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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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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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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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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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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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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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News & Publications
Home › News & Publications › Publications › 2007 Publications

2007 Publications

Adamska, M. et al. (2007) The evolutionary origin of hedgehog proteins. Curr Biol 17(19), R836-7. 10.1016/j.cub.2007.08.010
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Ahituv, N. et al. (2007) Deletion of ultraconserved elements yields viable mice. Plos Biology 5(9), 1906-1911. ARTN e234 DOI 10.1371/journal.pbio.0050234
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Allen, E. E. et al. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A 104(6), 1883-8. 10.1073/pnas.0604851104
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Alonso, C. et al. (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9(5), 1253-66. 10.1111/j.1462-2920.2007.01244.x
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Anderson, S. J. et al. (2007) Phenotypic and genetic variation among soybean rust isolates. Phytopathology 97(7), S4-S4.
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Arp, D. J. et al. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology 61, 503-528. DOI 10.1146/annurev.micro.61.080706.093449
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Auerbach, R. K. et al. (2007) Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. Plos One 2(8). ARTN e770 DOI 10.1371/journal.pone.0000770
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Bailey, Joseph M. et al. (2007) Confederate guerrilla : the Civil War memoir of Joseph M. Bailey. The Civil War in the West , xix, 148 p..
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Barns, S. M. et al. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73(9), 3113-6. 10.1128/AEM.02012-06
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Beckstrom-Sternberg, S. M. et al. (2007) Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One 2(9), e947. 10.1371/journal.pone.0000947
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Challacombe, J. F. et al. (2007) The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol 189(9), 3680-1. 10.1128/JB.00241-07
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Chistoserdova, L. et al. (2007) Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol 189(11), 4020-7. 10.1128/JB.00045-07
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Dalevi, D. et al. (2007) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. Bmc Bioinformatics 8. Artn 402 Doi 10.1186/1471-2105-8-402
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Field, D. et al. (2007) The positive role of the ecological community in the genomic revolution. Microb Ecol 53(3), 507-11. 10.1007/s00248-007-9206-5
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Fong, J. J. et al. (2007) A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals. Animal Conservation 10(4), 452-460. DOI 10.1111/j.1469-1795.2007.00131.x
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Fujita, M. K. et al. (2007) Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; squamata, gekkonidae). Molecular Biology and Evolution 24(12), 2775-2786. DOI 10.1093/molbev/msm212
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Giraud, E. et al. (2007) Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316(5829), 1307-12. 10.1126/science.1139548
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Gordon, L. et al. (2007) Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res 17(11), 1603-13. 10.1101/gr.6775107
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Gowda, M. et al. (2007) Interrogation of the RNA species in Magnaporthe grisea. Phytopathology 97(7), S42-S42.
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Grossman, A. R. et al. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10(2), 190-198. Doi 10.1016/J.Pbi.2007.01.012
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Gu, S. Y. et al. (2007) TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23(6), 764-766. Doi 10.1093/Bioinformatics/Btl643
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Horner-Devine, M. C. et al. (2007) A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88(6), 1345-1353. Doi 10.1890/06-0286
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Housman, D. C. et al. (2007) Heterogeneity of soil nutrients and subsurface biota in a dryland ecosystem. Soil Biology & Biochemistry 39(8), 2138-2149. Doi 10.1016/J.Soilbio.2007.03.015
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Hristova, K. R. et al. (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and Environmental Microbiology 73(22), 7347-7357. Doi 10.1128/Aem.01604-07
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Hugenholtz, P. et al. (2007) Riding giants. Environmental Microbiology 9(1), 5-5. Doi 10.1111/J.1462-2920.2006.01222_4.X
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Hugenholtz, P. et al. (2007) Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology 18(3), 235-236. Doi 10.1016/J.Copbio.2007.05.004
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Jansen, R. K. et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America 104(49), 19369-19374. DOI 10.1073/pnas.0709121104
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Jeffries, T. W. et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25(3), 319-26. 10.1038/nbt1290
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Johnson, S. L. et al. (2007) Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands. Environmental Microbiology 9(3), 680-689. Doi 10.1111/J.1462-2920.2006.01187.X
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Kalluri, U. C. et al. (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. Bmc Plant Biology 7. Artn 59Doi 10.1186/1471-2229-7-59
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Kamburov, A. et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. Bmc Genomics 8. Artn 460 Doi 10.1186/1471-2164-8-460
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Kane, S. R. et al. (2007) Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 189(5), 1931-45. 10.1128/JB.01259-06
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Kane, S. R. et al. (2007) Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of Bacteriology 189(5), 1931-1945. Doi 10.1128/Jb.01259-06
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Kazakov, A. E. et al. (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research 35, D407-D412. Doi 10.1093/Nar/Gkl865
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Kelleher, C. T. et al. (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal 50(6), 1063-1078. Doi 10.1111/J.1365-313x.2007.03112.X
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Larroux, C. et al. (2007) The NK homeobox gene cluster predates the origin of Hox genes. Current Biology 17(8), 706-710. Doi 10.1016/J.Cub.2007.03.008
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Leonardi, R. et al. (2007) Localization and regulation of mouse pantothenate kinase 2. FEBS Lett 581(24), 4639-44. 10.1016/j.febslet.2007.08.056
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Lo, I. et al. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135), 537-541. Doi 10.1038/Nature05624
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Lykidis, A. et al. (2007) Comparative genomics and evolution of eukaryotic phospholipid biosynthesis. Progress in Lipid Research 46(3-4), 171-199. Doi 10.1016/J.Plipres.2007.03.003
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Lykidis, A. et al. (2007) Genomics and evolution of eukaryotic phospholipid biosynthesis. Faseb Journal 21(6), A976-A976.
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Lykidis, A. et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of Bacteriology 189(6), 2477-2486. Doi 10.1128/Jb.01899-06
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Makarova, K. S. et al. (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2(9), e955. 10.1371/journal.pone.0000955
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Marcy, Y. et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America 104(29), 11889-11894. Doi 10.1073/Pnas.0704662104
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Markowitz, V. M. et al. (2007) Microbial genome data resources. Curr Opin Biotechnol 18(3), 267-72. 10.1016/j.copbio.2007.04.005
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Markowitz, V. M. et al. (2007) Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol 395, 35-56.
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Martin, F. N. et al. (2007) Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P-sojae. Current Genetics 51(5), 285-296. Doi 10.1007/S00294-007-0121-6
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Mavromatis, K. et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4(6), 495-500. Doi 10.1038/Nmeth1043
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McHardy, A. C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods 4(1), 63-72. Doi 10.1038/Nmeth976
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McMahon, K. D. et al. (2007) Integrating ecology into biotechnology. Current Opinion in Biotechnology 18(3), 287-292. Doi 10.1016/J.Copbio.2007.04.007
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McNeal, J. R. et al. (2007) Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology 5. Artn 55 Doi 10.1186/1741-7007-5-55
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McNeal, J. R. et al. (2007) Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. Bmc Plant Biology 7. Artn 57 Doi 10.1186/1471-2229-7-57
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Meier, S. et al. (2007) Continuous molecular evolution of protein-domain structures by single amino acid changes. Current Biology 17(2), 173-178. Doi 10.1016/J.Cub.2006.10.063
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Merchant, S. et al. (2007) Establishing potential chloroplast function through phylogenomics. Photosynthesis Research 91(2-3), 271-272.
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Merchant, S. S. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848), 245-251. Doi 10.1126/Science.1143609
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Minovitsky, S. et al. (2007) Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. Bmc Genomics 8. Artn 378 Doi 10.1186/1471-2164-8-378
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Montsant, A. et al. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43(3), 585-604. Doi 10.1111/J.1529-8817.2007.00342.X
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Moran, M. A. et al. (2007) Ecological genomics of marine roseobacters. Applied and Environmental Microbiology 73(14), 4559-4569. Doi 10.1128/Aem.02580-06
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Newton, I. L. G. et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315(5814), 998-1000. Doi 10.1126/Science.1138438
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Normand, P. et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp strains reflect host range and host plant biogeography. Genome Research 17(1), 7-15. Doi 10.1101/Gr.5798407
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Oudot-Le Secq, M. P. et al. (2007) Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Molecular Genetics and Genomics 277(4), 427-439. Doi 10.1007/S00438-006-0199-4
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Palenik, B. et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America 104(18), 7705-7710. Doi 10.1073/Pnas.0611046104
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Pel, H. J. et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2), 221-31. 10.1038/nbt1282
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Putnam, N. H. et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317(5834), 86-94. 10.1126/science.1139158
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Raubeson, L. A. et al. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. Bmc Genomics 8. Artn 174 Doi 10.1186/1471-2164-8-174
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Romeo, S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nature Genetics 39(4), 513-516. Doi 10.1038/Ng1984
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Sorek, R. et al. (2007) The birth of new exons: mechanisms and evolutionary consequences. RNA 13(10), 1603-8. 10.1261/rna.682507
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Sorek, R. et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318(5855), 1449-52. 10.1126/science.1147112
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Stein, L. Y. et al. (2007) Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol 9(12), 2993-3007. 10.1111/j.1462-2920.2007.01409.x
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Tanaka, S. et al. (2007) Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr D Biol Crystallogr 63(Pt 10), 1109-12. 10.1107/S090744490704228X
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Tang, Y. J. et al. (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73(12), 3859-64. 10.1128/AEM.02986-06
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Timme, R. E. et al. (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94(3), 302-12. 10.3732/ajb.94.3.302
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Udwary, D. W. et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences of the United States of America 104(25), 10376-10381. Doi 10.1073/Pnas.0700962104
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Vannini, C. et al. (2007) Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environmental Microbiology 9(2), 347-359. Doi 10.1111/J.1462-2920.2006.01144.X
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Visel, A. et al. (2007) Enhancer identification through comparative genomics. Seminars in Cell & Developmental Biology 18(1), 140-152. Doi 10.1016/J.Semcdb.2006.12.014
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von Mering, C. et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126-1130. Doi 10.1126/Science.1133420
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Warnecke, F. et al. (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8(12), 231. 10.1186/gb-2007-8-12-231
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Wong, R. et al. (2007) The story told by 100 shotgun sequenced microbial genomes - Why the clonability for genomes are different.. Plasmid 57(2), 239-239.
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Xie, G. et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Applied and Environmental Microbiology 73(11), 3536-3546. Doi 10.1128/Aem.00225-07
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Yamada, T. et al. (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. Isme Journal 1(3), 246-255. Doi 10.1038/Ismej.2007.28
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Yeager, C. M. et al. (2007) Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N-2-fixing members of biological soil crusts of the Colorado Plateau, USA. Fems Microbiology Ecology 60(1), 85-97. Doi 10.1111/J.1574-6941.2006.00265.X
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