Related papers: Method for finding metabolic properties based on t…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Weights of edges and nodes on food webs which are available from the empirical data hide much information about energy flows and biomass distributions in ecosystem. We define a set of variables related to weights for each species $i$,…
An extensive rewiring of cell metabolism supports enhanced proliferation in cancer cells. We propose a systems level approach to describe this phenomenon based on Flux Balance Analysis (FBA). The approach does not explicit a cell biomass…
The growth function of populations is central in biomathematics. The main dogma is the existence of density dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the population. One important…
We incorporate the generic hierarchical architecture of foodwebs into a "{\it unified}" model that describes both "micro" and "macro" evolutions within a single theoretical framework. This model describes the "micro" -evolution in detail by…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Probabilistic biological network growth models have been utilized for many tasks including but not limited to capturing mechanism and dynamics of biological growth activities, null model representation, capturing anomalies, etc. Well-known…
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…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
We examine the scaling law $B \propto M^{\alpha}$ which connects organismal metabolic rate $B$ with organismal mass $M$, where $\alpha$ is commonly held to be 3/4. Since simple dimensional analysis suggests $\alpha=2/3$, we consider this to…
Cell lineage statistics is a powerful tool for inferring cellular parameters, such as division rate, death rate or the population growth rate. Yet, in practice such an analysis suffers from a basic problem: how should we treat incomplete…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
A principle of evolutionary adaptation is applied to the Lotka--Volterra models, in particular to the food webs. We present a relatively simple computational algorithm of optimization with respect to a given criterion. This algorithm boils…
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…
The UK Biobank Imaging Study has acquired medical scans of more than 40,000 volunteer participants. The resulting wealth of anatomical information has been made available for research, together with extensive metadata including measurements…
Collective cellular movement plays a crucial role in many processes fundamental to health, including development, reproduction, infection, wound healing, and cancer. The emergent dynamics that arise in these systems are typically thought to…
Complex systems, in many different scientific sectors, show coarse-grain properties with simple growth laws with respect to fundamental microscopic algorithms. We propose a classification scheme of growth laws which includes human aging,…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…