相关论文: A mechanistic model of disjunctive metabolic symbi…

A hallmark of living systems is the ability to employ a common set of versatile building blocks that can self-organize into a multitude of different structures, in a way that can be controlled with minimal cost. This capability can only be…

If one isolated species (corporation) is supposed to evolve following the logistic mapping, then we are tempted to think that the dynamics of two species (corporations) can be expressed by a coupled system of two discrete logistic…

Mutualistic networks have attracted increasing attention in the ecological literature in the last decades as they play a key role in the maintenance of biodiversity. Here, we develop an analytical framework to study the structural stability…

Random non-reciprocal interactions between a large number of conserved densities are shown to enhance the stability of the system towards pattern formation. The enhanced stability is an exact result when the number of species approaches…

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…

In many social mammals, early life social adversity and social integration largely predict individual health, lifespan and reproductive success. Efforts in identifying the physiological mechanisms mediating the relationship between the…

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…

We investigate how the pattern of contacts between species in mutualistic ecosystems is affected by the phylogenetic proximity between the species of each guild. We develop several theoretical tools to measure that effect and we use them to…

Detecting associations between microbial compositions and sample characteristics is one of the most important tasks in microbiome studies. Most of the existing methods apply univariate models to single microbial species separately, with…

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 ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…

The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…

Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over non-motile cells. Since motility is energetically costly, cells must optimize their swimming speed and…

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…

To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…

Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…

We study molecular dynamics within populations of diffusively coupled cells under the assumption of fast diffusive exchange. As a technical tool, we propose conditions on boundedness and ultimate boundedness for systems with a singular…

Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…

Starting from common assumptions, we build a rate equation model for multi-strain disease dynamics in terms of immune repertoire classes. We then move to a strain-level description where a low-order closure reminiscent of a pair…

In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…