2018
(2018) Genomic features of bacterial adaptation to plants.
Nat Genet 50(1), 138-150.
10.1038/s41588-017-0012-9
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2017
(2017) Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.
Front Microbiol 8, 2264.
10.3389/fmicb.2017.02264
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(2017) Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.
mSphere 2(4).
10.1128/mSphereDirect.00257-17
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(2017) IMG/M: integrated genome and metagenome comparative data analysis system.
Nucleic Acids Res 45(D1), D507-D516.
10.1093/nar/gkw929
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(2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.
ISME J .
10.1038/s41396-017-0002-z
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(2017) Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.
Stand Genomic Sci 12, 67.
10.1186/s40793-017-0279-6
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(2017) The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils.
Sci Rep 7(1), 6008.
10.1038/s41598-017-06112-3
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(2017) Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.
PLoS One 12(5), e0177189.
10.1371/journal.pone.0177189
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(2017) Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.
PLoS One 12(5), e0177189.
10.1371/journal.pone.0177189
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(2017) Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.
mSystems 2(4).
10.1128/mSystems.00091-17
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(2017) A genomic perspective on stoichiometric regulation of soil carbon cycling.
ISME J .
10.1038/ismej.2017.115
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(2017) Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.
Nat Commun 8(1), 1507.
10.1038/s41467-017-01376-9
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(2017) A compendium of multi-omic sequence information from the Saanich Inlet water column.
Sci Data 4, 170160.
10.1038/sdata.2017.160
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(2017) Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes.
mSphere 2(5).
10.1128/mSphere.00277-17
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(2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders.
Proc Natl Acad Sci U S A .
10.1073/pnas.1703424114
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(2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders.
Proc Natl Acad Sci U S A 114(28), 7432-7437.
10.1073/pnas.1703424114
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(2017) Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities.
Front Microbiol 8, 88.
10.3389/fmicb.2017.00088
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(2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.
PeerJ 5, e3134.
10.7717/peerj.3134
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(2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.
PeerJ 5, e3134.
10.7717/peerj.3134
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(2017) Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.
BMC Res Notes 10(1), 367.
10.1186/s13104-017-2671-0
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(2017) Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.
Environ Sci Technol 51(5), 2944-2953.
10.1021/acs.est.6b04477
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(2017) The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil.
Appl Environ Microbiol 83(11).
10.1128/AEM.00275-17
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(2017) Patterns and drivers of fungal community depth stratification in Sphagnum peat.
FEMS Microbiol Ecol 93(7).
10.1093/femsec/fix082
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(2017) Lignocellulose pretreatment in a fungus-cultivating termite.
Proc Natl Acad Sci U S A 114(18), 4709-4714.
10.1073/pnas.1618360114
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(2017) Lignocellulose pretreatment in a fungus-cultivating termite.
Proc Natl Acad Sci U S A 114(18), 4709-4714.
10.1073/pnas.1618360114
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(2017) Metagenomic and metatranscriptomic analyses reveal structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited condition.
Appl Environ Microbiol .
10.1128/AEM.03508-16
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(2017) Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.
Mol Ecol 26(6), 1547-1556.
10.1111/mec.14011
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(2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Nat Biotechnol .
10.1038/nbt.3886
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(2017) The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.
MBio 8(1).
10.1128/mBio.01969-16
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(2017) Protein structure determination using metagenome sequence data.
Science 355(6322), 294-298.
10.1126/science.aah4043
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(2017) Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.
Nat Protoc 12(8), 1673-1682.
10.1038/nprot.2017.063
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(2017) Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity.
PeerJ 5, e3817.
10.7717/peerj.3817
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(2017) Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.
Nat Commun 8(1), 858.
10.1038/s41467-017-01086-2
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(2017) Giant viruses with an expanded complement of translation system components.
Science 356(6333), 82-85.
10.1126/science.aal4657
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(2017) Towards a balanced view of the bacterial tree of life.
Microbiome 5(1), 140.
10.1186/s40168-017-0360-9
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(2017) Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Nat Methods 14(11), 1063-1071.
10.1038/nmeth.4458
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(2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
Microbiome 5(1), 65.
10.1186/s40168-017-0287-1
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(2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
Microbiome 5(1), 65.
10.1186/s40168-017-0287-1
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(2017) NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.
BMC Res Notes 10(1), 278.
10.1186/s13104-017-2607-8
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(2017) Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
J Biomol Tech .
10.7171/jbt.17-2801-004
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(2017) Succession in the petroleum reservoir microbiome through an oil field production lifecycle.
ISME J .
10.1038/ismej.2017.78
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(2017) Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico.
Sci Rep 7(1), 16015.
10.1038/s41598-017-16375-5
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(2017) Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.
Elife 6.
10.7554/eLife.26580
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(2017) DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies.
ISME J , 112-123.
10.1038/ismej.2017.143
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2016
(2016) Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate.
Environ Microbiol 18(6), 1704-19.
10.1111/1462-2920.12819
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(2016) Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.
Frontiers in Microbiology 7, 25.
10.3389/fmicb.2016.00025
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(2016) Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
ISME J .
10.1038/ismej.2015.241
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(2016) Measurement of bacterial replication rates in microbial communities.
Nat Biotechnol 34(12), 1256-1263.
10.1038/nbt.3704
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(2016) Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.
New Phytol .
10.1111/nph.13697
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(2016) Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.
Nat Microbiol 1, 16146.
10.1038/nmicrobiol.2016.146
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(2016) Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria.
Front Microbiol 7, 606.
10.3389/fmicb.2016.00606
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(2016) Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation.
Appl Environ Microbiol 82(5), 1423-32.
10.1128/AEM.03014-15
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(2016) Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods.
Soil Biology & Biochemistry 96, 160-168.
10.1016/j.soilbio.2016.02.002
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(2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.
Nat Commun 7, 10476.
10.1038/ncomms10476
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(2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity.
Nature Microbiology , 15032.
10.1038/nmicrobiol.2015.32
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(2016) The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.
Frontiers in Microbiology 7, 150.
10.3389/fmicb.2016.00150
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(2016) Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments.
Microb Ecol 71(1), 100-12.
10.1007/s00248-015-0698-0
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(2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
ISME J .
10.1038/ismej.2016.42
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(2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
ISME J 10(10), 2365-75.
10.1038/ismej.2016.42
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(2016) The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).
Stand Genomic Sci 11, 17.
10.1186/s40793-016-0138-x
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(2016) 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.
Environ Microbiol .
10.1111/1462-2920.13234
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(2016) The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.
Environ Microbiol 18(12), 4755-4769.
10.1111/1462-2920.13366
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(2016) Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.
Microbiome 4(1), 56.
10.1186/s40168-016-0201-2
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(2016) Microbiome Data Science: Understanding Our Microbial Planet.
Trends Microbiol 24(6), 425-7.
10.1016/j.tim.2016.02.011
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(2016) BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.
BMC Bioinformatics 17(1), 435.
10.1186/s12859-016-1288-y
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(2016) Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Frontiers in Microbiology 7, 238.
10.3389/fmicb.2016.00238
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(2016) Facile Recoding of Selenocysteine in Nature.
Angew Chem Int Ed Engl 55(17), 5337-41.
10.1002/anie.201511657
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(2016) Transfer RNAs with novel cloverleaf structures.
Nucleic Acids Res .
10.1093/nar/gkw898
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(2016) Uncovering Earth's virome.
Nature .
10.1038/nature19094
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(2016) H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.
PeerJ 4, e1782.
10.7717/peerj.1782
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(2016) Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3.
Front Microbiol 7, 380.
10.3389/fmicb.2016.00380
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(2016) Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes.
Biogeochemistry 128(3), 353-368.
10.1007/s10533-016-0212-x
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(2016) Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.
Frontiers in Microbiology 7, 211.
10.3389/fmicb.2016.00211
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(2016) Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility.
Appl Environ Microbiol .
10.1128/AEM.03842-15
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(2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant.
Nat Commun 7, 12151.
10.1038/ncomms12151
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(2016) In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.
Sci Rep 6, 31362.
10.1038/srep31362
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2015
(2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes.
Microbiome 3, 5.
10.1186/s40168-015-0067-8
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(2015) Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.
ISME J 10(1), 210-24.
10.1038/ismej.2015.83
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(2015) Unusual biology across a group comprising more than 15% of domain Bacteria.
Nature 523(7559), 208-11.
10.1038/nature14486
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(2015) Elviz - exploration of metagenome assemblies with an interactive visualization tool.
BMC Bioinformatics 16, 130.
10.1186/s12859-015-0566-4
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(2015) Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.
Curr Biol 25(6), 690-701.
10.1016/j.cub.2015.01.014
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(2015) The integrated microbial genome resource of analysis.
Methods Mol Biol 1231, 289-95.
10.1007/978-1-4939-1720-4_18
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(2015) The Joint Genome Institute Offers Resources Beyond a Core Facility.
Microbe 10(7), 289-293.
10.1128/microbe.10.289.1
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(2015) IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.
MBio 6(4).
10.1128/mBio.00932-15
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(2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.
MBio 6(3), e00066-15.
10.1128/mBio.00066-15
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(2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.
MBio 6(3), e00066-15.
10.1128/mBio.00066-15
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(2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.
Front Microbiol 6, 1205.
10.3389/fmicb.2015.01205
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(2015) Lignin-modifying processes in the rhizosphere of arid land grasses.
Environ Microbiol 17(12), 4965-78.
10.1111/1462-2920.13020
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(2015) Lignin-Modifying Processes in the Rhizosphere of Aridland Grasses.
Environ Microbiol .
10.1111/1462-2920.13020
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(2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater.
ISME J .
10.1038/ismej.2015.2
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(2015) Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.
Environ Microbiol .
10.1111/1462-2920.12930
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(2015) Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function.
Front Microbiol 6, 1044.
10.3389/fmicb.2015.01044
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(2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
PeerJ 3, e1165.
10.7717/peerj.1165
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(2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
PeerJ 3, e1165.
10.7717/peerj.1165
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(2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
PeerJ 3, e1165.
10.7717/peerj.1165
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(2015) Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.
Environ Microbiol .
10.1111/1462-2920.12936
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(2015) Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.
PLoS One 10(12), e0143790.
10.1371/journal.pone.0143790
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(2015) Diverse uncultivated ultra-small bacterial cells in groundwater.
Nat Commun 6, 6372.
10.1038/ncomms7372
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(2015) Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System.
Trends Microbiol 23(11), 730-41.
10.1016/j.tim.2015.07.012
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(2015) Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.
Environ Microbiol .
10.1111/1462-2920.13095
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(2015) Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis.
ISME J .
10.1038/ismej.2015.155
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(2015) Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.
ISME J .
10.1038/ismej.2015.170
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(2015) Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.
ISME J .
10.1038/ismej.2015.170
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(2015) Insights into the bacterial community and its temporal succession during the fermentation of wine grapes.
Front Microbiol 6, 809.
10.3389/fmicb.2015.00809
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(2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes.
Mol Ecol .
10.1111/mec.13419
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(2015) Global diversity and biogeography of deep-sea pelagic prokaryotes.
ISME J .
10.1038/ismej.2015.137
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(2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.
Genome Res 25(4), 534-43.
10.1101/gr.183012.114
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(2015) Performance evaluation and tuning of BioPig for genomic analysis.
Proceedings of the 2015 International Workshop on Data-Intensive Scalable Computing Systems , 1-7.
10.1145/2831244.2831252
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(2015) Similar Microbial Communities Found on Two Distant Seafloor Basalts.
Frontiers in Microbiology 6.
ARTN 1409
10.3389/fmicb.2015.01409
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(2015) Similar Microbial Communities Found on Two Distant Seafloor Basalts.
Frontiers in Microbiology 6.
10.3389/fmicb.2015.01409
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(2015) Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.
ISME J .
10.1038/ismej.2015.162
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(2015) Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.
ISME J 9(9), 2094-107.
10.1038/ismej.2015.110
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(2015) A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses.
Microbiome 3, 62.
10.1186/s40168-015-0129-y
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(2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.
MBio 6(1).
10.1128/mBio.02288-14
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2014
(2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects.
MBio 5(6).
10.1128/mBio.02077-14
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(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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(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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(2014) Metagenomic sequencing of two salton sea microbiomes.
Genome Announc 2(1).
10.1128/genomeA.01208-13
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(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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(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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(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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(2014) The microbial ecology of permafrost.
Nat Rev Microbiol 12(6), 414-25.
10.1038/nrmicro3262
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(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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(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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(2014) Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples.
J Vis Exp (94).
10.3791/52117
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(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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(2014) FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.
Nucleic Acids Res .
10.1093/nar/gku702
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(2014) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.
Nucleic Acids Res .
10.1093/nar/gku950
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(2014) Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.
Sci Rep 4, 6480.
10.1038/srep06480
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(2014) A microarray for assessing transcription from pelagic marine microbial taxa.
ISME J .
10.1038/ismej.2014.1
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(2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.
Biotechnol Biofuels 7(1), 495.
10.1186/s13068-014-0180-0
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(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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(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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(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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(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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(2014) An environmental bacterial taxon with a large and distinct metabolic repertoire.
Nature 506(7486), 58-62.
10.1038/nature12959
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(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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(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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2013
(2013) Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean.
ISME J 7(2), 256-68.
10.1038/ismej.2012.108
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(2013) Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.
Appl Environ Microbiol 79(12), 3770-8.
10.1128/AEM.03833-12
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(2013) Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.
PLoS One 8(7), e68465.
10.1371/journal.pone.0068465
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(2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
Nat Commun 4, 1854.
10.1038/ncomms2884
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(2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites.
PLoS One 8(4), e61126.
10.1371/journal.pone.0061126
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(2013) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling.
Microbiome 1(1), 22.
10.1186/2049-2618-1-22.
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(2013) Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.
Front Microbiol 4, 95.
10.3389/fmicb.2013.00095
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(2013) The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem.
Front Microbiol 4, 67.
10.3389/fmicb.2013.00067
More Details
(2013) Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments.
Front Microbiol 4, 106.
10.3389/fmicb.2013.00106
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(2013) Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.
ISME J 7(3), 622-34.
10.1038/ismej.2012.132
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(2013) The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.
Front Microbiol 4, 323.
10.3389/fmicb.2013.00323
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(2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
J Comput Biol 20(10), 714-37.
10.1089/cmb.2013.0084
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(2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.
PLoS One 8(3), e59927.
10.1371/journal.pone.0059927
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(2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions.
Proc Natl Acad Sci U S A 110(16), 6548-53.
10.1073/pnas.1302837110
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(2013) Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill.
ISME J .
10.1038/ismej.2013.129
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(2013) Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.
Appl Environ Microbiol 79(9), 2932-43.
10.1128/AEM.03591-12
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(2013) Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.
PLoS One 8(9), e73827.
10.1371/journal.pone.0073827
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(2013) Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications.
PLoS Genet 9(1).
Artn E1003131Doi 10.1371/Journal.Pgen.1003131
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2012
(2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.
ISME J 6(9), 1688-701.
10.1038/ismej.2012.10
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(2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill.
Environ Microbiol 14(9), 2405-16.
10.1111/j.1462-2920.2012.02780.x
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(2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
Environ Microbiol 14(1), 207-27.
10.1111/j.1462-2920.2011.02593.x
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(2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community.
ISME J 6(9), 1702-14.
10.1038/ismej.2012.15
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(2012) Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay.
ISME J 6(4), 863-74.
10.1038/ismej.2011.142
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(2012) Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia.
MBio 3(1).
10.1128/mBio.00249-11
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(2012) Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.
Environ Microbiol 14(5), 1145-58.
10.1111/j.1462-2920.2011.02695.x
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(2012) Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris).
Microb Ecol 63(4), 719-25.
10.1007/s00248-011-9963-z
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(2012) Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia.
Biotechnol Bioeng 109(5), 1140-5.
10.1002/bit.24388
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(2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.
ISME J 6(3), 531-41.
10.1038/ismej.2011.131
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(2012) Differences in crop bacterial community structure between hoatzins from different geographical locations.
Research in Microbiology 163(3), 211-220.
DOI 10.1016/j.resmic.2012.01.001
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(2012) Microbes in thawing permafrost: the unknown variable in the climate change equation.
ISME J 6(4), 709-12.
10.1038/ismej.2011.163
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(2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria.
Appl Environ Microbiol 78(3), 752-8.
10.1128/AEM.07113-11
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(2012) Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion.
PLoS One 7(6), e39689.
10.1371/journal.pone.0039689
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(2012) A framework for human microbiome research.
Nature 486(7402), 215-21.
10.1038/nature11209
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(2012) Structure, function and diversity of the healthy human microbiome.
Nature 486(7402), 207-14.
10.1038/nature11234
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(2012) Unlocking the potential of metagenomics through replicated experimental design.
Nature Biotechnology 30(6), 513-520.
Doi 10.1038/Nbt.2235
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(2012) Defining the core Arabidopsis thaliana root microbiome.
Nature 488(7409), 86-90.
10.1038/nature11237
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(2012) Individual genome assembly from complex community short-read metagenomic datasets.
ISME J 6(4), 898-901.
10.1038/ismej.2011.147
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(2012) Individual genome assembly from complex community short-read metagenomic datasets.
ISME J 6(4), 898-901.
10.1038/ismej.2011.147
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(2012) IMG/M: the integrated metagenome data management and comparative analysis system.
Nucleic Acids Res 40(Database issue), D123-9.
10.1093/nar/gkr975
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(2012) IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.
PLoS One 7(7), e40151.
10.1371/journal.pone.0040151
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(2012) Effect of oxygen minimum zone formation on communities of marine protists.
ISME J 6(8), 1586-601.
10.1038/ismej.2012.7
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(2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.
Proc Natl Acad Sci U S A 109(33), 13272-7.
10.1073/pnas.1121464109
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(2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
Curr Opin Biotechnol 23(1), 9-15.
10.1016/j.copbio.2011.11.013
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(2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis.
Molecular Plant-Microbe Interactions 25(1), 28-36.
Doi 10.1094/Mpmi-08-11-0204
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(2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis.
Molecular Plant-Microbe Interactions 25(1), 28-36.
Doi 10.1094/Mpmi-08-11-0204
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(2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.
Environ Microbiol Rep 4(2), 248-56.
10.1111/j.1758-2229.2012.00328.x
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(2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem.
Plos One 7(6).
ARTN e38108
DOI 10.1371/journal.pone.0038108
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(2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips.
PLoS One 7(5), e36740.
10.1371/journal.pone.0036740
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(2012) Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis.
Isme Journal 6(7), 1427-1439.
DOI 10.1038/ismej.2011.200
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(2012) Global distribution of a wild alga revealed by targeted metagenomics.
Curr Biol 22(17), R675-7.
10.1016/j.cub.2012.07.054
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2011
(2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio.
ISME J 5(8), 1323-31.
10.1038/ismej.2011.14
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(2011) Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome.
Isme Journal 5(1), 161-164.
DOI 10.1038/ismej.2010.97
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(2011) Genomics for key players in the N cycle from guinea pigs to the next frontier.
Methods Enzymol 496, 289-318.
10.1016/B978-0-12-386489-5.00012-9
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(2011) Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil.
Plos One 6(4).
ARTN e19306
DOI 10.1371/journal.pone.0019306
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(2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard.
Stand Genomic Sci 4(2), 271-85.
10.4056/sigs.621069
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(2011) Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass.
Applied and Environmental Microbiology 77(16), 5804-5812.
Doi 10.1128/Aem.00032-11
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(2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Science 331(6016), 463-7.
10.1126/science.1200387
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(2011) Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.
J Allergy Clin Immunol 127(2), 372-381 e1-3.
10.1016/j.jaci.2010.10.048
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(2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium.
ISME J 5(1), 122-30.
10.1038/ismej.2010.125
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(2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.
Nature 480(7377), 368-71.
10.1038/nature10576
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(2011) ClaMS: A Classifier for Metagenomic Sequences.
Stand Genomic Sci 5(2), 248-53.
10.4056/sigs.2075298
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(2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies.
Science 333(6042), 646-8.
10.1126/science.1205760
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(2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction.
Biotechnol Bioeng 108(9), 2088-98.
10.1002/bit.23176
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(2011) Phage encoded H-NS: a potential achilles heel in the bacterial defence system.
PLoS One 6(5), e20095.
10.1371/journal.pone.0020095
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(2011) Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean.
Science 333(6047), 1296-1300.
DOI 10.1126/science.1203690
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(2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nature Biotechnology 29(5), 415-420.
Doi 10.1038/Nbt.1823
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2010
(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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(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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(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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(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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(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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(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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(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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2008
(2008) Identification of ancient remains through genomic sequencing.
Genome Research 18(8), 1347-1353.
DOI 10.1101/gr.076091.108
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(2008) Annotation of metagenome short reads using proxygenes.
Bioinformatics 24(16), I7-I13.
DOI 10.1093/bioinformatics/btn276
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(2008) Toward a standards-compliant genomic and metagenomic publication record.
OMICS 12(2), 157-60.
10.1089/omi.2008.A2B2
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(2008) Microbiology - Metagenomics.
Nature 455(7212), 481-483.
Doi 10.1038/455481a
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(2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal.
Genome Research 18(2), 293-297.
Doi 10.1101/Gr.6835308
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(2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Mol Syst Biol 4, 198.
10.1038/msb.2008.35
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(2008) IMG/M: a data management and analysis system for metagenomes.
Nucleic Acids Research 36, D534-D538.
Doi 10.1093/Nar/Gkm869
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(2008) Assembly of viral metagenomes from yellowstone hot springs.
Appl Environ Microbiol 74(13), 4164-74.
10.1128/AEM.02598-07
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(2008) A renaissance for the pioneering 16S rRNA gene.
Curr Opin Microbiol 11(5), 442-6.
10.1016/j.mib.2008.09.011
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(2008) The airborne metagenome in an indoor urban environment.
PLoS One 3(4), e1862.
10.1371/journal.pone.0001862
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(2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.
Isme Journal 2(11), 1146-1156.
DOI 10.1038/ismej.2008.48
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2006
(2006) An experimental metagenome data management and analysis system.
Bioinformatics 22(14), e359-67.
10.1093/bioinformatics/btl217
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