Related papers: Inferring resource competition in microbial commun…
Many systems can be described using graphs, or networks. Detecting communities in these networks can provide information about the underlying structure and functioning of the original systems. Yet this detection is a complex task and a…
Understanding the pattern formation in communities has been at the center of attention in various fields. Here we introduce a novel model, called an "information-particle model," which is based on the reaction-diffusion model and the…
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…
Many natural patterns, such as the distributions of blood particles in a blood sample, proteins on cell surfaces, biological populations in their habitat, galaxies in the universe, the sequence of human genes, and the fitness in…
Foraging is a widespread behavior, and being part of a group may bring several benefits compared to solitary foraging, such as collective pooling of information and reducing environmental uncertainty. Often theoretical models of collective…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
An outstanding open problem is whether collective social phenomena occurring over short timescales can systematically reduce cultural heterogeneity in the long run, and whether offline and online human interactions contribute differently to…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
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…
Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist…
Discrete time, spatially extended models play an important role in ecology, modelling population dynamics of species ranging from micro-organisms to birds. An important question is how 'bottom up', individual-based models can be…
The \emph{community}, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal…
In this paper we address the problem of inferring social structure and dominance relationships in a group of rhesus macaques (a species of monkey) using only position data captured using RFID tags. Automatic inference of the social…
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of…
We discuss a set of computational techniques, called Inductive Game Theory, for extracting strategic decision-making rules from time series data and constructing probabilistic social circuits. We construct these circuits by connecting…
The analysis of multilayer networks is among the most active areas of network science, and there are now several methods to detect dense "communities" of nodes in multilayer networks. One way to define a community is as a set of nodes that…
Collective systems that self-organise to maximise the group's ability to collect and distribute information can be successful in environments with high spatial and temporal variation. Such organisations are abundant in nature, as sharing…
This is the second of two papers dedicated to the relationship between population models of competition and biodiversity. Here we consider species assembly models where the population dynamics is kept far from fixed points through the…
In any ecosystem, the conditions of the environment and the characteristics of the species that inhabit it are entangled, co-evolving in space and time. We introduce a model that couples active agents with a dynamic environment, interpreted…
Organisms adapt to volatile environments by integrating sensory information with internal memory, yet their information processing is constrained by resource limitations. Such limitations can fundamentally alter optimal estimation…