JEFFREY L contact THORNE

Summary

Affiliation: North Carolina State University
Country: USA

Publications

  1. ncbi Protein evolution constraints and model-based techniques to study them
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
    Curr Opin Struct Biol 17:337-41. 2007
  2. ncbi Estimating the rate of evolution of the rate of molecular evolution
    J L Thorne
    Statistics Department, North Carolina State University, Raleigh 27695 8203, USA
    Mol Biol Evol 15:1647-57. 1998
  3. ncbi Models of protein sequence evolution and their applications
    J L Thorne
    Program in Statistical Genetics, Statistics Department, Box 8203, North Carolina State University, Raleigh, North Carolina 27695 8203, USA
    Curr Opin Genet Dev 10:602-5. 2000
  4. ncbi Population genetics without intraspecific data
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Institute for Advanced Study, Berlin, Germany
    Mol Biol Evol 24:1667-77. 2007
  5. ncbi Combining protein evolution and secondary structure
    J L Thorne
    Statistics Department, North Carolina State University, Raleigh 27695 8203, USA
    Mol Biol Evol 13:666-73. 1996
  6. ncbi Divergence time and evolutionary rate estimation with multilocus data
    Jeffrey L Thorne
    Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
    Syst Biol 51:689-702. 2002
  7. 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
  8. ncbi A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
    Tae Kun Seo
    Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Bioinformatics 18:115-23. 2002
  9. ncbi Dependence among sites in RNA evolution
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1525-37. 2006
  10. ncbi Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
    Tae Kun Seo
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Proc Natl Acad Sci U S A 102:4436-41. 2005

Research Grants

  1. Evolutionary inferences from protein-coding genes
    Jeffrey Thorne; Fiscal Year: 2007
  2. Evolutionary inferences from protein-coding genes
    JEFFREY L contact THORNE; Fiscal Year: 2010

Collaborators

Detail Information

Publications17

  1. ncbi Protein evolution constraints and model-based techniques to study them
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
    Curr Opin Struct Biol 17:337-41. 2007
    ....
  2. ncbi Estimating the rate of evolution of the rate of molecular evolution
    J L Thorne
    Statistics Department, North Carolina State University, Raleigh 27695 8203, USA
    Mol Biol Evol 15:1647-57. 1998
    ..The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences...
  3. ncbi Models of protein sequence evolution and their applications
    J L Thorne
    Program in Statistical Genetics, Statistics Department, Box 8203, North Carolina State University, Raleigh, North Carolina 27695 8203, USA
    Curr Opin Genet Dev 10:602-5. 2000
    ..Notable recent advances have been made in the treatment of insertion and deletion events, the estimation of amino-acid replacement rates, and the detection of positive selection...
  4. ncbi Population genetics without intraspecific data
    Jeffrey L Thorne
    Wissenschaftskolleg zu Berlin, Institute for Advanced Study, Berlin, Germany
    Mol Biol Evol 24:1667-77. 2007
    ..We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population genetic interpretation...
  5. ncbi Combining protein evolution and secondary structure
    J L Thorne
    Statistics Department, North Carolina State University, Raleigh 27695 8203, USA
    Mol Biol Evol 13:666-73. 1996
    ..For the evolution of sucrose synthase, a parametric bootstrap approach indicates that our model is statistically preferable to one that ignores secondary structure...
  6. ncbi Divergence time and evolutionary rate estimation with multilocus data
    Jeffrey L Thorne
    Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
    Syst Biol 51:689-702. 2002
    ..The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed...
  7. 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...
  8. ncbi A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
    Tae Kun Seo
    Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Bioinformatics 18:115-23. 2002
    ..We illustrate how these approximations can be exploited to determine which viral sample to sequence when samples representing different dates are available...
  9. ncbi Dependence among sites in RNA evolution
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 23:1525-37. 2006
    ..Potential applications of this procedure, including improved ancestral sequence inference and location of functionally interesting sites, are discussed...
  10. ncbi Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
    Tae Kun Seo
    Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695 7566, USA
    Proc Natl Acad Sci U S A 102:4436-41. 2005
    ..We discuss the applicability of the two-stage bootstrap idea to the Kishino-Hasegawa test and the Shimodaira-Hasegawa test...
  11. ncbi Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
    Tae Kun Seo
    Bioinformatics Research Center, Box 7566, North Carolina State University, NC, USA
    Mol Biol Evol 21:1201-13. 2004
    ..Our analysis of these data also suggests that rates have been positively correlated...
  12. ncbi Time flies, a new molecular time-scale for brachyceran fly evolution without a clock
    Brian M Wiegmann
    Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
    Syst Biol 52:745-56. 2003
    ..This study provides increased resolution of brachyceran phylogeny, and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms...
  13. ncbi Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach
    Tae Kun Seo
    Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Genetics 160:1283-93. 2002
    ..52 x 10(-5) to 5.02 x 10(-5). Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients...
  14. ncbi Protein evolution with dependence among codons due to tertiary structure
    Douglas M Robinson
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 20:1692-704. 2003
    ....
  15. ncbi Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution
    Masami Hasegawa
    The Institute of Statistical Mathematics, Minato ku, Tokyo, Japan
    Genes Genet Syst 78:267-83. 2003
    ..With denser taxonomic sampling and a more realistic model of molecular evolution, this Bayesian approach is expected to increase the accuracy of divergence time estimates...
  16. ncbi Testing for spatial clustering of amino acid replacements within protein tertiary structure
    Jiaye Yu
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA
    J Mol Evol 62:682-92. 2006
    ..These findings need to be reconciled with the common practice of basing evolutionary inferences on models that assume independent change among sites...
  17. ncbi Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach
    Elizabeth H Scholl
    Center for the Biology of Nematode Parasitism, Box 7253, North Carolina State University, Raleigh, NC 27695, USA
    Genome Biol 4:R39. 2003
    ..Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism...

Research Grants5

  1. Evolutionary inferences from protein-coding genes
    Jeffrey Thorne; Fiscal Year: 2007
    ..abstract_text> ..
  2. Evolutionary inferences from protein-coding genes
    JEFFREY L contact THORNE; Fiscal Year: 2010
    ..Via this improved understanding, we will develop statistical techniques for identifying which variation in protein-coding genes is likely to be deleterious to human health. ..