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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 › 2010 Publications

2010 Publications

Abt, B. et al. (2010) Complete genome sequence of Cellulomonas flavigena type strain (134). Stand Genomic Sci 3(1), 15-25. 10.4056/sigs.1012662
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Aklujkar, M. et al. (2010) The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments. Bmc Genomics 11. Artn 490 Doi 10.1186/1471-2164-11-490
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Allgaier, M. et al. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5(1), e8812. 10.1371/journal.pone.0008812
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Alverson, A. J. et al. (2010) Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27(6), 1436-1448. DOI 10.1093/molbev/msq029
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Anderson, I. et al. (2010) Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci 3(3), 315-24. 10.4056/sigs.1283367
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Ayala-del-Rio, H. L. et al. (2010) The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol 76(7), 2304-12. 10.1128/AEM.02101-09
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Baker, B. J. et al. (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A 107(19), 8806-11. 10.1073/pnas.0914470107
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Blanc, G. et al. (2010) The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell 22(9), 2943-55. 10.1105/tpc.110.076406
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Blow, M. J. et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42(9), 806-10. 10.1038/ng.650
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Brambilla, E. et al. (2010) Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847(T)). Standards in Genomic Sciences 3(2), 203-211. Doi 10.4056/Sigs.1183143
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Cannon, G. C. et al. (2010) Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation. Biochim Biophys Acta 1804(2), 382-92. 10.1016/j.bbapap.2009.09.026
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Chan, Y. F. et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327(5963), 302-5. 10.1126/science.1182213
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Chang, Y. J. et al. (2010) Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Stand Genomic Sci 3(1), 1-14. 10.4056/sigs.1002553
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Chapman, J. A. et al. (2010) The dynamic genome of Hydra. Nature 464(7288), 592-596. Doi 10.1038/Nature08830
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Chertkov, O. et al. (2010) Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci 2(3), 280-9. 10.4056/sigs.902116
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Cirstea, I. C. et al. (2010) A restricted spectrum of NRAS mutations causes Noonan syndrome. Nat Genet 42(1), 27-9. 10.1038/ng.497
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Clum, A. et al. (2010) Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci 2(2), 228-88. 10.4056/sigs.881234
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Copeland, A. et al. (2010) Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009). Standards in Genomic Sciences 2(3), 361-362. Doi 10.4056/Sigs.992408
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Cuvelier, M. L. et al. (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci U S A 107(33), 14679-84. 10.1073/pnas.1001665107
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DeAngelis, K. M. et al. (2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. Bioenergy Research 3(2), 146-158. DOI 10.1007/s12155-010-9089-z
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Dehal, P. S. et al. (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res 38(Database issue), D396-400. 10.1093/nar/gkp919
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Del Rio, T. G. et al. (2010) Complete genome sequence of Intrasporangium calvum type strain (7 KIPT). Standards in Genomic Sciences 3(3), 294-303. Doi 10.4056/Sigs.1263355
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Deli, A. et al. (2010) LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis. FEBS J 277(13), 2740-53. 10.1111/j.1742-4658.2010.07691.x
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Ditty, J. L. et al. (2010) Incorporating genomics and bioinformatics across the life sciences curriculum. PLoS Biol 8(8), e1000448. 10.1371/journal.pbio.1000448
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Djao, O. D. N. et al. (2010) Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1(T)). Standards in Genomic Sciences 3(3), 267-275. Doi 10.4056/Sigs.1233249
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Du, J. C. et al. (2010) Bifurcation and Enhancement of Autonomous-Nonautonomous Retrotransposon Partnership through LTR Swapping in Soybean. Plant Cell 22(1), 48-61. DOI 10.1105/tpc.109.068775
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Elkins, J. G. et al. (2010) Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T. J Bacteriol 192(22), 6099-100. 10.1128/JB.00950-10
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Engelbrektson, A. et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4(5), 642-7. 10.1038/ismej.2009.153
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Engelbrektson, A. et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4(5), 642-7. 10.1038/ismej.2009.153
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Ferris, P. et al. (2010) Evolution of an expanded sex-determining locus in Volvox. Science 328(5976), 351-4. 10.1126/science.1186222
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Foster, B. et al. (2010) Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Stand Genomic Sci 2(1), 1-8. 10.4056/sigs.571102
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Fritz-Laylin, L. K. et al. (2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140(5), 631-42. 10.1016/j.cell.2010.01.032
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Glavina Del Rio, T. et al. (2010) Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci 2(1), 87-95. 10.4056/sigs.661199
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Goker, M. et al. (2010) Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Stand Genomic Sci 3(1), 66-75. 10.4056/sigs.1072907
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Goker, M. et al. (2010) Complete genome sequence of Olsenella uli type strain (VPI D76D-27C). Stand Genomic Sci 3(1), 76-84. 10.4056/sigs.1082860
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Goode, D. L. et al. (2010) Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Res 20(3), 301-10. 10.1101/gr.102210.109
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Gotea, V. et al. (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20(5), 565-77. 10.1101/gr.104471.109
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Gowda, M. et al. (2010) Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Res 38(21), 7558-69. 10.1093/nar/gkq583
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Grim, C. J. et al. (2010) Genome sequence of hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and comparative genomics with V. cholerae. J Bacteriol 192(13), 3524-33. 10.1128/JB.00040-10
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Gronow, S. et al. (2010) Complete genome sequence of Veillonella parvula type strain (Te3). Stand Genomic Sci 2(1), 57-65. 10.4056/sigs.521107
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Grubbs, G. S. et al. (2010) The complete iodine and nitrogen nuclear electric quadrupole coupling tensors for fluoroiodoacetonitrile determined by chirped pulse Fourier transform microwave spectroscopy. Journal of Chemical Physics 132(2). Artn 024310 Doi 10.1063/1.3291619
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Guisinger, M. M. et al. (2010) Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae. J Mol Evol 70(2), 149-66. 10.1007/s00239-009-9317-3
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Haley, B. J. et al. (2010) Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol 10, 154. 10.1186/1471-2180-10-154
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Harmon-Smith, M. et al. (2010) Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300). Stand Genomic Sci 2(2), 220-7. 10.4056/sigs.811799
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Hasan, N. A. et al. (2010) Comparative genomics of clinical and environmental Vibrio mimicus. Proc Natl Acad Sci U S A 107(49), 21134-9. 10.1073/pnas.1013825107
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Hasan, N. A. et al. (2010) Comparative genomics of clinical and environmental Vibrio mimicus. Proc Natl Acad Sci U S A 107(49), 21134-9. 10.1073/pnas.1013825107
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Hather, G. J. et al. (2010) The United States of America and scientific research. PLoS One 5(8), e12203. 10.1371/journal.pone.0012203
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He, S. et al. (2010) Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods 7(10), 807-12. 10.1038/nmeth.1507
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He, S. M. et al. (2010) Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environmental Microbiology 12(5), 1205-1217. DOI 10.1111/j.1462-2920.2010.02163.x
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Hellsten, U. et al. (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328(5978), 633-6. 10.1126/science.1183670
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Hemme, C. L. et al. (2010) Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. Isme Journal 4(5), 660-672. DOI 10.1038/ismej.2009.154
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Hemme, C. L. et al. (2010) Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol 192(24), 6494-6. 10.1128/JB.01064-10
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Hirschman, L. et al. (2010) Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci 2(3), 357-60. 10.4056/sigs.802738
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Hollister, E. B. et al. (2010) Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol 88(1), 389-99. 10.1007/s00253-010-2789-7
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Hooper, S. D. et al. (2010) Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics 26(3), 295-301. DOI 10.1093/bioinformatics/btp687
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Hooper, S. D. et al. (2010) Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics 26(3), 295-301. DOI 10.1093/bioinformatics/btp687
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Human Microbiome Jumpstart Reference Strains, Consortium et al. (2010) A catalog of reference genomes from the human microbiome. Science 328(5981), 994-9. 10.1126/science.1183605
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Hyatt, D. et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119. 10.1186/1471-2105-11-119
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Hyten, D. L. et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. Bmc Genomics 11. Artn 38Doi 10.1186/1471-2164-11-38
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International Brachypodium Initiative et al. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282), 763-8. 10.1038/nature08747
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Ivanova, N. et al. (2010) Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Stand Genomic Sci 2(1), 96-106. 10.4056/sigs.69.1277
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Ivanova, N. et al. (2010) Complete genome sequence of Gordonia bronchialis type strain (3410). Stand Genomic Sci 2(1), 19-28. 10.4056/sigs.611106
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Ivanova, N. et al. (2010) Complete genome sequence of Geodermatophilus obscurus type strain (G-20). Stand Genomic Sci 2(2), 158-67. 10.4056/sigs.711311
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Ivanova, N. et al. (2010) A call for standardized classification of metagenome projects. Environ Microbiol 12(7), 1803-5. 10.1111/j.1462-2920.2010.02270.x
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Jackson, D. J. et al. (2010) Parallel evolution of nacre building gene sets in molluscs. Mol Biol Evol 27(3), 591-608. 10.1093/molbev/msp278
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Janssen, P. J. et al. (2010) The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 5(5), e10433. 10.1371/journal.pone.0010433
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Junier, P. et al. (2010) The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ Microbiol 12(10), 2738-54. 10.1111/j.1462-2920.2010.02242.x
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Kerfeld, C. A. et al. (2010) Open education, open minds. PLoS Biol 8(10). 10.1371/journal.pbio.1000508
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Kerfeld, C. A. et al. (2010) Bacterial microcompartments. Annu Rev Microbiol 64, 391-408. 10.1146/annurev.micro.112408.134211
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Kielak, A. et al. (2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol Ecol 71(1), 23-33. 10.1111/j.1574-6941.2009.00785.x
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Kim, M. Y. et al. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proceedings of the National Academy of Sciences of the United States of America 107(51), 22032-22037. DOI 10.1073/pnas.1009526107
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Kim, M. Y. et al. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci U S A 107(51), 22032-7. 10.1073/pnas.1009526107
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Kiss, H. et al. (2010) Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1). Stand Genomic Sci 3(2), 153-62. 10.4056/sigs.1153107
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Kiss, H. et al. (2010) Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460). Stand Genomic Sci 2(3), 270-9. 10.4056/sigs.892105
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Kunin, V. et al. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12(1), 118-23. 10.1111/j.1462-2920.2009.02051.x
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Kyrpides, N. et al. (2010) Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8. Stand Genomic Sci 3(1), 93-6. 10.4056/sigs.1022942
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Labutti, K. et al. (2010) Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Stand Genomic Sci 3(1), 85-92. 10.4056/sigs.1092865
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Labutti, K. et al. (2010) Complete genome sequence of Planctomyces limnophilus type strain (Mu 290). Stand Genomic Sci 3(1), 47-56. 10.4056/sigs.1052813
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Lail, K. et al. (2010) Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci 2(2), 176-85. 10.4056/sigs.741334
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Liolios, K. et al. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 38, D346-D354. Doi 10.1093/Nar/Gkp848
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Liolios, K. et al. (2010) Complete genome sequence of Thermobispora bispora type strain (R51(T)). Standards in Genomic Sciences 2(3), 318-326. Doi 10.4056/Sigs.962171
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Liolios, K. et al. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 38, D346-D354. Doi 10.1093/Nar/Gkp848
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Lykidis, A. et al. (2010) The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. Plos One 5(3). Artn E9729 Doi 10.1371/Journal.Pone.0009729
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Ma, L. J. et al. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464(7287), 367-373. Doi 10.1038/Nature08850
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Macagno, E. R. et al. (2010) Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. Bmc Genomics 11. Artn 407 Doi 10.1186/1471-2164-11-407
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Markowitz, V. M. et al. (2010) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Research 38, D382-D390. Doi 10.1093/Nar/Gkp887
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Markowitz, V. M. et al. (2010) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 38(Database issue), D382-90. 10.1093/nar/gkp887
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Martin, J. et al. (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. Bmc Bioinformatics 11. Artn S10 Doi 10.1186/1471-2105-11-S3-S10
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Martinez, D. et al. (2010) Annotation of Protein-Coding Genes in Fungal Genomes. Applied and Computational Mathematics 9, 56-65.
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Mavromatis, K. et al. (2010) Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Stand Genomic Sci 3(2), 136-44. 10.4056/sigs.1143106
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Mavromatis, K. et al. (2010) Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24(T)). Standards in Genomic Sciences 2(3), 290-299. Doi 10.4056/Sigs.952166
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Mavromatis, K. et al. (2010) Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T)). Standards in Genomic Sciences 2(1), 9-18. Doi 10.4056/Sigs.591104
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Mavromatis, K. et al. (2010) Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Stand Genomic Sci 3(2), 117-25. 10.4056/sigs.1113067
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Mavromatis, K. et al. (2010) Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Stand Genomic Sci 3(2), 136-44. 10.4056/sigs.1143106
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McCarren, J. et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A 107(38), 16420-7. 10.1073/pnas.1010732107
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McKinlay, J. B. et al. (2010) A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production. BMC Genomics 11, 680. 10.1186/1471-2164-11-680
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Miller, T. R. et al. (2010) Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 192(22), 6101-2. 10.1128/JB.01030-10
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Morgan, J. L. et al. (2010) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 5(4), e10209. 10.1371/journal.pone.0010209
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Nalbantoglu, U. et al. (2010) Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp tularensis A1 and Schu S4. Plos One 5(2). Artn E9007 Doi 10.1371/Journal.Pone.0009007
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Nicolas, F. E. et al. (2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res 38(16), 5535-41. 10.1093/nar/gkq301
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Nolan, M. et al. (2010) Complete genome sequence of Ferrimonas balearica type strain (PAT). Stand Genomic Sci 3(2), 174-82. 10.4056/sigs.1161239
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Nolan, M. et al. (2010) Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci 2(1), 29-37. 10.4056/sigs.631049
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Novichkov, P. S. et al. (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res 38(Database issue), D111-8. 10.1093/nar/gkp894
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Novichkov, P. S. et al. (2010) RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res 38(Web Server issue), W299-307. 10.1093/nar/gkq531
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Novichkov, P. S. et al. (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res 38(Database issue), D111-8. 10.1093/nar/gkp894
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Ochman, H. et al. (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol 8(11), e1000546. 10.1371/journal.pbio.1000546
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Ohm, R. A. et al. (2010) Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol 28(9), 957-63. 10.1038/nbt.1643
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Pati, A. et al. (2010) Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Stand Genomic Sci 2(3), 300-8. 10.4056/sigs.912121
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Pati, A. et al. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7(6), 455-7. 10.1038/nmeth.1457
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Pati, A. et al. (2010) Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2(1), 49-56. 10.4056/sigs.601105
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Pati, A. et al. (2010) Complete genome sequence of Brachyspira murdochii type strain (56-150). Stand Genomic Sci 2(3), 260-9. 10.4056/sigs.831993
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Pitluck, S. et al. (2010) Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). Stand Genomic Sci 3(3), 285-93. 10.4056/sigs.1253298
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Pitluck, S. et al. (2010) Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P). Stand Genomic Sci 3(2), 108-16. 10.4056/sigs.1133078
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Pope, P. B. et al. (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 107(33), 14793-8. 10.1073/pnas.1005297107
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Prochnik, S. E. et al. (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329(5988), 223-6. 10.1126/science.1188800
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Pukall, R. et al. (2010) Complete genome sequence of Conexibacter woesei type strain (ID131577). Stand Genomic Sci 2(2), 212-9. 10.4056/sigs.751339
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Pukall, R. et al. (2010) Complete genome sequence of Kribbella flavida type strain (IFO 14399). Stand Genomic Sci 2(2), 186-93. 10.4056/sigs.731321
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Raha, D. et al. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A 107(8), 3639-44. 10.1073/pnas.0911315106
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Ran, L. et al. (2010) Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One 5(7), e11486. 10.1371/journal.pone.0011486
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Reeve, W. et al. (2010) Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci 2(1), 77-86. 10.4056/sigs.43526
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Reeve, W. et al. (2010) Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Stand Genomic Sci 2(3), 347-56. 10.4056/sigs.852027
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Saunders, E. et al. (2010) Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci 2(1), 107-16. 10.4056/sigs.681272
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Saunders, E. et al. (2010) Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci 2(1), 107-16. 10.4056/sigs.681272
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Schmutz, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278), 178-83. 10.1038/nature08670
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Schmutz, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278), 178-83. 10.1038/nature08670
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Sieber, J. R. et al. (2010) The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environmental Microbiology 12(8), 2289-2301. DOI 10.1111/j.1462-2920.2010.02237.x
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Sikorski, J. et al. (2010) Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Stand Genomic Sci 3(3), 304-14. 10.4056/sigs.1273360
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Sikorski, J. et al. (2010) Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Stand Genomic Sci 3(2), 194-202. 10.4056/sigs.1173118
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Sikorski, J. et al. (2010) Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288). Stand Genomic Sci 3(1), 57-65. 10.4056/sigs.1062906
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Sikorski, J. et al. (2010) Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Stand Genomic Sci 2(2), 149-57. 10.4056/sigs.671209
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Sikorski, J. et al. (2010) Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci 2(2), 203-11. 10.4056/sigs.791633
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Sikorski, J. et al. (2010) Complete genome sequence of Meiothermus silvanus type strain (VI-R2). Stand Genomic Sci 3(1), 37-46. 10.4056/sigs.1042812
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Spring, S. et al. (2010) The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010, 690737. 10.1155/2010/690737
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Spring, S. et al. (2010) Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Stand Genomic Sci 2(1), 38-48. 10.4056/sigs.581048
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Spring, S. et al. (2010) Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci 2(3), 245-59. 10.4056/sigs.821804
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Srivastava, M. et al. (2010) Early evolution of the LIM homeobox gene family. BMC Biol 8, 4. 10.1186/1741-7007-8-4
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Srivastava, M. et al. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466(7307), 720-6. 10.1038/nature09201
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Stein, L. Y. et al. (2010) Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b. J Bacteriol 192(24), 6497-8. 10.1128/JB.01144-10
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Stone, C. L. et al. (2010) Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens phakopsora pachyrhizi and p. meibomiae. Mycologia 102(4), 887-97.
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Strnad, H. et al. (2010) Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol 192(13), 3545-6. 10.1128/JB.00366-10
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Suen, G. et al. (2010) An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet 6(9), e1001129. 10.1371/journal.pgen.1001129
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Tagmount, A. et al. (2010) The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PLoS One 5(2), e9327. 10.1371/journal.pone.0009327
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Tice, H. et al. (2010) Complete genome sequence of Nakamurella multipartita type strain (Y-104). Stand Genomic Sci 2(2), 168-75. 10.4056/sigs.721316
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Tindall, B. J. et al. (2010) Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci 3(1), 26-36. 10.4056/sigs.1032748
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Vanden Wymelenberg, A. et al. (2010) Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol 76(11), 3599-610. 10.1128/AEM.00058-10
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Visel, A. et al. (2010) Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464(7287), 409-12. 10.1038/nature08801
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Voelker, S. L. et al. (2010) Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar. Plant Physiol 154(2), 874-86. 10.1104/pp.110.159269
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von Jan, M. et al. (2010) Complete genome sequence of Archaeoglobus profundus type strain (AV18). Stand Genomic Sci 2(3), 327-46. 10.4056/sigs.942153
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Wagner-Dobler, I. et al. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. Isme Journal 4(1), 61-77. DOI 10.1038/ismej.2009.94
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Walker, C. B. et al. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107(19), 8818-23. 10.1073/pnas.0913533107
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Wang, S. et al. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 11(1), R8. 10.1186/gb-2010-11-1-r8
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Wang, S. et al. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 11(1), R8. 10.1186/gb-2010-11-1-r8
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Wang, Z. et al. (2010) SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol 10, 14. 10.1186/1471-2229-10-14
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Wei, D. et al. (2010) Laccase and its role in production of extracellular reactive oxygen species during wood decay by the brown rot basidiomycete Postia placenta. Appl Environ Microbiol 76(7), 2091-7. 10.1128/AEM.02929-09
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Wilson, A. et al. (2010) Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. J Biol Chem 285(24), 18364-75. 10.1074/jbc.M110.115709
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Wirth, R. et al. (2010) Complete genome sequence of Thermocrinis albus type strain (HI 11/12). Stand Genomic Sci 2(2), 194-202. 10.4056/sigs.761490
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Wortman, J. et al. (2010) A data analysis and coordination center for the human microbiome project. Genome Biology 11. Artn O13 Doi 10.1186/Gb-2010-11-S1-O13
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Woyke, T. et al. (2010) One bacterial cell, one complete genome. PLoS One 5(4), e10314. 10.1371/journal.pone.0010314
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Wurtzel, O. et al. (2010) A single-base resolution map of an archaeal transcriptome. Genome Research 20(1), 133-141. DOI 10.1101/gr.100396.109
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Yan, H. H. et al. (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant Journal 63(3), 353-365. DOI 10.1111/j.1365-313X.2010.04246.x
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Yasawong, M. et al. (2010) Complete genome sequence of Arcanobacterium haemolyticum type strain (11018(T)). Standards in Genomic Sciences 3(2), 126-135. Doi 10.4056/Sigs.1123072
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Yilmaz, S. et al. (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7(12), 943-4. 10.1038/nmeth1210-943
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Yilmaz, S. et al. (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods 7(12), 943-944. DOI 10.1038/nmeth1210-943
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Yilmaz, S. et al. (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. Isme Journal 4(10), 1352-1356. DOI 10.1038/ismej.2010.73
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Young, M. et al. (2010) Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. J Bacteriol 192(3), 841-60. 10.1128/JB.01254-09
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Young, M. et al. (2010) Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium. Journal of Bacteriology 192(3), 841-860. Doi 10.1128/Jb.01254-09
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