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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Image of Octopus Springs for the CSP annual call
    Letters of Intent are due April 12, 2021 for the annual Community Science Program (CSP) call focused on large-scale genomic science projects that address specific areas of special emphasis and exploit the diversity of JGI capabilities.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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News & Publications
Home › News & Publications › Publications › 2006 Publications

2006 Publications

Baker, S. E. et al. (2006) Aspergillus niger genomics: Past, present and into the future. Medical Mycology 44, S17-S21. Doi 10.1080/13693780600921037
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Beller, H. R. et al. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188(4), 1473-88. 10.1128/JB.188.4.1473-1488.2006
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Brodie, E. L. et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72(9), 6288-98. 10.1128/AEM.00246-06
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Budowle, B. et al. (2006) Quality sample collection, handling, and preservation for an effective microbial forensics program. Appl Environ Microbiol 72(10), 6431-8. 10.1128/AEM.01165-06
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Cai, Z. et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6, 77. 10.1186/1471-2148-6-77
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Carapelli, A. et al. (2006) The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Gene 376(2), 248-59. 10.1016/j.gene.2006.04.005
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Chain, P. S. et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 103(42), 15280-7. 10.1073/pnas.0606924103
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Coleman, M. L. et al. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311(5768), 1768-1770. Doi 10.1126/Science.1122050
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Collins, A. G. et al. (2006) Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Systematic Biology 55(1), 97-115. Doi 10.1080/10635150500433615
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Collins, A. G. et al. (2006) Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Systematic Biology 55(1), 97-115. Doi 10.1080/10635150500433615
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DeSantis, T. Z. et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 34, W394-W399. Doi 10.1093/Nar/Gkl244
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DeSantis, T. Z. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72(7), 5069-5072. Doi 10.1128/Aem.03006-05
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Doggett, N. A. et al. (2006) A 360-kb interchromosomal duplication of the human HYDIN locus. Genomics 88(6), 762-771. Doi 10.1016/J.Ygeno.2006.07.012
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Gowda, M. et al. (2006) Robust analysis of 5 '-transcript ends (5 '-RATE): a novel technique for transcriptome analysis and genome annotation. Nucleic Acids Research 34(19). Doi 10.1093/Nar/Gkl522
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Hallam, S. J. et al. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences of the United States of America 103(48), 18296-18301. Doi 10.1073/Pnas.0608549103
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Hallam, S. J. et al. (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. Plos Biology 4(4), 520-536. Artn E95 Doi 10.1371/Journal.Pbio.0040095
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Hixson, K. K. et al. (2006) Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 5(11), 3008-17. 10.1021/pr060179y
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Huerta, A. M. et al. (2006) Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes. Molecular Biology and Evolution 23(5), 997-1010. Doi 10.1093/Molbev/Msk004
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Huerta, A. M. et al. (2006) Selection for unequal densities of sigma(70) promoter-like signals in different regions of large bacterial genomes. Plos Genetics 2(11), 1740-1750. ARTN e185 DOI 10.1371/journal.pgen.0020185
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Imachi, H. et al. (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 72(3), 2080-2091. Doi 10.1128/Aem.72.3.2080-2091.2006
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Janga, S. C. et al. (2006) The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucleic Acids Research 34(14), 3980-3987. Doi 10.1093/Nar/Gkl563
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Klotz, M. G. et al. (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol 72(9), 6299-315. 10.1128/AEM.00463-06
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Krampis, K. et al. (2006) Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum. Molecular Plant-Microbe Interactions 19(12), 1329-1336. Doi 10.1094/Mpmi-19-1329
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Kuske, C. R. et al. (2006) Current and emerging technologies for the study of bacteria in the outdoor air. Current Opinion in Biotechnology 17(3), 291-296. Doi 10.1016/J.Copbio.2006.04.001
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Kuske, C. R. et al. (2006) Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes. Journal of Forensic Sciences 51(3), 548-558. Doi 10.1111/J.1556-4029.2006.00131.X
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Li, M. et al. (2006) Confidence-based classifier design. Pattern Recognition 39(7), 1230-1240. Doi 10.1016/J.Patcog.2006.01.010
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Li, M. K. et al. (2006) Confidence-based active learning. Ieee Transactions on Pattern Analysis and Machine Intelligence 28(8), 1251-1261.
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Liolios, K. et al. (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research 34, D332-D334. Doi 10.1093/Nar/Gkj145
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Loots, G. G. et al. (2006) Array2BIO: from microarray expression data to functional annotation of co-regulated genes. Bmc Bioinformatics 7. Artn 307 Doi 10.1186/1471-2105-7-307
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Maeder, D. L. et al. (2006) The Methanosarcina barkeri genome: Comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. Journal of Bacteriology 188(22), 7922-7931. Doi 10.1128/Jb.00810-06
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Maeder, D. L. et al. (2006) The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 188(22), 7922-31. 10.1128/JB.00810-06
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Makarova, K. et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103(42), 15611-6. 10.1073/pnas.0607117103
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Makarova, K. et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103(42), 15611-6. 10.1073/pnas.0607117103
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Markowitz, V. M. et al. (2006) An experimental metagenome data management and analysis system. Bioinformatics 22(14), e359-67. 10.1093/bioinformatics/btl217
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Markowitz, V. M. et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research 34, D344-D348. Doi 10.1093/Nar/Gkj024
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Martin, H. G. et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology 24(10), 1263-1269. Doi 10.1038/Nbt1247
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Martiny, J. B. H. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4(2), 102-112. Doi 10.1038/Nrmicro1341
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Mavromatis, K. et al. (2006) The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Journal of Bacteriology 188(11), 4015-4023. Doi 10.1128/Jb.01837-05
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Medina, M. et al. (2006) Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A 103(24), 9096-100. 10.1073/pnas.0602444103
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Merrill, L. et al. (2006) Composition of Bacillus species in aerosols from 11 US cities. Journal of Forensic Sciences 51(3), 559-565. Doi 10.1111/J.1556-4029.2006.00132.X
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Nosenko, T. et al. (2006) Chimeric plastid proteome in the florida "red tide" dinoflagellate Karenia brevis. Molecular Biology and Evolution 23(11), 2026-2038. Doi 10.1093/Molbev/Msl074
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Podsiadlowski, L. et al. (2006) The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda : Diplura): High genetic divergence in a morphologically uniform taxon. Gene 381, 49-61. Doi 10.1016/J.Gene.2006.06.009
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Prabhakar, S. et al. (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314(5800), 786. 10.1126/science.1130738
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Schulte, J. A. et al. (2006) A genetic perspective on the geographic association of taxa among and North American lizards of the Sceloporus magister complex (Squamata : Iguanidae : Phrynosomatinae). Molecular Phylogenetics and Evolution 39(3), 873-880. Doi 10.1016/J.Ympev.2005.04.033
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Scott, K. M. et al. (2006) The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. Plos Biology 4(12), 2196-2212. ARTN e383 DOI 10.1371/journal.pbio.0040383
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Siddaramappa, S. et al. (2006) Comparative analyses of two cryptic plasmids from Haemophilus somnus (Histophilus somni). Plasmid 55(3), 227-234. Doi 10.1016/J.Plasmid.2005.11.004
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Simison, W. B. et al. (2006) Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution 39(2), 562-567. Doi 10.1016/J.Ympev.2005.11.006
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Starkenburg, S. R. et al. (2006) Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology 72(3), 2050-2063. Doi 10.1128/Aem.72.3.2050-2063.2006
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Stillman, J. H. et al. (2006) Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes. Integrative and Comparative Biology 46(6), 919-930. Doi 10.1093/Icb/Icl007
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Tuskan, G. A. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793), 1596-1604. Doi 10.1126/Science.1128691
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Tyler, B. M. et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313(5791), 1261-1266. Doi 10.1126/Science.1128796
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Valles, Y. et al. (2006) Lophotrochozoan mitochondrial genomes. Integrative and Comparative Biology 46(4), 544-557. Doi 10.1093/Icb/Icj056
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Vanden Wymelenberg, A. et al. (2006) Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Fungal Genetics and Biology 43(5), 343-356. Doi 10.1016/J.Fgb.2006.01.003
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Warren, R. L. et al. (2006) Physical map-assisted whole-genome shotgun sequence assemblies. Genome Research 16(6), 768-775. Doi 10.1101/Gr.5090606
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Wei, X. M. et al. (2006) Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Archives of Microbiology 186(2), 107-118. Doi 10.1007/S00203-006-0126-4
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Weng, L. et al. (2006) Application of sequence-based methods in human microbial ecology. Genome Research 16(3), 316-322. Doi 10.1101/Gr.3676406
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Williams, L. E. et al. (2006) Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing. Applied and Environmental Microbiology 72(7), 4899-4906. Doi 10.1128/Aem.00354-06
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Woyke, T. et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443(7114), 950-955. Doi 10.1038/Nature05192
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Zhang, K. et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24(6), 680-686. Doi 10.1038/Nbt1214
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