2009 Publications

Anderson, I. et al. (2009) Complete genome sequence of Halorhabdus utahensis type strain (AX-2(T)). Standards in Genomic Sciences 1(3), 218-225. Doi 10.4056/Sigs.31864
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Anderson, I. J. et al. (2009) The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. Bmc Genomics 10. Artn 145 Doi 10.1186/1471-2164-10-145
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Baker, S. E. et al. (2009) Selection to sequence: opportunities in fungal genomics. Environ Microbiol 11(12), 2955-8. 10.1111/j.1462-2920.2009.02112.x
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Bickel, R. D. et al. (2009) Contrasting Patterns of Sequence Evolution at the Functionally Redundant bric A brac Paralogs in Drosophila melanogaster. Journal of Molecular Evolution 69(2), 194-202. DOI 10.1007/s00239-009-9265-y
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Blazewicz, J. et al. (2009) Whole genome assembly from 454 sequencing output via modified DNA graph concept. Computational Biology and Chemistry 33(3), 224-230. DOI 10.1016/j.compbiolchem.2009.04.005
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Bressler, J. et al. (2009) The INSIG2 rs7566605 genetic variant does not play a major role in obesity in a sample of 24,722 individuals from four cohorts. BMC Med Genet 10, 56. 10.1186/1471-2350-10-56
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Calton, M. A. et al. (2009) Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Human Molecular Genetics 18(6), 1140-1147. Doi 10.1093/Hmg/Ddn431
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Campbell, B. J. et al. (2009) Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 5(2), e1000362. 10.1371/journal.pgen.1000362
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Carbon, S. et al. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25(2), 288-9. 10.1093/bioinformatics/btn615
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Chain, P. S. et al. (2009) Genomics. Genome project standards in a new era of sequencing. Science 326(5950), 236-7. 10.1126/science.1180614
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Chovatia, M. et al. (2009) Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883). Stand Genomic Sci 1(3), 254-61. 10.4056/sigs.40645
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Cordeddu, V. et al. (2009) Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet 41(9), 1022-6. 10.1038/ng.425
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Donaher, N. et al. (2009) The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol Evol 1, 439-48. 10.1093/gbe/evp047
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Drainas, C. et al. (2009) Characterization and whole genome sequencing of Arthrobacter phenanthrenivorans, a new phenanthrene degrading bacterium. Febs Journal 276, 101-101.
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Dubchak, I. et al. (2009) Multiple whole-genome alignments without a reference organism. Genome Research 19(4), 682-689. DOI 10.1101/gr.081778.108
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Duncan, K. E. et al. (2009) Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ Sci Technol 43(20), 7977-84. 10.1021/es9013932
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Duncan, K. E. et al. (2009) Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ Sci Technol 43(20), 7977-84. 10.1021/es9013932
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Engelbrektson, A. et al. (2009) Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol 58(Pt 5), 663-70. 10.1099/jmm.0.47615-0
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Field, D. et al. (2009) Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7. Stand Genomic Sci 1(1), 68-71. 10.4056/sigs.25165
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Han, C. et al. (2009) Complete genome sequence of Kangiella koreensis type strain (SW-125). Stand Genomic Sci 1(3), 226-33. 10.4056/sigs.36635
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Harris, D. R. et al. (2009) Directed evolution of ionizing radiation resistance in Escherichia coli. J Bacteriol 191(16), 5240-52. 10.1128/JB.00502-09
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Hill, K. K. et al. (2009) Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol 7, 66. 10.1186/1741-7007-7-66
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Hill, K. K. et al. (2009) Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. BMC Biol 7, 66. 10.1186/1741-7007-7-66
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Ivanova, N. et al. (2009) Spreading of aqueous solutions of trisiloxanes and conventional surfactants over PTFE AF coated silicone wafers. Langmuir 25(6), 3564-70. 10.1021/la803679y
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Kazakov, A. E. et al. (2009) Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol 191(1), 52-64. 10.1128/JB.01175-08
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Keim, P. et al. (2009) The genome and variation of Bacillus anthracis. Mol Aspects Med 30(6), 397-405. 10.1016/j.mam.2009.08.005
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Keim, P. et al. (2009) The genome and variation of Bacillus anthracis. Mol Aspects Med 30(6), 397-405. 10.1016/j.mam.2009.08.005
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Kislyuk, A. et al. (2009) Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl 5(4), 458-77.
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Klein, M. G. et al. (2009) Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392(2), 319-33. 10.1016/j.jmb.2009.03.056
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Kouvelis, V. N. et al. (2009) Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. J Bacteriol 191(22), 7140-1. 10.1128/JB.01084-09
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Kristiansson, E. et al. (2009) ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25(20), 2737-8. 10.1093/bioinformatics/btp508
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Land, M. et al. (2009) Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Stand Genomic Sci 1(1), 21-8. 10.4056/sigs.1162
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Lane, T. W. et al. (2009) Digital Transcriptomic Analysis of Silicate Starvation Induced Triacylglycerol Formation in the Marine Diatom Thalassiosira Pseudonana.. Phycologia 48(4), 71-71.
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Larsson, P. et al. (2009) Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen. PLoS Pathog 5(6), e1000472. 10.1371/journal.ppat.1000472
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Lin-Jones, J. et al. (2009) Identification and Localization of Myosin Superfamily Members in Fish Retina and Retinal Pigmented Epithelium. Journal of Comparative Neurology 513(2), 209-223. Doi 10.1002/Cne.21958
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Masta, S. E. et al. (2009) Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol Phylogenet Evol 50(1), 117-28. 10.1016/j.ympev.2008.10.010
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Mavromatis, K. et al. (2009) Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System. Plos One 4(11). Artn E7979 Doi 10.1371/Journal.Pone.0007979
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Mavromatis, K. et al. (2009) Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One 4(1), e4192. 10.1371/journal.pone.0004192
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Mavromatis, K. et al. (2009) The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Standards in Genomic Sciences 1(1), 63-67. Doi 10.4056/Sigs.632
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McMurdie, P. J. et al. (2009) Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5(11), e1000714. 10.1371/journal.pgen.1000714
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Munk, C. et al. (2009) Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21). Stand Genomic Sci 1(3), 234-41. 10.4056/sigs.47643
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Nolan, M. et al. (2009) Complete genome sequence of Streptobacillus moniliformis type strain (9901). Stand Genomic Sci 1(3), 300-7. 10.4056/sigs.48727
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Nolan, M. et al. (2009) Complete genome sequence of Rhodothermus marinus type strain (R-10). Stand Genomic Sci 1(3), 283-90. 10.4056/sigs.46736
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Novichkov, P. S. et al. (2009) ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res 37(Database issue), D448-54. 10.1093/nar/gkn684
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Novichkov, P. S. et al. (2009) Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 191(1), 65-73. 10.1128/JB.01237-08
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O'Rourke, J. A. et al. (2009) Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. BMC Genomics 10, 376. 10.1186/1471-2164-10-376
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Pavlopoulos, G. A. et al. (2009) jClust: a clustering and visualization toolbox. Bioinformatics 25(15), 1994-6. 10.1093/bioinformatics/btp330
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Pearson, T. et al. (2009) Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 7, 78. 10.1186/1741-7007-7-78
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Pearson, T. et al. (2009) Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 7, 78. 10.1186/1741-7007-7-78
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Penn, K. et al. (2009) Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 3(10), 1193-203. 10.1038/ismej.2009.58
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Pukall, R. et al. (2009) Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134). Stand Genomic Sci 1(3), 262-9. 10.4056/sigs.41646
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Pukall, R. et al. (2009) Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Stand Genomic Sci 1(3), 234-41. 10.4056/sigs.37633
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Ratnere, I. et al. (2009) Obtaining comparative genomic data with the VISTA family of computational tools. Curr Protoc Bioinformatics Chapter 10, Unit 10 6. 10.1002/0471250953.bi1006s26
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Romeo, S. et al. (2009) Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest 119(1), 70-9. 10.1172/JCI37118
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Seidl, V. et al. (2009) Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. Bmc Genomics 10. Artn 567 Doi 10.1186/1471-2164-10-567
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Slavotinek, A. M. et al. (2009) Sequence variants in the HLX gene at chromosome 1q41-1q42 in patients with diaphragmatic hernia. Clinical Genetics 75(5), 429-439. DOI 10.1111/j.1399-0004.2009.01182.x
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Spring, S. et al. (2009) Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci 1(3), 242-53. 10.4056/sigs.39508
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Tindall, B. J. et al. (2009) Complete genome sequence of Halomicrobium mukohataei type strain (arg-2). Stand Genomic Sci 1(3), 270-7. 10.4056/sigs.42644
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Tschop, M. H. et al. (2009) Getting to the core of the gut microbiome. Nat Biotechnol 27(4), 344-6. 10.1038/nbt0409-344
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Van der Auwera, G. A. et al. (2009) Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie Van Leeuwenhoek 96(2), 193-204. 10.1007/s10482-009-9316-9
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Visel, A. et al. (2009) Functional autonomy of distant-acting human enhancers. Genomics 93(6), 509-13. 10.1016/j.ygeno.2009.02.002
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Visel, A. et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457(7231), 854-8. 10.1038/nature07730
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Visel, A. et al. (2009) Genomic views of distant-acting enhancers. Nature 461(7261), 199-205. 10.1038/nature08451
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Walsh, D. A. et al. (2009) Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones. Science 326(5952), 578-582. DOI 10.1126/science.1175309
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Walsh, D. A. et al. (2009) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326(5952), 578-82. 10.1126/science.1175309
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Ward, N. L. et al. (2009) Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils. Applied and Environmental Microbiology 75(7), 2046-2056. Doi 10.1128/Aem.02294-08
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Ward, N. L. et al. (2009) Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils. Applied and Environmental Microbiology 75(7), 2046-2056. Doi 10.1128/Aem.02294-08
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Warnecke, F. et al. (2009) A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts. Journal of Biotechnology 142(1), 91-95. DOI 10.1016/j.jbiotec.2009.03.022
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Wattam, A. R. et al. (2009) Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle. Journal of Bacteriology 191(11), 3569-3579. Doi 10.1128/Jb.01767-08
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Wu, D. et al. (2009) Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 4(1), e4207. 10.1371/journal.pone.0004207
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Wu, D. Y. et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462(7276), 1056-1060. Doi 10.1038/Nature08656
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Zhang, Z. et al. (2009) Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci U S A 106(9), 3219-24. 10.1073/pnas.0813400106
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