Related papers: Microbial correlation: a semi-parametric model for…
Quantification of microbial interactions from 16S rRNA and meta-genomic sequencing data is difficult due to their sparse nature, as well as the fact that the data only provides measures of relative abundance. In this paper, we propose using…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
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…
Contamination of water resources with pathogenic microorganisms excreted in human feces is a worldwide public health concern. Surveillance of fecal contamination is commonly performed by routine monitoring for a single type or a few types…
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…
Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These…
The human gastrointestinal tract is an environment that hosts an ecosystem of microorganisms essential to human health. Vital biological processes emerge from fundamental inter- and intra-species molecular interactions that influence the…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
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…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
We consider the complex data modeling problem motivated by the zero-inflated and overdispersed data from microbiome studies. Analyzing how microbiome abundance is associated with human biological features, such as BMI, is of great…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
Effective dietary monitoring is critical for managing Type 2 diabetes, yet accurately estimating caloric intake remains a major challenge. While continuous glucose monitors (CGMs) offer valuable physiological data, they often fall short in…
The human gut microbiota is a complex ecosystem that affects a range of human physiology. In order to explore the dynamics of the human gut microbiota, we used a system of ordinary differential equations to model mathematically the biomass…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
Many diseases are considered to be closely related to the changes in the gut microbial community, including colorectal cancer (CRC), which is one of the most common cancers in the world. The diagnostic classification and etiological…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Quantifying the relation between gut microbiome and body weight can provide insights into personalized strategies for improving digestive health. In this paper, we present an algorithm that predicts weight fluctuations using gut microbiome…
Statistical analysis of microbiome data is challenging. Bayesian multinomial logistic-normal (MLN) models have gained popularity due to their ability to account for the count compositional nature of these data, but existing approaches are…
Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…