Related papers: An Introduction to Rule-based Modeling of Immune R…
Immunology is the emerging research area which deals with the study of the immune system in any living organism. It is modelled through various computational and mathematical models to deal with the problem facing while to boost the immune…
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
The immune system can be thought as a complex network of different interacting elements. A cellular automaton, defined in shape-space, was recently shown to exhibit self-regulation and complex behavior and is, therefore, a good candidate to…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…
Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
We argue that immune system is an adaptive complex system. It is shown that it has emergent properties. Its network structure is of the small world network type. The network is of the threshold type, which helps in avoiding autoimmunity. It…
The immunological synapse is a patterned collection of different types of receptors and ligands that forms in the intercellular junction between T Cells and antigen presenting cells (APCs) during recognition. The synapse is implicated in…
Repertoire-level analysis of T cell receptors offers a biologically grounded signal for disease detection and immune monitoring, yet practical deployment is impeded by label sparsity, cohort heterogeneity, and the computational burden of…
This paper gives an introduction to rule-based modelling applied to topics in infectious diseases. Rule-based models generalise reaction-based models with reagents that have internal state and may be bound together to form complexes, as in…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational…