The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have been applied to infer the order and rate of occurrence of these mutations. Understanding and...

The level of differential gene expression may be defined as a fold change, a frequency of upregulation, or some other measure of the degree or extent of a difference in expression across groups of interest. On the basis of expression data for hundreds or thousands of genes, inferring which genes...

In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for...

Currently the practice of using existing biological knowledge in analyzing high throughput genomic and proteomic data is mainly for the purpose of validations. Here we take a different approach of incorporating biological knowledge into statistical analysis to improve statistical power and...

High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing step. Statistical...

Generalized linear models with covariate measurement error can be estimated by maximum likelihood using gllamm, a program that fits a large class of multilevel latent variable models (Rabe-Hesketh, Skrondal, and Pickles 2004). The program uses adaptive quadrature to evaluate the log likelihood,...

There is great interest in finding human genes expressed through pharmaceutical intervention, thus opening a genomic window into benefit and side-effect profiles of a drug. Human insight gained from FDA-required animal experiments has historically been limited, but in the case of gene expression...

The level of differential gene expression may be defined as a fold change, a frequency of upregulation, or some other measure of the degree or extent of a difference in expression across groups of interest. On the basis of expression data for hundreds or thousands of genes, inferring which genes...