TY - JOUR AU - Welch, R. A. AU - Burland, V. AU - Plunkett, G. AU - Redford, P. AU - Roesch, P. AU - Rasko, D. AU - Buckles, E. L. AU - Liou, S. R. AU - Boutin, A. AU - Hackett, J. PY - 2002 DA - 2002// TI - Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.252529799 DO - 10.1073/pnas.252529799 ID - Welch2002 ER - TY - JOUR AU - Thompson, J. R. AU - Pacocha, S. AU - Pharino, C. AU - Klepac-Ceraj, V. AU - Hunt, D. E. AU - Benoit, J. AU - Sarma-Rupavtarm, R. AU - Distel, D. L. AU - Polz, M. F. PY - 2005 DA - 2005// TI - Genotypic diversity within a natural coastal bacterioplankton population JO - Science VL - 307 UR - https://doi.org/10.1126/science.1106028 DO - 10.1126/science.1106028 ID - Thompson2005 ER - TY - JOUR AU - Tettelin, H. AU - Masignani, V. AU - Cieslewicz, M. J. AU - Donati, C. AU - Medini, D. AU - Ward, N. L. AU - Angiuoli, S. V. AU - Crabtree, J. AU - Jones, A. L. AU - Durkin, A. S. PY - 2005 DA - 2005// TI - Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome" JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0506758102 DO - 10.1073/pnas.0506758102 ID - Tettelin2005 ER - TY - JOUR AU - Konstantinidis, K. T. AU - Tiedje, J. M. PY - 2005 DA - 2005// TI - Genomic insights that advance the species definition for prokaryotes JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409727102 DO - 10.1073/pnas.0409727102 ID - Konstantinidis2005 ER - TY - JOUR AU - Tyson, G. W. AU - Chapman, J. AU - Hugenholtz, P. AU - Allen, E. E. AU - Ram, R. J. AU - Richardson, P. M. AU - Solovyev, V. V. AU - Rubin, E. M. AU - Rokhsar, D. S. AU - Banfield, J. F. PY - 2004 DA - 2004// TI - Community structure and metabolism through reconstruction of microbial genomes from the environment JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02340 DO - 10.1038/nature02340 ID - Tyson2004 ER - TY - JOUR AU - Steinberg, D. K. AU - Carlson, C. A. AU - Bates, N. R. AU - Johnson, R. H. AU - Michaels, A. F. AU - Knap, A. H. PY - 2001 DA - 2001// TI - Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biochemistry JO - Deep-Sea Research II VL - 48 UR - https://doi.org/10.1016/S0967-0645(00)00148-X DO - 10.1016/S0967-0645(00)00148-X ID - Steinberg2001 ER - TY - JOUR AU - Venter, J. C. AU - Remington, K. AU - Heidelberg, J. F. AU - Halpern, A. L. AU - Rusch, D. AU - Eisen, J. A. AU - Wu, D. AU - Paulsen, I. AU - Nelson, K. E. AU - Nelson, W. PY - 2004 DA - 2004// TI - Environmental genome shotgun sequencing of the Sargasso Sea JO - Science VL - 304 UR - https://doi.org/10.1126/science.1093857 DO - 10.1126/science.1093857 ID - Venter2004 ER - TY - JOUR AU - Dufresne, A. AU - Garczarek, L. AU - Partensky, F. PY - 2005 DA - 2005// TI - Accelerated evolution associated with genome reduction in a free-living prokaryote JO - Genome Biology VL - 6 UR - https://doi.org/10.1186/gb-2005-6-2-r14 DO - 10.1186/gb-2005-6-2-r14 ID - Dufresne2005 ER - TY - JOUR AU - Giovannoni, S. J. AU - Tripp, H. J. AU - Givan, S. AU - Podar, M. AU - Vergin, K. AU - Batista, D. AU - Bibbs, L. AU - Eads, J. AU - Richardson, T. H. AU - Noordewier, M. PY - 2005 DA - 2005// TI - Genome streamlining in a cosmopolitan oceanic bacterium JO - Science VL - 309 UR - https://doi.org/10.1126/science.1114057 DO - 10.1126/science.1114057 ID - Giovannoni2005 ER - TY - JOUR AU - Rappé, M. S. AU - Giovannoni, S. J. PY - 2003 DA - 2003// TI - The uncultured microbial majority JO - Annual Reviews Microbiology VL - 57 UR - https://doi.org/10.1146/annurev.micro.57.030502.090759 DO - 10.1146/annurev.micro.57.030502.090759 ID - Rappé2003 ER - TY - JOUR AU - Morris, R. M. AU - Cho, J. C. AU - Rappe, M. S. AU - Vergin, K. L. AU - Carlson, C. A. AU - Giovannoni, S. J. PY - 2005 DA - 2005// TI - Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site JO - Limnol Oceanography VL - 50 UR - https://doi.org/10.4319/lo.2005.50.5.1687 DO - 10.4319/lo.2005.50.5.1687 ID - Morris2005 ER - TY - JOUR AU - Giovannoni, S. J. AU - Stingl, U. PY - 2005 DA - 2005// TI - Molecular Diversity and Ecology of Microbial Plankton JO - Nature Insight VL - 437 UR - https://doi.org/10.1038/nature04158 DO - 10.1038/nature04158 ID - Giovannoni2005 ER - TY - JOUR AU - Rusch, D. B. AU - Halpern, A. L. AU - Sutton, G. AU - Heidelberg, K. B. AU - Williamson, S. AU - Yooseph, S. AU - Wu, D. AU - Eisen, J. A. AU - Hoffman, J. M. AU - Remington, K. PY - 2007 DA - 2007// TI - The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050077 DO - 10.1371/journal.pbio.0050077 ID - Rusch2007 ER - TY - JOUR AU - Rappé, M. S. AU - Connon, S. A. AU - Vergin, K. L. AU - Giovannoni, S. J. PY - 2002 DA - 2002// TI - Cultivation of the ubiquitous SAR11 marine bacterioplankton clade JO - Nature VL - 418 UR - https://doi.org/10.1038/nature00917 DO - 10.1038/nature00917 ID - Rappé2002 ER - TY - JOUR AU - Smith, R. L. AU - Huyer, A. AU - Fleischbein, J. PY - 2001 DA - 2001// TI - The coastal ocean off Oregon from 1961 to 2000: is there evidence of climate change or only of Los Niños? JO - Progress in Oceanography VL - 53 ID - Smith2001 ER - TY - JOUR AU - Brown, M. V. AU - Schwalbach, M. S. AU - Hewson, I. AU - Fuhrman, J. A. PY - 2005 DA - 2005// TI - Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series JO - Environ Microbiol VL - 7 UR - https://doi.org/10.1111/j.1462-2920.2005.00835.x DO - 10.1111/j.1462-2920.2005.00835.x ID - Brown2005 ER - TY - JOUR AU - Hallam, S. J. AU - Konstantinidis, K. T. AU - Putnam, N. AU - Schleper, C. AU - Watanabe, Y. AU - Sugahara, J. AU - Preston, C. AU - de la Torre, J. AU - Richardson, P. M. AU - DeLong, E. F. PY - 2006 DA - 2006// TI - Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0608549103 DO - 10.1073/pnas.0608549103 ID - Hallam2006 ER - TY - JOUR AU - Rasko, D. A. AU - Myers, G. S. AU - Ravel, J. PY - 2005 DA - 2005// TI - Visualization of comparative genomic analyses by BLAST score ratio JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-2 DO - 10.1186/1471-2105-6-2 ID - Rasko2005 ER - TY - JOUR AU - Coleman, M. L. AU - Sullivan, M. B. AU - Martiny, A. C. AU - Steglich, C. AU - Barry, K. AU - Delong, E. F. AU - Chisholm, S. W. PY - 2006 DA - 2006// TI - Genomic islands and the ecology and evolution of Prochlorococcus JO - Science VL - 311 UR - https://doi.org/10.1126/science.1122050 DO - 10.1126/science.1122050 ID - Coleman2006 ER - TY - JOUR AU - DeLong, E. F. PY - 2005 DA - 2005// TI - Microbial community genomics in the ocean JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1158 DO - 10.1038/nrmicro1158 ID - DeLong2005 ER - TY - JOUR AU - Price, M. N. AU - Huang, K. H. AU - Alm, E. J. AU - Arkin, A. P. PY - 2005 DA - 2005// TI - A novel method for accurate operon predictions in all sequenced prokaryotes JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki232 DO - 10.1093/nar/gki232 ID - Price2005 ER - TY - JOUR AU - Béjà, O. AU - Aravind, L. AU - Koonin, E. V. AU - Suzuki, M. AU - Hadd, A. AU - Nguyen, L. P. AU - Jovanovich, S. B. AU - Gates, C. M. AU - Feldman, R. A. AU - Spudich, J. L. PY - 2000 DA - 2000// TI - Bacterial rhodopsin: evidence for a new type of phototrophy in the sea JO - Science VL - 289 UR - https://doi.org/10.1126/science.289.5486.1902 DO - 10.1126/science.289.5486.1902 ID - Béjà2000 ER - TY - JOUR AU - Giovannoni, S. J. AU - Bibbs, L. AU - Cho, J. C. AU - Stapels, M. D. AU - Desiderio, R. AU - Vergin, K. L. AU - Rappe, M. S. AU - Laney, S. AU - Wilhelm, L. J. AU - Tripp, H. J. PY - 2005 DA - 2005// TI - Proteorhodopsin in the ubiquitous marine bacterium SAR11 JO - Nature VL - 438 UR - https://doi.org/10.1038/nature04032 DO - 10.1038/nature04032 ID - Giovannoni2005 ER - TY - JOUR AU - Dobrindt, U. AU - Hochhut, B. AU - Hentschel, U. AU - Hacker, J. PY - 2004 DA - 2004// TI - Genomic islands in pathogenic and environmental microorganisms JO - Nat Rev Microbiol VL - 2 UR - https://doi.org/10.1038/nrmicro884 DO - 10.1038/nrmicro884 ID - Dobrindt2004 ER - TY - JOUR AU - Hacker, J. AU - Carniel, E. PY - 2001 DA - 2001// TI - Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes JO - EMBO Rep VL - 2 UR - https://doi.org/10.1093/embo-reports/kve097 DO - 10.1093/embo-reports/kve097 ID - Hacker2001 ER - TY - JOUR AU - Rocap, G. AU - Larimer, F. W. AU - Lamerdin, J. AU - Malfatti, S. AU - Chain, P. AU - Ahlgren, N. A. AU - Arellano, A. AU - Coleman, M. AU - Hauser, L. AU - Hess, W. R. PY - 2003 DA - 2003// TI - Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01947 DO - 10.1038/nature01947 ID - Rocap2003 ER - TY - JOUR AU - Berg, O. G. AU - Kurland, C. G. PY - 2002 DA - 2002// TI - Evolution of microbial genomes: sequence acquisition and loss JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004050 DO - 10.1093/oxfordjournals.molbev.a004050 ID - Berg2002 ER - TY - JOUR AU - Lerat, E. AU - Daubin, V. AU - Ochman, H. AU - Moran, N. A. PY - 2005 DA - 2005// TI - Evolutionary origins of genomic repertoires in bacteria JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030130 DO - 10.1371/journal.pbio.0030130 ID - Lerat2005 ER - TY - JOUR AU - Nilsson, A. I. AU - Koskiniemi, S. AU - Eriksson, S. AU - Kugelberg, E. AU - Hinton, J. C. AU - Andersson, D. I. PY - 2005 DA - 2005// TI - Bacterial genome size reduction by experimental evolution JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0503654102 DO - 10.1073/pnas.0503654102 ID - Nilsson2005 ER - TY - JOUR AU - Rozen, D. E. AU - Schneider, D. AU - Lenski, R. E. PY - 2005 DA - 2005// TI - Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism JO - J Mol Evol VL - 61 UR - https://doi.org/10.1007/s00239-004-0322-2 DO - 10.1007/s00239-004-0322-2 ID - Rozen2005 ER - TY - JOUR AU - Cohan, F. M. PY - 2002 DA - 2002// TI - What are bacterial species? JO - Annu Rev Microbiol VL - 56 UR - https://doi.org/10.1146/annurev.micro.56.012302.160634 DO - 10.1146/annurev.micro.56.012302.160634 ID - Cohan2002 ER - TY - JOUR AU - Tamames, J. PY - 2001 DA - 2001// TI - Evolution of gene order conservation in prokaryotes JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-6-research0020 DO - 10.1186/gb-2001-2-6-research0020 ID - Tamames2001 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Kondrashov, A. S. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.GR-1619R DO - 10.1101/gr.GR-1619R ID - Wolf2001 ER - TY - JOUR AU - Huynen, M. A. AU - Bork, P. PY - 1998 DA - 1998// TI - Measuring genome evolution JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.11.5849 DO - 10.1073/pnas.95.11.5849 ID - Huynen1998 ER - TY - JOUR AU - Linton, D. AU - Karlyshev, A. V. AU - Wren, B. W. PY - 2001 DA - 2001// TI - Deciphering Campylobacter jejuni cell surface interactions from the genome sequence JO - Curr Opin Microbiol VL - 4 UR - https://doi.org/10.1016/S1369-5274(00)00161-2 DO - 10.1016/S1369-5274(00)00161-2 ID - Linton2001 ER - TY - JOUR AU - Proctor, L. M. AU - Fuhrman, J. A. PY - 1990 DA - 1990// TI - Viral mortality of marine bacteria and cyanobacteria JO - Nature VL - 343 UR - https://doi.org/10.1038/343060a0 DO - 10.1038/343060a0 ID - Proctor1990 ER - TY - CHAP AU - Vergin, K. L. AU - Tripp, H. J. AU - Wilhelm, L. J. AU - Denver, D. R. AU - Rappe, M. S. AU - Giovannoni, S. J. PY - 2007 DA - 2007// TI - High Intraspecific Recombination Rate in a Native Population of Candidatus Pelagibacter ubique (SAR11) BT - Environmental Microbiology ID - Vergin2007 ER - TY - JOUR AU - Bashford, D. AU - Chothia, C. AU - Lesk, A. M. PY - 1987 DA - 1987// TI - Determinants of a protein fold. Unique features of the globin amino acid sequences JO - J Mol Biol VL - 196 UR - https://doi.org/10.1016/0022-2836(87)90521-3 DO - 10.1016/0022-2836(87)90521-3 ID - Bashford1987 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Rocap, G. AU - Distel, D. L. AU - Waterbury, J. B. AU - Chisholm, S. W. PY - 2002 DA - 2002// TI - Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences JO - Appl Environ Microbiol VL - 68 UR - https://doi.org/10.1128/AEM.68.3.1180-1191.2002 DO - 10.1128/AEM.68.3.1180-1191.2002 ID - Rocap2002 ER - TY - JOUR AU - Holmes, A. J. AU - Gillings, M. R. AU - Nield, B. S. AU - Mabbutt, B. C. AU - Nevalainen, K. M. AU - Stokes, H. W. PY - 2003 DA - 2003// TI - The gene cassette metagenome is a basic resource for bacterial genome evolution JO - Environ Microbiol VL - 5 UR - https://doi.org/10.1046/j.1462-2920.2003.00429.x DO - 10.1046/j.1462-2920.2003.00429.x ID - Holmes2003 ER - TY - JOUR AU - Reiter, W. D. AU - Palm, P. AU - Yeats, S. PY - 1989 DA - 1989// TI - Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements JO - Nucleic Acids Res VL - 17 UR - https://doi.org/10.1093/nar/17.5.1907 DO - 10.1093/nar/17.5.1907 ID - Reiter1989 ER - TY - JOUR AU - Daubin, V. AU - Ochman, H. PY - 2004 DA - 2004// TI - Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2231904 DO - 10.1101/gr.2231904 ID - Daubin2004 ER - TY - CHAP AU - Pride, D. T. PY - 2005 DA - 2005// TI - A tool for analyzing substitutions and similarity in multiple alignments BT - Distributed by the author ID - Pride2005 ER - TY - JOUR AU - Rozas, J. AU - Sanchez-DelBarrio, J. C. AU - Messeguer, X. AU - Rozas, R. PY - 2003 DA - 2003// TI - DnaSP, DNA polymorphism analyses by the coalescent and other methods JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg359 DO - 10.1093/bioinformatics/btg359 ID - Rozas2003 ER - TY - STD TI - Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, et al.: CDD: a Conserved Domain Database for protein classification.Nucleic Acids Res 2005, (33 Database):D192-196. ID - ref48 ER - TY - STD TI - Oregon State University Giovanonni laboratory[http://www.mcb.oregonstate.edu/giovannoni/] UR - http://www.mcb.oregonstate.edu/giovannoni/ ID - ref49 ER -