2007 Publications

Adamska, M. et al. (2007) The evolutionary origin of hedgehog proteins. Curr Biol 17(19), R836-7. 10.1016/j.cub.2007.08.010
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Ahituv, N. et al. (2007) Deletion of ultraconserved elements yields viable mice. Plos Biology 5(9), 1906-1911. ARTN e234 DOI 10.1371/journal.pbio.0050234
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Allen, E. E. et al. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A 104(6), 1883-8. 10.1073/pnas.0604851104
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Alonso, C. et al. (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9(5), 1253-66. 10.1111/j.1462-2920.2007.01244.x
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Anderson, S. J. et al. (2007) Phenotypic and genetic variation among soybean rust isolates. Phytopathology 97(7), S4-S4.
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Arp, D. J. et al. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology 61, 503-528. DOI 10.1146/annurev.micro.61.080706.093449
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Auerbach, R. K. et al. (2007) Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. Plos One 2(8). ARTN e770 DOI 10.1371/journal.pone.0000770
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Bailey, Joseph M. et al. (2007) Confederate guerrilla : the Civil War memoir of Joseph M. Bailey. The Civil War in the West , xix, 148 p..
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Barns, S. M. et al. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73(9), 3113-6. 10.1128/AEM.02012-06
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Beckstrom-Sternberg, S. M. et al. (2007) Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One 2(9), e947. 10.1371/journal.pone.0000947
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Challacombe, J. F. et al. (2007) The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol 189(9), 3680-1. 10.1128/JB.00241-07
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Chistoserdova, L. et al. (2007) Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol 189(11), 4020-7. 10.1128/JB.00045-07
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Dalevi, D. et al. (2007) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. Bmc Bioinformatics 8. Artn 402 Doi 10.1186/1471-2105-8-402
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Field, D. et al. (2007) The positive role of the ecological community in the genomic revolution. Microb Ecol 53(3), 507-11. 10.1007/s00248-007-9206-5
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Fong, J. J. et al. (2007) A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals. Animal Conservation 10(4), 452-460. DOI 10.1111/j.1469-1795.2007.00131.x
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Fujita, M. K. et al. (2007) Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; squamata, gekkonidae). Molecular Biology and Evolution 24(12), 2775-2786. DOI 10.1093/molbev/msm212
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Giraud, E. et al. (2007) Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316(5829), 1307-12. 10.1126/science.1139548
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Gordon, L. et al. (2007) Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res 17(11), 1603-13. 10.1101/gr.6775107
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Gowda, M. et al. (2007) Interrogation of the RNA species in Magnaporthe grisea. Phytopathology 97(7), S42-S42.
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Gu, S. Y. et al. (2007) TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23(6), 764-766. Doi 10.1093/Bioinformatics/Btl643
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Horner-Devine, M. C. et al. (2007) A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88(6), 1345-1353. Doi 10.1890/06-0286
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Housman, D. C. et al. (2007) Heterogeneity of soil nutrients and subsurface biota in a dryland ecosystem. Soil Biology & Biochemistry 39(8), 2138-2149. Doi 10.1016/J.Soilbio.2007.03.015
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Hristova, K. R. et al. (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and Environmental Microbiology 73(22), 7347-7357. Doi 10.1128/Aem.01604-07
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Hugenholtz, P. et al. (2007) Riding giants. Environmental Microbiology 9(1), 5-5. Doi 10.1111/J.1462-2920.2006.01222_4.X
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Hugenholtz, P. et al. (2007) Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology 18(3), 235-236. Doi 10.1016/J.Copbio.2007.05.004
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Jansen, R. K. et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America 104(49), 19369-19374. DOI 10.1073/pnas.0709121104
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Johnson, S. L. et al. (2007) Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands. Environmental Microbiology 9(3), 680-689. Doi 10.1111/J.1462-2920.2006.01187.X
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Kamburov, A. et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. Bmc Genomics 8. Artn 460 Doi 10.1186/1471-2164-8-460
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Kane, S. R. et al. (2007) Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 189(5), 1931-45. 10.1128/JB.01259-06
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Kane, S. R. et al. (2007) Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of Bacteriology 189(5), 1931-1945. Doi 10.1128/Jb.01259-06
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Kazakov, A. E. et al. (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research 35, D407-D412. Doi 10.1093/Nar/Gkl865
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Larroux, C. et al. (2007) The NK homeobox gene cluster predates the origin of Hox genes. Current Biology 17(8), 706-710. Doi 10.1016/J.Cub.2007.03.008
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Leonardi, R. et al. (2007) Localization and regulation of mouse pantothenate kinase 2. FEBS Lett 581(24), 4639-44. 10.1016/j.febslet.2007.08.056
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Lo, I. et al. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135), 537-541. Doi 10.1038/Nature05624
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Lykidis, A. et al. (2007) Comparative genomics and evolution of eukaryotic phospholipid biosynthesis. Progress in Lipid Research 46(3-4), 171-199. Doi 10.1016/J.Plipres.2007.03.003
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Lykidis, A. et al. (2007) Genomics and evolution of eukaryotic phospholipid biosynthesis. Faseb Journal 21(6), A976-A976.
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Lykidis, A. et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of Bacteriology 189(6), 2477-2486. Doi 10.1128/Jb.01899-06
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Makarova, K. S. et al. (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2(9), e955. 10.1371/journal.pone.0000955
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Marcy, Y. et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America 104(29), 11889-11894. Doi 10.1073/Pnas.0704662104
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Martin, F. N. et al. (2007) Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P-sojae. Current Genetics 51(5), 285-296. Doi 10.1007/S00294-007-0121-6
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McHardy, A. C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods 4(1), 63-72. Doi 10.1038/Nmeth976
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McMahon, K. D. et al. (2007) Integrating ecology into biotechnology. Current Opinion in Biotechnology 18(3), 287-292. Doi 10.1016/J.Copbio.2007.04.007
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McNeal, J. R. et al. (2007) Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology 5. Artn 55 Doi 10.1186/1741-7007-5-55
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McNeal, J. R. et al. (2007) Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. Bmc Plant Biology 7. Artn 57 Doi 10.1186/1471-2229-7-57
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Meier, S. et al. (2007) Continuous molecular evolution of protein-domain structures by single amino acid changes. Current Biology 17(2), 173-178. Doi 10.1016/J.Cub.2006.10.063
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Merchant, S. et al. (2007) Establishing potential chloroplast function through phylogenomics. Photosynthesis Research 91(2-3), 271-272.
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Minovitsky, S. et al. (2007) Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. Bmc Genomics 8. Artn 378 Doi 10.1186/1471-2164-8-378
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Moran, M. A. et al. (2007) Ecological genomics of marine roseobacters. Applied and Environmental Microbiology 73(14), 4559-4569. Doi 10.1128/Aem.02580-06
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Newton, I. L. G. et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315(5814), 998-1000. Doi 10.1126/Science.1138438
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Normand, P. et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp strains reflect host range and host plant biogeography. Genome Research 17(1), 7-15. Doi 10.1101/Gr.5798407
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Oudot-Le Secq, M. P. et al. (2007) Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Molecular Genetics and Genomics 277(4), 427-439. Doi 10.1007/S00438-006-0199-4
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Pel, H. J. et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2), 221-31. 10.1038/nbt1282
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Raubeson, L. A. et al. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. Bmc Genomics 8. Artn 174 Doi 10.1186/1471-2164-8-174
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Romeo, S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nature Genetics 39(4), 513-516. Doi 10.1038/Ng1984
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Sorek, R. et al. (2007) The birth of new exons: mechanisms and evolutionary consequences. RNA 13(10), 1603-8. 10.1261/rna.682507
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Sorek, R. et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318(5855), 1449-52. 10.1126/science.1147112
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Stein, L. Y. et al. (2007) Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol 9(12), 2993-3007. 10.1111/j.1462-2920.2007.01409.x
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Tanaka, S. et al. (2007) Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr D Biol Crystallogr 63(Pt 10), 1109-12. 10.1107/S090744490704228X
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Tang, Y. J. et al. (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73(12), 3859-64. 10.1128/AEM.02986-06
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Timme, R. E. et al. (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94(3), 302-12. 10.3732/ajb.94.3.302
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Udwary, D. W. et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences of the United States of America 104(25), 10376-10381. Doi 10.1073/Pnas.0700962104
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Vannini, C. et al. (2007) Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environmental Microbiology 9(2), 347-359. Doi 10.1111/J.1462-2920.2006.01144.X
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Visel, A. et al. (2007) Enhancer identification through comparative genomics. Seminars in Cell & Developmental Biology 18(1), 140-152. Doi 10.1016/J.Semcdb.2006.12.014
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von Mering, C. et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126-1130. Doi 10.1126/Science.1133420
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Warnecke, F. et al. (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8(12), 231. 10.1186/gb-2007-8-12-231
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Wong, R. et al. (2007) The story told by 100 shotgun sequenced microbial genomes - Why the clonability for genomes are different.. Plasmid 57(2), 239-239.
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Xie, G. et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Applied and Environmental Microbiology 73(11), 3536-3546. Doi 10.1128/Aem.00225-07
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Yeager, C. M. et al. (2007) Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N-2-fixing members of biological soil crusts of the Colorado Plateau, USA. Fems Microbiology Ecology 60(1), 85-97. Doi 10.1111/J.1574-6941.2006.00265.X
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