Published Papers

1.     Gallant, J., H. Erlich, B.G. Hall, and T. Laffler.  1970.  Analysis of the RC function.  Cold Spring Harbor Symposium on Quantitative Biology. 35: 397 – 405.

2.      Hall, B. G. and J. Gallant.  1971.  Effect of the RC gene product on constitutive enzyme synthesis.  J. Mol. Biol. 61: 271-273.

3.      Hall, B. G. and J. Gallant.  1972.  Defective translation in RC cells.  Nature,
New Biology 237:  131-135.

4.      Hall, B. G. and J. Gallant.  1973.  On the rate of messenger decay during amino acid starvation.  J. Mol. Biol. 73: 121-124.

5.      Hall, B. G.  1973.  In vivo  complementation between wild type and mutant b-galactosidase in Escherichia coli .  J. Bacteriol.  114: 448 – 450.

6.      Hall, B. G. and D.L. Hartl.  1974.  Regulation of newly evolved enzymes. I.  Selection of a novel lactase regulated by lactose in Escherichia coli .   Genetics 81: 427 – 435.

7.      Hartl, D.L. and B.G. Hall.  1974.  A second naturally occurring b-galactosidase in E. coli .  Nature 248: 152-153.

8.      Hall, B. G. and D.L. Hartl.  1975.  Regulation of newly evolved enzymes. II.  The ebg repressor.  Genetics 81: 427-435.

9.      Hall, B. G.  1976.  Methyl-galactosidase activity:  An alternative evolutionary destination for the ebgAo gene.  J. Bacteriol.  126: 536-538.

10.    Hall, B. G.  1976.  Experimental evolution of a new enzymatic function:  Kinetic analysis of the ancestral (ebgo) and evolved (ebg+) enzymes.  J. Mol. Biol.  107: 71 – 84.

11.    Hall, B. G.  1977.  The number of mutations required to evolve a new lactase function in Escherichia coli .  J. Bacteriol. 129: 540-543.

12.    Hall, B. G. and N.D. Clarke.  1977.  Regulation of newly evolved enzymes.  III.  Evolution of the ebg  repressor during selection for enhanced lactase activity.  Genetics 85: 193-201.

13.    Hall, B. G. and E.C.R. Reeve.  1977.  A third b-galactosidase in a strain of Klebsiella  which possesses two Lac  genes.  J. Bacteriol.  132: 219-223.

14.    Hall, B. G.  1978.  Experimental evolution of a new enzymatic function.  II.  Evolution of multiple functions for EBG  enzyme in E. coli .  Genetics 89: 453-465.

15.    Hall, B. G.  1978.  Regulation of newly evolved enzymes.  IV.  Directed evolution of the EBG  repressor.  Genetics 90: 673 – 681.

16.    Hall, B. G.  1979.  Lactose metabolism involving phospho-b-galactosidase in Klebsiella .  J. Bacteriol.  138: 691-698.

17.    Hall, B. G.  1980.  Properties of b-galactosidase III:  Implications for entry of galactosides into Klebsiella .  J. Bacteriol. 142: 433-438.

18.    Rolseth, S.J., V. Fried, and B.G. Hall  1980.  A mutant ebg  enzyme that converts lactose into an inducer of the lac operon.  J. Bacteriol. 142: 1036 – 1039.

19.    Hall, B. G. and T. Zuzel.  1980.  Evolution of a new enzymatic function by recombination within a gene.  Proc. Nat. Acad. Sci. U.S. 77: 3529 – 3533.

20.    Hall, B. G.  1980.  On the evolution of new metabolic functions in diploid organisms.  Genetics 96: 1007 – 1017.

21.    Hall, B. G. and T. Zuzel.  1980.  The ebg  operon consists of at least two genes.  J. Bacteriol.  144:  1208 – 1211.

22.    Imai, K. and B.G. Hall.  1981.  Properties of the lactose transport system in Klebsiella  strain CT-1. J. Bacteriol. 145:  1459 – 1462.

23.    Hall, B. G.  1981.  Changes in the substrate specificities of an enzyme during directed evolution of new functions.  Biochemistry 20: 4042 – 4049.

24.    Baumann, P., L. Baumann and B.G. Hall.  1981.  Lactose utilization by Vibrio vulnificus .  Current Microbiology 6: 131 – 135.

25.    Hall, B. G.,  K. Imai, and C. Romano.  1982.  Genetics of the lac-PTS system of Klebsiella .  Genetical Research 39: 287 – 302.

26.    Hall, B. G.  1982.  Transgalactosylation activity of EBG b-galactosidase synthesizes allolactose from lactose.  J. Bacteriol.  150: 132 – 140.

27.    Hall, B. G.  1982.  Evolution of a regulated operon in the laboratory.  Genetics 101: 335 – 344.

28.    Hall, B. G.  1982.  A chromosomal mutation for citrate utilization by Escherichia coli  K12.  J. Bacteriol.  151: 269 – 273.

29.    Hall, B. G.  1982.  EVOLUTION ON A PETRI DISH:  using the evolved b-galactosidase system as a model for studying acquisitive evolution in the laboratory.  Evolutionary Biology 15: 85 – 149.

30.    Hall, B. G., M. Murray, S. Osborne, and M.L. Sinnott.  1983.  The catalytic consequences of experimental evolution.  Part III.  Construction of reaction profiles for hydrolysis of lactose by ebgo, ebga, and ebgb enzymes via measurements of the enzyme-catalyzed exchange of galactose-1-18O by 13C NMR spectroscopy.  J. Chem. Soc. Perkin II: 1595 -1598.

31.    Hall, B. G.  1983a.  Yeast thermotolerance does not require protein synthesis.  J. Bacteriol. 156: 1363 – 1365.

32.    Hall, B. G., S. Yokoyama and D. Calhoun.  1983.  Role of cryptic genes in microbial evolution.  Mol. Biol & Evol. 1: 109 – 124.

33.    Hall, B. G. 1983b.  Evolution of new metabolic functions in the laboratory. In Evolution of Genes and Proteins. ,  M. Nei and R. Koehn, eds.  Sinauer Assoc., Sunderland, MA pp 234 – 257.

34.    Kricker, M. and B.G. Hall.  1984.  Directed evolution of cellobiose utilization in Escherichia coli .  Mol. Biol. & Evol. 1: 171 -182.

35.    Stokes, H.W. and B.G. Hall.  1984.  Topological repression of gene activity by a transposable element.  Proc. Nat. Acad. Sci. U.S.  81: 6115 – 6119.

36.    Hall, B. G.  1984.  The evolved b-galactosidase system of Escherichia coli.  In:  Microorganisms as Model Systems for Studying Evolution .  R.P. Mortlock, ed.  Plenum Publishing Corp.  pp. 165 – 185.

37.    Hall, B. G.  1984.  Adaptation by acquisition of novel enzyme activities.  In: Current Perspectives in Microbial Ecology .  M.K. Klug and C.A. Reddy, eds.  ASM Publications, Washington, D.C. pp. 76 – 86.

38.    Slater, J.H., A.J. Weightman, and B.G. Hall.  1985.  Dehalogenase genes of Pseudomonas putida  PP3 on chromosomally located transposable elements.   Mol. Biol. & Evol. 2:  557-567.

39.    Stokes, H.W. and B.G. Hall.  1985.  Sequence of the ebgR  gene of E. coli:  Evidence that the EBG and LAC operons are descended from a common ancestor.  Mol. Biol. & Evol. 2: 478-483.

40.    Stokes, H.W. , P.W. Betts, and B.G. Hall.  1985.  Sequence of the ebgA  gene of E. coli :  Comparison with the lacZ  gene.  Mol. Biol. & Evol. 2: 469-477.

41.    Hall, B. G.  1986.  Enzyme Evolution.  In:  Comprehensive  Biotechnology.   Vol. I., M. Moo-Young, editor.  Pergammon Press, Oxford, U.K.  pp. 553 – 566.

42.    Hall, B. G., P.W. Betts, and M. Kricker.  1986.   Maintenance of the Cellobiose Utilization Genes of Escherichia coli  in a Cryptic State.  Mol. Biol. & Evol.3: 389-402.

43.    Kricker, M. and B.G. Hall. 1987. Biochemical Genetics of the Cellobiose Utilization System of Escherichia coli K12.  Genetics 115: 419-429.

44.    Hall, B. G. and P.W. Betts.  1987.  Cryptic Genes for Cellobiose Utilization in Natural Isolates of Escherichia coli.  Genetics 115:­ ­ 431-439.

45.    Hall, B. G.  and W. Faunce III. 1987. Functional Genes for Cellobiose Utilization in Natural Isolates of Escherichia coli.   J. Bacteriol. 169: 2713-2717.

46.    Parker, L.L., P.W. Betts,  and B.G. Hall. 1988.  Activation of a cryptic gene by excision of a DNA fragment..   J. Bacteriol. 170: 218-222.

47.    Hall, B. G.  1988. Widespread distribution of a deletion of the bgl  operon in natural isolates of Escherichia coli .   Mol. Biol. Evol. 5: 456-457.

48.    Parker, L.L., and B.G. Hall.  1988.  A fourth E. coli gene system with the potential to evolve b-glucoside utilization.  Genetics  119: 485-490.

49.    Hall, B. G.  1988.  Adaptive evolution that requires multiple spontaneous mutations.  I.  Mutations involving an insertion sequence.  Genetics 120: 887-897.

50.    Hall, B. G., L.L. Parker, P.W. Betts, R.F. DuBose, S.A. Sawyer, and D.L. Hartl.  1989.  IS103, a new insertion element in E. coli: Characterization and distribution in natural populations.  Genetics  121: 423-431.

51.    Hall, B. G.  1989.  Selection, Adaptation, and Bacterial Operons.  Genome 31: 265-271.

52.    Hall, B. G.  1989.  Adaptive Evolution  { A solicited popular science article} .  The World & I.  4: #3 (March) 276-283.

53.    Hall, B. G.  1989 .  Genetic Mobility { Book review of  “Mobile DNA”, edited by Berg and Howe} .  Science 245: 84-85.

54.    Hall, B. G. , P. W. Betts, and J. C. Wootton   1989.   DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes.  Genetics 123: 635-648.

55.    Parker, L. L. and B. G. Hall  1990.   Characterization and nucleotide sequence of the cryptic cel operon of E. coli K12.  Genetics 124:455-471.

56.    Parker, L. L. and B. G. Hall  1990.  Mechanisms of activation of the cryptic cel operon of E. coli K12.  Genetics 124:473-482.

57.    Hall, B. G.  1990.  Spontaneous point mutations that occur more often when they are advantageous than when they are neutral. Genetics 126: 5-16.

58.    Hall, B. G.  1990. Directed Evolution of a Bacterial Operon.  BioEssays 12: 551-558.

59.    Hall, B. G.  1991.  Increased Rates of Advantageous Mutations in Response to Environmental Challenges. ASM News 57: 82-86

60.    Hall, B. G. 1991.  Shortchanging Basic Science:  Why young scientists are discouraged.  Editorial in Los Angeles Times, April 7, Page M2.

61     Hall, B. G.  1991. Adaptive Evolution that Requires Multiple Spontaneous Mutations:  Mutations Involving Base Substitutions.  Proc. Nat. Acad. Sci. USA  88: 5882-5886.

62.    Hall, B. G.  1991.  Spectrum of mutations that occur under selective and non-selective conditions in E. coli. Genetica 84: 73-76.

63.    Hall, B. G., L. Xu and H. Ochman.  1991.  Physical map location of the asc operon of Escherichia coliK12.  J. Bacteriol. 173:5250.

64.    Hall, B. G. 1991.  Is the occurrence of some spontaneous mutations directed by environmental challenges?  New Biologist 3: 729-733.

65.    Elliott, A. C., K, S., Sinnott, M. L., Smith, P. J., Bommuswamy, J.,  Guo, Z., Hall, B. G., & Zhang, Y.  1992.  The catalytic consequences of experimental evolution.  Studies on the subunit structure of second (ebg) b-galactosidase of Escherichia coli, and on catalysis by  ebgab, an experimental evolvant containing two amino acid substitutions.   Biochem. J. 282: 155-164.

66.    Hall, B. G. 1992.  Selection-induced mutations occur in yeast.  Proc. Nat. Acad. Sci. USA 89: 4300-4303.

67.    Hall, B. G. and P.M. Sharp.  1992.  Molecular population genetics of Escherichia coli:  DNA sequence diversity at the celC, crr, and gutB loci of natural isolates.  Mol. Biol Evol.9: 654-665.

68.    Hall, B. G. and L. Xu.  1992.  Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coliK12.  Mol. Biol. Evol.9: 688-706.

69.    Hall, B. G.  1992.  Selection-induced Mutations.  Current Opinion in Genetics and Development 2:  943-946.

70.    Hall, B. G. and B. Hauer.  1993.  Acquisition of New Metabolic Activities by Microbial Populations, in “Molecular Evolution:  Producing the Biochemical Data.” E.A. Zimmer, T.J. White, R.L. Cann and A.C. Wilson, eds. Methods in Enzymology  244: 603-613.

71.    Srinivasan, K., A. Konstantindis, M.L. Sinnott, and B.G. Hall.  1993.  Large changes of transition state structure during experimental evolution of an enzyme.  Biochem. J. 291: 15-17.

72.    Hall, B. G.  1993.  The role of single-mutant intermediates in the generation of trpAB double revertants during prolonged selection.  J. Bacteriol. 175: 6411-6414.

73.    Xu, L. and B.G. Hall.  1994.  SASA: a simplified, reliable method for allele-specific amplification of polymorphic sites.  BioTechniques 16: 44-45.

74.    Hall, B. G.  1994.  On alternatives to selection-induced mutations in the Bgl operon of Escherichia coli. Mol. Biol. Evol. 11: 159-168.

75.    Hall, B. G.  1994. Selection or mutation:  Which, if either, comes first?  FEMS Microbiol. Lett. 117: 237-242.

76.    Hall, B. G.  1995.  Genetics of selection-induced mutations.  I.  uvrA, uvrB, uvrC, and uvrD are selection-induced specific mutator loci.   J. Mol. Evol. 40: 86-93.

77.    Hall, B. G.  1995.  Evolutionary potential of the ebgA gene. Mol. Biol. Evol. 12: 514-517.

78.    Hall, B. G.  1995.  Adaptive mutations in E. coli as a model for the multiple-mutation origins of tumors. Proc. Nat. Acad. Sci. USA.92: 5669-5673.

79.    Calugaru, S.V., B.G. Hall, and M.L. Sinnott.  1995. Catalysis by the large subunit of the second b-galactosidase of Escherichia coli in the absence of the small subunit. Biochem J.   312: 281-286

80.    Srinivasan, K., B.G. Hall, and M.L. Sinnott.  1995.  The catalytic consequences of experimental evolution.  Catalysis by a “third generation” evolvant of the second b-galactosidase of Escherichia coli, Ebgabcde, and by a “second generation” evolvant containing two supposedly “kinetically silent” mutations.  Biochem. J.  312: 971-977.

81.    Hall, B. G.  1997.  On the specificity of adaptive mutations.  Genetics 145: 39-44.

82.    Calugaru, S.V., Krishnan, S., Chany II, C.J., Hall, B. G., and Sinnott, M.L.  1997.  Larger increases in sensitivity to paracatalytic inactivation than in catalytic competence during experimental evolution of the second b-galactosidase of Escherichia coli.   Biochem J.  325: 117-121.

83.       Hall, B. G.  1997.  The rtn gene of Proteus vulgaris is actually from E. coli.  J. Bacteriol. 179: 2433-2434.

84.       Riesenfeld, C., M.  Everett, L.J.V.  Piddock, and B.G.  Hall.  1997 Adaptive mutations produce resistance to ciprofloxacin.  Antimicrob.  Agents Chemother. 41: 2059-2060

85.       Hall, B. G.  1998 Activation of the Bgl+ operon by adaptive mutations.  Mol. Biol. Evol. 15: 1-5

86.       Hall, B. G. 1998.  Adaptive Mutagenesis: A process that generates almost exclusively beneficial mutations.  Genetica 102/103: 109-125

87.       Hall, B. G.  1998  Adaptive mutagenesis at ebgR is regulated by PhoPQ.   J. Bacteriol. 180: 2862-2865.

88.       Hall, B.  G. and H.S. Malik  1998.  Determining the evolutionary potential of a gene.  Mol.  Biol.  Evol. 15: 1055-1061

89.       Raychaudhuri, S., J. Conrad, B. G. Hall, and J. Offengand  1998.  A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli.    RNA 4: 1407-1417.

90.       Hall, B. G.  1999.  The spectra of spontaneous growth-dependent and adaptive mutations at ebgR  J. Bacteriol. 181: 1149-1155.

91.       Hall, B. G. 1999. Experimental evolution  of Ebg enzyme provides clues about the evolution of catalysis and to evolutionary potential.  FEMS Microbiol. Lett. 174: 1-8.

92.       Hall, B. G. 1999  Toward an Understanding of Evolutionary Potential.  FEMS Microbiol. Lett.  178: 1-6.

93.       Thompson, J., S. B. Ruvinov, D. I. Freedberg and B. G. Hall.  1999 Cellobiose-6- Phosphate hydrolase (CelF) of Escherichia coli: characterization and assignment  to the unusual family 4 of Glycosylhydrolases.  J.  Bacteriol 181: 7339-7345.

94.       Hall, B. G.  1999   Transposable Elements as Activators of Cryptic Genes in E. coli.  Genetica  107 :181-187.

95        Hall, B. G.  2001  Phylogenetic Trees Made Easy:  A How-To Manual for Molecular Biologists.  Sinauer, Assoc. Sunderland, MA.

96.       Hall, B. G. 2001  Predicting Evolutionary Potential.  I.  Predicting the evolution of a Lactose-PTS system in E. coli.  Mol. Biol. Evol  18: 1389-1400.

97.       Thompson, J.,  S.A. Robrish, S. Immel, F.W. Lichtenthaler, B.G. Hall, and A. Pikis.  2001. Metabolism of sucrose and its five linkage-isomeric a-D-glucosyl-D-fructoses by Klebsiella pneumoniae: participation and properties of sucrose-6-phosphate hydrolase and phospho-a-glucosidase  J. Biol. Chem. 276: 37415-37425.

98.       Barlow, M. and B.G. Hall.  2002. Predicting Evolutionary Potential: In vitro Evolution Accurately Reproduces Natural Evolution of the TEM b-Lactamase. Genetics 160: 823-832.

99.       Barlow, M. and B.G. Hall.  2002.  Origins and evolution of the ampC b-lactamases of Citrobacter freundii. Antimicrob.  Agents Chemother. 46: 1190-1198.

100.     Barlow, M. and B.G. Hall.  2002  Phylogenetic analysis shows that the OXA b-lactamase genes have been on plasmids for millions of years.  J. Mol. Evol. 55: 314-321.

101.     Hall, B. G. 2002 Predicting evolution by in vitro evolution requires determining evolutionary pathways.  Antimicrob.  Agents Chemother: 46: 3035-3038.

102      Hall, B. G.  2002  Experimental evolution of antibiotic resistance.  APUA  Newsletter 20 No. 4: 4-5

103.     Hall, B. G. 2003  The EBG system of E. coli: Origin and evolution of a novel b-galactosidase for the metabolism of lactose.  Genetica 118: 143-156.

104.     Barlow, M. and B.G. Hall.  2003. Experimental Prediction of the Natural Evolution of Antibiotic Resistance.  Genetics 163: 1237-1241.

105.     Salipante, S. and B.G. Hall.  2003. Determining the limits of the evolutionary potential of an antibiotic resistance gene.  Mol. Biol. Evol. 20: 653-659.

106.     Barlow, M. and B.G. Hall.  2003. Experimental Prediction of the Evolution of Cefepime Resistance from the CMY-2 AmpC b-lactamase.  Genetics 164:  23-29.

107.       Hall, B. G., S. Salipante and M. Barlow. 2003. The metallo-b-lactamases fall into two distinct phylogenetic groups.   J. Mol. Evol 57: 249-254.

108.       Hall, B. G. and  M. Barlow.  2003. Structure based phylogenies of the serine b-lactamases.  J. Mol. Evol. 57: 255-260.

—.         Hall, B. G. 2003.  In vitro Sim: A program for simulating in vitro evolution experiments using the Barlow-Hall method.  Bellingham Research Institute.

109.       Salipante, S., M. Barlow, and B.G. Hall. 2003.  GeneHunter, a transposon tool for the identification and characterization of cryptic antibiotic resistance genes..  Antimicrob. Agents Chemother. 47: 3840-3845.

110.       Hall, B. G.  2004.   In vitro evolution predicts that  the IMP-1 metallo-b-lactamase does not have the potential to evolve increased activity toward imipenem.  Antimicrob. Agents. Chemother. 48: 1032-1033.

111.       Hall, B. G. 2004 .  Predicting the evolution of antibiotic resistance.  Nature Reviews Microbiology 2: 430-435

112.       Hall, B. G. and M. Barlow 2004.  Evolution of the serine b-lactamases: Past, Present and Future.  Drug Resistance Updates  7: 111-123.

113.     Hall, B. G.  2004  Phylogenetic Trees Made Easy:  A How-To Manual. 2nd Edition.  Sinauer, Assoc. Sunderland, MA.

114      Hall, B. G., S. Salipante and M. Barlow. 2004.  Independent origins of the Subgroup (B1 + B2) and the Subgroup B3 metallo-b-lactamases. J. Mol. Evol. 59: 132-140.

115.     Hall, B. G. 2005. Comparison of the Accuracies of Several Phylogenetic Methods Using Protein and DNA Sequences.  Mol. Biol Evol. 22: 792-802.

116.     Garau, G.  A. M.  Di Guilmi, and  B. G. Hall. 2005.  Structure-based phylogeny of the metallo-b-lactamases. Antimicrob. Agents and Chemother.  49:  2778-2784.

117.     Hall, B. G. and M. Barlow. 2005.  Revised Ambler Classification of b-lactamases.  J. Antimicrob. Chemother. 55:1050-1051

118.     Hall, B. G. and M. Barlow. 2006. Phylogenetic Analysis as a Tool for Molecular Epidemiology of Infectious Diseases. Annals of Epidemiology 16: 157-169.

119      Hall, B. G.  2006 Simple and accurate estimation of ancestral protein sequences.  Proc. Nat. Acad. Sci. USA 103: 5431-5436.

120.     Hall, B. G. 2006.  Predicting the evolution and emergence of new antibiotic-resistance genes: an important element in developing antibiotics and antibiotic therapeutic policy.  In Antimicrobial Resistance in Bacteria.  C. F. Amábile-Cuevas, editor.  Horizon Scientific Press , U.K.  pp. 149 – 166.

121.     Hall, B. G. 2007 Phylogenetic Trees Made Easy:  A How-To Manual. 3rd Edition.  Sinauer, Assoc. Sunderland, MA.

122.     Hall, B. G. 2008  Simulating DNA coding sequence evolution with EvolveAGene 3.  Mol. Biol. Evol.  25: 688-695.

—.       Hall, B. G. and M. Barlow.  2008  Barlow-Hall in vitro Evolution Protocol.  Available from Nature Precedings <;

123.     Hall, B. G.  2008.  How well does the HoT score reflect sequence alignment accuracy?  Mol. Biol. Evol. 25:  1576-1580.

124.     Hall, B. G., A. Pikis and J. Thompson.  2009.  Evolution and biochemistry of Family 4 glycosidases: implications for assigning enzyme function  in sequence annotations. Mol. Biol. Evol. 26: 2487-2497.

125.     Hall, B. G. 2009. Molecular Epidemiology of Mycobacterium leprae: a solid beginning.  Leprosy Review 80: 246-249.

126.     Gillis, T., V. Vissa, M. Matsuoka, S. Young, J.H. Richardus, R. Truman, B.G. Hall, P. Brennan, IDEAL Consortium Partners. 2009  Characterization of short tandem repeats for genotyping Mycobacterium lepraeLeprosy Review 80: 250-260.

127.     Hall, B. G., G.D. Ehrlich and F.Z. Hu.  2010.  Pan-genome analysis provides much higher strain typing resolution than does MLST. Microbiology 156: 1060-1068.

128.     Hall, B. G. and S. J. Salipante. 2010 Molecular Epidemiology of Mycobacterium leprae as Determined by Structure-Neighbor Clustering. J. Clinical Microbiology 46: 1997-2008.

129.     Hall, B. G. 2010.  A Mycobacterium leprae VNTR database.  Leprosy Review 81: 96-98.

130.     Hall, B. G. 2011. Phylogenetic Trees Made Easy:  A How-To Manual. 4th Edition.  Sinauer, Assoc. Sunderland, MA.

131.     Boissy, R., A. Ahmed, B. Janto1, J. Earl, B. G. Hall, J. S. Hogg, G. D. Pusch,, N. L. Hiller, E. Powell, J. Hayes, S. Yu, S. Kathju, P. Stoodley, J. C. Post, G. D. Ehrlich and Fen Z. Hu. 2011. Comparative Supragenomic Analyses among the Pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a Modification of the Finite Supragenome Model.  BMC Genomics 12: 187.

132.     Salipante, S.J. and B.G. Hall  2011 Towards the Molecular Epidemiology of Mycobacterium leprae: Strategies, Successes, and Shortcomings.  Infection, Genetics and Evolution 11: 1505-1513.

133.     Salipante, S.J. and B.G. Hall  2011 The Inadequacies of Minimum Spanning Trees in Molecular Epidemiology.  J. Clinical Microbiology 46: 3568-3575.

134.     Hall, B. G. 2011 Walter Fitch: Founder of a Journal, a Society and a Field.  Mol. Biol. Evol. 28: 3405-3409.

135.     Ahmed,  A., J. Earl, A. Retchless, S.L. Hillier, L.K. Rabe, T.L. Cherpes, E. Powell, B. Janto, R. Eutsey, N.L. Hiller, R. Boissy,  M.E. Dahlgren, B.G. Hall,  J.W. Costerton,  J.C. Post, F.Z. Hu, and G.D. Ehrlich  2012  Comparative genomic analyses of seventeen clinical isolates of Gardnerella vaginalis provides evidence of multiple genetically isolated clades consistent with sub-speciation into genovars.  J. Bacteriology 194: 3922-3937.

136.     Goulart, C. P. , M. Mahmudi, K. A. Crona, S. D. Jacobs, M. Kallmann, B. G. Hall, D. C. Greene, M. Barlow  2013 Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes.  PLOS One 8(2): e56040. doi:10.1371/journal.pone.0056040.

137.     Hall, B. G.  2013 Building Phylogenetic Trees from Molecular Data with MEGA.  Mol. Biol. Evol.  30: 1229-1235,  doi: 10.1093/molbev/mst012.

138.     Thompson, J., A. Pikis, J. Rich, B. G. Hall and S. G. Withers.  2013  α-Galacturonidase(s): a new class of Family 4 glycoside hydrolases with strict specificity and a unique active site motif.  2013 FEBS Lett. 587: 3322-3327. .

139.     Hall, B. G., L. Cardenas, and M. Barlow. 2013 Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes. PLoS ONE 8(7): e68901. doi:10.1371/journal.pone.0068901

140.     Hall, B. G.,  B.C. Kirkup,  M.C. Riley and M. Barlow  2013  Clustering Acinetobacter Strains by Optical Mapping.  Genome Biol. Evol. 5: 1176-1184; doi: 10.1093/gbe/evt085.

141.     Gardner, S. N. and B. G. Hall.  2013  When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.  PLoS One 8(12): e81760. doi:10.1371/journal.pone.0081760

142.     Hall, B. G., H. Acar, A. Nandipati and M. Barlow.  2014  Growth Rates Made Easy.  Mol. Biol. Evol. 31: 232-238doi:10.1093/molbev/mst197 .

143.     Hall, B.G.  2014  SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.  PLoS One  9(2): e90490. doi:10.1371/journal.pone.0090490

144.     Hall, B.G.  2015  Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP.  Cladistics 32: 90-99 (doi: 10.1111/cla.12113).

145.     Gardner, S.N., T. Slezak, and B.G. Hall.  2015.  kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genomes.  Bioinformatics 31: 2877-2878  doi: 10.1093/bioinformatics/btv271.

146.     Ankrum, A. and  B. G. Hall. 2017.  Population dynamics of Staphylococcus aureus in Cystic Fibrosis patients to determine transmission events utilizing WGS.  J. Clin. Microbiol. 55: 2143 – 2152. (doi:10.1128.JCM00164-17)

147.     Hall, B. G. 2017. Phylogenetic Trees Made Easy:  A How-To Manual. 5th Edition.  Sinauer, Assoc. Sunderland, MA.

148.     Mira, P., M. Barlow, and B. G. Hall.  2017. Statistical Package for Growth Rates Made Easy. Mol. Biol. Evol.  34: 3303-3309.  doi: 10.1093/molbev/msx255.

149.    Hall, B. G. 2018. Identifying Plasmids in Bacterial Genome Assemblies.  BioRxiv doi 10.1101/332049.

150.     Hall, B.G. 2021. Stress proteins as predictors of COVID-19 outcomes.  Cell Stress and Chaperones

151. Portia Mira , Pamela Yeh, Barry G. Hall 2022. Estimating microbial population density with optical density. PLOS ONE

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