Biochemical reaction systems in a cell exhibit stochastic behaviour, owing to the unpredictable nature of the molecular interactions. The fluctuations at the molecular level may lead to a different behaviour than that predicted by the deterministic m...
Markov chain perturbation theory is a rapidly developing subfield of the theory of stochastic processes. This review outlines emerging applications of this theory in the analysis of stochastic models of chemical reactions, with a particular focus on...
This paper aims to explain the transition to multicellularity as a consequence of the evolutionary response to stress. The proposed model is composed of three parts. The first part details stochastic biochemical kinetics within a reactor (potentially...
The parameter estimation (PE) of biochemical reactions is one of the most challenging tasks in systems biology given the pivotal role of these kinetic constants in driving the behavior of biochemical systems. PE is a non-convex, multi-modal, and non-...
The lymphocytic choriomeningitis virus (LCMV) is a non-cytopathic virus broadly used in fundamental immunology as a mouse model for acute and chronic virus infections. LCMV remains a cause of meningitis in humans, in particular the fatal LCMV infecti...
This paper analyses several mathematical games developed 50 years ago by Manfred Eigen and Ruthild Winkler in their famous book “Laws of the Game: How the Principles of Nature Govern Chance,” published for the first time in German in 1975...
Replication of Human Immunodeficiency Virus type 1 (HIV) in infected CD4+ T cells represents a key driver of HIV infection. The HIV life cycle is characterised by the heterogeneity of infected cells with respect to multiplicity of infection and the v...
The single-cell RNA-seq allows exploring the transcriptome for one cell at a time. By doing so, cellular regulation is pictured. One limitation is the dropout events phenomenon, where a gene is observed at a low or moderate expression level in one ce...
Minimal artificial cells (MACs) are self-assembled chemical systems able to mimic the behavior of living cells at a minimal level, i.e. to exhibit self-maintenance, self-reproduction and the capability of evolution. The bottom-up approach to the con...