Related papers: Method for finding metabolic properties based on t…
Understanding the links between diet, metabolic changes, and health outcomes is a key focus in nutritional science and broader biological research. Analyzing relationships, such as those between ultra-processed food (UPF) intake and…
Many natural patterns, such as the distributions of blood particles in a blood sample, proteins on cell surfaces, biological populations in their habitat, galaxies in the universe, the sequence of human genes, and the fitness in…
I consider how cell shape and environmental geometry affect the rate of nutrient capture and the consequent maximum growth rate of a cell, focusing on rod-like species like \textit{E.\ coli}. Simple modeling immediately implies that it is…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
We consider a general growth mechanism, which acts at cellular level and above (organs, systems and whole organisms). Using its mathematical representation, the growth equation, we study the growth and division mechanisms of amoeba and…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a…
Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental…
We present and critically discuss five commonly used mathematical models of the meal glucose rate of appearance in humans. Such models are key to simulation of the metabolism in healthy people, people with diabetes, and obese people, and…
This study develops a Bayesian semi-parametric model to examine the longitudinal growth and appetite phenotypes in children from the GUSTO cohort, with a focus on understanding the relationship between eating behaviours and growth outcomes…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
Background: Information processing in the brain requires large amounts of metabolic energy, the spatial distribution of which is highly heterogeneous reflecting complex activity patterns in the mammalian brain. Results: Here, it is found…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
Cancer cells are often seen to prefer glycolytic metabolism over oxidative phosphorylation even in the presence of oxygen-a phenomenon termed the Warburg effect. Despite significant strides in the decades since its discovery, a clear basis…
Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based…
In earlier work, we introduced a discrete Fibonacci-based ontogenetic model in which the metabolic scaling exponent $b(n)$ is treated as a dynamic function of an organism's developmental stage, and we estimated $b(n)$ for selected mammalian…
Complex networks, modeled as large graphs, received much attention during these last years. However, data on such networks is only available through intricate measurement procedures. Until recently, most studies assumed that these…