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Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a…
In this paper, models of the blood glucose (BG) dynamics in people with Type 1 diabetes (T1D) in response to moderate intensity aerobic activity are derived from physiology-based first principles and system identification experiments. We…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
Recent experiments have revealed that cytoplasms become glassy when their metabolism is suppressed, while they maintain fluidity in a living state. The mechanism of this active fluidization is not clear, especially for bacterial cytoplasms,…
The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine learning based biomarker development for multiple diseases and conditions. The microbiome is often analyzed…
Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and its associated malodour impacts the quality of life for many women. Clinical diagnosis primarily relies on microscopy to presumptively detect a…
The human microbiome has an important role in determining health. Mediation analyses quantify the contribution of the microbiome in the causal path between exposure and disease; however, current mediation models cannot fully capture the…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
As one of the most prevalent diseases worldwide, plaque formation in human arteries, known as atherosclerosis, is the focus of many research efforts. Previously, molecular communication (MC) models have been proposed to capture and analyze…
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…
With advances in high-resolution mass spectrometry technologies, metabolomics data are increasingly used to investigate biological mechanisms underlying associations between exposures and health outcomes in clinical and epidemiological…
More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…
Here we describe an "information based exchange" model of brain function that ascribes to neocortex, basal ganglia, and thalamus distinct network functions. The model allows us to analyze whole brain system set point measures, such as the…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…