相关论文: Representation of Dormant and Active Microbial Dyn…

Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…

Marine plankton play a crucial role in carbon storage, oxygen production, global climate, and ecosystem function. Planktonic ecosystems are embedded in a Lagrangian patches of water that are continuously moving, stretching, and diluting.…

An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…

Motility is a ubiquitous feature of microbial life on Earth, and is widely regarded as a promising biosignature candidate. In the search for motile organisms, it is therefore valuable to have rough estimates for the number of such microbes…

Understanding the assembly of ecosystems to estimate the number of species at different spatial scales is a challenging problem. Until now, maximum entropy approaches have lacked the important feature of considering space in an explicit…

Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…

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…

We present a mathematical model based on a system of partial differential equations (PDEs) with cross-diffusion and reaction terms to describe ecological interactions between multiple bacterial species and substrates within microaggregates,…

Thanks to recent technological advances, it is now possible to track with an unprecedented precision and for long periods of time the movement patterns of many living organisms in their habitat. The increasing amount of data available on…

Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal…

Microbial populations in the natural environment are likely to experience growth conditions very different from those of a typical laboratory xperiment. In particular, removal rates of biomass and substrate are unlikely to be balanced under…

The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…

Ecosystem respiration (Reco) represents a major component of the global carbon cycle, and accurate characterization of its dynamics is essential for a comprehensive understanding of ecosystem-climate interactions and the impacts of climate…

High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…

This paper introduces a novel approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from…

The increasing volume of ecologically and biologically relevant data has revealed a wide collection of emergent patterns in living systems. Analyzing different datasets, ranging from metabolic gene-regulatory to species interaction…

Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…

The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also…

Ecologists are interested in modeling the population growth of species in various ecosystems. Studying population dynamics can assist environmental managers in making better decisions for the environment. Traditionally, the sampling of…