2008 Pubs - DOE Joint Genome Institute

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
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
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
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
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
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
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
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
Bowler, C. et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456(7219), 239-44. 10.1038/nature07410
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
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
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
Christiaen, L. et al. (2008) The transcription/migration interface in heart precursors of Ciona intestinalis. Science 320(5881), 1349-52. 10.1126/science.1158170
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
Dalevi, D. et al. (2008) Annotation of metagenome short reads using proxygenes. Bioinformatics 24(16), I7-I13. DOI 10.1093/bioinformatics/btn276
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
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
Field, D. et al. (2008) The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 26(5), 541-547. Doi 10.1038/Nbt1360
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
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
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
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
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
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
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
Hess, M. et al. (2008) Thermoacidophilic proteins for biofuel production. Trends Microbiol 16(9), 414-9. 10.1016/j.tim.2008.06.001
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
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
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
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
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
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
Hugenholtz, P. et al. (2008) Microbiology – Metagenomics. Nature 455(7212), 481-483. Doi 10.1038/455481a
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
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
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
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
Kallimanis, A. et al. (2008) Identification of two 1-hydroxy-2-naphthoate dioxygenase genes in Arthrobacter sp strain Sphe3. Febs Journal 275, 409-409.
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
Katsaveli, K. et al. (2008) Microbial community shifts during the annual operation of Messolonghi solar saltern, Greece. Febs Journal 275, 282-282.
Katsaveli, K. et al. (2008) Microbial community shifts during the annual operation of Messolonghi solar saltern, Greece. Febs Journal 275, 282-282.
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
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
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
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
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
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
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
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
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
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
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
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
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
Mackelprang, R. et al. (2008) Paleontology. New tricks with old bones. Science 321(5886), 211-2. 10.1126/science.1161890
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
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
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
Martin, F. et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183), 88-U7. Doi 10.1038/Nature06556
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Prabhakar, S. et al. (2008) Human-specific gain of function in a developmental enhancer. Science 321(5894), 1346-50. 10.1126/science.1159974
Putnam, N. H. et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198), 1064-71. 10.1038/nature06967
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
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
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
Riley, M. et al. (2008) Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9, 210. 10.1186/1471-2164-9-210
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
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
Rubin, E. M. et al. (2008) Genomics of cellulosic biofuels. Nature 454(7206), 841-5. 10.1038/nature07190
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
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
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
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
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
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
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
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
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
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
Srivastava, M. et al. (2008) The Trichoplax genome and the nature of placozoans. Nature 454(7207), 955-60. 10.1038/nature07191
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
Tanaka, S. et al. (2008) Atomic-level models of the bacterial carboxysome shell. Science 319(5866), 1083-6. 10.1126/science.1151458
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
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
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
Tringe, S. G. et al. (2008) The airborne metagenome in an indoor urban environment. PLoS One 3(4), e1862. 10.1371/journal.pone.0001862
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
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
Valdes, J. et al. (2008) Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597. 10.1186/1471-2164-9-597
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
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
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
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
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
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
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
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
Yan, H. et al. (2008) Intergenic locations of rice centromeric chromatin. PLoS Biol 6(11), e286. 10.1371/journal.pbio.0060286
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
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
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