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Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics…
Network science plays an increasingly important role to model complex data in many scientific disciplines. One notable feature of network organization is community structure, which refers to clusters of tightly interconnected nodes. A…
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these…
Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
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…
The effects of climate change, urbanisation and agriculture are changing the way insects occupy habitats. Some species may utilise anthropogenic microhabitat features for their existence, either because they prefer them to natural features,…
Microbiome interventions provide valuable data about microbial ecosystem structure and dynamics. Despite their ubiquity in microbiome research, few rigorous data analysis approaches are available. In this study, we extend transfer…
The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Networks can model real-world systems in a variety of domains. Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology,…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to…
Temporal (or time-evolving) networks are commonly used to model complex systems and the evolution of their components throughout time. Although these networks can be analyzed by different means, visual analytics stands out as an effective…
Social media and social networks have already woven themselves into the very fabric of everyday life. This results in a dramatic increase of social data capturing various relations between the users and their associated artifacts, both in…
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
Real-world complex systems such as ecological communities and neuron networks are essential parts of our everyday lives. These systems are composed of units which interact through intricate networks. The ability to predict sudden changes in…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…