Asger Hobolth: Publications

Publications

Please send an email if you would like a copy of any of my papers.

Scally, A., Dutheil, J.Y., Hillier, L.W., Jordan, G.E., Goodhead, I., Herrero, J., Hobolth, A. et al. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature. In Press.

Tataru, P. and Hobolth, A. (2011). Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. BMC Bioinformatics, 12, 465 (highly accessed). paper poster talk
Hobolth, A. and Jensen, J.L. (2010). Summary statistics for endpoint-conditioned continuous-time Markov chains. Journal of Applied Probability, 48, 911-924. paper
The orangutan genome consortium (2011). Comparative and demographic analysis of orang-utan genomes Nature, 469, 529-533.
Hobolth, A., Dutheil, J., Hawks, J., Schierup, M., & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection. Genome Research, 21, 349-356.
T. Mailund, J.Y. Dutheil, A. Hobolth, G. Lunter and M.H. Schierup (2011). Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies using a Coalescent Hidden Markov Model. Link PLoS Genetics, 7(3).
Hobolth, A. , Andersen, L.N. and Mailund, T. (2011). On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics, 187, 1241-1243.
Asmussen, S. and Hobolth, A. (2011). Markov Bridges, Bisection and Variance Reduction. Thiele Research Report 01 (January 2011). To appear in MCQMC 2010 Proceedings.

Dutheil, J.Y. and Hobolth, A. (2010). Ancestral population genetics. To appear as Chapter in Springer book.

Dutheil, J.Y., Ganapathy, G., Hobolth, A., Mailund, T., Uyenoyama, M.K. and Schierup, M.H. (2009). Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183, 259-274.
Hobolth, A. and Stone, A.C. (2009). Efficient simulation from finite-state, continuous-time Markov chains with incomplete observations. Annals of Applied Statistics, 3, 1204-1231. pdf Electronic version in Euclid arXiv link
Hobolth, A. and Wiuf, C. (2009). The genealogy, site frequency spectrum and ages of two nested mutations. Theoretical Population Biology, 75, 260-265. pdf

Asmussen, S. and Hobolth, A. (2008). Bisection ideas in end-point conditioned Markov process simulation. In Proceedings of the 7th International Workshop on Rare Event Simulation (G. Rubino and B. Tuffin, eds.), 121-130. Rennes, France. pdf
Hobolth, A. (2008). A Markov Chain Monte Carlo Expectation Maximization algorithm for statistical analysis of DNA sequence evolution with neighbour-dependent substitution rates. Journal of Computational and Graphical Statistics, 17, 138-164. pdf
Hobolth, A., Uyenoyama, M.K. and Wiuf, C. (2008). Importance Sampling for the Infinite Sites Model. Statistical Applications in Genetics and Molecular Biology, 7, 31. pdf

Choi, S.C., Hobolth, A., Robinson, D.M., Kishino, H. and Thorne, J.L. (2007). Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution. Molecular Biology and Evolution, 24, 1769-1782.
Hobolth, A., Christensen, O.F., Mailund, T. and Schierup, M.H. (2007). Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics, 3, 294-304.
Frandsen, J., Hobolth, A., Jensen, E.B.V., Vestergaard-Poulsen, P. and Ã˜stergaard, L. (2007). Bayesian regularization of diffusion tensor images. Biostatistics, 8, 784-799.

Jonsdottir, K.Y., Hoffmann, L.M., Hobolth, A. and Jensen, E.B.V. (2006). On variance estimation in circular systematic sampling. Journal of Microscopy, 222, 212-216.
Hobolth, A., Nielsen, R., Wang, Y., Wu, F. and Tanksley, S.D. (2006). CpG+CpNpG analysis of protein coding sequences from tomato. Molecular Biology and Evolution, 23, 1318-1323. pdf

Christensen, O.F., Hobolth, A. and Jensen, J.L. (2005). Pseudo-likelihood analysis of context-dependent codon substitution models. Maphysto Research Report 2004-29, Department of Theoretical Statistics, University of Aarhus. Journal of Computational Biology, 12, 1166-1182.
Hobolth, A. and Jensen, J.L. (2005). Statistical inference in evolutionary models of DNA sequences via the EM algorithm. Statistical applications in Genetics and Molecular Biology, 4, 18. Web address.
JÃ¸rgensen, F.G., Hobolth, A., HornshÃ¸j, H., Bendixen, C., Fredholm, M. and Schierup, M.H. (2005). Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biology, 3, 2.
Hobolth, A. and Jensen, J.L. (2005). Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene. Journal of Computational Biology, 12, 186-203. pdf
Gardner, R.J., Hobolth, A., Jensen, E.B.V. and SÃ¸rensen, F.B. (2005). Shape discrimination by total curvature, with a view to cancer diagnostics. Journal of Microscopy, 217, 49-59.

Hannila, M., Jensen, E.B.V., Hobolth, A. and Nyengaard, J.R. (2004). Spatial particle shape modeling from planar central sections - a case study. Journal of Microscopy, 215, 183-190.

Hobolth, A. (2003). The spherical deformation model. Biostatistics, 4, 583-595. pdf.
Hobolth, A., Pedersen, J. and Jensen, E.B.V. (2003) A continuous parametric shape model. Annals of the Institute of Statistical Mathematics, 55, 227-242.

Hobolth, A. and Jensen, E.B.V. (2002). Stereological analysis of shape. Image Analysis and Stereology, 21, 23-29.
Hobolth, A. and Jensen, E.B.V. (2002). A note on design-based versus model-based variance estimation in stereology. Advances in Applied Probability (SGSA), 34, 484-490. pdf.
Hobolth, A., Pedersen, J. and Jensen, E.B.V. (2002). A deformable template model, with special reference to elliptical templates. Journal of Mathematical Imaging and Vision, 17, 131-137. pdf.
Hobolth, A., Kent, J.T. and Dryden, I.L. (2002). On the relation between edge and vertex modelling in shape analysis. Scandinavian Journal of Statistics, 29, 355-374. pdf.

Hobolth, A. and Jensen, E.B.V. (2000). Modelling stochastic changes in curve shape, with an application to cancer diagnostics. Advances in Applied Probability (SGSA), 32, 344-362. pdf.

Hobolth, A. and Yoshida, R. (2005) Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbour-joining and the EM algorithm. Algebraic Biology 2005, Computer Algebra in Biology, edited by H. Anai and K. Horimoto, 1, 41 - 50, Universal Academy Press, INC.

Hobolth, A. og Schauser, L. (2005). Statistiske modeller finder generne [Statistical models find the genes]. Aktuel Naturvidenskab, 6, 9-11. pdf. In Danish. Udvidede version: Genfinding og skjulte Markov-modeller [Extended version: Gene finding and hidden Markov models]. pdf.
Schierup, M.H., Mailund, T., Hobolth, A. and Vollertsen, A. (2007). DNA-statistik gør mennesket yngre. Aktuel Naturvidenskab, 3, 25-27. In Danish.