Molecular Networks
Cold atmospheric plasma (CAP) is a promising new agent for (selective) cancer treatment, but the underlying cause of the anti-cancer effect of CAP is not well understood yet. Among different theories and observations, one theory in…
The multiple futile cycle is a phosphorylation system in which a molecular substrate might be phosphorylated sequentially n times by means of an enzymatic mechanism. The system has been studied mathematically using reaction network theory…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…
We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven…
This document compares SRI's Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways. The…
We present a highly efficient and accurate hybrid stochastic simulation algorithm (HSSA) for the purpose of simulating a subset of biochemical reactions of large gene regulatory networks (GRN). The algorithm relies on the separability of a…
An incoherent feed-forward loop (IFFL) is a network motif known for its ability to accelerate responses and generate pulses. Though functions of IFFLs are well studied, most previous computational analysis of IFFLs used ordinary…
We consider the stochastic gene expression process with inter-state flip-flops. An exact steady-state solution to the master equation is calculated. One of the main goals in this paper is to investigate whether the probability distribution…
Eukaryotic cells transmit extracellular signal information to cellular interiors through the formation of a ternary complex made up of a ligand (or agonist), G-protein, and G-protein coupled receptor (GPCR). Previously formalized theories…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
Biological network alignment (NA) aims to find a node mapping between species' molecular networks that uncovers similar network regions, thus allowing for transfer of functional knowledge between the aligned nodes. However, current NA…
We consider a model of extracellular signal-regulated kinase (ERK) regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but loses these properties in the limit in which the mechanisms…
In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior,…