The regular models of a normal logic program are a particular type of partial (i.e. 3-valued) models which correspond to stable partial models with minimal undefinedness. In this paper, we explore graphical conditions on the dependency graph of a finite ground normal logic program to analyze the existence, unicity and number of regular models for the program […]
Tue, Oct 1, 2024
Chemical Reaction Networks (CRNs) are a standard formalism used in chemistry and biology to model complex molecular interaction systems. In the perspective of systems biology, they are a central tool to analyze the high-level functions of the cell in terms of their low-level molecular interactions. In the perspective of synthetic biology, they constitute a target programming language to implement in chemistry new functions either in vitro, in artificial vesicles, or in living cells […]
Mon, Jul 1, 2024
Boolean Networks (BNs) are widely used as a modeling formalism in several domains, notably systems biology and computer science. A fundamental problem in BN analysis is the enumeration of trap spaces, which are hypercubes in the state space that cannot be escaped once entered. Several methods have been proposed for enumerating trap spaces, however they often suffer from scalability and efficiency issues, particularly for large and complex models […]
Thu, Feb 1, 2024
Molecular interaction maps (MIMs) are static graphical representations depicting complex biochemical networks that can be formalized using one of the Systems Biology Graphical Notation languages. Regardless of their extensive coverage of various biological processes, they are limited in terms of dynamic insights. However, MIMs can serve as templates for developing dynamic computational models […]
Thu, Feb 1, 2024
Boolean network modeling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes. The recent use of trap spaces made a real breakthrough in that field allowing to consider medium-sized models that used to be out of reach […]
Fri, Sep 1, 2023
Cancer-associated fibroblasts (CAFs) are amongst the key players of the tumor microenvironment (TME) and are involved in cancer initiation, progression, and resistance to therapy. They exhibit aggressive phenotypes affecting extracellular matrix remodeling, angiogenesis, immune system modulation, tumor growth, and proliferation. CAFs phenotypic changes appear to be associated with metabolic alterations, notably a reverse Warburg effect that may drive fibroblasts transformation […]
Tue, Aug 1, 2023
Boolean Networks (BNs) are an efficient modeling formalism with applications in various research fields such as mathematics, computer science, and more recently systems biology. One crucial problem in the BN research is to enumerate all fixed points, which has been proven crucial in the analysis and control of biological systems. Indeed, in that field, BNs originated from the pioneering work of R […]
Tue, Aug 1, 2023
Abstract Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype […]
Sat, Jul 1, 2023
Rheumatoid Arthritis (RA) is an autoimmune disease characterized by a highly invasive pannus formation consisting mainly of Synovial Fibroblasts (RASFs). This pannus leads to cartilage, bone, and soft tissue destruction in the affected joint. RASFs’ activation is associated with metabolic alterations resulting from dysregulation of extracellular signals’ transduction and gene regulation […]
Thu, Dec 1, 2022
Boolean modelling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. This is even more true for very large models where such data is frequently missing and led to a constant increase in size of logical models à la Thomas. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes […]
Thu, Sep 1, 2022