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Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
We used a metacommunity of 49 discrete communities of aquatic invertebrates to analyze the dynamical relationship between community and metacommunity species distributions as a test of the neutral theory of biodiversity and biogeography. At…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
Molecular communication between biological entities is a new paradigm in communications. Recently, we studied molecular communication between two nodes formed from synthetic bacteria. Due to high randomness in behavior of bacteria, we used…
We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptake measurements of Synechocystis sp. PCC6803 with a…
Standard models of population dynamics focus on the the interaction, survival, and extinction of the competing species individually. Real ecological systems, however, are characterized by an abundance of species (or strategies, in the…
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…
Motivated by the phenomenology of transport through the Golgi apparatus of cells, we study a multi-species model with boundary injection of one species of particle, interconversion between the different species of particle, and driven…
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.…
The contact process is a simple infection spreading model showcasing an out-of-equilibrium phase transition between a macroscopically active and an inactive phase. Such absorbing state phase transitions are often sensitive to the presence…
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
Levels of sociality in nature vary widely. Some species are solitary; others live in family groups; some form complex multi-family societies. Increased levels of social interaction can allow for the spread of useful innovations and…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
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 built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be…
Indirect effects are powerful influences in ecosystems that may maintain species diversity and alter apparent relationships between species in surprising ways. Here, we applied Network Environ Analysis to 50 empirically-based trophic…
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…
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the…
Complex networks have been successfully used to describe the spread of diseases in populations of interacting individuals. Conversely, pairwise interactions are often not enough to characterize social contagion processes such as opinion…