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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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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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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