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    ear the town of Rifle, Colorado, lies the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 (SFA 2.0, sponsored by the DOE Office of Biological and Environmental Research—BER).
    Waiting to Respire
    UC Berkeley and JGI researchers joined forces and data sets to describe bacterial genomes for related (“sibling”) lineages that diverged from the bacterial tree before Cyanobacteria and its contemporaries. The information was then used to predict the metabolic strategies applied by a common ancestor to all five lineages.

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    Field researchers studying drought responses in Panicum hallii at the UT Austin Brackenridge Field Lab. (David Gilbert)
    A Model System for Perennial Grasses
    The DOE supports research programs for developing methods for converting plant biomass into sustainable fuels for cars and jets. By studying a close relative model species like Panicum hallii, researchers can develop crop improvement techniques that could be applied to the candidate bioenergy feedstock switchgrass.

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    At high temperature, S. paradoxus cells die in the act of cell division, as seen by the dyads with cell bodies shriveled away from the outer cell wall. (Images by Carly Weiss, courtesy of the Brem Lab)
    Mapping Heat Resistance in Yeasts
    In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.

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    Jorge Rodrigues is interested in the biological causes of methane flux variation in the Amazon rainforest. (Courtesy of Jorge Rodrigues)
    Methane Flux in the Amazon
    Wetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

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    Vampirovibrio chlorellavorus in yellow on green host. (Courtesy of Judith Brown)
    Infections and Host-Pathogen Interactions of Chlorella
    The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus is a globally important obligate pathogen of Chlorella species/strains, which are of interest as biofuel feedstocks.

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    Morphological diversity of Sordariales growing in the lab. Pierre Gladieux's proposal explores functional diversity in Neurospora and its relatives. (Pierre Gladieux, INRA Montpellier)
    Insights into Functional Diversity in Neurospora
    This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

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    Click on the image above or click here (https://youtu.be/iSEEw4Vs_B4) to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.
    Mining IMG/M for CRISPR-Associated Proteins
    Researchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

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    The Angelo Coast Range Reserve, from which soil samples were taken, protects thousands of acres of the upper watershed of South Fork of the Eel River (shown here) in Mendocino County. (Akos Kokai via Flickr, CC BY 2.0 https://www.flickr.com/photos/on_earth/17307333828/)
    DAS Tool for Genome Reconstruction from Metagenomes
    Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.

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    DOE JGI BOOST logo
    New Software Tools Streamline DNA Sequence Design-and-Build Process
    Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.

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    Cropped image of switchgrass microcosm showing established root network. (James Moran)
    FY 2019 FICUS EMSL-JGI Projects Selected
    Through the EMSL-JGI FICUS calls, users can combine EMSL’s unique imaging, omics and computational resources with cutting-edge genomics, DNA synthesis and complementary capabilities at JGI. This was the sixth FICUS call between EMSL and JGI since the collaborative science initiative was formed.

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    Preparing for a Sequence Data Deluge
    The approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

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    The molecule cyclic di-GMP plays a key role in controlling cellulose production and biofilm formation. To better understand cyclic di-GMP signaling pathways, the team developed the first chemiluminescent biosensor system for cyclic di-GMP and showed that it could be used to assay cyclic di-GMP in bacterial lysates. (Image courtesy of Hammond Lab, UC Berkeley)
    Innovative Technology Improves Our Understanding of Bacterial Cell Signaling
    Cyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).

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    One of the heated plots at the Harvard Forest (Jeff Blanchard)
    Hidden Giants in Forest Soils
    In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

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    Truffle orchard in Lorraine, France. (Francis Martin)
    Symbiosis a Driver of Truffle Diversity
    Truffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In Nature Ecology & Evolution, an international team sought insights into the ECM lifestyle of truffle-forming species. They conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.

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    Blyttiomyces helicus on spruce pollen grain. (Joyce Longcore)
    Expanding Fungal Diversity, One Cell at a Time
    In Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.

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News & Publications
Home › News & Publications › Publications › 2010 Publications

2010 Publications

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