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Understanding complex interactions within microbiomes is essential for exploring their roles in health and disease. However, constructing reliable microbiome networks often poses a challenge due to variations in the output of different…

An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…

More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…

Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…

Previous work has shown that species interacting in an ecosystem and actors transacting in an economic context may have notable similarities in behavior. However, the specific mechanism that may underlie similarities in nature and human…

Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…

Interactive networks representing user participation and interactions in specific "events" are highly dynamic, with communities reflecting collective behaviors that evolve over time. Predicting these community evolutions is crucial for…

In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant…

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving…

A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…

Community structure exists in many real-world networks and has been reported being related to several functional properties of the networks. The conventional approach was partitioning nodes into communities, while some recent studies start…

Ranking nodes in networks according to a defined measure of importance is an extensively studied task, with applications in ecology, economic trade networks, and social networks. This paper introduces a method based on a non-linear…

The gut microbiome, crucial for human health, presents challenges in analyzing its complex metaomic data due to high dimensionality and sparsity. Traditional methods struggle to capture its intricate relationships. We investigate graph…

Communities are not static; they evolve, split and merge, appear and disappear, i.e. they are product of dynamical processes that govern the evolution of the network. A good algorithm for community detection should not only quantify the…

Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…

Encounter-based network is a frequently-disconnected wireless ad-hoc network requiring immediate neighbors to store and forward aggregated data for information disseminations. Using traditional approaches such as gateways or firewalls for…

Community detection algorithms are fundamental tools that allow us to uncover organizational principles in networks. When detecting communities, there are two possible sources of information one can use: the network structure, and the…

The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…

Social networks existing among employees, customers or users of various IT systems have become one of the research areas of growing importance. A social network consists of nodes - social entities and edges linking pairs of nodes. In…