Related papers: Modeling microbial abundances and dysbiosis with b…
Accurate estimates of microbial species abundances are needed to advance our understanding of the role that microbiomes play in human and environmental health. However, artificially constructed microbiomes demonstrate that intuitive…
This paper investigates two environmental applications related to climate change, where observations consist of bounded counts. The binomial and beta-binomial (BB) models are commonly used for bounded count data, with the BB model offering…
One important problem in microbiome analysis is to identify the bacterial taxa that are associated with a response, where the microbiome data are summarized as the composition of the bacterial taxa at different taxonomic levels. This paper…
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…
Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is…
We wish to formally test for changes in the taxonomic diversity of a community, especially in the presence of high latent diversity. Drawing on the meta-analysis literature, we construct a model for diversity that accounts for covariate…
The advances of next-generation sequencing technology have accelerated study of the microbiome and stimulated the high throughput profiling of metagenomes. The large volume of sequenced data has encouraged the rise of various studies for…
The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the…
Beta-binomial/Poisson models have been used by many authors to model multivariate count data. Lora and Singer (Statistics in Medicine, 2008) extended such models to accommodate repeated multivariate count data with overdipersion in the…
Monitoring the distribution of microfossils in stratigraphic successions is an essential tool for biostratigraphic, evolutionary and paleoecologic/paleoceanographic studies. To estimate the relative abundance (%) of a given species, it is…
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
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…
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…
Differential abundance analysis is a key component of microbiome studies. Although dozens of methods exist there is currently no consensus on the preferred methods. While the correctness of results in differential abundance analysis is an…
Recent evidence suggests that analyzing the presence/absence of taxonomic features can offer a compelling alternative to differential abundance analysis in microbiome studies. However, standard approaches to differential prevalence analysis…
This study developed a new statistical model and method for analyzing the precision of binary measurement methods from collaborative studies. The model is based on beta-binomial distributions. In other words, it assumes that the sensitivity…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
In this paper, we propose a regression model where the response variable is beta prime distributed using a new parameterization of this distribution that is indexed by mean and precision parameters. The proposed regression model is useful…