Molecular Networks
Background: Radiation-induced leukopenia caused by low-dose exposure is frequently associated with Traditional Chinese Medicine (TCM) syndromes like "blood deficiency" and "fatigue syndrome". Ci Bai Capsule (CB) has been reported to enhance…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…
Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation.…
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…
We introduce the boundary reproduction number, adapted from the next generation matrix method, to assess whether an infusion of species will persist or become exhausted in a chemical reaction system. Our main contributions are as follows:…
In this essay, we investigate some relations between Chemical Reaction Networks (CRN) and Mathematical Epidemiology (ME) and report on several pleasant surprises which we had simply by putting these two topics together. Firstly, we propose…
Cell sensory transcription networks are the intracellular computation structure that regulates and drives cellular activity. Activity in these networks determines the the cell's ability to adapt to changes in its environment. Resilient…
Trajectory mutual information is frequently used to quantify information transfer in biochemical systems. Tractable solutions of the trajectory mutual information can be obtained via the widely used Linear-Noise Approximation (LNA) using…
The G-protein coupled receptors EP2 and EP4 both transduce the signal of the lipid messenger Prostaglandin E2 (PGE2). Changes in the cell response to PGE2 can have important effects on immunity and development of diseases, however, a…
Mathematical models of living cells have been successively refined with advancements in experimental techniques. A main concern is striking a balance between modelling power and the tractability of the associated mathematical analysis. In…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and…
Biochemical systems are inherently stochastic, particularly those with small-molecule populations. The spatial distribution of molecules plays a critical role and requires the inclusion of spatial coordinates in their analysis. Stochastic…
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities…
Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…
Stochastic fluctuations of molecular abundances are a ubiquitous feature of cellular processes and lead to significant cell-to-cell variability. Recent theoretical work established lower bounds for stochastic fluctuations in cells for broad…
Molecular chirality is critical to biochemical function, but it is unknown when chiral selectivity first became important in the evolutionary transition from geochemistry to biochemistry during the emergence of life. Here, we identify key…
The evolution of chemical reaction networks is often analyzed through kinetic models and energy landscapes, but these approaches fail to capture the deeper structural constraints governing complexity growth. In chemical reaction networks,…
A continuing frustration for origin of life scientists is that abiotic and, by extension, pre-biotic attempts to develop self-sustaining, evolving molecular systems tend to produce more dead-end substances than macromolecular products with…