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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…
1. In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Networks are widely used in the biological, physical, and social sciences as a concise mathematical representation of the topology of systems of interacting components. Understanding the structure of these networks is one of the outstanding…
In this paper, we study an adaptive spatial network. We consider an SIS (susceptible-infectedsusceptible) epidemic on the network, with a link/contact rewiring process constrained by spatial proximity. In particular, we assume that…
Hierarchically modular organization is a canonical network topology that is evolutionarily conserved in the nervous systems of animals. Within the network, neurons form directional connections defined by the growth of their axonal…
Causal effect estimation in networked systems is central to data-driven decision making. In such settings, interventions on one unit can spill over to others, and in complex physical or social systems, the interaction pathways driving these…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Network reconstruction is fundamental to understanding the dynamical behaviors of the networked systems. Many systems, modeled by multiplex networks with various types of interactions, display an entirely different dynamical behavior…
Many studies have been performed to characterize the dynamics and stability of the microbiome across a range of environmental contexts [Costello et al., 2012, Faust et al., 2015]. For example, it is often of interest to identify time…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Epidemics on complex networks is a widely investigated topic in the last few years, mainly due to the last pandemic events. Usually, real contact networks are dynamic, hence much effort has been invested in studying epidemics on evolving…
In many epidemiological and ecological contexts, there is a trade-off between infections and interactions. This arises because the links between individuals capable of spreading infections are also often associated with beneficial…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…