@article{hobolth_2008, title={A Markov chain Monte Carlo expectation maximization algorithm for statistical analysis of DNA sequence evolution with neighbor-dependent substitution rates}, volume={17}, ISSN={["1537-2715"]}, DOI={10.1198/106186008X289010}, abstractNote={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 rate of substitution at a site depends on the states of the neighboring sites. Neighbor-dependent substitution models are analytically intractable and must be analyzed using either approximate or simulation-based methods. We describe statistical inference of neighbor-dependent models using a Markov chain Monte Carlo expectation maximization (MCMC-EM) algorithm. In the MCMC-EM algorithm, the high-dimensional integrals required in the EM algorithm are estimated using MCMC sampling. The MCMC sampler requires simulation of sample paths from a continuous time Markov process, conditional on the beginning and ending states and the paths of the neighboring sites. An exact path sampling algorithm is developed for this purpose.}, number={1}, journal={JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, author={Hobolth, Asger}, year={2008}, month={Mar}, pages={138–162} }
 @article{hobolth_nielsen_wang_wu_tanksley_2006, title={CpG plus CpNpG analysis of protein-coding sequences from tomato}, volume={23}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msk017}, abstractNote={We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.}, number={6}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Hobolth, Asger and Nielsen, Rasmus and Wang, Ying and Wu, Feinan and Tanksley, Steven D.}, year={2006}, month={Jun}, pages={1318–1323} }
 @article{jonsdottir_hoffmann_hobolth_jensen_2006, title={On error prediction in circular systematic sampling}, volume={222}, ISSN={["1365-2818"]}, DOI={10.1111/j.1365-2818.2006.01589.x}, abstractNote={Summary}, journal={JOURNAL OF MICROSCOPY}, author={Jonsdottir, K. Y. and Hoffmann, L. M. and Hobolth, A. and Jensen, E. B. Vedel}, year={2006}, month={Jun}, pages={212–216} }