Related papers: Differential Analysis of Microbial Interaction Net…

One important problem in microbiome analysis is to identify the bacterial taxa that are associated with a response, where the microbiome data are summarized as the composition of the bacterial taxa at different taxonomic levels. This paper…

Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…

It is a fundamental challenge to understand how the function of a network is related to its structural organization. Adaptive dynamical networks represent a broad class of systems that can change their connectivity over time depending on…

With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…

Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades,…

Networked systems that occur in various domains, such as the power grid, the brain, and opinion networks, are known to obey conservation laws. For instance, electric networks obey Kirchoff's laws, and social networks display opinion…

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…

We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…

Digital networks have profoundly transformed the ways in which individuals interact, exchange information, and establish connections, leading to the emergence of phenomena such as virality, misinformation cascades, and online polarization.…

Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…

The study of how diseases spread has greatly benefited from advances in network modeling. Recently, a class of networks known as multilayer graphs has been shown to describe more accurately many real systems, making it possible to address…

The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…

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…

Many natural systems are organized as networks, in which the nodes (be they cells, individuals or populations) interact in a time-dependent fashion. The dynamic behavior of these networks depends on how these nodes are connected, which can…

In many complex systems, the dynamic processes that take place on a network and the changes in the network topology are intertwined. Here, we propose a model of coevolutionary dynamics of information spreading which is accompanied with link…

Interactions between units in phyical, biological, technological, and social systems usually give rise to intrincate networks with non-trivial structure, which critically affects the dynamics and properties of the system. The focus of most…

Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…

We predict disease-genes relations on the Human Interactome network using a methodology that jointly learns functional and connectivity patterns surrounding proteins. Contrary to other data structures, the Interactome is characterized by…

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…