Related papers: Testing for differential abundance in compositiona…
The target of inference in microbiome analyses is usually relative abundance (RA) because RA in a sample (e.g., stool) can be considered as an approximation of RA in an entire ecosystem (e.g., gut). However, inference on RA suffers from the…
Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a…
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…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Dimension reduction techniques are among the most essential analytical tools in the analysis of high-dimensional data. Generalized principal component analysis (PCA) is an extension to standard PCA that has been widely used to identify…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
High-dimensional compositional covariates, often derived from count data, are subject to measurement error and are frequently analyzed after aggregation along a prespecified tree to improve interpretability in applications such as…
Modern statistical analyses often involve testing large numbers of hypotheses. In many situations, these hypotheses may have an underlying tree structure that not only helps determine the order that tests should be conducted but also…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
Analyzing multivariate count data generated by high-throughput sequencing technology in microbiome research studies is challenging due to the high-dimensional and compositional structure of the data and overdispersion. In practice,…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
Compositional data sets are ubiquitous in science, including geology, ecology, and microbiology. In microbiome research, compositional data primarily arise from high-throughput sequence-based profiling experiments. These data comprise…
Compositional data are met in many different fields, such as economics, archaeometry, ecology, geology and political sciences. Regression where the dependent variable is a composition is usually carried out via a log-ratio transformation of…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…
Compositional data arise when count observations are normalised into proportions adding up to unity. To allow use of standard statistical methods, compositional proportions can be mapped from the simplex into the Euclidean space through the…
How can we learn generative models to sample data with arbitrary logical compositions of statistically independent attributes? The prevailing solution is to sample from distributions expressed as a composition of attributes' conditional…
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…
Recent attacks of various viruses with having deep and extensive impact at a global scale has warranted that microbiome be studied extensively and in a robust analytic framework. Microbiome typically refers to the collective genomes of such…
Current advances in next generation sequencing techniques have allowed researchers to conduct comprehensive research on microbiome and human diseases, with recent studies identifying associations between human microbiome and health outcomes…
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.…