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Algebra, Geometry and Topology of ERK Kinetics
The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death (Shaul and Seger in Biochim Biophys Acta...
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Information-Theoretic Analysis of a Model of CAR-4-1BB-Mediated NFκB Activation
Systems biology utilizes computational approaches to examine an array of biological processes, such as cell signaling, metabolomics and pharmacology....
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Cytotoxic Activity of Raphanus sativus Linn. on Selected Cancer Cell Lines and Mechanistic Pathways Predicted Through Mathematical Modeling
Studies have shown different effects of Raphanus sativus L. (RS) extract on different cancer cell types. However, the dynamics of gene regulation...
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Phenotype Control techniques for Boolean gene regulatory networks
Modeling cell signal transduction pathways via Boolean networks (BNs) has become an established method for analyzing intracellular communications...
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Model Reduction and Implicit–Explicit Runge–Kutta Schemes for Nonlinear Stiff Initial-Value Problems
The main goal of this paper is the use of the implicit–explicit Runge–Kutta method for finding the numerical approximate solutions for chemical...
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Multistationarity questions in reduced versus extended biochemical networks
We address several questions in reduced versus extended networks via the elimination or addition of intermediate complexes in the framework of...
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Modelling HIF-PHD Dynamics and Related Downstream Pathways
Hypoxia can represent a challenging condition for survival at different biological scales, from cells to organisms. The efficiency of the response to...
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A 3D Multiscale Model to Explore the Role of EGFR Overexpression in Tumourigenesis
The epidermal growth factor receptor (EGFR) signalling cascade is one of the main pathways that regulate the survival and division of mammalian...
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Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets
Pancreatic ductal adenocarcinoma is among the leading causes of cancer-related deaths globally due to its extreme difficulty to detect and treat....
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Construction of a New Model to Investigate Breast Cancer Data
Modelling is a way to describe the elements of the network/system, their states and their interactions with other elements in order to understand the...
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Integrative Network Analysis of Cancer Cell Signaling by High-Resolution Proteomics
Post-translational modifications (PTMs), such as phosphorylation, ubiquitination and acetylation, are known to be widely involved in the regulation...
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Modelling Keloids Dynamics: A Brief Review and New Mathematical Perspectives
Keloids are fibroproliferative disorders described by excessive growth of fibrotic tissue, which also invades adjacent areas (beyond the original...
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Mathematical Modeling of Cancer Signaling Addressing Tumor Heterogeneity
One of the obstacles for cancer therapies is the heterogeneity of cancers. Heterogeneity in signal transduction within the same cell population...
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Self-Organization of Tissues Through Biochemical and Mechanical Signals
Self-organization enables the emergence of patterns in systems without the need of an external causal agent. Instead, the interactions and the...
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Efficiency of Neuro-Nutrient Therapy in the Treatment of Neuropathologies
Brain being a complex organ is under the influence of many chemical messengers. Some like Serotonin and GABA exert a calming effect, while others...
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Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking...
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Bye bye, linearity, bye: quantification of the mean for linear CRNs in a random environment
Molecular reactions within a cell are inherently stochastic, and cells often differ in morphological properties or interact with a heterogeneous...
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An Axiomatic Approach to Reversible Computation
Undoing computations of a concurrent system is beneficial in many situations, e.g., in reversible debugging of multi-threaded programs and in...
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Noise control and utility: From regulatory network to spatial patterning
Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how...
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Control of Intracellular Molecular Networks Using Algebraic Methods
Many problems in biology and medicine have a control component. Often, the goal might be to modify intracellular networks, such as gene regulatory...
