Triplet periodicity (TP) is a distinctive feature of the protein coding sequences of both prokaryotic and eukaryotic genomes. In this work, we explored the TP difference inside and between 45 prokaryotic genomes. We constructed two hypotheses of TP distribution on a set of coding sequences and...

Approaches to Bayesian inference for problems with intractable likelihoods have become increasingly important in recent years. Approximate Bayesian computation (ABC) and “likelihood free” Markov chain Monte Carlo techniques are popular methods for tackling inference in these scenarios but...

In this paper we consider the problem of parameter inference for Markov jump process (MJP) representations of stochastic kinetic models. Since transition probabilities are intractable for most processes of interest yet forward simulation is straightforward, Bayesian inference typically proceeds...

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 binding behavior of molecules in nuclei of living cells can be studied through the analysis of images from fluorescence recovery after photobleaching experiments. However, there is still a lack of methodology for the statistical evaluation of FRAP data, especially for the joint analysis of...

An ordinal scale is commonly used to measure health status and disease related outcomes in hospital settings as well as in translational medical research. In addition, repeated measurements are common in clinical practice for tracking and monitoring the progression of complex diseases. Classical...