Titlebook: Computational Modeling of Signaling Networks; Lan K. Nguyen Book 2023 Springer Science+Business Media, LLC, part of Springer Nature 2023 C

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A Practical Guide for the Efficient Formulation and Calibration of Large, Energy- and Rule-Based Mod

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Design Principles Underlying Robust Adaptation of Complex Biochemical Networksosable into just two types of network building-blocks—opposer modules and balancer modules. Here we present an overview of the design principles that characterize all RPA-capable network topologies through a detailed examination of a collection of simple examples. We also introduce a diagrammatic me

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Multi-Dimensional Analysis of Biochemical Network Dynamics Using pyDYVIPACal to the field of synthetic biology. In this chapter, we will present a practical guide to the multidimensional exploration, analysis, and visualization of network dynamics using pyDYVIPAC, which is a tool ideally suited to these purposes implemented in Python. The utility of pyDYVIPAC will be demo

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Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulato regulatory and protein-protein interaction (PPI) links connecting signaling proteins or transcription factors or miRNAs to metabolic enzymes and their metabolites using network analysis and mathematical modeling. These cross-pathway links were shown to play important roles in metabolic reprogrammin

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Efficient Quantification of Extrinsic Fluctuations via Stochastic Simulations estimate these extrinsic fluctuations for experimentally constructed bidirectional transcriptional reporter systems along with the intrinsic variability. We use the Nanog transcriptional regulatory network and its variants to illustrate our numerical method. Our method reconciled experimental obser

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Meta-Dynamic Network Modelling for Biochemical Networkseals the range of possible protein dynamics for a given network topology. Since MDN modelling is integrated with traditional ODE modelling, it can also be used to investigate the underlying causal mechanics. This technique is particularly suited to the investigation of network behaviors in systems t

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Resolving Crosstalk Between Signaling Pathways Using Mathematical Modeling and Time-Resolved Single of p53 to genotoxic stress using time-resolved single cell data and perturbed NF-κB signaling by inhibiting the kinase IKK2. Employing a subpopulation-based modeling approach enabled us to identify multiple interaction points that are simultaneously affected by perturbation of NF-κB signaling. Henc