Related papers: Alignment of metabolic trajectories with applicati…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
This paper serves as a framework for designing advanced models for drug action on metabolism. Drug treatment may affect metabolism by either enhancing or inhibiting metabolic reactions comprising a metabolic network. We introduce the…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
With advances in high-resolution mass spectrometry technologies, metabolomics data are increasingly used to investigate biological mechanisms underlying associations between exposures and health outcomes in clinical and epidemiological…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…
A simple model is studied for the chemotactic movement of biological cells in the presence of a periodic chemical wave. It incorporates the feature of adaptation that may play an important role in allowing for ``rectified" chemotaxis:…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
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…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
Treatment of cancer involves heterogeneous, complex care pathways. The relationship between these longitudinal trajectories, baseline mental health, and prognostic outcomes remains poorly understood. We introduce an interpretable…
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
The goal of personalized decision making is to map a unit's characteristics to an action tailored to maximize the expected outcome for that unit. Obtaining high-quality mappings of this type is the goal of the dynamic regime literature. In…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can…