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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…
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…
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…
A key challenge in differential abundance analysis of microbial samples is that the counts for each sample are compositional, resulting in biased comparisons of the absolute abundance across study groups. Normalization-based differential…
Differential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false positive control challenging. Here, we show that the compositional effects can be…
It is largely taken for granted that differential abundance analysis is, by default, the best first step when analyzing genomic data. We argue that this is not necessarily the case. In this article, we identify key limitations that are…
Differential abundance tests in compositional data are essential and fundamental tasks in various biomedical applications, such as single-cell, bulk RNA-seq, and microbiome data analysis. However, because of the compositional constraint and…
Using a sample from a population to estimate the proportion of the population with a certain category label is a broadly important problem. In the context of microbiome studies, this problem arises when researchers wish to use a sample from…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
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…
The achievable level of precision on photospheric abundances of stars is a major limiting factor on investigations of exoplanet host star characteristics, the chemical histories of star clusters, and the evolution of the Milky Way and other…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
The analysis of human microbiome data is often based on dimension-reduced graphical displays and clustering derived from vectors of microbial abundances in each sample. Common to these ordination methods is the use of biologically motivated…
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…
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…
To analyse a very large data set containing lengthy variables, we adopt a sequential estimation idea and propose a parallel divide-and-conquer method. We conduct several conventional sequential estimation procedures separately, and properly…
Making informed decisions about model adequacy has been an outstanding issue for regression models with discrete outcomes. Standard assessment tools for such outcomes (e.g. deviance residuals) often show a large discrepancy from the…
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…
In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the…