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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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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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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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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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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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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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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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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.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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News & Publications
Home › News & Publications › Publications › 2015 Publications

2015 Publications

Abdul Rahman, N. et al. (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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Ai, C. et al. (2015) Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains. Genome Announc 3(5). 10.1128/genomeA.01142-15
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Alaba, O. A. et al. (2015) High-Resolution Linkage Map and Chromosome-Scale Genome Assembly for Cassava (Manihot esculenta Crantz) from 10 Populations. G3-Genes Genomes Genetics 5(1), 133-144. DOI 10.1534/g3.114.015008
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Alawi, M. et al. (2015) Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil. Genome Announc 3(2). 10.1128/genomeA.00270-15
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Albertin, C. B. et al. (2015) The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature 524(7564), 220-4. 10.1038/nature14668
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Alivisatos, A. P. et al. (2015) MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 350(6260), 507-8. 10.1126/science.aac8480
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Ardley, J. et al. (2015) High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil. Stand Genomic Sci 10, 126. 10.1186/s40793-015-0119-5
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Baker, S. E. et al. (2015) Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announc 3(2). 10.1128/genomeA.00074-15
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Baran, R. et al. (2015) Exometabolite niche partitioning among sympatric soil bacteria. Nat Commun 6, 8289. 10.1038/ncomms9289
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Beam, J.P. et al. (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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Beck, D. A. et al. (2015) Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environ Microbiol 17(3), 547-54. 10.1111/1462-2920.12736
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Belmann, P. et al. (2015) Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience 4, 47. 10.1186/s13742-015-0087-0
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Berben, T. et al. (2015) Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. Stand Genomic Sci 10, 105. 10.1186/s40793-015-0097-7
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Berben, T. et al. (2015) Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T). Stand Genomic Sci 10, 85. 10.1186/s40793-015-0078-x
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Berben, T. et al. (2015) Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification. Stand Genomic Sci 10, 84. 10.1186/s40793-015-0080-3
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Berry, D. et al. (2015) Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A 112(2), E194-203. 10.1073/pnas.1420406112
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Bianchetti, C. M. et al. (2015) Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem 290(19), 11819-32. 10.1074/jbc.M114.623579
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Billings, A. F. et al. (2015) Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci 10, 106. 10.1186/s40793-015-0100-3
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Boundy-Mills, K. et al. (2015) The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections. Appl Environ Microbiol 81(17), 5671-4. 10.1128/AEM.01176-15
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Bowers, R. M. et al. (2015) Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics 16(1), 856. 10.1186/s12864-015-2063-6
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Branco, S. et al. (2015) Genetic isolation between two recently diverged populations of a symbiotic fungus. Mol Ecol . 10.1111/mec.13132
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Brauer, S. L. et al. (2015) Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. Microbiology . 10.1099/mic.0.000117
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Brown, C. T. et al. (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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Brumm, P. J. et al. (2015) Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 10, 73. 10.1186/s40793-015-0031-z
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Brutnell, T. P. et al. (2015) Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. Annu Rev Plant Biol 66, 465-85. 10.1146/annurev-arplant-042811-105528
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Cadillo-Quiroz, H. et al. (2015) Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland. Genome Announc 3(6). 10.1128/genomeA.01280-15
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Cantor, M. et al. (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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Carr, S. A. et al. (2015) Abundant Atribacteria in deep marine sediment from the Adelie Basin, Antarctica. Front Microbiol 6, 872. 10.3389/fmicb.2015.00872
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Castelle, C. J. et al. (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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Chang, Y. et al. (2015) Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. Genome Biol Evol 7(6), 1590-601. 10.1093/gbe/evv090
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Chapman, J. A. et al. (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 16, 26. 10.1186/s13059-015-0582-8
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Checcucci, A. et al. (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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Chochois, V. et al. (2015) Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments. Plant Physiol 168(3), 953-67. 10.1104/pp.15.00095
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Choi, D. H. et al. (2015) High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. Stand Genomic Sci 10, 98. 10.1186/s40793-015-0088-8
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Christen, M. et al. (2015) Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis. ACS Synth Biol 4(8), 927-34. 10.1021/acssynbio.5b00087
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Christensen, G. A. et al. (2015) Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. J Bacteriol 197(1), 29-39. 10.1128/JB.02083-14
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Chubukov, V. et al. (2015) Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC. Appl Environ Microbiol 81(14), 4690-6. 10.1128/AEM.01102-15
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Cohen, M. F. et al. (2015) Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1. Genome Announc 3(3). 10.1128/genomeA.00646-15
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Couturier, M. et al. (2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. Biotechnol Biofuels 8, 216. 10.1186/s13068-015-0407-8
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Couturier, M. et al. (2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. Biotechnol Biofuels 8, 216. 10.1186/s13068-015-0407-8
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 10, 80. 10.1186/s40793-015-0074-1
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci 10, 79. 10.1186/s40793-015-0072-3
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. Stand Genomic Sci 10, 31. 10.1186/s40793-015-0018-9
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. Stand Genomic Sci 10, 13. 10.1186/1944-3277-10-13
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T). Stand Genomic Sci 10, 64. 10.1186/s40793-015-0048-3
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 10, 80. 10.1186/s40793-015-0074-1
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De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci 10, 79. 10.1186/s40793-015-0072-3
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Dedysh, S. N. et al. (2015) Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase. Genome Announc 3(2). 10.1128/genomeA.01555-14
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Deng, K. et al. (2015) Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol 3, 153. 10.3389/fbioe.2015.00153
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Dhillon, B. et al. (2015) Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci U S A 112(11), 3451-6. 10.1073/pnas.1424293112
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Dore, J. et al. (2015) Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytol . 10.1111/nph.13546
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Eichorst, S. A. et al. (2015) Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol . 10.1093/femsec/fiv106
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Eshraghi, L. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia. Stand Genomic Sci 10, 87. 10.1186/s40793-015-0073-2
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Evans, J. et al. (2015) Diversity and Population Structure of Northern Switchgrass as Revealed Through Exome Capture Sequencing. Plant J . 10.1111/tpj.13041
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Fiedler, Jason D. et al. (2015) High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing. The Plant Genome 8(2). 10.3835/plantgenome2014.10.0065
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Firrincieli, A. et al. (2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 6, 978. 10.3389/fmicb.2015.00978
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Fitzgerald, T. L. et al. (2015) Brachypodium as an emerging model for cereal-pathogen interactions. Ann Bot 115(5), 717-31. 10.1093/aob/mcv010
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Floudas, D. et al. (2015) Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol 76, 78-92. 10.1016/j.fgb.2015.02.002
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Gao, X. Y. et al. (2015) Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China. Stand Genomic Sci 10, 1. 10.1186/1944-3277-10-1
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Gaudana, S. B. et al. (2015) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria. Photosynth Res 126(1), 99-109. 10.1007/s11120-014-0059-8
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Gaudana, S. B. et al. (2015) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria. Photosynth Res 126(1), 99-109. 10.1007/s11120-014-0059-8
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Gilbert, D. et al. (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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Goordial, J. et al. (2015) Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost. Stand Genomic Sci 10, 61. 10.1186/s40793-015-0043-8
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Gordon, S. P. et al. (2015) Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing. PLoS One 10(7), e0132628. 10.1371/journal.pone.0132628
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Gutierrez, T. et al. (2015) Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 3(2). 10.1128/genomeA.00207-15
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Gutierrez, T. et al. (2015) Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium. Genome Announc 3(4). 10.1128/genomeA.00793-15
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Gutierrez, T. et al. (2015) Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 3(3). 10.1128/genomeA.00672-15
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Haase, N. J. et al. (2015) Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis. G3 (Bethesda) 5(8), 1593-602. 10.1534/g3.115.017665
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Hadjithomas, M. et al. (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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Hahnke, R. L. et al. (2015) High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci 10, 46. 10.1186/s40793-015-0032-y
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Hamilton, R. et al. (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3(3). 10.1128/genomeA.00515-15
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Haushalter, R. W. et al. (2015) Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production. Metab Eng 30, 1-6. 10.1016/j.ymben.2015.04.003
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He, S. et al. (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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He, S. et al. (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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Hedlund, B. P. et al. (2015) High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism. Genome Announc 3(6). 10.1128/genomeA.01410-15
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Hedlund, B. P. et al. (2015) Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'. Curr Opin Microbiol 25, 136-45. 10.1016/j.mib.2015.06.008
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Hedlund, B. P. et al. (2015) High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism. Genome Announc 3(6). 10.1128/genomeA.01410-15
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Hedrick, P. W. et al. (2015) Examining the cause of high inbreeding depression: analysis of whole-genome sequence data in 28 selfed progeny of Eucalyptus grandis. New Phytol . 10.1111/nph.13639
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Hemme, C. L. et al. (2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 6, 1205. 10.3389/fmicb.2015.01205
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Hudson, C. M. et al. (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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Hug, L. A. et al. (2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J . 10.1038/ismej.2015.2
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Hug, L. A. et al. (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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Hultman, J. et al. (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521(7551), 208-12. 10.1038/nature14238
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Huntemann, M. et al. (2015) The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 10, 86. 10.1186/s40793-015-0077-y
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Hwang, C. et al. (2015) Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. Genome Announc 3(1). 10.1128/genomeA.01449-14
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Inskeep, W. P. et al. (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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Kalyuzhnaya, M. G. et al. (2015) Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment. Genome Announc 3(2). 10.1128/genomeA.00103-15
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Kang, D. D. et al. (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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Kantor, R. S. et al. (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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Kato, S. et al. (2015) Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria. Frontiers in Microbiology 6. ARTN 1265 10.3389/fmicb.2015.01265
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Kazakov, A. E. et al. (2015) sigma54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics 16, 919. 10.1186/s12864-015-2176-y
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Kemp, D. W. et al. (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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Kirby, J. et al. (2015) Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate. Appl Environ Microbiol 81(1), 130-8. 10.1128/AEM.02920-14
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Kohler, A. et al. (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists (vol 47, pg 410, 2015). Nature Genetics 47(4), 410-415.
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Kotak, M. et al. (2015) Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes. Genome Announc 3(2). 10.1128/genomeA.00060-15
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Kourist, R. et al. (2015) Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems. MBio 6(4). 10.1128/mBio.00918-15
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Labonte, J. M. et al. (2015) Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J . 10.1038/ismej.2015.48
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Lam, K. K. et al. (2015) FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads. Bioinformatics . 10.1093/bioinformatics/btv280
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Lao, J. et al. (2015) Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum). Proteomics . 10.1002/pmic.201400487
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Lau, S. C. et al. (2015) Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group. Stand Genomic Sci 10, 51. 10.1186/s40793-015-0050-9
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Laviad, S. et al. (2015) High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 10, 21. 10.1186/s40793-015-0003-3
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Laviad, S. et al. (2015) High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 10, 29. 10.1186/s40793-015-0010-4
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Lebeis, S. L. et al. (2015) Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science . 10.1126/science.aaa8764
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Lee, L. L. et al. (2015) Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and "Thermoanaerobacter cellulolyticus". Genome Announc 3(3). 10.1128/genomeA.00440-15
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Lichius, A. et al. (2015) Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 16, 326. 10.1186/s12864-015-1526-0
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Liu, L. et al. (2015) A Xyloglucan Backbone 6-O-Acetyltransferase from Brachypodium distachyon Modulates Xyloglucan Xylosylation. Mol Plant . 10.1016/j.molp.2015.11.004
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Lizhen Shi et al. (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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Lowe, C. J. et al. (2015) The deuterostome context of chordate origins. Nature 520(7548), 456-65. 10.1038/nature14434
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Lozano, R. et al. (2015) Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC Genomics 16, 360. 10.1186/s12864-015-1554-9
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Luef, B. et al. (2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6, 6372. 10.1038/ncomms7372
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Mak, W. S. et al. (2015) Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun 6, 10005. 10.1038/ncomms10005
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Markowitz, V. M. et al. (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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Markowitz, V. M. et al. (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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Matsuda, Y. et al. (2015) A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis. Cytogenet Genome Res . 10.1159/000381292
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Mazur, A. et al. (2015) High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland. Stand Genomic Sci 10, 36. 10.1186/s40793-015-0029-6
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McCarthy, S. et al. (2015) Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution. Appl Environ Microbiol . 10.1128/AEM.03225-15
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McCarthy, S. et al. (2015) Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives. Genome Announc 3(3). 10.1128/genomeA.00549-15
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McIlroy, S. J. et al. (2015) High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov. Stand Genomic Sci 10, 23. 10.1186/s40793-015-0013-1
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McTaggart, T. L. et al. (2015) Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment. Genome Announc 3(1). 10.1128/genomeA.01511-14
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McTaggart, T. L. et al. (2015) Draft genomes of two strains of flavobacterium isolated from lake washington sediment. Genome Announc 3(1). 10.1128/genomeA.01597-14
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McTaggart, T. L. et al. (2015) Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment. Genome Announc 3(1). 10.1128/genomeA.01587-14
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McTaggart, T. L. et al. (2015) Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment. Genome Announc 3(1). 10.1128/genomeA.01588-14
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Medema, Marnix H. et al. (2015) Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 11(9), 625-631. 10.1038/nchembio.1890
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Mhamdi, R. et al. (2015) High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci 10, 34. 10.1186/s40793-015-0005-1
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Min, B. et al. (2015) Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation. J Biotechnol 211, 42-43. 10.1016/j.jbiotec.2015.06.426
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Muchero, W. et al. (2015) High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. BMC Genomics 16, 24. 10.1186/s12864-015-1215-z
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Mukherjee, S. et al. (2015) Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Stand Genomic Sci 10, 18. 10.1186/1944-3277-10-18
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Mukherjee, S. et al. (2015) High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 10, 8. 10.1186/1944-3277-10-8
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Munoz-Amatriain, M. et al. (2015) Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J . 10.1111/tpj.12959
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Muraguchi, H. et al. (2015) Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea. PLoS One 10(10), e0141586. 10.1371/journal.pone.0141586
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Nagy, L. G. et al. (2015) Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Mol Biol Evol . 10.1093/molbev/msv337
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Ngan, Chew Yee et al. (2015) Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nature Plants 1(1). 10.1038/nplants.2015.107 http://www.nature.com/articles/nplants2015107#supplementary-information
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Nobu, M. K. et al. (2015) Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J . 10.1038/ismej.2014.256
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Nobu, M. K. et al. (2015) Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME J . 10.1038/ismej.2015.97
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Ntougias, S. et al. (2015) High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. Stand Genomic Sci 10, 52. 10.1186/s40793-015-0052-7
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Olsen, M. T. et al. (2015) The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol 6, 604. 10.3389/fmicb.2015.00604
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Oulas, A. et al. (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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Oyserman, B. O. et al. (2015) Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J . 10.1038/ismej.2015.155
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Paul, B. G. et al. (2015) Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat Commun 6, 6585. 10.1038/ncomms7585
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Pernice, M. C. et al. (2015) Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME J . 10.1038/ismej.2015.170
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Petit, E. et al. (2015) Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 10(6), e0118285. 10.1371/journal.pone.0118285
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Piao, H. et al. (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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Plaza, D. F. et al. (2015) Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode. G3 (Bethesda) 6(1), 87-98. 10.1534/g3.115.023069
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Plett, J. M. et al. (2015) The Mutualist Laccaria bicolor Expresses a Core Gene Regulon During the Colonization of Diverse Host Plants and a Variable Regulon to Counteract Host-Specific Defenses. Mol Plant Microbe Interact 28(3), 261-73. 10.1094/MPMI-05-14-0129-FI
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Quinn, J. Y. et al. (2015) SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biol 13(12), e1002310. 10.1371/journal.pbio.1002310
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Ramsay, B. D. et al. (2015) High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announc 3(2). 10.1128/genomeA.00092-15
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Ray, J. et al. (2015) Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announc 3(3). 10.1128/genomeA.00322-15
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Reeve, W. et al. (2015) A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci 10, 14. 10.1186/1944-3277-10-14
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Reeve, W. et al. (2015) High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. Stand Genomic Sci 10, 54. 10.1186/s40793-015-0049-2
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Rellan-Alvarez, R. et al. (2015) GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. Elife 4. 10.7554/eLife.07597
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Rooney, E. A. et al. (2015) Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a. Genome Announc 3(4). 10.1128/genomeA.00797-15
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Roux, S. et al. (2015) Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4. 10.7554/eLife.08490
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Sakamoto, M. et al. (2015) High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum. Stand Genomic Sci 10, 48. 10.1186/s40793-015-0045-6
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Salazar, G. et al. (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol . 10.1111/mec.13419
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Salazar, G. et al. (2015) Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME J . 10.1038/ismej.2015.137
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Schicklberger, M. et al. (2015) Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte. Genome Announc 3(3). 10.1128/genomeA.00607-15
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Schwessinger, B. et al. (2015) Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses. PLoS Pathog 11(3), e1004809. 10.1371/journal.ppat.1004809
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Septer, A. N. et al. (2015) Bright luminescence of Vibrio fischeri aconitase mutants reveals a connection between citrate and the Gac/Csr regulatory system. Mol Microbiol 95(2), 283-96. 10.1111/mmi.12864
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Seshadri, R. et al. (2015) Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. Sci Rep 5, 16825. 10.1038/srep16825
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Sevcikova, T. et al. (2015) Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?. Sci Rep 5, 10134. 10.1038/srep10134
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Sharma, M.K. et al. (2015) Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes. Bioenerg Res , 1-14. 10.1007/s12155-015-9667-1
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Sharon, I. et al. (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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Sharp, C. E. et al. (2015) Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki. Genome Announc 3(3). 10.1128/genomeA.00644-15
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Shetty, A. R. et al. (2015) Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand Genomic Sci 10, 55. 10.1186/s40793-015-0041-x
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Shi, L., et al. (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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Siegel, J. B. et al. (2015) Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A 112(12), 3704-9. 10.1073/pnas.1500545112
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Silva, L. P. et al. (2015) Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment. Curr Opin Biotechnol 34, 209-216. 10.1016/j.copbio.2015.03.015
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Simirenko, L. et al. (2015) The Joint Genome Institute's synthetic biology internal review process. Journal of Responsible Innovation 2(1), 133-136. 10.1080/23299460.2014.1002058
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Singer, E. et al. (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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Singh, R. et al. (2015) Complete Genome Sequence of an Evolved Thermotoga maritima Isolate. Genome Announc 3(3). 10.1128/genomeA.00557-15
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Smalley, N. E. et al. (2015) Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of the new species Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol . 10.1099/ijs.0.000190
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Smedley, D. et al. (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 43(W1), W589-98. 10.1093/nar/gkv350
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Song, Q. et al. (2015) SNP Assay Development for Linkage Map Construction, Anchoring Whole Genome Sequence and Other Genetic and Genomic Applications in Common Bean. G3 (Bethesda) . 10.1534/g3.115.020594
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Sun, C. L. et al. (2015) Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J . 10.1038/ismej.2015.162
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Tennessen, K. et al. (2015) ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J . 10.1038/ismej.2015.100
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Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. Stand Genomic Sci 10, 33. 10.1186/s40793-015-0007-z
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Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York. Stand Genomic Sci 10, 24. 10.1186/s40793-015-0008-y
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Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama. Stand Genomic Sci 10, 27. 10.1186/s40793-015-0006-0
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Tisa, L. S. et al. (2015) Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina. Genome Announc 3(4). 10.1128/genomeA.00889-15
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Tiwari, R. et al. (2015) Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. Stand Genomic Sci 10, 113. 10.1186/s40793-015-0115-9
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Tremblay, J. et al. (2015) Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 6, 771. 10.3389/fmicb.2015.00771
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Tripp, H. J. et al. (2015) Toward a standard in structural genome annotation for prokaryotes. Stand Genomic Sci 10, 45. 10.1186/s40793-015-0034-9
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Tschitschko, B. et al. (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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Varghese, N. J. et al. (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res 43(14), 6761-71. 10.1093/nar/gkv657
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Walworth, N. et al. (2015) Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Proc Natl Acad Sci U S A 112(14), 4251-6. 10.1073/pnas.1422332112
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Wang, X. et al. (2015) Bayesian Spatial-Temporal Modeling of Ecological Zero-Inflated Count Data. Statistica Sinica 25(1), 189-204. DOI 10.5705/ss.2013.212w
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Weinmaier, T. et al. (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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Wetmore, K. M. et al. (2015) Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio 6(3), e00306-15. 10.1128/mBio.00306-15
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Whitman, W. B. et al. (2015) Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci 10, 26. 10.1186/s40793-015-0017-x
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Woyke, T. et al. (2015) Function-driven single-cell genomics. Microb Biotechnol 8(1), 38-9. 10.1111/1751-7915.12247
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Yang, S. et al. (2015) Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics 16, 882. 10.1186/s12864-015-2070-7
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Yang, X. et al. (2015) A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 207(3), 491-504. 10.1111/nph.13393
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Yassin, A. F. et al. (2015) High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)). Stand Genomic Sci 10, 50. 10.1186/s40793-015-0036-7
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Yates, R. et al. (2015) High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. Stand Genomic Sci 10, 44. 10.1186/s40793-015-0020-2
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Young, D. et al. (2015) Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation. PLoS One 10(6), e0130381. 10.1371/journal.pone.0130381
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Youssef, N. H. et al. (2015) In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3). PLoS One 10(6), e0127499. 10.1371/journal.pone.0127499
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Yung, M. C. et al. (2015) Tn-seq of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance. J Bacteriol . 10.1128/JB.00382-15
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Zhou, A. et al. (2015) Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J . 10.1038/ismej.2015.45
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Zhou, J. et al. (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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