Molecular Networks
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Deterministic reaction networks (RNs) are tools to model diverse biological phenomena characterized by particle systems, when there are abundant number of particles. Examples include but are not limited to biochemistry, molecular biology,…
Alterations in the human gut bacteriome can be associated with human health issues, such as type-2 diabetes and cardiovascular disease. Both external and internal factors can drive changes in the composition and in the interactions of the…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species $X$ catalyzes its own formation. From the perspective of chemical kinetics, autocatalysts show a regime of super-linear growth. Given a…
We consider the problem of binomiality of the steady state ideals of biochemical reaction networks. We are interested in finding polynomial conditions on the parameters such that the steady state ideal of a chemical reaction network is…
We study real steady state varieties of the dynamics of chemical reaction networks. The dynamics are derived using mass action kinetics with parametric reaction rates. The models studied are not inherently parametric in nature. Rather, our…
We consider the problem of testing whether the points in a complex or real variety with non-zero coordinates form a multiplicative group or, more generally, a coset of a multiplicative group. For the coset case, we study the notion of…
Does regulation in the genome use collective behavior, similar to the way the brain or deep neural networks operate? Here I make the case for why having a genomic network capable of a high level of computation would be strongly selected…
The dynamics of a mathematical model of the Calvin cycle, which is part of photosynthesis, is analysed. Since diffusion of ATP is included in the model a system of reaction-diffusion equations is obtained. It is proved that for a suitable…
Kinetic models of biochemical systems used in the modern literature often contain hundreds or even thousands of variables. While these models are convenient for detailed simulations, their size is often an obstacle to deriving mechanistic…
To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein-protein interaction networks integrating…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
Gene regulatory networks are comprised of biochemical reactions, which are inherently stochastic. Each reaction channel contributes to this stochasticity in different measure. In this paper we study the stochastic dynamics of protein…
Biological processes at the cellular level are stochastic in nature, and the immune response system is no different. Therefore, models that attempt to explain this system need to also incorporate noise or fluctuations that can account for…
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…
Stochastic reaction networks are a fundamental model to describe interactions between species where random fluctuations are relevant. The master equation provides the evolution of the probability distribution across the discrete state space…
Healthy human prostate epithelial cells have the unique ability to produce and secrete large amounts of citrate into the lumen of the prostate. Citrate is a Krebs cycle metabolite produced in the condensation reaction between acetyl-CoA and…
The novelty of new human coronavirus COVID-19/SARS-CoV-2 and the lack of effective drugs and vaccines gave rise to a wide variety of strategies employed to fight this worldwide pandemic. Many of these strategies rely on the repositioning of…