Molecular interaction maps (MIMs) are static graphical representations depicting complex biochemical networks that can be formalized using one of the Systems Biology Graphical …
Introduction The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic …
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 …
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. …
Abstract Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a …
Rheumatoid Arthritis (RA) is an autoimmune disease characterized by a highly invasive pannus formation consisting mainly of Synovial Fibroblasts (RASFs). This pannus leads to …
Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to …
The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses …
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and …
Motivation: Personalized medicine aims at providing patient-tailored therapeutics based on multi-type data towards improved treatment outcomes. Chronotherapy that consists in …
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must …
Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides …
Biochemical reaction networks are one of the most widely used formalism in systems biology to describe the molecular mechanisms of high-level cell processes. However modellers …
Thomas's necessary conditions for the existence of multiple steady states in gene networks have been proved by Soulé with high generality for dynamical systems defined by …
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the …
In Mathematical Biology, many dynamical models of biochemical reaction systems are presented with Ordinary Differential Equations (ODE). Once kinetic parameter values are fixed, …
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing …
In this paper we study the problem of deciding the existence of a subgraph epimorphism between two graphs. Our interest in this variant of graph matching problem stems from the …