Barry G Hall

Summary

Publications

  1. pmc Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model
    Robert Boissy
    Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA 15212, USA
    BMC Genomics 12:187. 2011
  2. pmc Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations
    Barry G Hall
    Bellingham Research Institute, Bellingham, WA, USA
    Mol Biol Evol 26:2487-97. 2009
  3. pmc Measures of clade confidence do not correlate with accuracy of phylogenetic trees
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, United States of America
    PLoS Comput Biol 3:e51. 2007
  4. pmc Molecular epidemiology of Mycobacterium leprae as determined by structure-neighbor clustering
    Barry G Hall
    Bellingham Research Institute, 218 Chuckanut Point Rd, Bellingham, WA 98229, USA
    J Clin Microbiol 48:1997-2008. 2010
  5. doi request reprint How well does the HoT score reflect sequence alignment accuracy?
    Barry G Hall
    Bellingham Research Institute
    Mol Biol Evol 25:1576-80. 2008
  6. doi request reprint Towards the molecular epidemiology of Mycobacterium leprae: strategies, successes, and shortcomings
    Stephen J Salipante
    Bellingham Research Institute, Bellingham, WA 98229, USA
    Infect Genet Evol 11:1505-13. 2011
  7. doi request reprint Simulating DNA coding sequence evolution with EvolveAGene 3
    Barry G Hall
    Bellingham Research Institute, Bellingham, WA, USA
    Mol Biol Evol 25:688-95. 2008
  8. pmc Inadequacies of minimum spanning trees in molecular epidemiology
    Stephen J Salipante
    Bellingham Research Institute, Bellingham, Washington, USA
    J Clin Microbiol 49:3568-75. 2011
  9. doi request reprint Building phylogenetic trees from molecular data with MEGA
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, USA
    Mol Biol Evol 30:1229-35. 2013
  10. pmc Clustering acinetobacter strains by optical mapping
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, USA
    Genome Biol Evol 5:1176-84. 2013

Collaborators

Detail Information

Publications26

  1. pmc Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model
    Robert Boissy
    Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA 15212, USA
    BMC Genomics 12:187. 2011
    ....
  2. pmc Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations
    Barry G Hall
    Bellingham Research Institute, Bellingham, WA, USA
    Mol Biol Evol 26:2487-97. 2009
    ....
  3. pmc Measures of clade confidence do not correlate with accuracy of phylogenetic trees
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, United States of America
    PLoS Comput Biol 3:e51. 2007
    ....
  4. pmc Molecular epidemiology of Mycobacterium leprae as determined by structure-neighbor clustering
    Barry G Hall
    Bellingham Research Institute, 218 Chuckanut Point Rd, Bellingham, WA 98229, USA
    J Clin Microbiol 48:1997-2008. 2010
    ....
  5. doi request reprint How well does the HoT score reflect sequence alignment accuracy?
    Barry G Hall
    Bellingham Research Institute
    Mol Biol Evol 25:1576-80. 2008
    ..However, HoT scores are overestimates of alignment accuracy in general, with the extent of overestimation depending on the method used for multiple sequence alignment...
  6. doi request reprint Towards the molecular epidemiology of Mycobacterium leprae: strategies, successes, and shortcomings
    Stephen J Salipante
    Bellingham Research Institute, Bellingham, WA 98229, USA
    Infect Genet Evol 11:1505-13. 2011
    ..Lastly, we critically evaluate the strengths and shortcomings of leprosy research, and present recommendations for future work that will hopefully shed light on some of the disease's most fundamental mysteries...
  7. doi request reprint Simulating DNA coding sequence evolution with EvolveAGene 3
    Barry G Hall
    Bellingham Research Institute, Bellingham, WA, USA
    Mol Biol Evol 25:688-95. 2008
    ....
  8. pmc Inadequacies of minimum spanning trees in molecular epidemiology
    Stephen J Salipante
    Bellingham Research Institute, Bellingham, Washington, USA
    J Clin Microbiol 49:3568-75. 2011
    ..It is our hope this algorithm will become the new "gold standard" approach for analyzing MSTs for molecular epidemiology so that this generally useful computational approach can be used informatively and to its full potential...
  9. doi request reprint Building phylogenetic trees from molecular data with MEGA
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, USA
    Mol Biol Evol 30:1229-35. 2013
    ..MEGA is available for use on PCs and Macs from www.megasoftware.net...
  10. pmc Clustering acinetobacter strains by optical mapping
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, USA
    Genome Biol Evol 5:1176-84. 2013
    ..Minimum spanning trees of the two clusters that included sequenced genomes are presented. The programs we have developed provide a more rigorous approach for analyzing optical map data than previously existed. ..
  11. pmc Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, United States of America
    PLoS ONE 8:e68901. 2013
    ..Experimentally, we apply the method to screening a set of 98 isolates to distinguishing E. coli from Shigella, and EHEC from non-EHEC E. coli strains and show that all isolates are correctly identified. ..
  12. pmc Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
    Barry G Hall
    Bellingham Research Institute, 218 Chuckanut Point Rd, Bellingham, WA 98229, USA
    Microbiology 156:1060-8. 2010
    ....
  13. pmc Simple and accurate estimation of ancestral protein sequences
    Barry G Hall
    Bellingham Research Institute, 218 Chuckanut Point Road, Bellingham, WA 98229, USA
    Proc Natl Acad Sci U S A 103:5431-6. 2006
    ..A highly accurate method for correcting the estimated sequences is introduced, and it is shown that the correction permits inferring the sequences of ancient protein sequences with a very high degree of accuracy...
  14. pmc Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627 0211, USA
    Genetics 160:823-32. 2002
    ..Additionally, our results predict that a phenotype not yet observed among TEM beta-lactamases in nature-resistance to cefepime-is likely to arise in nature...
  15. pmc Structure-based phylogeny of the metallo-beta-lactamases
    Gianpiero Garau
    Laboratoire de Cristallographie Macromoléulaire, Institut de Biologie Structural Jean Pierre Ebel, CEA CNRS UJF, Grenoble, France
    Antimicrob Agents Chemother 49:2778-84. 2005
    ..The presence of genes from Eubacteria, Archaebacteria, and Eukaryota on that tree is consistent with a very ancient origin of the metallo-beta-lactamase family...
  16. ncbi request reprint Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences
    Barry G Hall
    Biology Department, University of Rochester, USA
    Mol Biol Evol 22:792-802. 2005
    ....
  17. ncbi request reprint Independent origins of subgroup Bl + B2 and subgroup B3 metallo-beta-lactamases
    Barry G Hall
    Biology Department, University of Rochester, Rochester, NY 14627, USA
    J Mol Evol 59:133-41. 2004
    ..These results lend additional support to the proposal that the metallo-beta-lactamases should be divided into two distinct classes...
  18. ncbi request reprint The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose
    Barry G Hall
    Biology Department, Hutchinson Hall, River Campus, University of Rochester, Rochester, NY 14627 0211, USA
    Genetica 118:143-56. 2003
    ..The analysis of free-energy profiles for the wildtype and all of the various evolved Ebg enzymes has permitted rejection of the Albery-Knowles hypothesis that relates likely changes in free-energy profiles to evolutionary change...
  19. pmc Origin and evolution of the AmpC beta-lactamases of Citrobacter freundii
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627, USA
    Antimicrob Agents Chemother 46:1190-8. 2002
    ..These results suggest that selection for increased resistance to beta-lactam antibiotics has not been a significant force directing the evolution of the C. freundii ampC alleles found in beta-lactam-resistant clinical isolates...
  20. ncbi request reprint Phylogenetic analysis shows that the OXA beta-lactamase genes have been on plasmids for millions of years
    Miriam Barlow
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Evol 55:314-21. 2002
    ..That observation contradicts the commonly held impression that mobilization of antibiotic resistance genes is strictly the result of modern use of antibiotics...
  21. ncbi request reprint Determining the limits of the evolutionary potential of an antibiotic resistance gene
    Stephen J Salipante
    Biology Department, University of Rochester, USA
    Mol Biol Evol 20:653-9. 2003
    ..typhimurium LT2 has the potential to evolve increased aminoglycoside resistance in nature. The practical implications of being able to determine the evolutionary limits for other antibiotic resistance genes are discussed...
  22. pmc Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627 0211, USA
    Genetics 164:23-9. 2003
    ..Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles...
  23. ncbi request reprint The metallo-beta-lactamases fall into two distinct phylogenetic groups
    Barry G Hall
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Evol 57:249-54. 2003
    ..We present phylogenies of these two groups and suggest a new classification scheme for the beta-lactamases...
  24. ncbi request reprint Structure-based phylogenies of the serine beta-lactamases
    Barry G Hall
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Evol 57:255-60. 2003
    ..From those phylogenies, we show that the Class A and Class D beta-lactamases are sister taxa and that the divergence of the Class C beta-lactamases pre-dated the divergence of the Class A and Class D beta-lactamases...
  25. ncbi request reprint Evolution of the serine beta-lactamases: past, present and future
    Barry G Hall
    Department of Biology, University of Rochester, Rochester, NY, USA
    Drug Resist Updat 7:111-23. 2004
    ..We also discuss a method that is being used to predict the future evolution of beta-lactamases in response to selection with new drugs...
  26. ncbi request reprint Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases
    Barry G Hall
    Biology Department, University of Rochester, Rochester, NY, USA
    Ann Epidemiol 16:157-69. 2006
    ..When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates...