Related papers: A Statistical Perspective on the Challenges in Mol…
Today there are approximately 85,000 chemicals regulated under the Toxic Substances Control Act, with around 2,000 new chemicals introduced each year. It is impossible to screen all of these chemicals for potential toxic effects either via…
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…
Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging…
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…
Quantitative analysis of the dynamics of tiny cellular and sub-cellular structures, known as particles, in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous…
In microbial studies, samples are often treated under different experimental conditions and then tested for microbial survival. A technique, dating back to the 1880's, consists of diluting the samples several times and incubating each…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
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…
Multivariate statistical analysis is concerned with observations on several variables which are thought to possess some degree of inter-dependence. Driven by problems in genetics and the social sciences, it first flowered in the earlier…
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…
We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
We study a statistical procedure based on higher criticism (HC) to address the sparse multi-stream quickest change-point detection problem. Namely, we aim to detect a potential change in the distribution of multiple data streams at some…
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Reasoning from sequences of raw sensory data is a ubiquitous problem across fields ranging from medical devices to robotics. These problems often involve using long sequences of raw sensor data (e.g. magnetometers, piezoresistors) to…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…