Related papers: Differential Analysis of Microbial Interaction Net…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
The modeling of the spreading of communicable diseases has experienced significant advances in the last two decades or so. This has been possible due to the proliferation of data and the development of new methods to gather, mine and…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…
Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
Contagion processes, representing the spread of infectious diseases, information, or social behaviors, are often schematized as taking place on networks, which encode for instance the interactions between individuals. The impact of the…
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…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
In this article we develop a highly integrated effective degree approach to modeling epidemic and awareness spreading processes on multiplex networks coupled with awareness-dependent adaptive rewiring. This approach keeps track of the…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
We investigate structural transitions in adaptive networks where node states remain fixed and only the connections evolve via state-dependent rewiring. Using a general framework characterized by probabilistic rules for disconnection and…
Inflammatory bowel diseases (IBD) are complex diseases in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when they are exposed to yet unclear environmental factors. The complexity of this class…
Many networks are important because they are substrates for dynamical systems, and their pattern of functional connectivity can itself be dynamic -- they can functionally reorganize, even if their underlying anatomical structure remains…
Models of disease spreading are critical for predicting infection growth in a population and evaluating public health policies. However, standard models typically represent the dynamics of disease transmission between individuals using…