Related papers: Cross-study analyses of microbial abundance using …
Estimating and testing for differences in molecular phenotypes (e.g. gene expression, chromatin accessibility, transcription factor binding) across conditions is an important part of understanding the molecular basis of gene regulation.…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
The emergent dynamics of complex systems often arise from the internal dynamical interactions among different elements and hence is to be modeled using multiple variables that represent the different dynamical processes. When such systems…
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…
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…
Ex-post harmonisation is one of many data preprocessing processes used to combine the increasingly vast and diverse sources of data available for research and analysis. Documenting provenance and ensuring the quality of multi-source…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
The \emph{community}, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
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…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry…
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…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…
Meta-analysis, because of both logistical convenience and statistical efficiency, is widely popular for synthesizing information on common parameters of interest across multiple studies. We propose developing a generalized meta-analysis…
In practice, observations are often contaminated by noise, making the resulting sample covariance matrix to be an information-plus-noise-type covariance matrix. Aiming to make inferences about the spectra of the underlying true covariance…
In many applications, data can be heterogeneous in the sense of spanning latent groups with different underlying distributions. When predictive models are applied to such data the heterogeneity can affect both predictive performance and…