Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome modelRobert Boissy
Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA 15212, USA
BMC Genomics 12:187. 2011
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- 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
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- 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
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- 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
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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...
- 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...
- Simulating DNA coding sequence evolution with EvolveAGene 3
Barry G Hall
Bellingham Research Institute, Bellingham, WA, USA
Mol Biol Evol 25:688-95. 2008
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- 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...
- 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
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- 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...
- Structure-based phylogeny of the metallo-beta-lactamases
Gianpiero Garau
, 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...
Comparison of the accuracies of several phylogenetic methods using protein and DNA sequencesBarry G Hall
Biology Department, University of Rochester, USA
Mol Biol Evol 22:792-802. 2005
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- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
