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2008 Publications

Alvarez Retuerto, A. I. et al. (2008) Association of common variants in the Joubert syndrome gene (AHI1) with autism. Hum Mol Genet 17(24), 3887-96. 10.1093/hmg/ddn291
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Anderson, I. et al. (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. Journal of Bacteriology 190(8), 2957-2965. Doi 10.1128/Jb.01949-07
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Anderson, S. J. et al. (2008) Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi. Mol Ecol Resour 8(6), 1310-2. 10.1111/j.1755-0998.2008.02272.x
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Angiuoli, S. V. et al. (2008) Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 12(2), 137-41. 10.1089/omi.2008.0017
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Auger, S. et al. (2008) The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains. Applied and Environmental Microbiology 74(4), 1276-1280. Doi 10.1128/Aem.02242-07
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Blow, M. J. et al. (2008) Identification of ancient remains through genomic sequencing. Genome Research 18(8), 1347-1353. DOI 10.1101/gr.076091.108
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Bluhm, B. H. et al. (2008) Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth. BMC Genomics 9, 523. 10.1186/1471-2164-9-523
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Boore, J. L. et al. (2008) Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philosophical Transactions of the Royal Society B-Biological Sciences 363(1496), 1445-1451. DOI 10.1098/rstb.2007.2234
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Bowler, C. et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456(7219), 239-44. 10.1038/nature07410
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Breznak, J. A. et al. (2008) Spirochaeta cellobiosiphila sp. nov., a facultatively anaerobic, marine spirochaete. Int J Syst Evol Microbiol 58(Pt 12), 2762-8. 10.1099/ijs.0.2008/001263-0
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Cai, Z. Q. et al. (2008) Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions. Journal of Molecular Evolution 67(6), 696-704. DOI 10.1007/s00239-008-9180-7
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Chivian, D. et al. (2008) Environmental genomics reveals a single-species ecosystem deep within earth. Science 322(5899), 275-278. DOI 10.1126/science.1155495
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Christiaen, L. et al. (2008) The transcription/migration interface in heart precursors of Ciona intestinalis. Science 320(5881), 1349-52. 10.1126/science.1158170
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Coyne, R. S. et al. (2008) Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. Bmc Genomics 9. Artn 562Doi 10.1186/1471-2164-9-562
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Dalevi, D. et al. (2008) Annotation of metagenome short reads using proxygenes. Bioinformatics 24(16), I7-I13. DOI 10.1093/bioinformatics/btn276
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De Val, S. et al. (2008) Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors. Cell 135(6), 1053-1064. DOI 10.1016/j.cell.2008.10.049
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Elkins, J. G. et al. (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A 105(23), 8102-7. 10.1073/pnas.0801980105
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Field, D. et al. (2008) The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 26(5), 541-547. Doi 10.1038/Nbt1360
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Field, D. et al. (2008) Foreword to the Special Issue on the Fifth Genomic Standards Consortium Workshop. Omics-a Journal of Integrative Biology 12(2), 99-99. DOI 10.1089/omi.2008.0013
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Garcia, E. et al. (2008) Molecular characterization of L-413C, a P2-related plague diagnostic bacteriophage. Virology 372(1), 85-96. DOI 10.1016/j.virol.2007.10.032
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Garrity, G. M. et al. (2008) Toward a standards-compliant genomic and metagenomic publication record. OMICS 12(2), 157-60. 10.1089/omi.2008.A2B2
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Gomez, L. D. et al. (2008) Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis. Biotechnol Biofuels 1(1), 15. 10.1186/1754-6834-1-15
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Grimson, A. et al. (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455(7217), 1193-7. 10.1038/nature07415
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Haberle, R. C. et al. (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. Journal of Molecular Evolution 66(4), 350-361. DOI 10.1007/s00239-008-9086-4
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Hendrix, D. A. et al. (2008) Promoter elements associated with RNA Pol 11 stalling in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America 105(22), 7762-7767. DOI 10.1073/pnas.0802406105
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Hess, M. et al. (2008) Thermoacidophilic proteins for biofuel production. Trends Microbiol 16(9), 414-9. 10.1016/j.tim.2008.06.001
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Hess, M. et al. (2008) Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. Extremophiles 12(3), 351-364. DOI 10.1007/s00792-008-0139-9
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Hirschman, L. et al. (2008) Habitat-Lite: A GSC case study based on free text terms for environmental metadata. Omics-a Journal of Integrative Biology 12(2), 129-136. DOI 10.1089/omi.2008.0016
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Holland, L. Z. et al. (2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research 18(7), 1100-1111. DOI 10.1101/gr.073676.107
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Hooper, S. D. et al. (2008) A Molecular Study of Microbe Transfer between Distant Environments. Plos One 3(7). Artn E2607 Doi 10.1371/Journal.Pone.0002607
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Horton, A. et al. (2008) Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Development Genes and Evolution 218(11-12), 613-628. DOI 10.1007/s00427-008-0249-5
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Horton, A. C. et al. (2008) Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev Genes Evol 218(11-12), 613-28. 10.1007/s00427-008-0249-5
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Hugenholtz, P. et al. (2008) Microbiology - Metagenomics. Nature 455(7212), 481-483. Doi 10.1038/455481a
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Hwang, J. S. et al. (2008) Cilium evolution: Identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes. Molecular Biology and Evolution 25(9), 2009-2017. DOI 10.1093/molbev/msn154
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Isabel, S. et al. (2008) Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species. Journal of Bacteriology 190(22), 7548-7558. Doi 10.1128/Jb.01067-08
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Isabel, S. et al. (2008) Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species. Journal of Bacteriology 190(22), 7548-7558. Doi 10.1128/Jb.01067-08
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Ishoey, T. et al. (2008) Genomic sequencing of single microbial cells from environmental samples. Current Opinion in Microbiology 11(3), 198-204. DOI 10.1016/j.mib.2008.05.006
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Kallimanis, A. et al. (2008) Identification of two 1-hydroxy-2-naphthoate dioxygenase genes in Arthrobacter sp strain Sphe3. Febs Journal 275, 409-409.
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Kalyuzhnaya, M. G. et al. (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotechnology 26(9), 1029-1034. Doi 10.1038/Nbt.1488
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Katsaveli, K. et al. (2008) Microbial community shifts during the annual operation of Messolonghi solar saltern, Greece. Febs Journal 275, 282-282.
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Katsaveli, K. et al. (2008) Microbial community shifts during the annual operation of Messolonghi solar saltern, Greece. Febs Journal 275, 282-282.
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King, N. et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451(7180), 783-788. Doi 10.1038/Nature06617
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Kraaijeveld, K. et al. (2008) The evolution of sperm and non-sperm producing organs in male Drosophila. Biological Journal of the Linnean Society 94(3), 505-512. DOI 10.1111/j.1095-8312.2008.01030.x
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Kunin, V. et al. (2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research 18(2), 293-297. Doi 10.1101/Gr.6835308
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Kunin, V. et al. (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4, 198. 10.1038/msb.2008.35
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Kunin, V. et al. (2008) A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 72(4), 557-78, Table of Contents. 10.1128/MMBR.00009-08
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Labbe, J. et al. (2008) A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies. New Phytol 180(2), 316-28. 10.1111/j.1469-8137.2008.02614.x
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Lapidus, A. et al. (2008) Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact 171(2), 236-49. 10.1016/j.cbi.2007.03.003
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Larroux, C. et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 25(5), 980-96. 10.1093/molbev/msn047
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Leary, R. J. et al. (2008) Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proceedings of the National Academy of Sciences of the United States of America 105(42), 16224-16229. DOI 10.1073/pnas.0808041105
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Lee, J. H. et al. (2008) Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9, 247. 10.1186/1471-2164-9-247
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Liolios, K. et al. (2008) The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36(Database issue), D475-9. 10.1093/nar/gkm884
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Loh, Y. H. et al. (2008) Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biol 9(7), R113. 10.1186/gb-2008-9-7-r113
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Macey, J. R. et al. (2008) Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic data. Molecular Phylogenetics and Evolution 49(3), 1015-1018. DOI 10.1016/j.ympev.2008.08.024
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Mackelprang, R. et al. (2008) Paleontology. New tricks with old bones. Science 321(5886), 211-2. 10.1126/science.1161890
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Marco, E. J. et al. (2008) ARHGEF9 disruption in a female patient is associated with X linked mental retardation and sensory hyperarousal. Journal of Medical Genetics 45(2), 100-105. DOI 10.1136/jmg.2007.052324
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Markowitz, V. M. et al. (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research 36, D534-D538. Doi 10.1093/Nar/Gkm869
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Markowitz, V. M. et al. (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 36(Database issue), D528-33. 10.1093/nar/gkm846
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Martin, F. et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183), 88-U7. Doi 10.1038/Nature06556
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Martinez, D. et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26(5), 553-60. 10.1038/nbt1403
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Masta, S. E. et al. (2008) Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Mol Biol Evol 25(5), 949-59. 10.1093/molbev/msn051
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Mattes, T. E. et al. (2008) The genome of Polaromonas sp strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Applied and Environmental Microbiology 74(20), 6405-6416. Doi 10.1128/Aem.00197-08
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Mccoy, S. R. et al. (2008) The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. Bmc Evolutionary Biology 8. Artn 130 Doi 10.1186/1471-2148-8-130
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Merritt, W. M. et al. (2008) Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med 359(25), 2641-50. 10.1056/NEJMoa0803785
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Mueller, R. L. et al. (2008) Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. Zoology (Jena) 111(3), 218-30. 10.1016/j.zool.2007.07.010
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Norton, J. M. et al. (2008) Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol 74(11), 3559-72. 10.1128/AEM.02722-07
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Oda, Y. et al. (2008) Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proc Natl Acad Sci U S A 105(47), 18543-8. 10.1073/pnas.0809160105
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Opperman, C. H. et al. (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci U S A 105(39), 14802-7. 10.1073/pnas.0805946105
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Peterson, S. B. et al. (2008) Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ Microbiol 10(10), 2692-703. 10.1111/j.1462-2920.2008.01690.x
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Pierce, E. et al. (2008) The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 10(10), 2550-73. 10.1111/j.1462-2920.2008.01679.x
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Pierce, E. et al. (2008) The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 10(10), 2550-73. 10.1111/j.1462-2920.2008.01679.x
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Podar, M. et al. (2008) A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 9(11), R158. 10.1186/gb-2008-9-11-r158
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Podar, M. et al. (2008) A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 9(11), R158. 10.1186/gb-2008-9-11-r158
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Prabhakar, S. et al. (2008) Human-specific gain of function in a developmental enhancer. Science 321(5894), 1346-50. 10.1126/science.1159974
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Putnam, N. H. et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198), 1064-71. 10.1038/nature06967
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Quesada, T. et al. (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytol 180(2), 408-20. 10.1111/j.1469-8137.2008.02586.x
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Ralph, S. G. et al. (2008) Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. Bmc Genomics 9. Artn 57Doi 10.1186/1471-2164-9-57
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Rensing, S. A. et al. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319(5859), 64-69. DOI 10.1126/science.1150646
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Riley, M. et al. (2008) Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9, 210. 10.1186/1471-2164-9-210
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Rodrigues, D. F. et al. (2008) Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics 9, 547. 10.1186/1471-2164-9-547
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Romeo, S. et al. (2008) Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 40(12), 1461-5. 10.1038/ng.257
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Rubin, E. M. et al. (2008) Genomics of cellulosic biofuels. Nature 454(7206), 841-5. 10.1038/nature07190
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Satou, Y. et al. (2008) Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 9(10), R152. 10.1186/gb-2008-9-10-r152
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Schoenfeld, T. et al. (2008) Assembly of viral metagenomes from yellowstone hot springs. Appl Environ Microbiol 74(13), 4164-74. 10.1128/AEM.02598-07
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Schwarz, J. A. et al. (2008) Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics 9, 97. 10.1186/1471-2164-9-97
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Sela, D. A. et al. (2008) The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America 105(48), 18964-18969. DOI 10.1073/pnas.0809584105
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Sela, D. A. et al. (2008) The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America 105(48), 18964-18969. DOI 10.1073/pnas.0809584105
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Shoemaker, R. C. et al. (2008) Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome 51(4), 294-302. 10.1139/G08-010
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Sievert, S. M. et al. (2008) Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Applied and Environmental Microbiology 74(4), 1145-1156. Doi 10.1128/Aem.01844-07
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Smith, D. R. et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research 18(10), 1638-1642. DOI 10.1101/gr.077776.108
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Smith, D. R. et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research 18(10), 1638-1642. DOI 10.1101/gr.077776.108
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Sorek, R. et al. (2008) CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6(3), 181-186. Doi 10.1038/Nrmicro1793
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Srivastava, M. et al. (2008) The Trichoplax genome and the nature of placozoans. Nature 454(7207), 955-60. 10.1038/nature07191
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Starkenburg, S. R. et al. (2008) Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Appl Environ Microbiol 74(9), 2852-63. 10.1128/AEM.02311-07
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Tanaka, S. et al. (2008) Atomic-level models of the bacterial carboxysome shell. Science 319(5866), 1083-6. 10.1126/science.1151458
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Theofilopoulos, S. et al. (2008) Novel function of the human presqualene diphosphate phosphatase as a type II phosphatidate phosphatase in phosphatidylcholine and triacylglyceride biosynthesis pathways. Biochimica Et Biophysica Acta-Molecular and Cell Biology of Lipids 1781(11-12), 731-742. DOI 10.1016/j.bbalip.2008.09.001
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Torriani, S. F. et al. (2008) Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola. Fungal Genet Biol 45(5), 628-37. 10.1016/j.fgb.2007.12.005
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Tringe, S. G. et al. (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11(5), 442-6. 10.1016/j.mib.2008.09.011
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Tringe, S. G. et al. (2008) The airborne metagenome in an indoor urban environment. PLoS One 3(4), e1862. 10.1371/journal.pone.0001862
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Tringe, S. G. et al. (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11(5), 442-6. 10.1016/j.mib.2008.09.011
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Tsiamis, G. et al. (2008) Prokaryotic community profiles at different operational stages of a Greek solar saltern. Research in Microbiology 159(9-10), 609-627. DOI 10.1016/j.resmic.2008.09.007
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Valdes, J. et al. (2008) Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597. 10.1186/1471-2164-9-597
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Valles, Y. et al. (2008) Group II introns break new boundaries: presence in a bilaterian's genome. PLoS One 3(1), e1488. 10.1371/journal.pone.0001488
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Van Brabant, B. et al. (2008) Laying the foundation for a genomic rosetta stone: Creating information hubs through the use of consensus identifiers. Omics-a Journal of Integrative Biology 12(2), 123-127. DOI 10.1089/omi.2008.0020
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Visel, A. et al. (2008) Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet 40(2), 158-60. 10.1038/ng.2007.55
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Weiner, R. M. et al. (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40(T). Plos Genetics 4(5). ARTN e1000087 DOI 10.1371/journal.pgen.1000087
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Wickett, N. J. et al. (2008) Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Mol Biol Evol 25(2), 393-401. 10.1093/molbev/msm267
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Wilson, A. et al. (2008) A photoactive carotenoid protein acting as light intensity sensor. Proceedings of the National Academy of Sciences of the United States of America 105(33), 12075-12080. DOI 10.1073/pnas.0804636105
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Wrighton, K. C. et al. (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. Isme Journal 2(11), 1146-1156. DOI 10.1038/ismej.2008.48
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Wu, M. et al. (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9(10), R151. 10.1186/gb-2008-9-10-r151
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Yan, H. et al. (2008) Intergenic locations of rice centromeric chromatin. PLoS Biol 6(11), e286. 10.1371/journal.pbio.0060286
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Yang, X. H. et al. (2008) The F-Box Gene Family Is Expanded in Herbaceous Annual Plants Relative to Woody Perennial Plants. Plant Physiology 148(3), 1189-1200. DOI 10.1104/pp.108.121921
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Yeates, T. O. et al. (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6(9), 681-91. 10.1038/nrmicro1913
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Yin, T. et al. (2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 18(3), 422-30. 10.1101/gr.7076308
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