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One primary goal of human microbiome studies is to predict host traits based on human microbiota. However, microbial community sequencing data present significant challenges to the development of statistical methods. In particular, the…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
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…
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…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
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…
Detecting associations between microbial compositions and sample characteristics is one of the most important tasks in microbiome studies. Most of the existing methods apply univariate models to single microbial species separately, with…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
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…
The role of the microbiome in disease pathogenesis is an emerging field with strong evidence suggesting that dysbiosis is associated with precancerous and cancerous states. Microbiome data present substantial challenges for causal mediation…
Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic…
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…
Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU…
The task of reconstructing a matrix given a sample of observedentries is known as the matrix completion problem. It arises ina wide range of problems, including recommender systems, collaborativefiltering, dimensionality reduction, image…
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…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…