Related papers: Inferring microbial interactions with their enviro…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
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…
In this work, we introduce a computational model for the study of the host-bacteria interaction and the influence of the intestinal microbiota on the behavior and feeding pattern of an individual. The model is based on digital entities,…
Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
When making predictions about ecosystems, we often have available a number of different ecosystem models that attempt to represent their dynamics in a detailed mechanistic way. Each of these can be used as simulators of large-scale…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Alterations in the human gut bacteriome can be associated with human health issues, such as type-2 diabetes and cardiovascular disease. Both external and internal factors can drive changes in the composition and in the interactions of the…
Swarm robotics has potential for a wide variety of applications, but real-world deployments remain rare due to the difficulty of predicting emergent behaviors arising from simple local interactions. Traditional engineering approaches design…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The metabolism of an organism is regulated at the cellular level, yet is strongly influenced by its environment. The precise metabolomic study of living organisms is currently hampered by measurement sensitivity: most metabolomic…
Metabolic networks are complex systems that comprise hundreds of chemical reactions which synthesize biomass molecules from chemicals in an organism's environment. The metabolic network of any one organism is encoded by a metabolic…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods.…
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…
Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to…