Profile Hidden Markov Models (pHMMs) are widely used to model nucleotide or protein sequence families. In many applications, a sequence family classified into several subfamilies is given and each subfamily is modeled separately by one pHMM. A major drawback of this approach is the difficulty of...

An important challenge in system biology is the inference of biological networks from postgenomic data. Among these biological networks, a gene transcriptional regulatory network focuses on interactions existing between transcription factors (TFs) and and their corresponding target genes. A...

Illumina bead arrays are microarrays that contain a random number of technical replicates (beads) for every probe (bead type) within the same array. Typically around 30 beads are placed at random positions on the array surface, which opens unique opportunities for quality control. Most...

We present a method for improving the power of linkage analysis by detecting chromosome segments shared identical by descent (IBD) by individuals not known to be related. Existing Markov chain Monte Carlo methods sample descent patterns on pedigrees conditional on observed marker data. These...

For a better understanding of the biology of an organism, a complete description is needed of all regions of the genome that are actively transcribed. Tiling arrays are used for this purpose. They allow for the discovery of novel transcripts and the assessment of differential expression between...

The advent of high-throughput biotechnologies, which can efficiently measure gene expression on a global basis, has led to the creation and population of correspondingly rich databases and compendia. Such repositories have the potential to add enormous scientific value beyond that provided by...

Testing for unequal variances is usually performed in order to check the validity of the assumptions that underlie standard tests for differences between means (the t-test and anova). However, existing methods for testing for unequal variances (Levene's test and Bartlett's test) are notoriously...

This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation...

We explore the use of generalized t priors on regression coefficients to help understand the nature of association signal within hit regions of genome-wide association studies. The particular generalized t distribution we adopt is a Student distribution on the absolute value of its argument. For...