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

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

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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

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

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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

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

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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

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

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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

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

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

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News & Publications
Home › News & Publications › Publications › 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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