Related papers: Using micro- and macro-level network metrics unvei…
Nowadays, epidemic models provide an appropriate tool for describing the propagation of biological viruses in human or animal populations, or rumours and other kinds of information in social networks and malware in both computer and ad hoc…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
Propagation of contagion in networks depends on the graph topology. This paper is concerned with studying the time-asymptotic behavior of the extended contact processes on static, undirected, finite-size networks. This is a contact process…
Inter neuron communication happens through the exchange of neurotransmitters at the synapse by a process known as exocytosis. This makes exocytosis a fundamental process of information exchange in the body. The exocytosis process has a…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
Understanding the modular structure and central elements of complex biological networks is critical for uncovering system-level mechanisms in disease. Here, we constructed weighted gene co-expression networks from bulk RNA-seq data of…
Under many physiological and pathological conditions such as division and migration, cells undergo dramatic deformations, under which their mechanical integrity is supported by cytoskeletal networks (i.e. intermediate filaments, F-actin,…
Immune cells coordinate their efforts for the correct and efficient functioning of the immune system (IS). Each cell type plays a distinct role and communicates with other cell types through mediators such as cytokines, chemokines and…
We seek to identify genes involved in Parkinson's Disease (PD) by combining information across different experiment types. Each experiment, taken individually, may contain too little information to distinguish some important genes from…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
Approaches to gene interactions based on sign epistasis have been highly influential in recent time. Sign epistasis is useful for relating local and global properties of fitness landscapes, as well as for analyzing evolutionary trajectories…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
The history of infections and epidemics holds famous examples where understanding, containing and ultimately treating an outbreak began with understanding its mode of spread. Influenza, HIV and most computer viruses, spread person to…
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…
Understanding the complex relationships of biomarkers in diabetes is pivotal for advancing treatment strategies, a pressing need in diabetes research. This study applies Bayesian network structure learning to analyze the Shanghai Type 1 and…
Genetic interactions play an important role in the progression of complex diseases, providing explanation of variations in disease phenotype missed by main genetic effects. Comparatively, there are fewer investigations on prognostic…
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…
Parkinsons disease (PD) is a movement disorder and the second most common neurodengerative disease but despite its relative abundance, there are no clinically accepted neuroimaging biomarkers to make prognostic predictions or differentiate…