John P Huelsenbeck

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc A compound poisson process for relaxing the molecular clock
    J P Huelsenbeck
    Department of Biology, University of Rochester, New York 14627, USA
    Genetics 154:1879-92. 2000
  2. ncbi Empirical and hierarchical Bayesian estimation of ancestral states
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 50:351-66. 2001
  3. ncbi Effect of nonindependent substitution on phylogenetic accuracy
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 48:317-28. 1999
  4. ncbi Testing a covariotide model of DNA substitution
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Biol Evol 19:698-707. 2002
  5. ncbi Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:155-65. 2002
  6. ncbi Inferring the root of a phylogenetic tree
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:32-43. 2002
  7. ncbi Bayesian inference of phylogeny and its impact on evolutionary biology
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 294:2310-4. 2001
  8. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
  9. ncbi A Bayesian framework for the analysis of cospeciation
    J P Huelsenbeck
    Department of Biology, University of Rochester, New York 14627, USA
    Evolution 54:352-64. 2000
  10. ncbi Accommodating phylogenetic uncertainty in evolutionary studies
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 288:2349-50. 2000

Detail Information

Publications11

  1. pmc A compound poisson process for relaxing the molecular clock
    J P Huelsenbeck
    Department of Biology, University of Rochester, New York 14627, USA
    Genetics 154:1879-92. 2000
    ..This model should prove useful for estimating divergence times when substitution rates vary across lineages...
  2. ncbi Empirical and hierarchical Bayesian estimation of ancestral states
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 50:351-66. 2001
    ..We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis...
  3. ncbi Effect of nonindependent substitution on phylogenetic accuracy
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 48:317-28. 1999
    ..Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process...
  4. ncbi Testing a covariotide model of DNA substitution
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Biol Evol 19:698-707. 2002
    ..I show that in nine of the genes examined a covariotide model provides a better explanation of the data than a model that does not allow constraints to change over time...
  5. ncbi Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:155-65. 2002
    ..The geographic origin of modern human mtDNA is inferred to be in Africa, although support for this hypothesis was ambiguous for data from an early paper...
  6. ncbi Inferring the root of a phylogenetic tree
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:32-43. 2002
    ..We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results...
  7. ncbi Bayesian inference of phylogeny and its impact on evolutionary biology
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 294:2310-4. 2001
    ....
  8. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
    ..The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo...
  9. ncbi A Bayesian framework for the analysis of cospeciation
    J P Huelsenbeck
    Department of Biology, University of Rochester, New York 14627, USA
    Evolution 54:352-64. 2000
    ..In particular, it does not assume that the host or parasite phylogenies are known without error; many alternative phylogenies are sampled in proportion to their probability of being correct...
  10. ncbi Accommodating phylogenetic uncertainty in evolutionary studies
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 288:2349-50. 2000
    ..We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies...
  11. ncbi Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    Gautam Altekar
    Department of Computer Science, University of Rochester, USA
    Bioinformatics 20:407-15. 2004
    ..Metropolis coupled MCMC [(MC)(3)], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time...