相关论文: A Phylogeny-based Test of Mediation Effect in Micr…
Mediation analysis for survival outcomes is challenging. Most existing methods quantify the treatment effect using the hazard ratio (HR) and attempt to decompose the HR into the direct effect of treatment plus an indirect, or mediated,…
Common psychiatric and brain disorders are highly heritable and affected by a number of genetic risk factors, yet the mechanism by which these genetic factors contribute to the disorders through alterations in brain structure and function…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
The Complete Mediation Test (CMT) serves as a specialized approach of mediation analysis to assess whether an independent variable A, influences an outcome variable Y exclusively through a mediator M, without any direct effect. An…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
Mediation analysis is a useful tool to evaluate surrogate endpoints in clinical trials. We propose a novel method, the M-survival learner, for estimating heterogeneous indirect treatment effects in the presence of censored outcomes. The…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
Environmental health studies are increasingly measuring endogenous omics data ($\boldsymbol{M}$) to study intermediary biological pathways by which an exogenous exposure ($\boldsymbol{A}$) affects a health outcome ($\boldsymbol{Y}$), given…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to…
Mediation analysis seeks to identify and quantify the paths by which an exposure affects an outcome. Intermediate variables which are effected by the exposure and which effect the outcome are known as mediators. There exists extensive work…
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…
This article presents a novel methodology for detecting multiple biomarkers in high-dimensional mediation models by utilizing a modified Least Absolute Shrinkage and Selection Operator (LASSO) alongside Pathway LASSO. This approach…
Bacterial Vaginosis (BV) affects nearly 23-29% of women worldwide and increases risk of miscarriage, preterm birth, and sexually transmitted infections. It involves a shift in the vaginal microbiome from Lactobacillus dominance to a diverse…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…