The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous ...

We propose a simple model for interaction between gene candidates in the two strands of bacterial DNA (deoxyribonucleic acid). Our model assumes that 'final' genes appear in one of the two strands, ...

Haplotype inference is an indispensable technique in medical science, especially in genome-wide association studies. Although the conventional method of inference using the expectation-maximization ...

Extracting regulatory motifs 1 from DNA sequences seems to be all the rage these days. Take your favorite cluster of coexpressed genes, and with some luck you might hope to find a short pattern of ...