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The generalized Lotka-Volterra (gLV) equations, a classic model from theoretical ecology, describe the population dynamics of a set of interacting species. As the number of species in these systems grow in number, their dynamics become…
The generalized Lotka-Volterra (gLV) equations model the microbiome as a collection of interacting ecological species. Here we use a particular experimentally-derived gLV model of C. difficile infection (CDI) as a case study to generate…
The state space is a fundamental concept for describing the trajectory of a dynamic system. Depending on its form, it can highlight certain changes over time while ignoring others. This is particularly the case for the spaces associated…
Inferring microbial community structure based on temporal metagenomics data is an important goal in microbiome studies. The deterministic generalized Lotka-Volterra differential (GLV) equations have been used to model the dynamics of…
Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalised medicine. The generalised Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and…
Classical approaches to ecological stability rely on fully connected interaction models, yet real ecosystems are sparse and structured--a feature that qualitatively reshapes their collective dynamics. Here, we establish a thermodynamically…
Species-rich ecosystems often exhibit multiple stable states with distinct species compositions. Yet, the factors determining the likelihood of each state's occurrence remain poorly understood. Here, we characterize and explain the…
Ecological resilience refers to the ability of a system to retain its state when subject to state variables perturbations or parameter changes. While understanding and quantifying resilience is crucial to anticipate the possible regime…
The generalized Lotka-Volterra (GLV) equations with quenched random interactions have been extensively used to investigate the stability and dynamics of complex ecosystems. However, the standard linear interaction model suffers from…
We investigate the outcome of generalised Lotka-Volterra dynamics of ecological communities with random interaction coefficients and non-linear feedback. We show in simulations that the saturation of non-linear feedback stabilises the…
Changes in environmental or system parameters often drive major biological transitions, including ecosystem collapse, disease outbreaks, and tumor development. Analyzing the stability of steady states in dynamical systems provides critical…
Compositional data, where only relative abundances are available, are common in microbiome and other high-throughput sequencing studies. Log ratios between groups of variables serve as key biomarkers in these settings. However, selecting…
How do interactions between species influence their spatial distribution in an ecosystem? To answer this question, we introduce a spatially-extended ecosystem of Generalized Lotka-Volterra type, where species can diffuse and interactions…
Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential…
Recent advances in metagenomics have revealed macroecological patterns or "laws" describing robust statistical regularities across microbial communities. Stochastic logistic models (SLMs), which treat species as independent -- akin to ideal…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
In this work we study the stability of the equilibria reached by ecosystems formed by a large number of species. The model we focus on are Lotka-Volterra equations with symmetric random interactions. Our theoretical analysis, confirmed by…
Ecological systems are governed by complex interactions which are mainly nonlinear. In order to capture this complexity and nonlinearity, statistical models recently gained popularity. However, although these models are commonly applied in…
For years, a main focus of ecological research has been to better understand the complex dynamical interactions between species which comprise food webs. Using the connectance properties of a widely explored synthetic food web called the…
Stochastic, spatially extended models for predator-prey interaction display spatio-temporal structures that are not captured by the Lotka-Volterra mean-field rate equations. These spreading activity fronts reflect persistent correlations…