Nuclear Magnetic Resonance (NMR) spectroscopy is a key experimental technique used to study protein structure, dynamics, and interactions. NMR methods face the bottleneck of spectral analysis, in particular determining the resonance assignments, which help define the mapping between atoms in the...

Array Comparative Genomic Hybridization (aCGH) is an array-based technology which provides simultaneous spot assays of relative genetic abundance (RGA) levels at multiple sites across the genome. These spot assays are spatially correlated with respect to genomic location and, as a result, the...

In a recent article in PLoS Genetics, Bock et al., (2006) undertake an extensive computational epigenetics analysis of the ability of DNA sequence-derived features, capturing attributes such as tetramer frequencies, repeats and predicted structure, to predict the methylation status of CpG...

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is...

We describe statistical inference in continuous time Markov processes of DNA sequences related by a phylogenetic tree. The maximum likelihood estimator can be found by the expectation maximization (EM) algorithm and an expression for the information matrix is also derived. We provide explicit...

Markov models provide a natural framework for modeling cellular and molecular level changes over time. Kalbfleisch and Lawless propose using a Chi-squared statistic for assessing the appropriateness of assuming a first-order, homogeneous Markov process. While this statistic provides a global...

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...

Statistical inference of graphical models has become an important tool in the reconstruction of biological networks of the type which model, for example, gene regulatory interactions. In particular, the construction of a score-based Bayesian posterior density over the space of models provides an...

We propose here a review of the methods available to compute pattern statistics on text generated by a Markov source. Theoretical, but also numerical aspects are detailed for a wide range of techniques (exact, Gaussian, large deviations, binomial and compound Poisson). The SPatt package...