W J Bruno

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. pmc Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes
    Peter T Hraber
    Theoretical Biology and Biophysics, T 10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545, USA
    Virol J 3:103. 2006
  2. ncbi request reprint Modeling residue usage in aligned protein sequences via maximum likelihood
    W J Bruno
    Los Alamos National Laboratory, New Mexico 87545, USA
    Mol Biol Evol 13:1368-74. 1996
  3. ncbi request reprint Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction
    W J Bruno
    Los Alamos National Laboratory, New Mexico 87545, USA
    Mol Biol Evol 17:189-97. 2000
  4. ncbi request reprint Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies
    A L Halpern
    Los Alamos National Laboratory, New Mexico, USA
    Mol Biol Evol 15:910-7. 1998
  5. ncbi request reprint Finding regulatory elements using joint likelihoods for sequence and expression profile data
    I Holmes
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA
    Proc Int Conf Intell Syst Mol Biol 8:202-10. 2000
  6. ncbi request reprint Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition
    D D Pollock
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    Mol Biol Evol 17:1854-8. 2000
  7. ncbi request reprint Major structural determinants of transmembrane proteins identified by principal component analysis
    J M Koshi
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico 87545, USA
    Proteins 34:333-40. 1999
  8. ncbi request reprint Evolutionary HMMs: a Bayesian approach to multiple alignment
    I Holmes
    Group T10, Los Alamos National Laboratory, NM 87545, USA
    Bioinformatics 17:803-20. 2001

Collaborators

Detail Information

Publications8

  1. pmc Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes
    Peter T Hraber
    Theoretical Biology and Biophysics, T 10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545, USA
    Virol J 3:103. 2006
    ..This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions...
  2. ncbi request reprint Modeling residue usage in aligned protein sequences via maximum likelihood
    W J Bruno
    Los Alamos National Laboratory, New Mexico 87545, USA
    Mol Biol Evol 13:1368-74. 1996
    ..The ability of this method to discard misleading phylogenetic effects allows the biochemical propensities of different positions in a sequence to be more clearly observed and interpreted...
  3. ncbi request reprint Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction
    W J Bruno
    Los Alamos National Laboratory, New Mexico 87545, USA
    Mol Biol Evol 17:189-97. 2000
    ..Weighbor appears to be relatively immune to the "long branches attract" and "long branch distracts" drawbacks observed with neighbor joining, BIONJ, and parsimony...
  4. ncbi request reprint Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies
    A L Halpern
    Los Alamos National Laboratory, New Mexico, USA
    Mol Biol Evol 15:910-7. 1998
    ..Site-to-site differences in rates, as well as synonymous/nonsynonymous and first/second/third-codon-position differences, arise as a natural consequence of the site-to-site differences in amino acid frequencies...
  5. ncbi request reprint Finding regulatory elements using joint likelihoods for sequence and expression profile data
    I Holmes
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA
    Proc Int Conf Intell Syst Mol Biol 8:202-10. 2000
    ..A program, called kimono, that implements this algorithm has been developed: the source code is freely available on the Internet...
  6. ncbi request reprint Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition
    D D Pollock
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    Mol Biol Evol 17:1854-8. 2000
    ....
  7. ncbi request reprint Major structural determinants of transmembrane proteins identified by principal component analysis
    J M Koshi
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico 87545, USA
    Proteins 34:333-40. 1999
    ..In a further analysis, we examine trends for some of the PCA axes over averaged transmembrane alpha helices, and find interesting results for aromaticity...
  8. ncbi request reprint Evolutionary HMMs: a Bayesian approach to multiple alignment
    I Holmes
    Group T10, Los Alamos National Laboratory, NM 87545, USA
    Bioinformatics 17:803-20. 2001
    ..The individual sampling and maximization steps of the algorithm require no more computational resources than pairwise alignment...