Related papers: Differential Analysis of Microbial Interaction Net…
Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…
Learning the structure of Bayesian networks from data provides insights into underlying processes and the causal relationships that generate the data, but its usefulness depends on the homogeneity of the data population, a condition often…
To simplify mathematical models of disease spread, we often assume equal contact rates among hosts, but real-world scenarios differ. Network-based frameworks help capture these complexities and structural variations in actual systems. We…
Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…
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…
Reconstructing network connectivity from the collective dynamics of a system typically requires access to its complete continuous-time evolution although these are often experimentally inaccessible. Here we propose a theory for revealing…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the behaviour of individual populations. This process is driven by the cross-feeding networks that structure these communities,…
This paper investigates the dynamics of infectious diseases with a non-exponentially distributed infectious period. This is achieved by considering a multi-stage infection model on networks. Using pairwise approximation with a standard…
We consider multiple diseases spreading in a static Configuration Model network. We make standard assumptions that infection transmits from neighbor to neighbor at a disease-specific rate and infected individuals recover at a…
Biochemistry, ecology, and neuroscience are examples of prominent fields aiming at describing interacting systems that exhibit non-trivial couplings to complex, ever-changing environments. We have recently shown that linear interactions and…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
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…
We develop a new ensemble of modular random graphs in which degree-degree correlations can be different in each module and the inter-module connections are defined by the joint degree-degree distribution of nodes for each pair of modules.…
Recent work in modeling the coupling between disease dynamics and dynamic social network geometry has led to the examination of how human interactions force a rewiring of connections in a population. Rewiring of the network may be…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…