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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 › 2004 Publications

2004 Publications

Ahituv, N. et al. (2004) Exploiting human-fish genome comparisons for deciphering gene regulation. Human Molecular Genetics 13, R261-R266. Doi 10.1093/Hmg/Ddh229
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Armbrust, E. V. et al. (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306(5693), 79-86. Doi 10.1126/Science.1101156
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Baroukh, N. et al. (2004) Analysis of apolipoprotein A5, C3, and plasma triglyceride concentrations in genetically engineered mice. Arteriosclerosis Thrombosis and Vascular Biology 24(7), 1297-1302. Doi 10.1161/01.Atv.0000130463.68272.1d
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Bensasson, D. et al. (2004) Genes without frontiers?. Heredity 92(6), 483-489. Doi 10.1038/Sj.Hdy.6800451
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Boffelli, D. et al. (2004) Convergent evolution in primates and an insectivore. Genomics 83(1), 19-23. Doi 10.1016/S0888-7543(03)00148-4
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Boffelli, D. et al. (2004) Comparative genomics at the vertebrate extremes. Nature Reviews Genetics 5(6), 456-465. Doi 10.1038/Nrg1350
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Boffelli, D. et al. (2004) Intraspecies sequence comparisons for annotating genomes. Genome Research 14(12), 2406-2411. Doi 10.1101/Gr.3199704
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Bolotin, A. et al. (2004) Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nature Biotechnology 22(12), 1554-1558. Doi 10.1038/Nbt1034
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Boore, J. L. et al. (2004) Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. Bmc Genomics 5. Artn 67 Doi 10.1186/1471-2164-5-67
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Boore, J. L. et al. (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Molecular Biology and Evolution 21(8), 1492-1503. Doi 10.1093/Molbev/Msh090
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Brudno, M. et al. (2004) Automated whole-genome multiple alignment of rat, mouse, and human. Genome Research 14(4), 685-692. Doi 10.1101/Gr.2067704
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Cooper, G. M. et al. (2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Research 14(4), 539-548. Doi 10.1101/Gr.2034704
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Eichenbaum-Voline, S. et al. (2004) Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia. Arteriosclerosis Thrombosis and Vascular Biology 24(1), 167-174. Doi 10.1161/01.Atv.0000099881.83261.D4
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Epting, C. L. et al. (2004) Stem cell antigen-1 is necessary for cell-cycle withdrawal and myoblast differentiation in C2C12 cells. Journal of Cell Science 117(25), 6185-6195. Doi 10.1242/Jcs.01548
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Frazer, K. A. et al. (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research 32, W273-W279. Doi 10.1093/Nar/Gkh458
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Gatesy, J. et al. (2004) Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of Crocodylia. Systematic Biology 53(2), 342-355. Doi 10.1080/10635150490423971
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Gibbs, R. A. et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982), 493-521. Doi 10.1038/Nature02426
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Ginige, M. P. et al. (2004) Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied and Environmental Microbiology 70(1), 588-596. Doi 10.1128/Aem.70.1.588-596.2004
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Grimwood, J. et al. (2004) The DNA sequence and biology of human chromosome 19. Nature 428(6982), 529-535. Doi 10.1038/Nature02399
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Grimwood, J. et al. (2004) The DNA sequence and biology of human chromosome 19. Nature 428(6982), 529-535. Doi 10.1038/Nature02399
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Hallam, S. J. et al. (2004) Reverse methanogenesis: Testing the hypothesis with environmental genomics. Science 305(5689), 1457-1462. Doi 10.1126/Science.1100025
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Helfenbein, K. G. et al. (2004) The mitochondrial genome of Phoronis architecta - Comparisons demonstrate that phoronids are Lophotrochozoan protostomes. Molecular Biology and Evolution 21(1), 153-157. Doi 10.1093/Molbev/Msh011
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Helfenbein, K. G. et al. (2004) The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proceedings of the National Academy of Sciences of the United States of America 101(29), 10639-10643. Doi 10.1073/Pnas.0400941101
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Huber, T. et al. (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20(14), 2317-2319. Doi 10.1093/Bioinformatics/Bth226
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Hugenholtz, P. et al. (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). International Journal of Systematic and Evolutionary Microbiology 54, 2049-2051. Doi 10.1099/Ijs.0.03028-0
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Imanishi, T. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. Plos Biology 2(6), 856-875. ARTN e162 DOI 10.1371/journal.pbio.0020162
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International Human Genome Sequencing Consortium. et al. (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011), 931-45. 10.1038/nature03001
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Joyce, W. G. et al. (2004) Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles. Journal of Paleontology 78(5), 989-1013. Doi 10.1666/0022-3360(2004)078<0989:Dapftc>2.0.Co;2
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Kim, J. et al. (2004) Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2. Genomics 84(1), 47-58. Doi 10.1016/J.Ygeno.2004.02.007
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Larimer, F. W. et al. (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnology 22(1), 55-61. Doi 10.1038/Nbt923
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Lavrov, D. V. et al. (2004) Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society B-Biological Sciences 271(1538), 537-544. Doi 10.1098/Rspb.2003.2631
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Leem, S. H. et al. (2004) Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements. Genome Research 14(2), 239-246. Doi 10.1101/Gr.1929904
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Li, T. T. et al. (2004) Genetic variation responsible for mouse strain differences in integrin alpha(2) expression is associated with altered platelet responses to collagen. Blood 103(9), 3396-3402. Doi 10.1182/Blood-2003-10-3721
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Macey, J. R. et al. (2004) Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Molecular Phylogenetics and Evolution 33(1), 22-31. Doi 10.1016/J.Ympev.2004.05.003
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Martin, J. et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature 432(7020), 988-94. 10.1038/nature03187
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Martinez, D. et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology 22(6), 695-700. 10.1038/nbt967
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Masta, S. E. et al. (2004) The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Molecular Biology and Evolution 21(5), 893-902. 10.1093/molbev/msh096
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Mueller, R. L. et al. (2004) Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc Natl Acad Sci U S A 101(38), 13820-5. 10.1073/pnas.0405785101
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Nobrega, M. A. et al. (2004) Comparative genomic analysis as a tool for biological discovery. Journal of Physiology-London 554(1), 31-39. Doi 10.1113/Jphysiol.2003.050948
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Nobrega, M. A. et al. (2004) Megabase deletions of gene deserts result in viable mice. Nature 431(7011), 988-93. 10.1038/nature03022
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Olivier, M. et al. (2004) Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11. Genomics 83(5), 912-923. Doi 10.1016/J.Ygeno.2003.11.016
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Parham, J. F. et al. (2004) Evolutionary distinctiveness of the extinct Yunnan box turtle (Cuora yunnanensis) revealed by DNA from an old museum specimen. Proceedings of the Royal Society B-Biological Sciences 271, S391-S394. Doi 10.1098/Rsbl.2004.0217
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Parra, M. et al. (2004) Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitate expression of diverse tissue-specific isoforms. Genomics 84(4), 637-646. Doi 10.1016/J.Ygeno.2004.06.004
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Predki, P. F. et al. (2004) Rolling circle amplification for sequencing templates. Methods Mol Biol 255, 189-96. 10.1385/1-59259-752-1:189
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Rodionov, D. A. et al. (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biology 5(11), R90. 10.1186/gb-2004-5-11-r90
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Ruiz-Trillo, I. et al. (2004) Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. Molecular Phylogenetics and Evolution 33(2), 321-332. Doi 10.1016/J.Ympev.2004.06.002
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Sangwan, P. et al. (2004) Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Applied and Environmental Microbiology 70(10), 5875-5881. Doi 10.1128/Aem.70.10.5875-5881.2004
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Schmutz, J. et al. (2004) The DNA sequence and comparative analysis of human chromosome 5. Nature 431(7006), 268-74. 10.1038/nature02919
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Schoenborn, L. et al. (2004) Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Applied and Environmental Microbiology 70(7), 4363-4366. Doi 10.1128/Aem.70.7.4363-4366.2004
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Shah, N. et al. (2004) Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics 20(5), 636-U122. Doi 10.1093/Bioinformatics/Btg459
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Stuart, B. L. et al. (2004) Molecular phylogeny of the critically endangered Indochinese box turtle (Cuora galbinifrons). Molecular Phylogenetics and Evolution 31(1), 164-177. Doi 10.1016/S1055-7903(03)00258-6
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Symula, D. J. et al. (2004) Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling. Mammalian Genome 15(1), 1-13. Doi 10.1007/S00335-002-2228-X
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Townsend, T. M. et al. (2004) Molecular phylogenetics of Squamata: The position of snakes, Amphisbaenians, and Dibamids, and the root of the Squamate tree. Systematic Biology 53(5), 735-757. Doi 10.1080/10635150490522340
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Tyson, G. W. et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978), 37-43. Doi 10.1038/Nature02340
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Wang, Q. F. et al. (2004) Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons. Human Molecular Genetics 13(10), 1049-1056. Doi 10.1093/Hmg/Ddh121
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Wong, G. K. S. et al. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432(7018), 717-722. Doi 10.1038/Nature03156
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Wyman, S. K. et al. (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17), 3252-3255. Doi 10.1093/Bioinformatics/Bth352
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Zheng, P. et al. (2004) Identification of a novel enhancer of brain expression near the apoE gene cluster by comparative genomics. Biochimica Et Biophysica Acta-Gene Structure and Expression 1676(1), 41-50. Doi 10.1016/J.Bbaexp.2003.10.007
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