相关论文: A Phylogeny-based Test of Mediation Effect in Micr…
Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and…
Multilevel selection occurs when short-term individual-level reproductive interests conflict with longer-term group-level fitness effects. Detecting and quantifying this phenomenon is key to understanding evolution of traits ranging from…
Mediation analysis is concerned with the decomposition of the total effect of an exposure on an outcome into the indirect effect through a given mediator, and the remaining direct effect. This is ideally done using longitudinal measurements…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
Although many exciting applications of molecular communication (MC) systems are envisioned to be at microscale, the MC testbeds reported so far are mostly at macroscale. To link the macroworld to the microworld, we propose and demonstrate a…
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Recent advances in single-cell technologies have advanced our understanding of gene regulation and cellular heterogeneity at single-cell resolution. Single-cell data contain both gene expression levels and the proportion of expressing…
We consider Bayesian high-dimensional mediation analysis to identify among a large set of correlated potential mediators the active ones that mediate the effect from an exposure variable to an outcome of interest. Correlations among…
Mediation analysis breaks down the causal effect of a treatment on an outcome into an indirect effect, acting through a third group of variables called mediators, and a direct effect, operating through other mechanisms. Mediation analysis…
Microbiome omics data including 16S rRNA reveal intriguing dynamic associations between the human microbiome and various disease states. Drastic changes in microbiota can be associated with factors like diet, hormonal cycles, diseases, and…
Understanding causal mechanisms is crucial for explaining and generalizing empirical phenomena. Causal mediation analysis offers statistical techniques to quantify the mediation effects. Although numerous methods have been developed for…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Mapping genotypes to phenotypes (G2P) is a fundamental goal in biology. So called PhyloG2P methods are a relatively new set of tools that leverage replicated evolution in phylogenetically independent lineages to identify genomic regions…
Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
In oncology the efficacy of novel therapeutics often differs across patient subgroups, and these variations are difficult to predict during the initial phases of the drug development process. The relation between the power of randomized…