Asger Hobolth: Publications
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Publications
Please send an email if you would like a copy of any of my papers.
2012
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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.
2011
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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
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Hobolth, A. and Jensen, J.L. (2010).
Summary statistics for endpoint-conditioned continuous-time Markov chains.
Journal of Applied Probability,
48, 911-924.
paper
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The orangutan genome consortium (2011).
Comparative and demographic analysis of orang-utan genomes
Nature,
469, 529-533.
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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.
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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).
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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.
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Asmussen, S. and Hobolth, A. (2011).
Markov Bridges, Bisection and Variance Reduction.
Thiele Research Report 01 (January 2011).
To appear in MCQMC 2010 Proceedings.
2010
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Dutheil, J.Y. and Hobolth, A. (2010).
Ancestral population genetics.
To appear as Chapter in Springer book.
2009
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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.
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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
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Hobolth, A. and Wiuf, C. (2009).
The genealogy, site frequency spectrum and ages of two nested
mutations.
Theoretical Population Biology,
75, 260-265.
pdf
2008
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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
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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
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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
2007
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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.
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Frandsen, J., Hobolth, A., Jensen, E.B.V.,
Vestergaard-Poulsen, P. and Østergaard, L. (2007).
Bayesian regularization of diffusion tensor images.
Biostatistics, 8, 784-799.
2006
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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.
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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
2005
- 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.
- Jørgensen, F.G., Hobolth, A., Hornshøj, 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 Sørensen,
F.B. (2005). Shape discrimination by total curvature, with a
view to cancer diagnostics.
Journal of Microscopy, 217, 49-59.
2004
- 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.
2003
- 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.
2002
- 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.
2000
- 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.
Conference papers
- 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.
Submitted papers
Popularisation
- 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.