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kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.

Gardner SN, Slezak T, Hall BG.

Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271. Epub 2015 Apr 25.


Dead wrong: the growing list of racial/ethnic disparities in childhood mortality.

Flores G, Escala MK, Hall BG.

J Pediatr. 2015 Apr;166(4):790-3. doi: 10.1016/j.jpeds.2015.02.001. No abstract available.


SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.

Hall BG.

PLoS One. 2014 Feb 28;9(2):e90490. doi: 10.1371/journal.pone.0090490. eCollection 2014.


Growth rates made easy.

Hall BG, Acar H, Nandipati A, Barlow M.

Mol Biol Evol. 2014 Jan;31(1):232-8. doi: 10.1093/molbev/mst187. Epub 2013 Oct 28.


Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.

Hall BG, Cardenas H, Barlow M.

PLoS One. 2013 Jul 23;8(7):e68901. doi: 10.1371/journal.pone.0068901. Print 2013.


Clustering acinetobacter strains by optical mapping.

Hall BG, Kirkup BC, Riley MC, Barlow M.

Genome Biol Evol. 2013;5(6):1176-84. doi: 10.1093/gbe/evt085.


Building phylogenetic trees from molecular data with MEGA.

Hall BG.

Mol Biol Evol. 2013 May;30(5):1229-35. doi: 10.1093/molbev/mst012. Epub 2013 Mar 13.


Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes.

Goulart CP, Mahmudi M, Crona KA, Jacobs SD, Kallmann M, Hall BG, Greene DC, Barlow M.

PLoS One. 2013;8(2):e56040. doi: 10.1371/journal.pone.0056040. Epub 2013 Feb 13.


α-Galacturonidase(s): a new class of Family 4 glycoside hydrolases with strict specificity and a unique CHEV active site motif.

Thompson J, Pikis A, Rich J, Hall BG, Withers SG.

FEBS Lett. 2013 Mar 18;587(6):799-803. doi: 10.1016/j.febslet.2013.02.004. Epub 2013 Feb 14.


Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars.

Ahmed A, Earl J, Retchless A, Hillier SL, Rabe LK, Cherpes TL, Powell E, Janto B, Eutsey R, Hiller NL, Boissy R, Dahlgren ME, Hall BG, Costerton JW, Post JC, Hu FZ, Ehrlich GD.

J Bacteriol. 2012 Aug;194(15):3922-37. doi: 10.1128/JB.00056-12. Epub 2012 May 18.


Remembrances of Walter M. Fitch.

Hall BG, Ayala FJ, McClure MA.

Mol Biol Evol. 2011 Dec;28(12):3405-9. doi: 10.1093/molbev/msr260. No abstract available.


Inadequacies of minimum spanning trees in molecular epidemiology.

Salipante SJ, Hall BG.

J Clin Microbiol. 2011 Oct;49(10):3568-75. doi: 10.1128/JCM.00919-11. Epub 2011 Aug 17.


Towards the molecular epidemiology of Mycobacterium leprae: strategies, successes, and shortcomings.

Salipante SJ, Hall BG.

Infect Genet Evol. 2011 Oct;11(7):1505-13. doi: 10.1016/j.meegid.2011.06.003. Epub 2011 Jun 25. Review.


Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model.

Boissy R, Ahmed A, Janto B, Earl J, Hall BG, Hogg JS, Pusch GD, Hiller LN, Powell E, Hayes J, Yu S, Kathju S, Stoodley P, Post JC, Ehrlich GD, Hu FZ.

BMC Genomics. 2011 Apr 13;12:187. doi: 10.1186/1471-2164-12-187.


A Mycobacterium leprae VNTR database.

Hall BG.

Lepr Rev. 2010 Jun;81(2):96-8. No abstract available.


Molecular epidemiology of Mycobacterium leprae as determined by structure-neighbor clustering.

Hall BG, Salipante SJ.

J Clin Microbiol. 2010 Jun;48(6):1997-2008. doi: 10.1128/JCM.00149-10. Epub 2010 Mar 29.


Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing.

Hall BG, Ehrlich GD, Hu FZ.

Microbiology. 2010 Apr;156(Pt 4):1060-8. doi: 10.1099/mic.0.035188-0. Epub 2009 Dec 17.


Molecular epidemiology of Mycobacterium leprae: a solid beginning.

Hall BG.

Lepr Rev. 2009 Sep;80(3):246-9. No abstract available.


Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations.

Hall BG, Pikis A, Thompson J.

Mol Biol Evol. 2009 Nov;26(11):2487-97. doi: 10.1093/molbev/msp162. Epub 2009 Jul 22.

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