Related papers: Microbial correlation: a semi-parametric model for…
A biological pathway represents a set of genes that serves a particular cellular or a physiological function. The genes within the same pathway are expected to function together and hence may interact with each other. It is also known that…
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…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
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…
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While…
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…
Biological sequencing data consist of read counts, e.g. of specified taxa and often exhibit sparsity (zero-count inflation) and overdispersion (extra-Poisson variability). As most sequencing techniques provide an arbitrary total count,…
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…
The role of the microbiome in disease pathogenesis is an emerging field with strong evidence suggesting that dysbiosis is associated with precancerous and cancerous states. Microbiome data present substantial challenges for causal mediation…
The gut microbiome significantly influences responses to cancer therapies, including immunotherapies, primarily through its impact on the metabolome. Despite some studies on effects of specific microbial genera on individual metabolites,…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…
Motivation: There is a growing need to integrate mechanistic models of biological processes with computational methods in healthcare in order to improve prediction. We apply data assimilation in the context of Type 2 diabetes to understand…