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Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae.

Richards VP, Velsko IM, Alam T, Zadoks RN, Manning SD, Pavinski Bitar PD, Hasler HB, Crestani C, Springer G, Probert B, Town CD, Stanhope MJ.

Mol Biol Evol. 2019 Jul 27. pii: msz169. doi: 10.1093/molbev/msz169. [Epub ahead of print]


White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability.

Marra NJ, Stanhope MJ, Jue NK, Wang M, Sun Q, Pavinski Bitar P, Richards VP, Komissarov A, Rayko M, Kliver S, Stanhope BJ, Winkler C, O'Brien SJ, Antunes A, Jorgensen S, Shivji MS.

Proc Natl Acad Sci U S A. 2019 Feb 19. pii: 201819778. doi: 10.1073/pnas.1819778116. [Epub ahead of print]


Transcriptome-Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks.

Bernard AM, Richards VP, Stanhope MJ, Shivji MS.

J Hered. 2018 Oct 31;109(7):771-779. doi: 10.1093/jhered/esy045.


Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy.

Marra NJ, Richards VP, Early A, Bogdanowicz SM, Pavinski Bitar PD, Stanhope MJ, Shivji MS.

BMC Genomics. 2017 Jan 30;18(1):87. doi: 10.1186/s12864-016-3411-x.


Blastocystis Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons.

Jacob AS, Andersen LO, Bitar PP, Richards VP, Shah S, Stanhope MJ, Stensvold CR, Clark CG.

Genome Biol Evol. 2016 Dec 14;8(11):3340-3350.


Laser capture microdissection microscopy and genome sequencing of the avian malaria parasite, Plasmodium relictum.

Lutz HL, Marra NJ, Grewe F, Carlson JS, Palinauskas V, Valkiūnas G, Stanhope MJ.

Parasitol Res. 2016 Dec;115(12):4503-4510. Epub 2016 Sep 21.


Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents.

Lutz HL, Patterson BD, Kerbis Peterhans JC, Stanley WT, Webala PW, Gnoske TP, Hackett SJ, Stanhope MJ.

Mol Phylogenet Evol. 2016 Jun;99:7-15. doi: 10.1016/j.ympev.2016.03.004. Epub 2016 Mar 12.


Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species.

Huguet-Tapia JC, Lefebure T, Badger JH, Guan D, Pettis GS, Stanhope MJ, Loria R.

Appl Environ Microbiol. 2016 Jan 29;82(7):2146-2155. doi: 10.1128/AEM.03504-15.


Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli.

Richards VP, Lefébure T, Pavinski Bitar PD, Dogan B, Simpson KW, Schukken YH, Stanhope MJ.

PLoS One. 2015 Mar 25;10(3):e0119799. doi: 10.1371/journal.pone.0119799. eCollection 2015. Erratum in: PLoS One. 2015;10(7):e0133222.


A unique open reading frame within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance.

Kaspar J, Ahn SJ, Palmer SR, Choi SC, Stanhope MJ, Burne RA.

Mol Microbiol. 2015 May;96(3):463-82. doi: 10.1111/mmi.12948. Epub 2015 Mar 4.


Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation.

Dogan B, Suzuki H, Herlekar D, Sartor RB, Campbell BJ, Roberts CL, Stewart K, Scherl EJ, Araz Y, Bitar PP, Lefébure T, Chandler B, Schukken YH, Stanhope MJ, Simpson KW.

Inflamm Bowel Dis. 2014 Nov;20(11):1919-32. doi: 10.1097/MIB.0000000000000183.


Phylogenomics and the dynamic genome evolution of the genus Streptococcus.

Richards VP, Palmer SR, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ.

Genome Biol Evol. 2014 Apr;6(4):741-53. doi: 10.1093/gbe/evu048.


Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment.

Richards VP, Choi SC, Pavinski Bitar PD, Gurjar AA, Stanhope MJ.

BMC Genomics. 2013 Dec 27;14:920. doi: 10.1186/1471-2164-14-920.


Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).

Richards VP, Suzuki H, Stanhope MJ, Shivji MS.

BMC Genomics. 2013 Oct 11;14:697. doi: 10.1186/1471-2164-14-697.


Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans.

Palmer SR, Miller JH, Abranches J, Zeng L, Lefebure T, Richards VP, Lemos JA, Stanhope MJ, Burne RA.

PLoS One. 2013 Apr 16;8(4):e61358. doi: 10.1371/journal.pone.0061358. Print 2013. Erratum in: PLoS One. 2013;8(11). doi:10.1371/annotation/ffff8cd5-b8fa-4d3c-a993-e5169198f1e6.


Core-gene-encoded peptide regulating virulence-associated traits in Streptococcus mutans.

Kim JN, Stanhope MJ, Burne RA.

J Bacteriol. 2013 Jun;195(12):2912-20. doi: 10.1128/JB.00189-13. Epub 2013 Apr 19.


Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA.

PLoS One. 2013;8(3):e60465. doi: 10.1371/journal.pone.0060465. Epub 2013 Mar 28.


Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).

Lin C, den Bakker HC, Suzuki H, Lefébure T, Ponnala L, Sun Q, Stanhope MJ, Wiedmann M, Duhamel GE.

Genome Announc. 2013 Jan;1(1). pii: e00215-12. doi: 10.1128/genomeA.00215-12. Epub 2013 Feb 21.


A galactose-specific sugar: phosphotransferase permease is prevalent in the non-core genome of Streptococcus mutans.

Zeng L, Xue P, Stanhope MJ, Burne RA.

Mol Oral Microbiol. 2013 Aug;28(4):292-301. doi: 10.1111/omi.12025. Epub 2013 Feb 20.


Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species.

Richards VP, Lefébure T, Pavinski Bitar PD, Stanhope MJ.

Infect Genet Evol. 2013 Mar;14:200-13. doi: 10.1016/j.meegid.2012.12.010. Epub 2012 Dec 29. Erratum in: Infect Genet Evol. 2014 Jan;21:506-7.


Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis.

Richards VP, Zadoks RN, Pavinski Bitar PD, Lefébure T, Lang P, Werner B, Tikofsky L, Moroni P, Stanhope MJ.

BMC Microbiol. 2012 Dec 18;12:293. doi: 10.1186/1471-2180-12-293.


Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans.

Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ.

Mol Biol Evol. 2013 Apr;30(4):881-93. doi: 10.1093/molbev/mss278. Epub 2012 Dec 10.


Outcome of infection of C57BL/6 IL-10(-/-) mice with Campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo.

Bell JA, Jerome JP, Plovanich-Jones AE, Smith EJ, Gettings JR, Kim HY, Landgraf JR, Lefébure T, Kopper JJ, Rathinam VA, St Charles JL, Buffa BA, Brooks AP, Poe SA, Eaton KA, Stanhope MJ, Mansfield LS.

Microb Pathog. 2013 Jan;54:1-19. doi: 10.1016/j.micpath.2012.08.001. Epub 2012 Aug 31.


Progress dissecting the oral microbiome in caries and health.

Burne RA, Zeng L, Ahn SJ, Palmer SR, Liu Y, Lefebure T, Stanhope MJ, Nascimento MM.

Adv Dent Res. 2012 Sep;24(2):77-80. doi: 10.1177/0022034512449462. Review.


Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae.

Lefébure T, Richards VP, Lang P, Pavinski-Bitar P, Stanhope MJ.

PLoS One. 2012;7(5):e37607. doi: 10.1371/journal.pone.0037607. Epub 2012 May 30.


Replacing and additive horizontal gene transfer in Streptococcus.

Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope MJ, Siepel A.

Mol Biol Evol. 2012 Nov;29(11):3309-20. doi: 10.1093/molbev/mss138. Epub 2012 May 21.


Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae.

Suzuki H, Lefébure T, Bitar PP, Stanhope MJ.

BMC Genomics. 2012 Jan 24;13:38. doi: 10.1186/1471-2164-13-38.


Functional bias of positively selected genes in Streptococcus genomes.

Suzuki H, Stanhope MJ.

Infect Genet Evol. 2012 Mar;12(2):274-7. doi: 10.1016/j.meegid.2011.11.004. Epub 2011 Dec 3.


Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.

Richards VP, Lang P, Bitar PD, Lefébure T, Schukken YH, Zadoks RN, Stanhope MJ.

Infect Genet Evol. 2011 Aug;11(6):1263-75. doi: 10.1016/j.meegid.2011.04.019. Epub 2011 Apr 22.


Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ.

Genome Biol Evol. 2011;3:168-85. doi: 10.1093/gbe/evr006. Epub 2011 Jan 31.


Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.

Lefébure T, Bitar PD, Suzuki H, Stanhope MJ.

Genome Biol Evol. 2010;2:646-55. doi: 10.1093/gbe/evq048. Epub 2010 Aug 4.


Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts.

Lang P, Lefebure T, Wang W, Pavinski Bitar P, Meinersmann RJ, Kaya K, Stanhope MJ.

Appl Environ Microbiol. 2010 Mar;76(6):1913-25. doi: 10.1128/AEM.01753-09. Epub 2010 Jan 22.


Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter.

Lefébure T, Stanhope MJ.

Genome Res. 2009 Jul;19(7):1224-32. doi: 10.1101/gr.089250.108. Epub 2009 Mar 20.


Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray comparative genomic hybridization.

Lang P, Lefébure T, Wang W, Zadoks RN, Schukken Y, Stanhope MJ.

Infect Genet Evol. 2009 Mar;9(2):179-88. doi: 10.1016/j.meegid.2008.10.015. Epub 2008 Nov 14.


Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development.

Stanhope MJ, Lefébure T, Walsh SL, Becker JA, Lang P, Pavinski Bitar PD, Miller LA, Italia MJ, Amrine-Madsen H.

Infect Genet Evol. 2008 May;8(3):331-9. doi: 10.1016/j.meegid.2008.02.001. Epub 2008 Feb 14.


The relative frequency of intraspecific lateral gene transfer of penicillin binding proteins 1a, 2b, and 2x, in amoxicillin resistant Streptococcus pneumoniae.

Stanhope MJ, Walsh SL, Becker JA, Miller LA, Lefébure T, Lang P, Bitar PD, Amrine-Madsen H.

Infect Genet Evol. 2007 Jul;7(4):520-34. Epub 2007 Mar 30.


Molecules consolidate the placental mammal tree.

Springer MS, Stanhope MJ, Madsen O, de Jong WW.

Trends Ecol Evol. 2004 Aug;19(8):430-8.


Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans.

Burk-Herrick A, Scally M, Amrine-Madsen H, Stanhope MJ, Springer MS.

Mamm Genome. 2006 Mar;17(3):257-70. Epub 2006 Mar 3.


Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread.

Stanhope MJ, Walsh SL, Becker JA, Italia MJ, Ingraham KA, Gwynn MN, Mathie T, Poupard JA, Miller LA, Brown JR, Amrine-Madsen H.

Antimicrob Agents Chemother. 2005 Oct;49(10):4315-26.


A retroposon analysis of Afrotherian phylogeny.

Nishihara H, Satta Y, Nikaido M, Thewissen JG, Stanhope MJ, Okada N.

Mol Biol Evol. 2005 Sep;22(9):1823-33. Epub 2005 Jun 1.


Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV.

Stanhope MJ, Brown JR, Amrine-Madsen H.

Infect Genet Evol. 2004 Mar;4(1):15-9.


The use of composite taxa in supermatrices.

Springer MS, Scally M, Madsen O, de Jong WW, Douady CJ, Stanhope MJ.

Mol Phylogenet Evol. 2004 Mar;30(3):883-4. No abstract available.


"Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis.

Douady CJ, Scally M, Springer MS, Stanhope MJ.

Mol Phylogenet Evol. 2004 Mar;30(3):778-88.


Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials.

Amrine-Madsen H, Scally M, Westerman M, Stanhope MJ, Krajewski C, Springer MS.

Mol Phylogenet Evol. 2003 Aug;28(2):186-96.


The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews).

Douady CJ, Catzeflis F, Raman J, Springer MS, Stanhope MJ.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8325-30. Epub 2003 Jun 23.


Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens.

Brown JR, Gentry D, Becker JA, Ingraham K, Holmes DJ, Stanhope MJ.

EMBO Rep. 2003 Jul;4(7):692-8.

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