Menzerath’s law, the tendency of Z (the mean size of the parts) to decrease as X (the number of parts) increases, is found in language, music and genomes. Recently, it has been argued that the presence of the law in genomes is an inevitable consequence of the fact that Z=Y/X, which would imply...

In genetic association studies, detecting disease-genotype association is a primary goal. We study seven robust test statistics for such association when the underlying genetic model is unknown, for data on disease status (case or control) and genotype (three genotypes of a biallelic genetic...

Stochastic systems in biology often exhibit substantial variability within and between cells. This variability, as well as having dramatic functional consequences, provides information about the underlying details of the system’s behavior. It is often desirable to infer properties of the...

Background: Identifying differentially expressed genes has been an important and widely used approach to investigate gene functions and molecular mechanisms. A related issue that has drawn much less attention but is equally important is the identification of constantly expressed genes across...

We assess the accuracy of various state-of-the-art statistics and machine learning methods for reconstructing gene and protein regulatory networks in the context of circadian regulation. Our study draws on the increasing availability of gene expression and protein concentration time series for...

This paper uses a Bayesian formulation of a clustering procedure to identify gene-gene interactions under case-control studies, called the Algorithm via Bayesian Clustering to Detect Epistasis (ABCDE). The ABCDE uses Dirichlet process mixtures to model SNP marker partitions, and uses the Gibbs...

Risk prediction models can link high-dimensional molecular measurements, such as DNA methylation, to clinical endpoints. For biological interpretation, often a sparse fit is desirable. Different molecular aggregation levels, such as considering DNA methylation at the CpG, gene, or chromosome...

We present a novel characterization of the generalized family wise error rate: kFWER. The interpretation allows researchers to view kFWER as a function of the test statistics rather than current methods based on p-values. Using this interpretation we present several theorems and methods...

We have developed a modified Patient Rule-Induction Method (PRIM) as an alternative strategy for analyzing representative samples of non-experimental human data to estimate and test the role of genomic variations as predictors of disease risk in etiologically heterogeneous sub-samples. A...

Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study...