In most cases where clustering of data is desirable, the underlying data distribution to be clustered is unconstrained. However clustering of site types in a discretely structured linear array, as is often desired in studies of linear sequences such as DNA, RNA or proteins, represents a problem...

There has been much interest in reconstructing bi-directional regulatory networks linking the circadian clock to metabolism in plants. A variety of reverse engineering methods from machine learning and computational statistics have been proposed and evaluated. The emphasis of the present paper...

The increasing availability of ChIP-seq data demands for advanced statistical tools to analyze the results of such experiments. The inherent features of high-throughput sequencing output call for a modelling framework that can account for the spatial dependency between neighboring regions of the...

Complex diseases are often characterized by coordinated expression alterations of genes and proteins which are grouped together in a molecular network. Identifying such interconnected and jointly altered gene/protein groups from functional omics data and a given molecular interaction network is...

The literature shows that classifiers perform differently across datasets and that correlations within datasets affect the performance of classifiers. The question that arises is whether the correlation structure within datasets differ significantly across diseases. In this study, we evaluated...

We explore the probabilistic structure of DNA in a number of bacterial genomes and conclude that a form of Markovianness is present at the boundaries between coding and non-coding regions, that is, the sequence of START and STOP codons annotated for the bacterial genome. This sequence is shown...

Conservative statistical tests are often used in complex multiple testing settings in which computing the type I error may be difficult. In such tests, the reported p-value for a hypothesis can understate the evidence against the null hypothesis and consequently statistical power may be lost....

It has been proposed recently that differentially variable CpG methylation (DVC) may contribute to transcriptional aberrations in human diseases. In large scale epigenetic studies, potential confounders could affect the observed methylation variabilities and need to be accounted for. In this...