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Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV. 2015. Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes. Front. Microbiol. 6:123. doi: 10.3389/fmicb.2015.00123
Zhuang Y, Zhang H, Hannick L & Lin S. 2015. Metatranscriptome profiling reveals versatile N-utrient utilization, CO2 limitation, oxidative stress, and active toxin production in an Alexandrium fundyense bloom. Harmful Algae 42, 60-70. full-text
Colston SM, Fullmer M, Beka L, Lamy B, Gogarten JP, Graf J. 2014. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 5(6):e02136-14. doi:10.1128/mBio.02136-14.
Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT. 2014. Population and genomic analysis of the genus Halorubrum. Frontiers in Microbiol, 5:140. doi: 10.3389/fmicb.2014.00140
Ram Mohan N, Fullmer MS, Makkay AM, Wheeler RW, Ventosa A, Naor A, Gogarten JP, Papke RT. 2014. Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Frontiers in Microbiol 5:143. doi: 10.3389/fmicb.2014.00143
Soucy SM, Fullmer MS, Papke RT, Gogarten JP. 2014. Inteins as indicators of gene flow in the halobacteria. Front. Microbiol. 5:299. doi: 10.3389/fmicb.2014.00299
Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM. 2013. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 8(12):e84300. doi: 10.1371/journal.pone.0084300
Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP. 2013. Distribution and Evolution of the Mobile vma-1b Intein. Molecular Biology and Evolution 30 (12): 2676-2687 doi: 10.1093/molbev/mst164
Butzin N, Secinaro M, Swithers KS, Gogarten JP, Noll K. 2013. Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12. Applied and Environmental Microbiology 79 (22) 7006-7012 doi: 10.1128/AEM.01800-13
Green AG, Swithers KS, Gogarten JF, Gogarten JP. 2013. Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum. Molecular Biology and Evolution 30 (11): 2463-2474 doi:10.1093/molbev/mst145
Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R. 2013. Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics 29(5): 571-9. doi:10.1093/bioinformatics/btt021
Jue NK, Murphy MB, Kasowitz SD, Quershi SM, Obergfell CJ, Rosin LF, Foley RJ, O’Neill RJ, O’Neill MJ. 2013. Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach. BMC Genomics 14: 150. doi:10.1186/1471-2164-14-150
Lasek-Nesselquist E, Gogarten JP. 2013. The effects of model choice and mitigating bias on the ribosomal tree of life. Molecular Phylogenetics and Evolution 69(1): 17-38. doi: 10.1016/j.ympev.2013.05.006.
Les, DH, Tippery, NP. 2013. In time and with water … the systematics of alismatid monocotyledons. in P. Wilkin, ed. Early Events in Monocot Evolution. Cambridge University Press. Link Buy
Lewis PO, Xie W, Chen MH, Fan Y, Kuo L. 2013. Posterior predictive Bayesian phylogenetic model selection. Systematic Biology 0(0):1–13. doi:10.1093/sysbio/syt068.
Liu Y, Forrest LL, Bainard J, Budkem JM, Goffinet B. 2013. Organellar genome, nuclear ribosomal DNA repeat unit and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses. Molecular Phylogenetics Evolution 66:1089-1094. doi: 10.1016/j.ympev.2012.12.006
O’Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D. 2013. pLogo: a probabilistic approach to visualizing sequence motifs. Nature Methods 10(12): 1211-1212. doi: 10.1038/nmeth.2646.
Wang W, Liu Y, Yu SX, Gao TG, Chen ZD. 2013. Gymnaconitum, a new genus of Ranunculaceae endemic to the Qinghai-Tibetan Plateau. Taxon 62(4): 713-722. doi: 10.12705/624.10
Zhuang Y, Zhang H & Lin S. 2013. Polyadenylation of 18S rRNA in algae1. Journal of Phycology 49: 570-579. full-text
2012 back to top
Andam CP, Harlow TJ, Papke RT, Gogarten JP. 2012. Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. BMC Evolutionary Biology 12:85. doi:10.1186/1471-2148-12-85
Bomar L, Graf J. 2012. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. Biol. Bull. 223: 155-166. pmid: 22983040
Chou MF, Prisic S, Lubner JM, Church GM, Husson RN, Schwartz D. 2012. Using bacteria to determine protein kinase specificity and predict target substrates. PLoS ONE 7(12): e52747. doi: 10.1371/journal.pone.0052747
Fournier GP, Andam CP, Alm EJ, Gogarten JP. 2012. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Origins of Life and Evolution of Biospheres 41(6): 621–632. doi: 10.1007/s11084-011-9261-2
Fučíková K, Flechtner VR, Lewis LA. 2012. Revision of the genus Bracteacoccus Tereg (Chlorophyceae, Chlorophyta) based on a phylogenetic approach. Nova Hedwigia 96(1-2): 15-59. doi: 10.1127/0029-5035/2012/0067
Fučíková K, Lewis LA. 2012. Intersection of Chlorella, Muriella, and Bracteacoccus: resurrecting the genus Chromochloris Kol & Chodat (Chlorophyceae, Chlorophyta). Fottea 12(1): 83-93. full-text
Henry CS, Brooks SJ, Duelli P, Johnson JB, Wells MLM, Mochizuki A. 2012. Parallel evolution in courtship songs of North American and European green lacewings (Neuroptera: Chrysopidae). Biological Journal of the Linnaean Society 105: 776-796. doi: 10.1111/j.1095-8312.2011.01845.x
Lapierre P, Lasek-Nesselquist E, Gogarten JP. 2012. The impact of HGT on phylogenomic reconstruction methods. Briefings in Bioinformatics 15(1): 79-90. doi:10.1093/bib/bbs050
Liu Y, Budke JM, Goffinet B. 2012. Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): Rapid radiation suggests rampant homoplasy in sporophyte evolution. Molecular Phylogenetics and Evolution 62: 130-145. doi: 10.1016/j.ympev.2013.05.006.
Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre, P, Gogarten JP, Xu Y. 2012. Quartet decomposition server: a platform for analyzing phylogenetic trees. BMC Bioinformatics 13: 123. doi:10.1186/1471-2105-13-123
Martínez-Solano I, Peralta-García A, Jockusch EL, Wake DB, Vázquez-Domínguez E, and Parra-Olea G. 2012. Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: mitochondrial-nuclear DNA discordance and the evolutionary history of B. major. Molecular Phylogenetics and Evolution, 63: 131-149. doi: 10.1016/j.ympev.2011.12.026
McManus HA, Fučíková K, Lewis LA, Haugen P. 2012. Invasion of protein coding genes by green algal ribosomal group I introns. Molecular Phylogenetics and Evolution 62(1): 109-116. doi: 10.1016/j.ympev.2011.09.027
Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U. 2012. Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids. Curr. Biol. 22(15): 1444-1448. doi: 10.1016/j.cub.2012.05.056
Ngunjiri JM, Lee CW, Ali A, Marcus PI. 2012. Influenza virus interferon-inducing particle efficiency is reversed in avian and mammalian cells, and enhanced in cells co-infected with defective-interfering particles. J Interferon Cytokine Res. 32(6): 280-285. doi: 10.1089/jir.2011.0102
Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM. 2012. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs. PLoS One. 7(6):e40236. doi:10.1371/journal.pone.0040236
Phansalkar R, Lapierre P, Mellone BG. 2012. Evolutionary insights into the role of the essential centromere protein CAL1 in Drosophila. Chromosome Res. 20(5): 493-504. doi: 10.1007/s10577-012-9299-7.
Ruiz-Arce R, Barr NB, Owen CL, Thomas DB, McPheron BA. 2012. Phylogeography of the West Indian fruit fly, Anastrepha obliqua inferred with mtDNA sequencing. J Econ Entomol. 105(6): 2147-2160. pmid: 23356081
Santoferrara LF, McManus GB, Alder VA. 2012. Utility of genetic markers and morphology for species discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist 164(1):24-36. doi:10.1016/j.protis.2011.12.002.
Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM, Butzin NC. 2012. Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales. Genome Biology and Evolution 4(8): 842-851. doi:10.1093/gbe/evs057
Swithers KS, Soucy SM, Gogarten JP. 2012. The Role of Reticulate Evolution in Creating Innovation and Complexity. Int Journal of Evolutionary Biology. Article ID 418964. doi:10.1155/2012/418964
Tippery NP, Fučíková K, Lewis PO, and Lewis LA. 2012. Probing the monophyly of the Sphaeropleales (Chlorophyceae) using data from five genes. Journal of Phycology 48: 1482-1493. doi: 10.1111/jpy.12003
Williams D, Gogarten JP, Papke RT. 2012. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biology and Evolution 4(12): 1223-1244. doi:10.1093/gbe/evs098
Wu X, Oh MH, Kim HS, Schwartz D, Imai BS, Yau PM, Clouse SD, Huber SC. 2012. Transphosphorylation of E. coli proteins during production of recombinant protein kinases provides a robust system to characterize kinase specificity. Front Plant Sci 3:262. doi: 10.3389/fpls.2012.00262
2011 back to top
Andam CP, Gogarten JP. 2011. Biased gene transfer in microbial evolution. (Analysis) Nature Reviews Microbiology 9(7): 543-555. doi:10.1038/nrmicro2593
Andam CP, Gogarten JP. 2011. Biased gene transfer and its implications for the concept of lineage. Biology Direct 6:47. doi: 10.1186/1745-6150-6-47
Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L. 2011. Home and away – the evolutionary dynamics of homing endonucleases. BMC Evolutionary Biology 11:324. doi: 10.1186/1471-2148-11-324
Bohunická M, Johansen JR, Fučíková K. 2011. Tapinothrix clintonii sp. nov. (Pseudanabaenaceae, Cyanobacteria), a new species at the nexus of five genera. Fottea 11(1): 127–140. full-text
Collins AJ, Nyholm SV. 2011. Draft genome of Phaeobacter gallaeciensis ANG1; a dominant member of the accessory nidamental gland of Euprymna scolopes. J Bacteriol 193(13): 3397–3398. doi: 10.1128/JB.05139-11
Fournier GP, Dick AA, Williams D, Gogarten JP (2011). Evolution of the Archaea: Emerging views on origins and phylogeny. Res. Microbiol. 162(1):92-98. doi: 10.1016/j.resmic.2010.09.016
Fučíková K, Rada JC, Lewis LA. 2011. The tangled taxonomic history of Dictyococcus, Bracteacoccus, and Pseudomuriella (Chlorophyceae, Chlorophyta) and their distinction based on a phylogenetic perspective. Phycologia 50: 422–429. doi: 10.2216/10-69.1
Fučíková K, Rada JC, Lukešová A, Lewis LA. 2011. Cryptic Diversity within the Genus Pseudomuriella Hanagata (Chlorophyta, Chlorophyceae, Sphaeropleales) Assessed Using Four Barcode Markers. Nova Hedwigia 93(1-2):29-46. doi:10.1127/0029-5035/2011/0093-0029
Jockusch EL, Martínez-Solano I, Hansen RW, Wake DB. 2011. Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species. Zootaxa 3190:1-30. full-text
Marshall DC, Hill KBR, Cooley JR, Simon C. 2011. Hybridization, mitochondrial DNA taxonomy, and prediction of the early stages of reproductive isolation: Lessons from New Zealand cicadas of the genus Kikihia. Systematic Biology 60(4): 482-502. doi: 10.1093/sysbio/syr017.
McManus HA, Lewis LA. 2011. Molecular phylogenetic relationships in the freshwater family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), with an emphasis on Pediastrum duplex. Journal of Phycology 47: 152-163. doi: 10.1111/j.1529-8817.2010.00940.x
Schleicher TS and Nyholm SV. 2011. “Characterizing the Host and Symbiont Proteomes in the Association Between the Bobtail Squid, Euprymna scolopes, and the Bacterium, Vibrio fischeri. PLoS ONE 6(10): e25649 doi: 10.1371/journal.pone.0025649
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. 2011. Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores. J Bacteriol 193(20):5869-70. doi: 10.1128/JB.05923-11
Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J (2011). Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data. PLoS ONE 6(2). doi: 10.1371/journal.pone.0016751
Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P. 2011. Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PLoS ONE. 6(8). doi: 10.1371/journal.pone.0023774
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. 2011. 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. J Bacteriol 193(19): 5566-7. doi: 10.1128/JB.05828-11
Tippery NP, Les DH. 2011. Phylogenetic relationships and morphological evolution in Nymphoides (Menyanthaceae). Systematic Botany 36(4): 1101-1113. doi: 10.1600/036364411X605092
Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP. 2011. A Rooted Net of Life. Biology Direct 6:45. doi:10.1186/1745-6150-6-45
2010 back to top
Andam CP, Williams D, Gogarten JP. 2010. Biased gene transfer mimics patterns created through shared ancestry. Proc. Natl. Acad. Sci. 107(23). doi: 10.1073/pnas.1001418107
Andam CP, Williams D, Gogarten JP. 2010. Natural Taxonomy in Light of Horizontal Gene Transfer (Special Issue on the Tree of Life). Biology and Philosophy 24(4): 589-602. doi: 10.1007/s10539-010-9212-8
Fournier GP, Gogarten JP. 2010. Rooting the Ribosomal Tree of Life. Molecular Biology and Evolution 27(8): 1792-1801. doi: 10.1093/molbev/msq057
Fournier GP, Neumann JE, Gogarten JP. 2010. Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders. PLoS ONE 5(3): e9437. doi: 10.1371/journal.pone.0009437
Hall JD, Fučíková K, Lo C, Lewis LA, Karol KG. 2010. An assessment of proposed DNA barcodes in freshwater green algae. Cryptogamie, Algologie 31 (4): 529-555. full-text
Marshall DC. 2010. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Systematic Biology 59(1):108-17. doi: 10.1093/sysbio/syp080
Poptsova MS, Gogarten JP. 2010. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156(7):1909-17. doi: 10.1099/mic.0.033811-0
Lee Y-J, Hill KBR. 2010. Systematic revision of the genus Psithyristria Stål (Hemiptera: Cicadidae) with seven new species and a molecular phylogeny of the genus and higher taxa. Systematic Entomology 35: 277-305. doi: 10.1111/j.1365-3113.2009.00509.x
Williams D, Gogarten JP, Lapierre P. 2010. Filling the gaps in the genomic landscape. Genome Biology 11:103. doi:10.1186/gb-2010-11-2-103
2009 back to top
Bajrami B, Shi Y, Lapierre P, Yao X. 2009. Shifting Unoccupied Space in Peptide Mass Spectrum by Esterification. J Am Soc Mass Spectrom. 20(11): 2124-34. doi: 10.1016/j.jasms.2009.07.005
Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR. 2009. Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics 10(1): 468. doi: 10.1186/1471-2164-10-468.
Fournier G. 2009. Horizontal gene transfer and the evolution of methanogenic pathways. Methods Mol Biol. 532:163-79. doi: 10.1007/978-1-60327-853-9_9
Fournier GP, Huang JL, Gogarten JP. 2009. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2009.0033
Fyler CA, Caira JN, Jensen K. 2009. Five new species of Acanthobothrium (Cestoda: Tetraphyllidea) from an unusual species of Himantura (Rajiformes: Dasyatidae) from northern Australia. Folia Parasitologica. 56(2): 107-28. full-text
Hill KBR, Simon C, Marshall DC, Chambers GK. 2009. Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelli. Journal of Biogeography 36: 675-692. doi: 10.1111/j.1365-2699.2008.02036.x
Huang J, Gogarten JP. 2009. Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol. 2009; 532:127-39. doi: 10.1007/978-1-60327-853-9_7
Lapierre P, Gogarten JP. 2009. Estimating the size of the bacterial pan-genome. Trends in Genetics 25(3): 107-10. doi: 10.1016/j.tig.2008.12.004
Les DH, Murray NM, Tippery NP. 2009. Taxonomic Studies of Pondweeds (Potamogetonaceae) with an Emphasis on Potamogeton vaseyi and P. gemmiparus, Two Imperiled Aquatic Plants. Systematic Botany 34(4):643-651. doi: 10.1600/036364409790139727
Marshall DC, Hill KBR, Fontaine KM, Buckley TR, Simon C. 2009. Glacial refugia in a maritime temperate climate: Cicada (Kikihia subalpina) phylogeography in New Zealand. Molecular Ecology 18: 1995-2009. full-text
Martínez-Solano I, Lawson R. 2009. Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay. BMC Evol Biol. 9:38. doi:10.1186/1471-2148-9-38
Olendzenski L, Gogarten JP. 2009. Evolution of genes and organisms: The tree/web of life in light of horizontal gene transfer. Annals of the New York Academy of Sciences 1178: 137-145. doi: 10.1111/j.1749-6632.2009.04998.x
Olendzenski L, Gogarten JP. 2009. Gene transfer: who benefits? Methods Mol Biol. 532: 3-9. doi: 10.1007/978-1-60327-853-9_1
Papke RT. 2009. A critique of prokaryotic species concepts. Methods Mol Biol. 532: 379-95. doi: 10.1007/978-1-60327-853-9_22
Poptsova M. 2009. Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. 532: 227-40. doi: 10.1007/978-1-60327-853-9_13
Shi Y, Bajrami B, Yao X. 2009. Passive and Active Fragment Ion Mass Defect Labeling: Distinct Proteomics Potential of Iodine-Based Reagents. Anal Chem. 81(15):6438-48. doi: 10.1021/ac9008034
Swithers KS, Gogarten JP, Fournier GP. 2009. Trees in the Web of Life. Journal of Biology 8:54. doi:10.1186/jbiol160
Swithers KS, Senejani AG, Fournier GP, Gogarten JP. 2009. Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements. BMC Evolutionary Biology 9: 303. doi:10.1186/1471-2148-9-303
Tippery NP, Les DH, Regalado JC, Averyanov LV, Long VN, Raven PH. 2009. Transfer of Villarsia cambodiana to Nymphoides (Menyanthaceae). Systematic Botany 34(4): 18–823. full-text
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP. 2009. Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution 1: 325-339. doi: 10.1093/gbe/evp032
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, and Noll KM. 2009. On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales. Proc Nat Acad Sci. 106(14): 5865-70. doi: 10.1073/pnas.0901260106
2008 back to top
Huang J, Gogarten JP. 2008. Concerted gene recruitment in early plant evolution. Genome Biology 9(7): R109. doi:10.1186/gb-2008-9-7-r109
Marshall DC, Slon K, Cooley JR, Hill KBR. 2008. Steady Plio-Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada radiation. Molecular Phylogenetics and Evolution 48: 1054-1066. doi: 10.1016/j.ympev.2008.05.007