Publications: Johann Peter Gogarten

• 2023

• Neighboring inteins interfere with one another's homing capacity.
  Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U
  PNAS nexus (2023) 2(11):pgad354 PMC419797 10.1101/GR.849004
• Protocol for an agent-based model of recombination in bacteria playing a public goods game.
  Lee IPA, Eldakar OT, Gogarten JP, Andam CP
  STAR protocols (2023) 4(4):102733 PMC10405257 10.1016/j.xpro.2023.102733
• Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria.
  Lee IPA, Eldakar OT, Gogarten JP, Andam CP
  iScience (2023) 26(8):107344 PMC3240628 10.1038/s41579-021-00650-4
• The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.
  Gosselin SP, Arsenault DR, Jennings CA, Gogarten JP
  Genes (2023) 14(2): PMC1079044 10.1073/pnas.33.9.253
• A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.
  Podgorski JM, Freeman K, Gosselin S, Huet A, Conway JF, Bird M, Grecco J, Patel S, Jacobs-Sera D, Hatfull G, Gogarten JP, Ravantti J, White SJ
  Structure (London, England : 1993) (2023) 31(3):282-294.e5 PMC4044616 10.1128/JVI.01629-15

• 2021

• Bacterial cooperation through horizontal gene transfer.
  Lee IPA, Eldakar OT, Gogarten JP, Andam CP
  Trends in ecology & evolution (2021) 37(3):223-232 10.1016/j.tree.2021.11.006
• An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.
  Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP
  Genome biology and evolution (2021) 13(9): PMC8483891 10.1093/gbe/evab187
• Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support.
  Gosselin S, Fullmer MS, Feng Y, Gogarten JP
  Systematic biology (2021) 71(2):396-409 PMC2667022 10.1002/9781118960608.obm00010.pub2
• The Evolutionary Origins of Extreme Halophilic Archaeal Lineages.
  Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP
  Genome biology and evolution (2021) 13(8): PMC8350355 10.1093/gbe/evab166

• 2020

• Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.
  Makkay AM, Louyakis AS, Ram-Mohan N, Gophna U, Gogarten JP, Papke RT
  Scientific reports (2020) 10(1):22297 PMC7749143 10.1038/s41598-020-79296-w
• Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum.
  Pyatibratov MG, Syutkin AS, Quax TEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV
  MicrobiologyOpen (2020) 9(7):e1047 PMC7349177 10.1002/mbo3.1047

• 2019

• Identification and characterization of putative Aeromonas spp. T3SS effectors.
  Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP
  PloS one (2019) 14(6):e0214035 PMC6548356 10.1371/journal.pone.0214035
• Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21.
  Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP
  Microbiology resource announcements (2019) 8(12): PMC6430316 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 (2019) 10(3): PMC6471742 10.3390/genes10030233

• 2018

• 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) 9(4): (PMC6058295) 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) 12(10):2559-2574 (PMC6154966) 10.1038/s41396-018-0166-1
• 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) 9(3): (PMC5867893) 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) 9(3): (PMC5867850) 10.3390/genes9030129

• 2016

• 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. (2016) 107:338-344
• Is LUCA a thermophilic progenote?
  Gogarten JP, Deamer D
  Nat Microbiol (2016) 1:16229
• Does Sequence Conservation Provide Evidence for Biological Function?
  Omer S, Harlow TJ, Gogarten JP
  Trends Microbiol. (2016) 25(1):11-18
• 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) 7:1342 (PMC5014874)
• 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) 113(32):E4654-61 (PMC4987785)

• 2015

• 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) 6:728 (PMC4523029)
• Horizontal gene transfer: building the web of life.
  Soucy SM, Huang J, Gogarten JP
  Nat. Rev. Genet. (2015) 16(8):472-82
• Ancient horizontal gene transfer and the last common ancestors.
  Fournier GP, Andam CP, Gogarten JP
  BMC Evol. Biol. (2015) 15:70 (PMC4427996)
• 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) 6:123 (PMC4337385)

• 2014

• 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) 5(6):e02136 (PMC4251997)
• Inteins as indicators of gene flow in the halobacteria.
  Soucy SM, Fullmer MS, Papke RT, Gogarten JP
  Front Microbiol (2014) 5:299 (PMC4071816)
• 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) 9(6):e98844 (PMC4044049)
• 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) 5:143 (PMC3988388)
• 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) 5:140 (PMC3990103)
• 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 (2014) 8(12):e84300 (PMC3877268)

• 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) 30(12):2676-87
• Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12.
  Butzin NC, Secinaro MA, Swithers KS, Gogarten JP, Noll KM
  Appl. Environ. Microbiol. (2013) 79(22):7006-12 (PMC3811540)
• 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) 30(11):2463-74
• The effects of model choice and mitigating bias on the ribosomal tree of life.
  Lasek-Nesselquist E, Gogarten JP
  Mol. Phylogenet. Evol. (2013) 69(1):17-38
• Systematic inference of highways of horizontal gene transfer in prokaryotes.
  Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R
  Bioinformatics (2013) 29(5):571-9

• 2012

• Pre-Posting and OLEB.
  Schwartz AW, Cleaves HJ, Gogarten JP
  Orig Life Evol Biosph (2012) 42(6):517
• Quantifying homologous replacement of loci between haloarchaeal species.
  Williams D, Gogarten JP, Papke RT
  Genome Biol Evol (2012) 4(12):1223-44 (PMC3542582)
• The impact of HGT on phylogenomic reconstruction methods.
  Lapierre P, Lasek-Nesselquist E, Gogarten JP
  Brief. Bioinformatics (2012) 15(1):79-90
• The role of reticulate evolution in creating innovation and complexity.
  Swithers KS, Soucy SM, Gogarten JP
  Int J Evol Biol (2012) 2012:418964 (PMC3403396)
• 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 (PMC3509894)
• 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 (PMC3387000)
• 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) 12:85 (PMC3436685)
• 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) 13:123 (PMC3447714)
• Ecology. How bacterial lineages emerge.
  Papke RT, Gogarten JP
  Science (2012) 336(6077):45-6

• 2011

• 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) 41(6):621-32
• Home and away- the evolutionary dynamics of homing endonucleases.
  Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L
  BMC Evol. Biol. (2011) 11:324 (PMC3229294)
• 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) 193(20):5869-70 (PMC3187219)
• Biased gene transfer and its implications for the concept of lineage.
  Andam CP, Gogarten JP
  Biol. Direct (2011) 6:47 (PMC3191353)
• A rooted net of life.
  Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP
  Biol. Direct (2011) 6:45 (PMC3189188)
• 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) 193(19):5566-7 (PMC3187421)
• Detecting highways of horizontal gene transfer.
  Bansal MS, Banay G, Gogarten JP, Shamir R
  J. Comput. Biol. (2011) 18(9):1087-114
• 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 (PMC3158100)
• Biased gene transfer in microbial evolution.
  Andam CP, Gogarten JP
  Nat. Rev. Microbiol. (2011) 9(7):543-55
• Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer.
  Andam CP, Fournier GP, Gogarten JP
  FEMS Microbiol. Rev. (2011) 35(5):756-67
• 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) 6(2):e16751 (PMC3040217)

• 2010

• Evolution of the Archaea: emerging views on origins and phylogeny.
  Fournier GP, Dick AA, Williams D, Gogarten JP
  Res. Microbiol. (2010) 162(1):92-8
• Biased gene transfer mimics patterns created through shared ancestry.
  Andam CP, Williams D, Gogarten JP
  Proc. Natl. Acad. Sci. U.S.A. (2010) 107(23):10679-84 (PMC2890805)
• Using comparative genome analysis to identify problems in annotated microbial genomes.
  Poptsova MS, Gogarten JP
  Microbiology (Reading, Engl.) (2010) 156(Pt 7):1909-17
• Filling the gaps in the genomic landscape.
  Williams D, Gogarten JP, Lapierre P
  Genome Biol. (2010) 11(2):103 (PMC2872866)
• Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders.
  Fournier GP, Neumann JE, Gogarten JP
  PLoS ONE (2010) 5(3):e9437 (PMC2830423)
• Rooting the ribosomal tree of life.
  Fournier GP, Gogarten JP
  Mol. Biol. Evol. (2010) 27(8):1792-801
• Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements.
  Swithers KS, Senejani AG, Fournier GP, Gogarten JP
  BMC Evol. Biol. (2010) 9:303 (PMC2814812)

• 2009

• Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer.
  Olendzenski L, Gogarten JP
  Ann. N. Y. Acad. Sci. (2009) 1178:137-45
• Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.
  Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR
  BMC Genomics (2009) 10:468 (PMC2770080)
• Prokaryotic evolution and the tree of life are two different things.
  Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W
  Biol. Direct (2009) 4:34 (PMC2761302)
• Trees in the web of life.
  Swithers KS, Gogarten JP, Fournier GP
  J. Biol. (2009) 8(6):54 (PMC2737374)
• Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.
  Fournier GP, Huang J, Gogarten JP
  Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2009) 364(1527):2229-39 (PMC2873001)
• On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.
  Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM
  Proc. Natl. Acad. Sci. U.S.A. (2009) 106(14):5865-70 (PMC2667022)
• Ancient gene transfer as a tool in phylogenetic reconstruction.
  Huang J, Gogarten JP
  Methods Mol. Biol. (2009) 532:127-39
• Gene transfer: who benefits?
  Olendzenski L, Gogarten JP
  Methods Mol. Biol. (2009) 532:3-9
• Estimating the size of the bacterial pan-genome.
  Lapierre P, Gogarten JP
  Trends Genet. (2009) 25(3):107-10
• Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.
  Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP
  Genome Biol Evol (2009) 1:325-39 (PMC2817427)

• 2008

• Concerted gene recruitment in early plant evolution.
  Huang J, Gogarten JP
  Genome Biol. (2008) 9(7):R109 (PMC2530860)
• Unsupervised learning in detection of gene transfer.
  Hamel L, Nahar N, Poptsova MS, Zhaxybayeva O, Gogarten JP
  J. Biomed. Biotechnol. (2008) 2008:472719 (PMC2288707)
• Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales.
  Noll KM, Lapierre P, Gogarten JP, Nanavati DM
  BMC Evol. Biol. (2008) 8:7 (PMC2246101)

• 2007

• Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia.
  Fournier GP, Gogarten JP
  J. Bacteriol. (2007) 190(3):1124-7 (PMC2223567)
• Signature of a primitive genetic code in ancient protein lineages.
  Fournier GP, Gogarten JP
  J. Mol. Evol. (2007) 65(4):425-36
• A hyperconserved protein in Prochlorococcus and marine Synechococcus.
  Zhaxybayeva O, Gogarten JP, Doolittle WF
  FEMS Microbiol. Lett. (2007) 274(1):30-4
• Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
  Huang J, Gogarten JP
  Genome Biol. (2007) 8(6):R99 (PMC2394758)
• The evolution of eukaryotes.
  Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA
  Science (2007) 316(5824):542-3; author reply 542-3
• BranchClust: a phylogenetic algorithm for selecting gene families.
  Poptsova MS, Gogarten JP
  BMC Bioinformatics (2007) 8:120 (PMC1853112)
• Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
  Senejani AG, Gogarten JP
  Int. J. Biol. Sci. (2007) 3(4):205-11 (PMC1802021)
• The power of phylogenetic approaches to detect horizontally transferred genes.
  Poptsova MS, Gogarten JP
  BMC Evol. Biol. (2007) 7:45 (PMC1847511)

• 2006

• Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
  Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR
  Genome Res. (2006) 17(1):7-15 (PMC1716269)
• Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.
  Gogarten JP, Hilario E
  BMC Evol. Biol. (2006) 6:94 (PMC1654191)
• Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
  Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT
  Genome Res. (2006) 16(9):1099-108 (PMC1557764)
• Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
  Huang J, Gogarten JP
  Trends Genet. (2006) 22(7):361-6
• Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species.
  Lapierre P, Shial R, Gogarten JP
  Syst. Appl. Microbiol. (2006) 29(1):15-23
• Ancient gene duplications and the root(s) of the tree of life.
  Zhaxybayeva O, Lapierre P, Gogarten JP
  Protoplasma (2006) 227(1):53-64

• 2005

• Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains.
  Morandi A, Zhaxybayeva O, Gogarten JP, Graf J
  J. Bacteriol. (2005) 187(18):6561-4 (PMC1236645)
• Horizontal gene transfer, genome innovation and evolution.
  Gogarten JP, Townsend JP
  Nat. Rev. Microbiol. (2005) 3(9):679-87
• The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic.
  Huang J, Xu Y, Gogarten JP
  Mol. Biol. Evol. (2005) 22(11):2142-6
• PentaPlot: a software tool for the illustration of genome mosaicism.
  Hamel L, Zhaxybayeva O, Gogarten JP
  BMC Bioinformatics (2005) 6:139 (PMC1177926)
• Were arachnids the first to use combinatorial peptide libraries?
  Sollod BL, Wilson D, Zhaxybayeva O, Gogarten JP, Drinkwater R, King GF
  Peptides (2005) 26(1):131-9

• 2004

• A hybrid clustering approach to recognition of protein families in 114 microbial genomes.
  Harlow TJ, Gogarten JP, Ragan MA
  BMC Bioinformatics (2004) 5:45 (PMC420232)
• Genome mosaicism and organismal lineages.
  Zhaxybayeva O, Lapierre P, Gogarten JP
  Trends Genet. (2004) 20(5):254-60
• Cladogenesis, coalescence and the evolution of the three domains of life.
  Zhaxybayeva O, Gogarten JP
  Trends Genet. (2004) 20(4):182-7
• Visualization of the phylogenetic content of five genomes using dekapentagonal maps.
  Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP
  Genome Biol. (2004) 5(3):R20 (PMC395770)

• 2003

• Spliceosomal introns: new insights into their evolution.
  Zhaxybayeva O, Gogarten JP
  Curr. Biol. (2003) 13(19):R764-6
• An improved probability mapping approach to assess genome mosaicism.
  Zhaxybayeva O, Gogarten JP
  BMC Genomics (2003) 4(1):37 (PMC222983)
• Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.
  Raymond J, Zhaxybayeva O, Gogarten JP, Blankenship RE
  Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2003) 358(1429):223-30 (PMC1693105)
• Gene transfer: gene swapping craze reaches eukaryotes.
  Gogarten JP
  Curr. Biol. (2003) 13(2):R53-4

• 2002

• Prokaryotic evolution in light of gene transfer.
  Gogarten JP, Doolittle WF, Lawrence JG
  Mol. Biol. Evol. (2002) 19(12):2226-38
• Whole-genome analysis of photosynthetic prokaryotes.
  Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE
  Science (2002) 298(5598):1616-20
• Inteins: structure, function, and evolution.
  Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E
  Annu. Rev. Microbiol. (2002) 56:263-87
• Multi site polyadenylation and transcriptional response to stress of a vacuolar type H+-ATPase subunit A gene in Arabidopsis thaliana.
  Magnotta SM, Gogarten JP
  BMC Plant Biol. (2002) 2:3 (PMC103671)
• Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.
  Zhaxybayeva O, Gogarten JP
  BMC Genomics (2002) 3:4 (PMC100357)

• 2001

• The intein of the Thermoplasma A-ATPase A subunit: structure, evolution and expression in E. coli.
  Senejani AG, Hilario E, Gogarten JP
  BMC Biochem. (2001) 2:13 (PMC60005)