S V Muse

Summary

Affiliation: North Carolina State University
Country: USA

Publications

  1. ncbi request reprint Evolution of duplicated alpha-tubulin genes in ciliates
    Rachel L Israel
    Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
    Evolution 56:1110-22. 2002
  2. ncbi request reprint Examining rates and patterns of nucleotide substitution in plants
    S V Muse
    Department of Statistics, North Carolina State University, Raleigh 27695 8203, USA
    Plant Mol Biol 42:25-43. 2000
  3. ncbi request reprint Positively selected sites in the Arabidopsis receptor-like kinase gene family
    Errol Strain
    Bioinformatics Research Center, Campus Box 7566, North Carolina State University, Raleigh, NC, 27695 7566, USA
    J Mol Evol 61:325-32. 2005
  4. ncbi request reprint HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
  5. ncbi request reprint Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
  6. doi request reprint Detecting signatures of selection from DNA sequences using Datamonkey
    Art F Y Poon
    Antiviral Research Center, Department of Pathology, University of California San Diego, La Jolla, CA, USA
    Methods Mol Biol 537:163-83. 2009
  7. ncbi request reprint A simple hierarchical approach to modeling distributions of substitution rates
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, San Diego, California, USA
    Mol Biol Evol 22:223-34. 2005
  8. ncbi request reprint A genetic algorithm approach to detecting lineage-specific variation in selection pressure
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:478-85. 2005
  9. pmc Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1
    Selene Zárate
    Antiviral Research Center, 150 W Washington St, Ste 100, San Diego, CA 92103, USA
    J Virol 81:6643-51. 2007
  10. ncbi request reprint Column sorting: rapid calculation of the phylogenetic likelihood function
    Sergei L Kosakovsky Pond
    Department of Mathematics, University of Arizona, Tucson, Arizona 85271, USA
    Syst Biol 53:685-92. 2004

Research Grants

  1. Biostatistics Training in the Omics Era
    Spencer Muse; Fiscal Year: 2007
  2. HyPhy: Molecular Evolutionary Analyses
    Sergei L Kosakovsky Pond; Fiscal Year: 2010

Collaborators

Detail Information

Publications16

  1. ncbi request reprint Evolution of duplicated alpha-tubulin genes in ciliates
    Rachel L Israel
    Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
    Evolution 56:1110-22. 2002
    ....
  2. ncbi request reprint Examining rates and patterns of nucleotide substitution in plants
    S V Muse
    Department of Statistics, North Carolina State University, Raleigh 27695 8203, USA
    Plant Mol Biol 42:25-43. 2000
    ..Evolutionary rates are seen to be quite variable, both among genes and among plant lineages. However, there are hints, particularly in the chloroplast, that individual factors can have important effects on many genes simultaneously...
  3. ncbi request reprint Positively selected sites in the Arabidopsis receptor-like kinase gene family
    Errol Strain
    Bioinformatics Research Center, Campus Box 7566, North Carolina State University, Raleigh, NC, 27695 7566, USA
    J Mol Evol 61:325-32. 2005
    ....
  4. ncbi request reprint HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
    ..AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  5. ncbi request reprint Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  6. doi request reprint Detecting signatures of selection from DNA sequences using Datamonkey
    Art F Y Poon
    Antiviral Research Center, Department of Pathology, University of California San Diego, La Jolla, CA, USA
    Methods Mol Biol 537:163-83. 2009
    ..org) provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in the presence of recombinant sequences...
  7. ncbi request reprint A simple hierarchical approach to modeling distributions of substitution rates
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, San Diego, California, USA
    Mol Biol Evol 22:223-34. 2005
    ..We also demonstrate this discretization scheme in the context of codon models specifically aimed at identifying individual sites undergoing adaptive or purifying evolution...
  8. ncbi request reprint A genetic algorithm approach to detecting lineage-specific variation in selection pressure
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:478-85. 2005
    ..We illustrate our methods on primate lysozyme sequences and compare them with previous methods applied to the same data sets...
  9. pmc Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1
    Selene Zárate
    Antiviral Research Center, 150 W Washington St, Ste 100, San Diego, CA 92103, USA
    J Virol 81:6643-51. 2007
    ....
  10. ncbi request reprint Column sorting: rapid calculation of the phylogenetic likelihood function
    Sergei L Kosakovsky Pond
    Department of Mathematics, University of Arizona, Tucson, Arizona 85271, USA
    Syst Biol 53:685-92. 2004
    ..The modifications will provide faster likelihood algorithms, which will allow likelihood methods to be applied to larger sets of taxa and to include more thorough searches of the tree topology space...
  11. ncbi request reprint Evolutionary model selection with a genetic algorithm: a case study using stem RNA
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California, San Diego, USA
    Mol Biol Evol 24:159-70. 2007
    ..In addition, the new method provides the foundation for rigorous selection and comparison of substitution models for other types of sequence data...
  12. ncbi request reprint Site-to-site variation of synonymous substitution rates
    Sergei Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, USA
    Mol Biol Evol 22:2375-85. 2005
    ..We discuss how failure to model synonymous rate variation in the model can lead to misidentification of sites as positively selected...
  13. ncbi request reprint PowerMarker: an integrated analysis environment for genetic marker analysis
    Kejun Liu
    Bioinformatics Research Center, North Carolina State University Raleigh, 27695 7566, USA
    Bioinformatics 21:2128-9. 2005
    ..It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker...
  14. ncbi request reprint Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes
    Laura A Katz
    Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
    Mol Biol Evol 21:555-62. 2004
    ....
  15. pmc Genomic analysis of closely related astroviruses
    Errol Strain
    Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
    J Virol 82:5099-103. 2008
    ..In addition, the analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection...
  16. ncbi request reprint Genome architecture drives protein evolution in ciliates
    Rebecca A Zufall
    Department of Biological Sciences, Smith College, USA
    Mol Biol Evol 23:1681-7. 2006
    ..Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution...

Research Grants3

  1. Biostatistics Training in the Omics Era
    Spencer Muse; Fiscal Year: 2007
    ..Students in both options will share a core set of courses designed to provide essential training in statistics, genomic science, and bioinformatics, and to enhance the sense of student community. ..
  2. HyPhy: Molecular Evolutionary Analyses
    Sergei L Kosakovsky Pond; Fiscal Year: 2010
    ....