Bugs as Features (Part I): Concepts and Foundations for the Compositional Data Analysis of the Microbiome-Gut-Brain Axis [PDF]
, 2022 There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis. While our techniques to measure the presence and abundance of these microbes have been steadily improving, the ...
arxiv +2 more sources
Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression [PDF]
, 2014 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 microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ...
Charles K. Fisher, Pankaj Mehta
openalex +3 more sources
Rough Set Microbiome Characterisation [PDF]
arXiv, 2021 Microbiota profiles measure the structure of microbial communities in a defined environment (known as microbiomes). In the past decade, microbiome research has focused on health applications as a result of which the gut microbiome has been implicated in the development of a broad range of diseases such as obesity, inflammatory bowel disease, and major ...
arxiv
Aggregating Knockoffs for False Discovery Rate Control with an Application to Gut Microbiome Data [PDF]
Entropy 23(2021) 230, 2019 Recent discoveries suggest that our gut microbiome plays an important role in our health and wellbeing. However, the gut microbiome data are intricate; for example, the microbial diversity in the gut makes the data high-dimensional. While there are dedicated high-dimensional methods, such as the lasso estimator, they always come with the risk of false ...
arxiv +1 more source
HT-MMIOW: A Hypothesis Test approach for Microbiome Mediation using Inverse Odds Weighting [PDF]
arXiv, 2023 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 high dimensional, correlated, and compositional nature of microbiome data and do not typically accommodate ...
arxiv
Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis [PDF]
Annals of Applied Statistics 2013, Vol. 7, No. 1, 418-442, 2013 With the development of next generation sequencing technology, researchers have now been able to study the microbiome composition using direct sequencing, whose output are bacterial taxa counts for each microbiome sample. One goal of microbiome study is to associate the microbiome composition with environmental covariates.
arxiv +1 more source
Multivariate Log-Contrast Regression with Sub-Compositional Predictors: Testing the Association Between Preterm Infants' Gut Microbiome and Neurobehavioral Outcomes [PDF]
arXiv, 2020 The so-called gut-brain axis has stimulated extensive research on microbiomes. One focus is to assess the association between certain clinical outcomes and the relative abundances of gut microbes, which can be presented as sub-compositional data in conformity with the taxonomic hierarchy of bacteria. Motivated by a study for identifying the microbes in
arxiv
Microbiome-derived bile acids contribute to elevated antigenic response and bone erosion in rheumatoid arthritis [PDF]
arXiv, 2023 Rheumatoid arthritis (RA) is a chronic, disabling and incurable autoimmune disease. It has been widely recognized that gut microbial dysbiosis is an important contributor to the pathogenesis of RA, although distinct alterations in microbiota have been associated with this disease.
arxiv
Control of ecological outcomes through deliberate parameter changes in a model of the gut microbiome [PDF]
Phys. Rev. E 101, 052402 (2020), 2019 The generalized Lotka-Volterra (gLV) equations are a mathematical proxy for ecological dynamics. We focus on a gLV model of the gut microbiome, in which the evolution of the gut microbial state is determined in part by pairwise inter-species interaction parameters that encode environmentally-mediated resource competition between microbes. We develop an
arxiv +1 more source
A Bayesian Nonparametric Approach for Identifying Differentially Abundant Taxa in Multigroup Microbiome Data with Covariates [PDF]
arXiv, 2022 Scientific studies in the last two decades have established the central role of the microbiome in disease and health. Differential abundance analysis seeks to identify microbial taxa associated with sample groups defined by a factor such as disease subtype, geographical region, or environmental condition.
arxiv