Related papers: Ecology theory disentangles microbial dichotomies
We introduce a new model for large scale evolution and extinction in which species are organized into food chains. The system evolves by two processes: origination/speciation and extinction. In the model, extinction of a given species can…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
The living organism is considered as an open system, whereas Prigogine's approach to the thermodynamics of such systems is used. The approach allows one to formulate the law of individual growth and development (ontogenesis) of the living…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
The coupling between evolutionary and ecological changes (eco-evolutionary dynamics) has been shown to be relevant among diverse species, and is also of interest outside of ecology, i.e. in cancer evolution. These dynamics play an important…
What makes living things special is how they manage matter, energy, and entropy. A general theory of organismal metabolism should therefore be quantified in these three currencies while capturing the unique way they flow between individuals…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an…
The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by…
Species coexistence is one of the central themes in modern ecology. Coexistence is a prerequisite of biological diversity. However, the question arises how biodiversity can be reconciled with the statement of competition theory, which…
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose…
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose,…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others.…
We introduce a simple computational model that, with a microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the so generated evolutionary tree…
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…
Modeling of growth (or decay) curves arises in many fields such as microbiology, epidemiology, marketing, and econometrics. Parametric forms like Logistic and Gompertz are often used for modeling such monotonic patterns. While useful for…
Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using game theory with parameters renormalized by diffusion. Contrary to…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…