Cawley et al. (2004) have recently mapped the locations of binding sites for three transcription factors along human chromosomes 21 and 22 using ChIP-Chip experiments. ChIP-Chip experiments are a new approach to the genome-wide identification of transcription factor binding sites and consist of...

Providing information about the risk of disease and clinical factors that may increase or decrease a patient's risk of disease is standard medical practice. Although case-control studies provide evidence of strong associations between diseases and risk factors, clinicians need to be able to...

Analysis of viral strand sequence data and viral replication capacity could potentially lead to biological insights regarding the replication ability of HIV-1. Determining specific target codons on the viral strand will facilitate the manufacturing of target specific antiretrovirals. Various...

In van der Laan and Dudoit (2003) we propose and theoretically study a unified loss function based statistical methodology, which provides a road map for estimation and performance assessment. Given a parameter of interest which can be described as the minimizer of the population mean of a loss...

Multiple transcription factors coordinately control transcriptional regulation of genes in eukaryotes. Although multiple computational methods consider the identification of individual transcription factor binding sites (TFBSs), very few focus on the interactions between these sites. We consider...

The present article proposes general single-step multiple testing procedures for controlling Type I error rates defined as arbitrary parameters of the distribution of the number of Type I errors, such as the generalized family-wise error rate. A key feature of our approach is the test statistics...

The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics (step-down maxT), while the second relies on minima of unadjusted p-values (step-down minP). A key feature...

Suppose that we observe a sample of independent and identically distributed realizations of a random variable. Assume that the parameter of interest can be defined as the minimizer, over a suitably defined parameter space, of the expectation (with respect to the distribution of the random...

The accompanying articles by Dudoit et al. (2003b) and van der Laan et al. (2003) provide single-step and step-down resampling-based multiple testing procedures that asymptotically control the family-wise error rate (FWER) for general null hypotheses and test statistics. The proposed procedures...

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs motif sampler) model binding sites...