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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 › 2003 Publications

2003 Publications

Azumi, K. et al. (2003) Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics 55(8), 570-581. Doi 10.1007/S00251-003-0606-5
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Boffelli, D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299(5611), 1391-1394. Doi 10.1126/Science.1081331
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Bray, N. et al. (2003) Avid: A Global Alignment Program. Genome Research 13(1), 97-102. Doi 10.1101/Gr.789803
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Chain, P. et al. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology 185(9), 2759-2773. Doi 10.1128/Jb.185.9.2759-2773.2003
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Cheng, J. F. et al. (2003) Comparative and functional analysis of cardiovascular-related genes. Pharmacogenomics 4(5), 571-582. Doi 10.1517/Phgs.4.5.571.23794
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Couronne, O. et al. (2003) Strategies and tools for whole-genome alignments. Genome Research 13(1), 73-80. Doi 10.1101/Gr.762503
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Dubchak, I. et al. (2003) Multi-species sequence comparison: the next frontier in genome annotation. Genome Biology 4(12). Artn 122 Doi 10.1186/Gb-2003-4-12-122
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Feil, H. et al. (2003) Site-directed disruption of the fimA and fimF fimbrial genes of Xylella fastidiosa. Phytopathology 93(6), 675-682. Doi 10.1094/Phyto.2003.93.6.675
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Frazer, K. A. et al. (2003) Cross-species sequence comparisons: A review of methods and available resources. Genome Research 13(1), 1-12. Doi 10.1101/Gr.222003
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Gibson-Brown, J. J. et al. (2003) A proposal to sequence the amphioxus genome submitted to the joint genome institute of the US department of energy. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 300B(1), 5-22. Doi 10.1002/Jez.B.00042
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Grogan, J. L. et al. (2003) Basal chromatin modification at the IL-4 gene in helper T cells. Journal of Immunology 171(12), 6672-6679.
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Grossman, A. R. et al. (2003) Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryotic Cell 2(6), 1137-1150. Doi 10.1128/Ec.2.6.1137-1150.2003
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Hallam, S. J. et al. (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Applied and Environmental Microbiology 69(9), 5483-5491. Doi 10.1128/Aem.69.9.5483-5491.2003
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Huby, T. et al. (2003) Regulation of the expression of the apolipoprotein(a) gene - Evidence for a regulatory role of the 5 ' distal apolipoprotein(a) transcription control region enhancer in yeast artificial chromosome transgenic mice. Arteriosclerosis Thrombosis and Vascular Biology 23(9), 1633-1639. Doi 10.1161/01.Atv.0000084637.01883.Ca
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Ishida, T. et al. (2003) Endothelial lipase is a major determinant of HDL level. Journal of Clinical Investigation 111(3), 347-355. Doi 10.1172/Jci200316306
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Murphy, M. B. et al. (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Research 31(18). ARTN e110 DOI 10.1093/nar/gng110
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Nardi, F. et al. (2003) Response to comment on "Hexapod origins: Monophyletic or paraphyletic?". Science 301(5639).
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Nardi, F. et al. (2003) Hexapod origins: Monophyletic or paraphyletic?. Science 299(5614), 1887-1889. Doi 10.1126/Science.1078607
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Nobrega, M. A. et al. (2003) Scanning human gene deserts for long-range enhancers. Science 302(5644), 413-413. Doi 10.1126/Science.1088328
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Palenik, B. et al. (2003) The genome of a motile marine Synechococcus. Nature 424(6952), 1037-1042. Doi 10.1038/Nature01943
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Passamonti, M. et al. (2003) Molecular evolution and recombination in gender-associated mitochondrial DNAs of the manila clam Tapes philippinarum. Genetics 164(2), 603-611.
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Pennacchio, L. A. et al. (2003) Insights from human/mouse genome comparisons. Mammalian Genome 14(7), 429-436. Doi 10.1007/S00335-002-4001-1
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Pennacchio, L. A. et al. (2003) Human-mouse comparative genomics: Successes and failures to reveal functional regions of the human genome. Cold Spring Harbor Symposia on Quantitative Biology 68, 303-309. Doi 10.1101/Sqb.2003.68.303
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Pennacchio, L. A. et al. (2003) Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice. Arteriosclerosis Thrombosis and Vascular Biology 23(4), 529-534. Doi 10.1161/01.Atv.0000054194.78240.45
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Pennacchio, L. A. et al. (2003) Comparative genomic tools and databases: providing insights into the human genome. Journal of Clinical Investigation 111(8), 1099-1106. Doi 10.1172/Jci200317842
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Pennacchio, L. A. et al. (2003) Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome. Cold Spring Harb Symp Quant Biol 68, 303-9.
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Rocap, G. et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424(6952), 1042-1047. Doi 10.1038/Nature01947
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Santini, S. et al. (2003) Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Research 13(6), 1111-1122. Doi 10.1101/Gr.700503
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Satou, Y. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - I. Genes for bHLH transcription factors. Development Genes and Evolution 213(5-6), 213-221. Doi 10.1007/S00427-003-0319-7
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Saunders, N. F. W. et al. (2003) Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Research 13(7), 1580-1588. Doi 10.1101/Gr.1180903
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Shen, X. et al. (2003) Genome-wide examination of myoblast cell cycle withdrawal during differentiation. Developmental Dynamics 226(1), 128-138. Doi 10.1002/Dvdy.10200
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Terajima, D. et al. (2003) Identification of candidate genes encoding the core components of the cell death machinery in the Ciona intestinalis genome. Cell Death and Differentiation 10(6), 749-753. Doi 10.1038/Sj.Cdd.4401223
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Vu-Dac, N. et al. (2003) Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators. Journal of Biological Chemistry 278(20), 17982-17985. Doi 10.1074/Jbc.M212191200
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Wada, S. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - II. Genes for homeobox transcription factors. Development Genes and Evolution 213(5-6), 222-234. Doi 10.1007/S00427-003-0321-0
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Yagi, K. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - III. Genes for Fox, ETS, nuclear receptors and NF kappa B. Development Genes and Evolution 213(5-6), 235-244. Doi 10.1007/S00427-003-0322-Z
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