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A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method is based on translating the structural and…
Known graphical conditions for the generic or global convergence to equilibria of the dynamical system arising from a reaction network are shown to be invariant under the so-called successive removal of intermediates, a systematic procedure…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination…
The standard analysis of reaction networks based on deterministic rate equations fails in confined geometries, commonly encountered in fields such as astrochemistry, thin film growth and cell biology. In these systems the small reactant…
We propose a novel method of reconstructing the topology and interaction functions for a general oscillator network. An ensemble of initial phases and the corresponding instantaneous frequencies is constructed by repeating random…
We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
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…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…