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Microbial communities analysis is drawing growing attention due to the rapid development of high-throughput sequencing techniques nowadays. The observed data has the following typical characteristics: it is high-dimensional, compositional…
High-throughput sequencing technology allows us to test the compositional difference of bacteria in different populations. One important feature of human microbiome data is that it often includes a large number of zeros. Such data can be…
Ongoing advances in microbiome profiling have allowed unprecedented insights into the molecular activities of microbial communities. This has fueled a strong scientific interest in understanding the critical role the microbiome plays in…
Substudies of the Childhood Asthma Management Program [Control. Clin. Trials 20 (1999) 91-120; N. Engl. J. Med. 343 (2000) 1054-1063] seek to identify patient characteristics associated with asthma symptoms and lung function. To determine…
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…
Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual differences between patients contributes to the difficulty to…
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…
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to…
High-dimensional compositional data arise naturally in many applications such as metagenomic data analysis. The observed data lie in a high-dimensional simplex, and conventional statistical methods often fail to produce sensible results due…
This paper is motivated by the recent interest in the analysis of high dimen- sional microbiome data. A key feature of this data is the presence of `structural zeros' which are microbes missing from an observation vector due to an…
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…
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…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
A great deal of effort has been devoted to discovering a particular genetic disorder, but its classification across a broad spectrum of disorder classes and types remains elusive. Early diagnosis of genetic disorders enables timely…
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…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
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…