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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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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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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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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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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.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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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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