相关论文: An Empirical Bayes Regression for Multi-tissue eQT…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…
Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression…
Kelly (2007, hereafter K07) described an efficient algorithm, using Gibbs sampling, for performing linear regression in the fairly general case where non-zero measurement errors exist for both the covariates and response variables, where…
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect…
In genome-wide association studies (GWASs), there is an increasing need for detecting the associations between a genetic variant and multiple traits. In studies of complex diseases, it is common to measure several potentially correlated…
Recent genome-wide association studies (GWAS) have uncovered the genetic basis of complex traits, but show an under-representation of non-European descent individuals, underscoring a critical gap in genetic research. Here, we assess whether…
A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…
Genetic Network Programming (GNP) is an evolutionary algorithm that extends Genetic Programming (GP). It is typically used in agent control problems. In contrast to GP, which employs a tree structure, GNP utilizes a directed graph…
Understanding the genetic underpinnings of complex traits and diseases has been greatly advanced by genome-wide association studies (GWAS). However, a significant portion of trait heritability remains unexplained, known as ``missing…
In this paper we derive one- and two-sample multivariate empirical Bayes statistics (the $\mathit{MB}$-statistics) to rank genes in order of interest from longitudinal replicated developmental microarray time course experiments. We first…
Single-cell transcriptomic data approximates the abundance of proteins at a high resolution, but its noisiness necessitates transformation by a pipeline of methods before analysis and inference. In the absence of robust validation of these…
We consider a Nonparametric Empirical Bayes (NPEB) framework. Let $Y_i$ be random variables, $Y_i \sim f(y|\theta_i)$, $i=1,...,n$, where $\theta_i \sim G$, and $\theta_i \in \Theta$ are independent. The variables $Y_i $ are conditionally…
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…
Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…
Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study…
Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can…
Motivated by genome-wide association studies, we consider a standard linear model with one additional random effect in situations where many predictors have been collected on the same subjects and each predictor is analyzed separately.…
We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in…
Learning latent expression themes that best express complex patterns in a sample is a central problem in data mining and scientific research. For example, in computational biology we seek a set of salient gene expression themes that explain…