ArticleScientific reports2015
DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- Benchmarking tools for a priori identifiability analysis.Bioinformatics (Oxford, England) · 2023Article
- A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems.Scientific reports · 2023Article
- libRoadRunner 2.0: a high performance SBML simulation and analysis library.Bioinformatics (Oxford, England) · 2023Article
- Multi-Dimensional Analysis of Biochemical Network Dynamics Using pyDYVIPAC.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Bayesian parameter estimation for dynamical models in systems biology.PLoS computational biology · 2022Article
- Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers.Cell reports · 2021Article
- Modeling the Nonlinear Dynamics of Intracellular Signaling Networks.Bio-protocol · 2021Article
- Article
- Exploratory Data Analysis of Adverse Birth Outcomes and Exposure to Oxides of Nitrogen Using Interactive Parallel Coordinates Plot Technique.Scientific reports · 2020Article
- Simple Rho GTPase Dynamics Generate a Complex Regulatory Landscape Associated with Cell Shape.Biophysical journal · 2020Article
- Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR.Scientific reports · 2018Article
- Exploring and visualizing multidimensional data in translational research platforms.Briefings in bioinformatics · 2017Article
- Mechanisms of Cell Polarization.Current opinion in systems biology · 2017Article
- Structural Identifiability of Dynamic Systems Biology Models.PLoS computational biology · 2016Article
- Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches.Cell systems · 2016Article
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4 authors.
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Abstract
Biochemical networks are dynamic and multi-dimensional systems, consisting of tens or hundreds of molecular components. Diseases such as cancer commonly arise due to changes in the dynamics of signalling and gene regulatory networks caused by genetic alternations. Elucidating the network dynamics in health and disease is crucial to better understand the disease mechanisms and derive effective therapeutic strategies. However, current approaches to analyse and visualise systems dynamics can often provide only low-dimensional projections of the network dynamics, which often does not present the multi-dimensional picture of the system behaviour. More efficient and reliable methods for multi-dimensional systems analysis and visualisation are thus required. To address this issue, we here present an integrated analysis and visualisation framework for high-dimensional network behaviour which exploits the advantages provided by parallel coordinates graphs. We demonstrate the applicability of the framework, named "Dynamics Visualisation based on Parallel Coordinates" (DYVIPAC), to a variety of signalling networks ranging in topological wirings and dynamic properties. The framework was proved useful in acquiring an integrated understanding of systems behaviour.
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