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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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News & Publications
Home › News & Publications › Publications › 2006 Publications

2006 Publications

Baker, S. E. et al. (2006) Aspergillus niger genomics: Past, present and into the future. Medical Mycology 44, S17-S21. Doi 10.1080/13693780600921037
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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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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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Markowitz, V. M. et al. (2006) An experimental metagenome data management and analysis system. Bioinformatics 22(14), e359-67. 10.1093/bioinformatics/btl217
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Markowitz, V. M. et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research 34, D344-D348. Doi 10.1093/Nar/Gkj024
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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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Tuskan, G. A. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793), 1596-1604. Doi 10.1126/Science.1128691
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Tyler, B. M. et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313(5791), 1261-1266. Doi 10.1126/Science.1128796
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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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Vanden Wymelenberg, A. et al. (2006) Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Fungal Genetics and Biology 43(5), 343-356. Doi 10.1016/J.Fgb.2006.01.003
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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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