Asger Hobolth

Summary

Affiliation: University of Aarhus
Country: Denmark

Publications

  1. ncbi Statistical inference in evolutionary models of DNA sequences via the EM algorithm
    Asger Hobolth
    Bioinformatics Research Center, University of Aarhus, Denmark
    Stat Appl Genet Mol Biol 4:Article18. 2005
  2. pmc Importance sampling for the infinite sites model
    Asger Hobolth
    Aarhus University
    Stat Appl Genet Mol Biol 7:Article32. 2008
  3. ncbi CpG + CpNpG analysis of protein-coding sequences from tomato
    Asger Hobolth
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1318-23. 2006
  4. pmc Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    Asger Hobolth
    Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 3:e7. 2007
  5. pmc Ancestral population genomics: the coalescent hidden Markov model approach
    Julien Y Dutheil
    Bioinformatics Research Center, Aarhus University, C F Møllers Allé 8, Bldg 1110, DK 8000 Aarhus C, Denmark
    Genetics 183:259-74. 2009
  6. pmc A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species
    Thomas Mailund
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    PLoS Genet 8:e1003125. 2012
  7. ncbi Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates
    Ole F Christensen
    Bioinformatics Research Center, University of Aarhus, Denmark
    J Comput Biol 12:1166-82. 2005
  8. pmc Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model
    Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, Denmark
    PLoS Genet 7:e1001319. 2011
  9. ncbi Quantifying the impact of protein tertiary structure on molecular evolution
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, NC, USA
    Mol Biol Evol 24:1769-82. 2007
  10. pmc Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, DK 8000 Aarhus C, Denmark
    Genome Res 21:349-56. 2011

Collaborators

Detail Information

Publications21

  1. ncbi Statistical inference in evolutionary models of DNA sequences via the EM algorithm
    Asger Hobolth
    Bioinformatics Research Center, University of Aarhus, Denmark
    Stat Appl Genet Mol Biol 4:Article18. 2005
    ..We provide explicit analytical solutions for the EM algorithm and information matrix...
  2. pmc Importance sampling for the infinite sites model
    Asger Hobolth
    Aarhus University
    Stat Appl Genet Mol Biol 7:Article32. 2008
    ..The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavaré (1994)...
  3. ncbi CpG + CpNpG analysis of protein-coding sequences from tomato
    Asger Hobolth
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1318-23. 2006
    ..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...
  4. pmc Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    Asger Hobolth
    Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 3:e7. 2007
    ....
  5. pmc Ancestral population genomics: the coalescent hidden Markov model approach
    Julien Y Dutheil
    Bioinformatics Research Center, Aarhus University, C F Møllers Allé 8, Bldg 1110, DK 8000 Aarhus C, Denmark
    Genetics 183:259-74. 2009
    ..We expect that this framework will prove useful for population genomics and provide exciting insights into genome evolution...
  6. pmc A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species
    Thomas Mailund
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    PLoS Genet 8:e1003125. 2012
    ..We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation...
  7. ncbi Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates
    Ole F Christensen
    Bioinformatics Research Center, University of Aarhus, Denmark
    J Comput Biol 12:1166-82. 2005
    ..The pseudo-likelihood estimates are shown to be very accurate, and from analyzing 348 human-mouse coding sequences we conclude that the incorporation of a CpG effect improves the fit of the model considerably...
  8. pmc Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model
    Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, Denmark
    PLoS Genet 7:e1001319. 2011
    ..We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection...
  9. ncbi Quantifying the impact of protein tertiary structure on molecular evolution
    Sang Chul Choi
    Bioinformatics Research Center, North Carolina State University, NC, USA
    Mol Biol Evol 24:1769-82. 2007
    ..Although their influences on rates of evolution vary among protein families, we find that the mean impacts of solvent accessibility and pairwise interactions are about the same...
  10. pmc Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, DK 8000 Aarhus C, Denmark
    Genome Res 21:349-56. 2011
    ..Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny...
  11. ncbi Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene
    Asger Hobolth
    Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark
    J Comput Biol 12:186-203. 2005
    ..This unified model is particularly useful for a detailed characterization of DNA sequences with a common gene. We illustrate the model on a variety of homologous sequences...
  12. pmc Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains
    Paula Tataru
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    BMC Bioinformatics 12:465. 2011
    ..In applications past evolutionary events (exact times and types of changes) are unaccessible and the past must be inferred from DNA sequence data observed in the present...
  13. doi The genealogy, site frequency spectrum and ages of two nested mutant alleles
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
    Theor Popul Biol 75:260-5. 2009
    ..We show that the age of the youngest mutation does not depend on the frequency of the single mutant allele and that the frequency spectra for the single mutant allele and the zero mutant allele are the same...
  14. pmc Algorithms for hidden markov models restricted to occurrences of regular expressions
    Paula Tataru
    Bioinformatics Research Centre, Aarhus University, C F Møllers Allé 8, DK 8000 Aarhus C, Denmark
    Biology (Basel) 2:1282-95. 2013
    ..We furthermore show that using this distribution in the decoding algorithms improves the predictive power of the model. ..
  15. ncbi Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data
    Paula Tataru
    Bioinformatics Research Centre, Aarhus University, Aarhus, 8000, Denmark
    Syst Biol . 2016
    ..We conclude with a brief overview of the multi-allelic process with a general mutation model. [Allele frequency, diffusion, inference, moments, selection, Wright-Fisher.]...
  16. pmc Inference Under a Wright-Fisher Model Using an Accurate Beta Approximation
    Paula Tataru
    Bioinformatics Research Centre, Aarhus University, Aarhus C 8000, Denmark
    Genetics 201:1133-41. 2015
    ..We additionally illustrate, using both simulated and real data, how the beta with spikes can be used for inference of divergence times between populations with comparable performance to an existing state-of-the-art method. ..
  17. doi Efficient computation in the IM model
    Lars Nørvang Andersen
    Bioinformatics Research Centre, Aarhus University, C F Møllers Allé 8, Aarhus C, 8000, Aarhus, Denmark
    J Math Biol 68:1423-51. 2014
    ..Finally, we show how the performance depends on the parameters in the model. ..
  18. doi Markovian approximation to the finite loci coalescent with recombination along multiple sequences
    Asger Hobolth
    Bioinformatics Research Center, Aarhus University, Denmark Electronic address
    Theor Popul Biol 98:48-58. 2014
    ..We compare our Markov approximation to other sequential Markov chains and discuss various applications. ..
  19. pmc Comparative analysis of protein coding sequences from human, mouse and the domesticated pig
    Frank Grønlund Jørgensen
    Department of Ecology and Genetics, University of Aarhus, Aarhus C, Denmark
    BMC Biol 3:2. 2005
    ....
  20. ncbi The spherical deformation model
    Asger Hobolth
    Department of Mathematical Sciences, University of Aarhus, Ny Munkegade, 8000 Aarhus C, Denmark
    Biostatistics 4:583-95. 2003
    ..We use maximum-likelihood-based inference for this purpose and demonstrate the suggested methods on real data...
  21. ncbi Bayesian regularization of diffusion tensor images
    Jesper Frandsen
    Department of Neuroradiology, Centre for Functionally Integrative Neuroscience, Arhus University Hospital, Arhus, Denmark
    Biostatistics 8:784-99. 2007
    ..In this paper, we develop a Bayesian procedure for regularizing the diffusion tensor field, fully utilizing the available 3D information of fiber orientation. The use of the procedure is exemplified on synthetic and in vivo data...