Genome sequence and transcriptome profiles of pathogenic fungusComputational and structural biotechnology journal · 2021Article
- Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread.BMC genomics · 2020Article
- Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways.Frontiers in physiology · 2018Article
- Systemic network analysis identifies XIAP and IκBα as potential drug targets in TRAIL resistant BRAF mutated melanoma.NPJ systems biology and applications · 2018Article
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Authors and funding
4 authors.
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Abstract
motivationMathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically.
resultsWe have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. AVAILABILITY AND IMPLEMENTATION: FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. CONTACT: thomas.sauter@uni.lu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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