Molecular Networks
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of…
Deciding whether and where a system of parametrized ordinary differential equations displays bistability, that is, has at least two asymptotically stable steady states for some choice of parameters, is a hard problem. For systems modeling…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Gene expression is a random or noisy process. The process consists of several random events among which the reinitiation of transcription by RNAP is an important one. The RNAP molecules can bind the gene only after the promoter gets…
The amyloid $\beta$ peptide (A$\beta$42), whose aggregation is associated with Alzheimer's disease, is an amphiphatic peptide with a high propensity to self-assemble. A$\beta$42 has a net negative charge at physiological pH and modulations…
The current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by researchers globally with the aim of resolving this disruptive crisis. This investigation process…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Directed protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network.…
SARS-CoV-2 coronavirus infection is mediated by the binding of its spike protein to the angiotensin-converting enzyme 2 (ACE2), which plays a pivotal role in the renin-angiotensin system (RAS). The study of RAS dysregulation due to…
Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…
Oscillations play a major role in a number of biological systems, from predator-prey models of ecology to circadian clocks. In this paper we focus on the question of whether oscillations exist within dual-site phosphorylation systems.…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…
In a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
In a molecular communication network, transmitters and receivers communicate by using signalling molecules. At the receivers, the signalling molecules react, via a chain of chemical reactions, to produce output molecules. The counts of…
Non-genetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong…
We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a…
Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. It was first identified in Wuhan, China, and has since spread causing a global pandemic. Various studies have been performed to understand the…
Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…