2006 Publications

Beller, H. R. et al. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188(4), 1473-88. 10.1128/JB.188.4.1473-1488.2006
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Brodie, E. L. et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72(9), 6288-98. 10.1128/AEM.00246-06
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Budowle, B. et al. (2006) Quality sample collection, handling, and preservation for an effective microbial forensics program. Appl Environ Microbiol 72(10), 6431-8. 10.1128/AEM.01165-06
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Cai, Z. et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6, 77. 10.1186/1471-2148-6-77
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Carapelli, A. et al. (2006) The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Gene 376(2), 248-59. 10.1016/j.gene.2006.04.005
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Chain, P. S. et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103(42), 15280-7. 10.1073/pnas.0606924103
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Coleman, M. L. et al. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311(5768), 1768-1770. Doi 10.1126/Science.1122050
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Collins, A. G. et al. (2006) Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Systematic Biology 55(1), 97-115. Doi 10.1080/10635150500433615
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Collins, A. G. et al. (2006) Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Systematic Biology 55(1), 97-115. Doi 10.1080/10635150500433615
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DeSantis, T. Z. et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34, W394-W399. Doi 10.1093/Nar/Gkl244
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DeSantis, T. Z. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72(7), 5069-5072. Doi 10.1128/Aem.03006-05
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Doggett, N. A. et al. (2006) A 360-kb interchromosomal duplication of the human HYDIN locus. Genomics 88(6), 762-771. Doi 10.1016/J.Ygeno.2006.07.012
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Gowda, M. et al. (2006) Robust analysis of 5 '-transcript ends (5 '-RATE): a novel technique for transcriptome analysis and genome annotation. Nucleic Acids Research 34(19). Doi 10.1093/Nar/Gkl522
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Hallam, S. J. et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences of the United States of America 103(48), 18296-18301. Doi 10.1073/Pnas.0608549103
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Hallam, S. J. et al. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. Plos Biology 4(4), 520-536. Artn E95 Doi 10.1371/Journal.Pbio.0040095
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Hixson, K. K. et al. (2006) Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 5(11), 3008-17. 10.1021/pr060179y
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Huerta, A. M. et al. (2006) Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes. Molecular Biology and Evolution 23(5), 997-1010. Doi 10.1093/Molbev/Msk004
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Huerta, A. M. et al. (2006) Selection for unequal densities of sigma(70) promoter-like signals in different regions of large bacterial genomes. Plos Genetics 2(11), 1740-1750. ARTN e185 DOI 10.1371/journal.pgen.0020185
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Imachi, H. et al. (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 72(3), 2080-2091. Doi 10.1128/Aem.72.3.2080-2091.2006
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Janga, S. C. et al. (2006) The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucleic Acids Research 34(14), 3980-3987. Doi 10.1093/Nar/Gkl563
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Klotz, M. G. et al. (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol 72(9), 6299-315. 10.1128/AEM.00463-06
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Krampis, K. et al. (2006) Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum. Molecular Plant-Microbe Interactions 19(12), 1329-1336. Doi 10.1094/Mpmi-19-1329
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Kuske, C. R. et al. (2006) Current and emerging technologies for the study of bacteria in the outdoor air. Current Opinion in Biotechnology 17(3), 291-296. Doi 10.1016/J.Copbio.2006.04.001
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Kuske, C. R. et al. (2006) Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes. Journal of Forensic Sciences 51(3), 548-558. Doi 10.1111/J.1556-4029.2006.00131.X
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Li, M. et al. (2006) Confidence-based classifier design. Pattern Recognition 39(7), 1230-1240. Doi 10.1016/J.Patcog.2006.01.010
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Li, M. K. et al. (2006) Confidence-based active learning. Ieee Transactions on Pattern Analysis and Machine Intelligence 28(8), 1251-1261.
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Liolios, K. et al. (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research 34, D332-D334. Doi 10.1093/Nar/Gkj145
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Loots, G. G. et al. (2006) Array2BIO: from microarray expression data to functional annotation of co-regulated genes. Bmc Bioinformatics 7. Artn 307 Doi 10.1186/1471-2105-7-307
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Maeder, D. L. et al. (2006) The Methanosarcina barkeri genome: Comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. Journal of Bacteriology 188(22), 7922-7931. Doi 10.1128/Jb.00810-06
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Maeder, D. L. et al. (2006) The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 188(22), 7922-31. 10.1128/JB.00810-06
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Makarova, K. et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103(42), 15611-6. 10.1073/pnas.0607117103
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Martin, H. G. et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology 24(10), 1263-1269. Doi 10.1038/Nbt1247
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Martiny, J. B. H. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4(2), 102-112. Doi 10.1038/Nrmicro1341
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Mavromatis, K. et al. (2006) The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Journal of Bacteriology 188(11), 4015-4023. Doi 10.1128/Jb.01837-05
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Medina, M. et al. (2006) Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A 103(24), 9096-100. 10.1073/pnas.0602444103
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Merrill, L. et al. (2006) Composition of Bacillus species in aerosols from 11 US cities. Journal of Forensic Sciences 51(3), 559-565. Doi 10.1111/J.1556-4029.2006.00132.X
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Nosenko, T. et al. (2006) Chimeric plastid proteome in the florida "red tide" dinoflagellate Karenia brevis. Molecular Biology and Evolution 23(11), 2026-2038. Doi 10.1093/Molbev/Msl074
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Podsiadlowski, L. et al. (2006) The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda : Diplura): High genetic divergence in a morphologically uniform taxon. Gene 381, 49-61. Doi 10.1016/J.Gene.2006.06.009
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Prabhakar, S. et al. (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314(5800), 786. 10.1126/science.1130738
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Schulte, J. A. et al. (2006) A genetic perspective on the geographic association of taxa among and North American lizards of the Sceloporus magister complex (Squamata : Iguanidae : Phrynosomatinae). Molecular Phylogenetics and Evolution 39(3), 873-880. Doi 10.1016/J.Ympev.2005.04.033
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Scott, K. M. et al. (2006) The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. Plos Biology 4(12), 2196-2212. ARTN e383 DOI 10.1371/journal.pbio.0040383
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Siddaramappa, S. et al. (2006) Comparative analyses of two cryptic plasmids from Haemophilus somnus (Histophilus somni). Plasmid 55(3), 227-234. Doi 10.1016/J.Plasmid.2005.11.004
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Simison, W. B. et al. (2006) Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution 39(2), 562-567. Doi 10.1016/J.Ympev.2005.11.006
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Starkenburg, S. R. et al. (2006) Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology 72(3), 2050-2063. Doi 10.1128/Aem.72.3.2050-2063.2006
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Stillman, J. H. et al. (2006) Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes. Integrative and Comparative Biology 46(6), 919-930. Doi 10.1093/Icb/Icl007
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Valles, Y. et al. (2006) Lophotrochozoan mitochondrial genomes. Integrative and Comparative Biology 46(4), 544-557. Doi 10.1093/Icb/Icj056
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Warren, R. L. et al. (2006) Physical map-assisted whole-genome shotgun sequence assemblies. Genome Research 16(6), 768-775. Doi 10.1101/Gr.5090606
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Wei, X. M. et al. (2006) Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Archives of Microbiology 186(2), 107-118. Doi 10.1007/S00203-006-0126-4
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Weng, L. et al. (2006) Application of sequence-based methods in human microbial ecology. Genome Research 16(3), 316-322. Doi 10.1101/Gr.3676406
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Williams, L. E. et al. (2006) Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing. Applied and Environmental Microbiology 72(7), 4899-4906. Doi 10.1128/Aem.00354-06
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Woyke, T. et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443(7114), 950-955. Doi 10.1038/Nature05192
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Zhang, K. et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24(6), 680-686. Doi 10.1038/Nbt1214
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