Related papers: Inferring resource competition in microbial commun…

The collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained…

Resource are often not uniformly distributed within a population. Spatial variations of concentration of a resource, change the fitness of competing strategies locally. The notion of fitness varying with respect to both genotype and…

In many biological systems, natural selection acts simultaneously on multiple levels of organization. This scenario typically presents an evolutionary conflict between the incentive of individuals to cheat and the collective incentive to…

Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…

We study a model of competition for resource through a chemostat-type model where species consume the common resource that is constantly supplied. We assume that the species and resources are characterized by a continuous trait. As already…

Explaining biodiversity is a fundamental issue in ecology. A long-standing puzzle lies in the paradox of the plankton: many species of plankton feeding on a limited variety of resources coexist, apparently flouting the competitive exclusion…

Habitat fragmentation, often driven by human activities, alters ecological landscapes by disrupting connectivity and reshaping species interactions. In such fragmented environments, habitats can be modeled as networks, where individuals…

Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…

We develop a trait-based model founded on the hypothesis that biological systems evolve and organize to maximize entropy production by dissipating chemical and electromagnetic potentials over longer time scales than abiotic processes by…

Collective sensing is an emergent phenomenon which enables individuals to estimate a hidden property of the environment through the observation of social interactions. Previous work on collective sensing shows that gregarious individuals…

The dynamics of dispersal-structured populations, consisting of competing individuals that are characterized by different diffusion coefficients but are otherwise identical, is investigated. Competition is taken into account through…

The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…

Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…

The far-reaching consequences of ecological interactions in the dynamics of biological communities remain an intriguing subject. For decades, competition has been a cornerstone in ecological processes, but mounting evidence shows that…

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical…

Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…

Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of…

Community detection and hierarchy extraction are usually thought of as separate inference tasks on networks. Considering only one of the two when studying real-world data can be an oversimplification. In this work, we present a generative…

Range migrations in response to climate change, invasive species and the emergence of novel ecosystems highlight the importance of temporal turnover in community composition as a fundamental part of global change in the Anthropocene.…

Networks built to model real world phenomena are characeterised by some properties that have attracted the attention of the scientific community: (i) they are organised according to community structure and (ii) their structure evolves with…