Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive optimal sequence weights that minimize the sum of the variances of the estimators of base frequency...

In the field of molecular evolution genome substitution models with neighbour dependent substitution rates have recently received much attention. It is well-known that substitution of nucleotides does not occur independently of neighbouring nucleotides, but there has been less focus on the...

With the rapid growth of entire genome data, reconstructing the phylogenetic relationship among different genomes has become a hot topic in comparative genomics. Maximum likelihood approach is one of the various approaches, and has been very successful. However, there is no reported study for...

The development of an organism represents a complex dynamic process, which is controlled by a network of genes and multiple environmental factors. Programmed cell death (PCD), a physiological cell suicide process, occurs during the development of most organisms and is, typically, a complex...

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances of the transformed intensities become approximately independent of their expected values. The...

We propose an original statistical method to estimate how the occurrences of a given process along a genome, genes or motifs for instance, may be influenced by the occurrences of a second process. More precisely, the aim is to detect avoided and/or favored distances between two motifs, for...

Maximum Likelihood (ML) is used as a standard method for estimating divergence times in phylogenetic trees. The method is consistent and hence the precision can be improved by analyzing longer sequences. In this paper we show that the precision can be improved also by including more taxa to the...

We describe a method for the generation of knowledge-based potentials and apply it to the observed torsional angles of known protein structures. The potential is derived using Bayesian reasoning, and is useful as a prior for further such reasoning in the presence of additional data. The...