Bret Larget

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. pmc The estimation of tree posterior probabilities using conditional clade probability distributions
    Bret Larget
    Departments of Botany and Statistics, University of Wisconsin, Madison, WI 53706, USA
    Syst Biol 62:501-11. 2013
  2. ncbi request reprint A Bayesian approach to the estimation of ancestral genome arrangements
    Bret Larget
    Department of Botany, University of Wisconsin, Madison, USA
    Mol Phylogenet Evol 36:214-23. 2005
  3. ncbi request reprint Bayesian estimation of concordance among gene trees
    Cecile Ane
    Department of Statistics, University of Wisconsin, USA
    Mol Biol Evol 24:412-26. 2007
  4. ncbi request reprint A bayesian analysis of metazoan mitochondrial genome arrangements
    Bret Larget
    Department of Botany, University of Wisconsin at Madison, USA
    Mol Biol Evol 22:486-95. 2005
  5. ncbi request reprint A Bayesian model of AFLP marker evolution and phylogenetic inference
    Ruiyan Luo
    University of Wisconsin, Madison, WI, USA
    Stat Appl Genet Mol Biol 6:Article11. 2007
  6. pmc An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species
    Raul Correa
    Department of Botany, University of Wisconsin Madison, Madison, WI 53706, USA
    New Phytol 193:494-503. 2012
  7. pmc Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria
    Matias J Cafaro
    Department of Bacteriology, University of Wisconsin, Madison, 4325 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
    Proc Biol Sci 278:1814-22. 2011
  8. doi request reprint A Bayesian perspective on a non-parsimonious parsimony model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 57:406-19. 2008
  9. doi request reprint Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics
    Clemens Lakner
    Department of Biological Science, Section Ecology and Evolution, Florida State University, Tallahassee, Florida 32306 4120, USA
    Syst Biol 57:86-103. 2008
  10. ncbi request reprint Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004

Research Grants

  1. Improving Bayesian Phylogeny
    Bret Larget; Fiscal Year: 2006

Detail Information

Publications13

  1. pmc The estimation of tree posterior probabilities using conditional clade probability distributions
    Bret Larget
    Departments of Botany and Statistics, University of Wisconsin, Madison, WI 53706, USA
    Syst Biol 62:501-11. 2013
    ..Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample...
  2. ncbi request reprint A Bayesian approach to the estimation of ancestral genome arrangements
    Bret Larget
    Department of Botany, University of Wisconsin, Madison, USA
    Mol Phylogenet Evol 36:214-23. 2005
    ..We compare and contrast a Bayesian approach with a parsimony approach to infer phylogenies and ancestral arrangements from genome arrangement data by re-analyzing a number of previously published data sets...
  3. ncbi request reprint Bayesian estimation of concordance among gene trees
    Cecile Ane
    Department of Statistics, University of Wisconsin, USA
    Mol Biol Evol 24:412-26. 2007
    ..We demonstrate the method on a set of 106 genes from 8 yeast species...
  4. ncbi request reprint A bayesian analysis of metazoan mitochondrial genome arrangements
    Bret Larget
    Department of Botany, University of Wisconsin at Madison, USA
    Mol Biol Evol 22:486-95. 2005
    ..We present summaries of Bayesian posterior distributions of tree topology on the basis of these two data sets...
  5. ncbi request reprint A Bayesian model of AFLP marker evolution and phylogenetic inference
    Ruiyan Luo
    University of Wisconsin, Madison, WI, USA
    Stat Appl Genet Mol Biol 6:Article11. 2007
    ..We compare the results of our analysis with a clustering method based on Nei and Li's restriction-site distance and a two-state Bayesian analysis using MrBayes...
  6. pmc An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species
    Raul Correa
    Department of Botany, University of Wisconsin Madison, Madison, WI 53706, USA
    New Phytol 193:494-503. 2012
    ..We identify methods to reduce false positives and false negatives in the future. 11_11B can be viewed as a potential speciation gene, illustrating the value of transgenomics for studying the molecular basis of reproductive isolation...
  7. pmc Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria
    Matias J Cafaro
    Department of Bacteriology, University of Wisconsin, Madison, 4325 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
    Proc Biol Sci 278:1814-22. 2011
    ..Our findings support a model that many fungus-growing ants maintain specialized Pseudonocardia symbionts that help with garden defence...
  8. doi request reprint A Bayesian perspective on a non-parsimonious parsimony model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 57:406-19. 2008
    ....
  9. doi request reprint Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics
    Clemens Lakner
    Department of Biological Science, Section Ecology and Evolution, Florida State University, Tallahassee, Florida 32306 4120, USA
    Syst Biol 57:86-103. 2008
    ..Our results have important implications for developers of Bayesian MCMC implementations and for the large group of users of Bayesian phylogenetics software...
  10. ncbi request reprint Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004
    ....
  11. ncbi request reprint Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees"
    Fredrik Ronquist
    School of Computational Science, Florida State University, Tallahassee, FL 32306 4120, USA
    Science 312:367; author reply 367. 2006
    ..However, the conditions leading to their results are artificial. Standard MCMC convergence diagnostics would detect the problem in real data, and correction of the model misspecification would solve it...
  12. ncbi request reprint Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics
    Mark T Holder
    School of Computational Science, Florida State University, Tallahassee, 32306 4120, USA
    Syst Biol 54:961-5. 2005
  13. ncbi request reprint Potential applications and pitfalls of Bayesian inference of phylogeny
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biology, University of California San Diego, La Jolla, CA 92093 0116, USA
    Syst Biol 51:673-88. 2002
    ..The results of a Bayesian analysis should be examined with respect to the sensitivity of the results to the priors used and the reliability of the Markov chain Monte Carlo approximation of the probabilities of trees...

Research Grants4

  1. Improving Bayesian Phylogeny
    Bret Larget; Fiscal Year: 2006
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