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Identification and characterization of putative Aeromonas spp. T3SS effectors.

Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP.

PLoS One. 2019 Jun 4;14(6):e0214035. doi: 10.1371/journal.pone.0214035. eCollection 2019.


Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21.

Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP.

Microbiol Resour Announc. 2019 Mar 21;8(12). pii: e00096-19. doi: 10.1128/MRA.00096-19.


The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.

Fullmer MS, Ouellette M, Louyakis AS, Papke RT, Gogarten JP.

Genes (Basel). 2019 Mar 19;10(3). pii: E233. doi: 10.3390/genes10030233.


Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients.

Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J.

MBio. 2018 Jul 24;9(4). pii: e01328-18. doi: 10.1128/mBio.01328-18.


Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire.

Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S.

ISME J. 2018 Oct;12(10):2559-2574. doi: 10.1038/s41396-018-0166-1. Epub 2018 Jun 28.


Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.

Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U.

Genes (Basel). 2018 Mar 20;9(3). pii: E172. doi: 10.3390/genes9030172.


Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.

Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT.

Genes (Basel). 2018 Feb 27;9(3). pii: E129. doi: 10.3390/genes9030129.


Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction.

Dick AA, Harlow TJ, Gogarten JP.

Mol Phylogenet Evol. 2017 Feb;107:338-344. doi: 10.1016/j.ympev.2016.11.016. Epub 2016 Nov 26.


Is LUCA a thermophilic progenote?

Gogarten JP, Deamer D.

Nat Microbiol. 2016 Nov 25;1:16229. doi: 10.1038/nmicrobiol.2016.229. No abstract available.


Does Sequence Conservation Provide Evidence for Biological Function?

Omer S, Harlow TJ, Gogarten JP.

Trends Microbiol. 2017 Jan;25(1):11-18. doi: 10.1016/j.tim.2016.09.010. Epub 2016 Oct 20. Review.


Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.

Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV, Balunas MJ.

Front Microbiol. 2016 Sep 8;7:1342. doi: 10.3389/fmicb.2016.01342. eCollection 2016.


Impact of a homing intein on recombination frequency and organismal fitness.

Naor A, Altman-Price N, Soucy SM, Green AG, Mitiagin Y, Turgeman-Grott I, Davidovich N, Gogarten JP, Gophna U.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4654-61. doi: 10.1073/pnas.1606416113. Epub 2016 Jul 26.


The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis.

Fullmer MS, Soucy SM, Gogarten JP.

Front Microbiol. 2015 Jul 21;6:728. doi: 10.3389/fmicb.2015.00728. eCollection 2015. No abstract available.


Horizontal gene transfer: building the web of life.

Soucy SM, Huang J, Gogarten JP.

Nat Rev Genet. 2015 Aug;16(8):472-82. doi: 10.1038/nrg3962. Review.


Ancient horizontal gene transfer and the last common ancestors.

Fournier GP, Andam CP, Gogarten JP.

BMC Evol Biol. 2015 Apr 22;15:70. doi: 10.1186/s12862-015-0350-0.


Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.

Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV.

Front Microbiol. 2015 Feb 23;6:123. doi: 10.3389/fmicb.2015.00123. eCollection 2015.


Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J.

MBio. 2014 Nov 18;5(6):e02136. doi: 10.1128/mBio.02136-14.


Inteins as indicators of gene flow in the halobacteria.

Soucy SM, Fullmer MS, Papke RT, Gogarten JP.

Front Microbiol. 2014 Jun 26;5:299. doi: 10.3389/fmicb.2014.00299. eCollection 2014.


AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y.

PLoS One. 2014 Jun 3;9(6):e98844. doi: 10.1371/journal.pone.0098844. eCollection 2014.


Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT.

Front Microbiol. 2014 Apr 9;5:143. doi: 10.3389/fmicb.2014.00143. eCollection 2014.


Population and genomic analysis of the genus Halorubrum.

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT.

Front Microbiol. 2014 Apr 11;5:140. doi: 10.3389/fmicb.2014.00140. eCollection 2014.


Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM.

PLoS One. 2013 Dec 31;8(12):e84300. doi: 10.1371/journal.pone.0084300. eCollection 2013.


Distribution and evolution of the mobile vma-1b intein.

Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP.

Mol Biol Evol. 2013 Dec;30(12):2676-87. doi: 10.1093/molbev/mst164. Epub 2013 Sep 18.


Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12.

Butzin NC, Secinaro MA, Swithers KS, Gogarten JP, Noll KM.

Appl Environ Microbiol. 2013 Nov;79(22):7006-12. doi: 10.1128/AEM.01800-13. Epub 2013 Sep 6.


Reconstruction of ancestral 16S rRNA reveals mutation bias in the evolution of optimal growth temperature in the Thermotogae phylum.

Green AG, Swithers KS, Gogarten JF, Gogarten JP.

Mol Biol Evol. 2013 Nov;30(11):2463-74. doi: 10.1093/molbev/mst145. Epub 2013 Aug 21.


The effects of model choice and mitigating bias on the ribosomal tree of life.

Lasek-Nesselquist E, Gogarten JP.

Mol Phylogenet Evol. 2013 Oct;69(1):17-38. doi: 10.1016/j.ympev.2013.05.006. Epub 2013 May 22.


Systematic inference of highways of horizontal gene transfer in prokaryotes.

Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R.

Bioinformatics. 2013 Mar 1;29(5):571-9. doi: 10.1093/bioinformatics/btt021. Epub 2013 Jan 17.


Pre-Posting and OLEB.

Schwartz AW, Cleaves HJ, Gogarten JP.

Orig Life Evol Biosph. 2012 Dec;42(6):517. doi: 10.1007/s11084-012-9317-y. No abstract available.


Quantifying homologous replacement of loci between haloarchaeal species.

Williams D, Gogarten JP, Papke RT.

Genome Biol Evol. 2012;4(12):1223-44. doi: 10.1093/gbe/evs098.


The impact of HGT on phylogenomic reconstruction methods.

Lapierre P, Lasek-Nesselquist E, Gogarten JP.

Brief Bioinform. 2014 Jan;15(1):79-90. doi: 10.1093/bib/bbs050. Epub 2012 Aug 20.


The role of reticulate evolution in creating innovation and complexity.

Swithers KS, Soucy SM, Gogarten JP.

Int J Evol Biol. 2012;2012:418964. doi: 10.1155/2012/418964. Epub 2012 Jul 12.


Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.

Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM, Butzin NC.

Genome Biol Evol. 2012;4(8):730-9. doi: 10.1093/gbe/evs057. Epub 2012 Jul 12.


Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs.

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM.

PLoS One. 2012;7(6):e40236. doi: 10.1371/journal.pone.0040236. Epub 2012 Jun 29.


Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.

Andam CP, Harlow TJ, Papke RT, Gogarten JP.

BMC Evol Biol. 2012 Jun 13;12:85. doi: 10.1186/1471-2148-12-85.


Quartet decomposition server: a platform for analyzing phylogenetic trees.

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y.

BMC Bioinformatics. 2012 Jun 7;13:123.


Ecology. How bacterial lineages emerge.

Papke RT, Gogarten JP.

Science. 2012 Apr 6;336(6077):45-6. doi: 10.1126/science.1219241. No abstract available.


Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life.

Fournier GP, Andam CP, Alm EJ, Gogarten JP.

Orig Life Evol Biosph. 2011 Dec;41(6):621-32. doi: 10.1007/s11084-011-9261-2. Epub 2011 Dec 27. Erratum in: Orig Life Evol Biosph. 2012 Aug;42(4):377.


Home and away- the evolutionary dynamics of homing endonucleases.

Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L.

BMC Evol Biol. 2011 Nov 4;11:324. doi: 10.1186/1471-2148-11-324.


Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores.

Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Saunders E, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Lykidis A, Land ML, Brettin T, Stetter KO, Nelson KE, Gogarten JP, Noll KM.

J Bacteriol. 2011 Oct;193(20):5869-70. doi: 10.1128/JB.05923-11.


Biased gene transfer and its implications for the concept of lineage.

Andam CP, Gogarten JP.

Biol Direct. 2011 Sep 23;6:47. doi: 10.1186/1745-6150-6-47.


A rooted net of life.

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP.

Biol Direct. 2011 Sep 21;6:45. doi: 10.1186/1745-6150-6-45.


Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea.

Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM.

J Bacteriol. 2011 Oct;193(19):5566-7. doi: 10.1128/JB.05828-11.


Detecting highways of horizontal gene transfer.

Bansal MS, Banay G, Gogarten JP, Shamir R.

J Comput Biol. 2011 Sep;18(9):1087-114. doi: 10.1089/cmb.2011.0066.


Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.

Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P.

PLoS One. 2011;6(8):e23774. doi: 10.1371/journal.pone.0023774. Epub 2011 Aug 18.


Biased gene transfer in microbial evolution.

Andam CP, Gogarten JP.

Nat Rev Microbiol. 2011 Jun 13;9(7):543-55. doi: 10.1038/nrmicro2593. Review.


Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.

Andam CP, Fournier GP, Gogarten JP.

FEMS Microbiol Rev. 2011 Sep;35(5):756-67. doi: 10.1111/j.1574-6976.2011.00274.x. Epub 2011 May 20. Review.


Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data.

Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J.

PLoS One. 2011 Feb 16;6(2):e16751. doi: 10.1371/journal.pone.0016751.


Evolution of the Archaea: emerging views on origins and phylogeny.

Fournier GP, Dick AA, Williams D, Gogarten JP.

Res Microbiol. 2011 Jan;162(1):92-8. doi: 10.1016/j.resmic.2010.09.016. Epub 2010 Oct 27.


Biased gene transfer mimics patterns created through shared ancestry.

Andam CP, Williams D, Gogarten JP.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10679-84. doi: 10.1073/pnas.1001418107. Epub 2010 May 21.


Using comparative genome analysis to identify problems in annotated microbial genomes.

Poptsova MS, Gogarten JP.

Microbiology. 2010 Jul;156(Pt 7):1909-17. doi: 10.1099/mic.0.033811-0. Epub 2010 Apr 29. Review.


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