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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 › 2014 Publications

2014 Publications

Ardley, J. et al. (2014) Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598. Stand Genomic Sci 9, 5. 10.1186/1944-3277-9-5
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Axen, S. D. et al. (2014) A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 10(10), e1003898. 10.1371/journal.pcbi.1003898
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Aylward, F. O. et al. (2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6). 10.1128/mBio.02077-14
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Bartholome, J. et al. (2014) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol . 10.1111/nph.13150
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Beck, D. A. et al. (2014) The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes. PLoS One 9(7), e102458. 10.1371/journal.pone.0102458
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Becker, E. A. et al. (2014) Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet 10(11), e1004784. 10.1371/journal.pgen.1004784
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Beissinger, T. M. et al. (2014) A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics 196(3), 829-40. 10.1534/genetics.113.160655
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Biddle, A. S. et al. (2014) The complete genome sequence of Clostridium indolis DSM 755(T.). Stand Genomic Sci 9(3), 1089-104. 10.4056/sigs.5281010
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Billis, K. et al. (2014) Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation. PLoS One 9(10), e109738. 10.1371/journal.pone.0109738
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Blaby, I. K. et al. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci . 10.1016/j.tplants.2014.05.008
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Blanc-Mathieu, R. et al. (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 15, 1103. 10.1186/1471-2164-15-1103
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Breider, S. et al. (2014) Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 9(3), 687-703. 10.4056/sigs.3828824
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Byrne, R. T. et al. (2014) Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife 3, e01322. 10.7554/eLife.01322
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Campbell, A. G. et al. (2014) Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environ Microbiol . 10.1111/1462-2920.12461
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Chaib De Mares, M. et al. (2014) Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita. New Phytol . 10.1111/nph.13140
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Chang, P. J. et al. (2014) Force measurements of a magnetic micro actuator proposed for a microvalve array. Journal of Micromechanics and Microengineering 24(3). 10.1088/0960-1317/24/3/034005
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Childs, K. L. et al. (2014) Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass. Plant Genome 7(2). Doi 10.3835/Plantgenome2013.12.0041
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Cho, Y. et al. (2014) Transcriptional responses of the Bdtf1-deletion mutant to the phytoalexin brassinin in the necrotrophic fungus Alternaria brassicicola. Molecules 19(8), 10717-32. 10.3390/molecules190810717
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Cimermancic, P. et al. (2014) Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters. Cell 158(2), 412-421. Doi 10.1016/J.Cell.2014.06.034
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Clingenpeel, S. et al. (2014) Effects of sample treatments on genome recovery via single-cell genomics. ISME J . 10.1038/ismej.2014.92
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Clingenpeel, S. et al. (2014) Reconstructing each cell's genome within complex microbial communities-dream or reality?. Front Microbiol 5, 771. 10.3389/fmicb.2014.00771
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Coleman-Derr, D. et al. (2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5(283), 283. 10.3389/fmicb.2014.00283
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Collavino, M. M. et al. (2014) nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2 -fixing community dynamics. Environ Microbiol 16(10), 3211-23. 10.1111/1462-2920.12423
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Deng, K. et al. (2014) Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol 9(7), 1470-9. 10.1021/cb5000289
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Dmytrenko, O. et al. (2014) The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15(1), 924. 10.1186/1471-2164-15-924
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Duanmu, D. et al. (2014) Marine algae and land plants share conserved phytochrome signaling systems. Proc Natl Acad Sci U S A . 10.1073/pnas.1416751111
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Dubchak, I. et al. (2014) An integrative computational approach for prioritization of genomic variants. PLoS One 9(12), e114903. 10.1371/journal.pone.0114903
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Durham, B. P. et al. (2014) Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genomic Sci 9(3), 632-45. 10.4056/sigs.4998989
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Earl, D. et al. (2014) Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res 24(12), 2077-89. 10.1101/gr.174920.114
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Erbilgin, O. et al. (2014) Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides. Applied and Environmental Microbiology 80(7), 2193-2205. Doi 10.1128/Aem.03887-13
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Evans, L. M. et al. (2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46(10), 1089-96. 10.1038/ng.3075
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Field, D. et al. (2014) Genomic standards consortium projects. Stand Genomic Sci 9(3), 599-601. 10.4056/sigs.5559680
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Field, E. K. et al. (2014) Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J . 10.1038/ismej.2014.183
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Gallo, A. et al. (2014) Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius. Int J Food Microbiol 179, 10-7. 10.1016/j.ijfoodmicro.2014.03.013
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Gan, F. et al. (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science 345(6202), 1312-7. 10.1126/science.1256963
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Gao, D. et al. (2014) Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris). Front Plant Sci 5, 339. 10.3389/fpls.2014.00339
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Garau, G. et al. (2014) Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of Medicago murex and M. polymorpha. Stand Genomic Sci 9, 4. 10.1186/1944-3277-9-4
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Gaudana, S. B. et al. (2014) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase C uptake by cyanobacteria. Photosynth Res . 10.1007/s11120-014-0059-8
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Ghylin, T. W. et al. (2014) Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J . 10.1038/ismej.2014.135
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Goker, M. et al. (2014) Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 9(3), 1076-88. 10.4056/sigs.5138968
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Goker, M. et al. (2014) Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci 9(3), 1105-17. 10.4056/sigs.3016383
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Golberg, A. et al. (2014) Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies. Biofuels Bioproducts & Biorefining-Biofpr 8(1), 67-82. Doi 10.1002/Bbb.1438
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Golberg, A. et al. (2014) Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water. PLoS One 9(1), e86341. 10.1371/journal.pone.0086341
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Gordon, S. P. et al. (2014) Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines. Plant J . 10.1111/tpj.12569
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Gostincar, C. et al. (2014) Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. BMC Genomics 15, 549. 10.1186/1471-2164-15-549
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Grigoriev, I. V. et al. (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42(Database issue), D699-704. 10.1093/nar/gkt1183
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Haider, B. et al. (2014) Omega: an Overlap-graph de novo Assembler for Metagenomics. Bioinformatics . 10.1093/bioinformatics/btu395
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Hawley, E. R. et al. (2014) Metagenomic sequencing of two salton sea microbiomes. Genome Announc 2(1). 10.1128/genomeA.01208-13
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Hawley, E. R. et al. (2014) Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics . 10.1016/j.margen.2014.06.003
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Hawley, E. R. et al. (2014) Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 9(3), 1259-74. 10.4056/sigs.5029016
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Hedlund, B. P. et al. (2014) Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter". Extremophiles 18(5), 865-75. 10.1007/s00792-014-0664-7
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Heins, R. A. et al. (2014) Phylogenomically Guided Identification of Industrially Relevant GH1 beta-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. Acs Chemical Biology 9(9), 2082-2091. 10.1021/Cb500244v
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Heller, P. et al. (2014) ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. Bioinformatics . 10.1093/bioinformatics/btu417
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Hess, J. et al. (2014) Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi. Genome Biol Evol 6(7), 1564-78. 10.1093/gbe/evu121
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Hillson, NathanJ et al. (2014) j5 DNA Assembly Design Automation. DNA Cloning and Assembly Methods 1116, 245-269. 10.1007/978-1-62703-764-8_17
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Hirsch, C. N. et al. (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26(1), 121-35. 10.1105/tpc.113.119982
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Hori, C. et al. (2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood. PLoS Genet 10(12), e1004759. 10.1371/journal.pgen.1004759
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Howe, A. C. et al. (2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13), 4904-9. 10.1073/pnas.1402564111
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Hurley, J. M. et al. (2014) Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A 111(48), 16995-7002. 10.1073/pnas.1418963111
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International Wheat Genome Sequencing, Consortium et al. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194), 1251788. 10.1126/science.1251788
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Ivanova, N. N. et al. (2014) Stop codon reassignments in the wild. Science 344(6186), 909-13. 10.1126/science.1250691
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Jansson, J. K. et al. (2014) The microbial ecology of permafrost. Nat Rev Microbiol 12(6), 414-25. 10.1038/nrmicro3262
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Jay, Z. J. et al. (2014) Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 80(1), 294-305. 10.1128/AEM.02860-13
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Kamke, J. et al. (2014) The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 9(1), e87353. 10.1371/journal.pone.0087353
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Kashtan, N. et al. (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344(6182), 416-20. 10.1126/science.1248575
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Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Stand Genomic Sci 9, 7. 10.1186/1944-3277-9-7
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Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. Stand Genomic Sci 9, 6. 10.1186/1944-3277-9-6
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Kis-Papo, T. et al. (2014) Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum. Nat Commun 5, 3745. 10.1038/ncomms4745
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Kouvelis, V. N. et al. (2014) Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer. Genome Announc 2(1). 10.1128/genomeA.00845-13
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Kruse, T. et al. (2014) Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. J Bacteriol . 10.1128/JB.02370-14
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Kuever, J. et al. (2014) Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 9(3), 821-39. 10.4056/sigs.5209235
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Kuo, A. et al. (2014) Expanding genomics of mycorrhizal symbiosis. Front Microbiol 5, 582. 10.3389/fmicb.2014.00582
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Kyrpides, N. C. et al. (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 12(8), e1001920. 10.1371/journal.pbio.1001920
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Kyrpides, N. C. et al. (2014) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci 9(3), 1278-84. 10.4056/sigs.5068949
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Lamendella, R. et al. (2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 5, 130. 10.3389/fmicb.2014.00130
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Lassila, J. K. et al. (2014) Assembly of robust bacterial microcompartment shells using building blocks from an organelle of unknown function. J Mol Biol 426(11), 2217-28. 10.1016/j.jmb.2014.02.025
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Leverenz, R. L. et al. (2014) Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection. Plant Cell 26(1), 426-37. 10.1105/tpc.113.118588
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Lewis, S. M., Gross, S., Visel, A., Kelly, M. and Morrow, W. et al. (2014) Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock. GCB Bioenergy . 10.1111/gcbb.12116
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Lim, Y. W. et al. (2014) Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J Vis Exp (94). 10.3791/52117
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Linshiz, G. et al. (2014) PR-PR: cross-platform laboratory automation system. ACS Synth Biol 3(8), 515-24. 10.1021/sb4001728
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Lowry, D. B. et al. (2014) The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. New Phytol . 10.1111/nph.13027
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Marcussen, T. et al. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345(6194), 1250092. 10.1126/science.1250092
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Markowitz, V. M. et al. (2014) IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res 42(Database issue), D568-73. 10.1093/nar/gkt919
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Markowitz, V. M. et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42(Database issue), D560-7. 10.1093/nar/gkt963
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Martin, J. A. et al. (2014) A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 4, 4519. 10.1038/srep04519
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Mason, O. U. et al. (2014) Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Front Microbiol 5, 332. 10.3389/fmicb.2014.00332
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Matzke, N. J. et al. (2014) Bayesian analysis of congruence of core genes in prochlorococcus and synechococcus and implications on horizontal gene transfer. PLoS One 9(1), e85103. 10.1371/journal.pone.0085103
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Meier-Kolthoff, J.P. et al. (2014) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9, 2. 10.1186/1944-3277-9-2
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Moulin, L. et al. (2014) Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Stand Genomic Sci 9(3), 763-74. 10.4056/sigs.4861021
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Mukherjee, S. et al. (2014) Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One 9(1), e86731. 10.1371/journal.pone.0086731
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Myburg, A. A. et al. (2014) The genome of Eucalyptus grandis. Nature 509(7505), 356-62. 10.1038/nature13308
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Nagy, L. G. et al. (2014) Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Commun 5, 4471. 10.1038/ncomms5471
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Nandasena, K. et al. (2014) Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)). Stand Genomic Sci 9(3), 462-72. 10.4056/sigs.4458283
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Nobu, M. K. et al. (2014) The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol . 10.1111/1462-2920.12444
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Nobu, M. K. et al. (2014) Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph. Genome Announc 2(1). 10.1128/genomeA.01064-13
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Nordberg, H. et al. (2014) The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res 42(Database issue), D26-31. 10.1093/nar/gkt1069
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Ntougias, S. et al. (2014) High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway. Stand Genomic Sci 9(3), 783-93. 10.4056/sigs.5088950
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O'Connor, R. M. et al. (2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A 111(47), E5096-104. 10.1073/pnas.1413110111
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Pedersen, K. et al. (2014) Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announc 2(3). 10.1128/genomeA.00509-14
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Reeve, W. et al. (2014) Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128. Stand Genomic Sci 9(3), 602-13. 10.4056/sigs.4929626
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Reeve, W. et al. (2014) Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. Stand Genomic Sci 9(3), 514-26. 10.4056/sigs.4938652
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Reeve, W. et al. (2014) Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas. Stand Genomic Sci 9(3), 1159-67. 10.4056/sigs.5249382
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Reeve, W. et al. (2014) Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. Stand Genomic Sci 9(3), 473-83. 10.4056/sigs.4828625
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Riedel, T. et al. (2014) Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9(3), 1333-45. 10.4056/sigs.4909790
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Scheuner, C. et al. (2014) Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 9, 10. 10.1186/1944-3277-9-10
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Singan, V. R. et al. (2014) Precision Drug Targeting: Understanding the Intracellular Transport Mechanism. Journal of Investigative Genomics 2(1). 10.15406/jig.2015.02.00011
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Singh, G. et al. (2014) Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia. J Clin Microbiol 52(7), 2430-8. 10.1128/JCM.01626-13
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Tas, N. et al. (2014) Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J . 10.1038/ismej.2014.36
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Terpolilli, J. et al. (2014) Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. Stand Genomic Sci 9(3), 527-39. 10.4056/sigs.4988693
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Thiel, T. et al. (2014) Complete genome sequence of Anabaena variabilis ATCC 29413. Stand Genomic Sci 9(3), 562-73. 10.4056/sigs.3899418
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Toome, M. et al. (2014) Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951. Genome Announc 2(3). 10.1128/genomeA.00539-14
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Visser, M. et al. (2014) Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci 9(3), 655-75. 10.4056/sigs.4718645
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Wagner, M. R. et al. (2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17(6), 717-26. 10.1111/ele.12276
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Walker, R. et al. (2014) Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia. Stand Genomic Sci 9(3), 551-61. 10.4056/sigs.5008793
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Walker, R. et al. (2014) Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia. Stand Genomic Sci 9(3), 1168-80. 10.4056/sigs.5018795
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Willems, A. et al. (2014) Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan. Stand Genomic Sci 9(3), 484-94. 10.4056/sigs.4848627
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Williams, T. J. et al. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J . 10.1038/ismej.2014.18
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Wilson, J. G. et al. (2014) Draft Genome Sequence of Enterobacter cloacae Strain JD6301. Genome Announc 2(3). 10.1128/genomeA.00381-14
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Wright, J. J. et al. (2014) Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. ISME J 8(2), 455-68. 10.1038/ismej.2013.152
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Wu, G. A. et al. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32(7), 656-62. 10.1038/nbt.2906
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Wu, Y. W. et al. (2014) MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2, 26. 10.1186/2049-2618-2-26
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Xie, G. et al. (2014) Recruiting human microbiome shotgun data to site-specific reference genomes. PLoS One 9(1), e84963. 10.1371/journal.pone.0084963
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Yamamoto, K. et al. (2014) Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge. Genome Announc 2(5). 10.1128/genomeA.00876-14
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Yamamoto, K. et al. (2014) Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor. Genome Announc 2(5). 10.1128/genomeA.00870-14
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Youssef, N. H. et al. (2014) Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. ISME J . 10.1038/ismej.2014.141
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Zhou, Y. et al. (2014) High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China. Stand Genomic Sci 9(3), 1020-30. 10.4056/sigs.5449586
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Ziemert, N. et al. (2014) Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A 111(12), E1130-9. 10.1073/pnas.1324161111
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