Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD effects. We investigated the statistical properties of a class of...

As a consequence of the large p small n characteristic for microarray data, hypothesis tests based on individual genes often result in low average power. There are several proposed tests that attempt to improve power. Among these, the FS test that was developed using the concept of James-Stein...

Quantitative trait loci (QTL) mapping often results in data on a number of traits that have well-established causal relationships. Many multi-trait QTL mapping methods that account for the correlation among multiple traits have been developed to improve the statistical power and the precision of...

Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values published in the genomic literature are often computed...

High correlations were obtained between probes in seemingly unrelated probe sets, following an examination of the data from thousands of Affymetrix GeneChips. Investigation revealed that these unexpected correlations were between probes that were adjacent to high-valued probes. Using carefully...

We present a new methodology for discriminating genomic symbolic sequences, which combines wavelet analysis and a self-organizing map algorithm. Wavelets are used to extract variation across various scales in the oligonucleotide patterns of a sequence. The variation is quantified by the...

Regional co-expression refers to the phenomenon of contiguous genes exhibiting similar expression patterns. Among others, DNA copy number aberrations may be causally involved in regional co-expression. We propose a random coefficients model to explain regional co-expression from DNA copy number...

We present a method for estimating and providing a confidence interval for the number of DNA replication origins in the genome of the yeast Kluyveromyces lactis. The method requires an initial set of verified sites from which a position specific frequency matrix (PSFM) can be constructed. We...

We consider the problem of locating multiple interacting quantitative trait loci (QTL) influencing traits measured in counts. In many applications the distribution of the count variable has a spike at zero. Zero-inflated generalized Poisson regression (ZIGPR) allows for an additional probability...

There has been increasing interest in predicting patients' survival after therapy by investigating gene expression microarray data. In the regression and classification models with high-dimensional genomic data, boosting has been successfully applied to build accurate predictive models and...