News & Publications

2007 Pubs

Adamska, M. et al. (2007) The evolutionary origin of hedgehog proteins. Curr Biol 17(19), R836-7. 10.1016/j.cub.2007.08.010
Ahituv, N. et al. (2007) Deletion of ultraconserved elements yields viable mice. Plos Biology 5(9), 1906-1911. ARTN e234 DOI 10.1371/journal.pbio.0050234
Allen, E. E. et al. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A 104(6), 1883-8. 10.1073/pnas.0604851104
Alonso, C. et al. (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9(5), 1253-66. 10.1111/j.1462-2920.2007.01244.x
Anderson, S. J. et al. (2007) Phenotypic and genetic variation among soybean rust isolates. Phytopathology 97(7), S4-S4.
Arp, D. J. et al. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology 61, 503-528. DOI 10.1146/annurev.micro.61.080706.093449
Auerbach, R. K. et al. (2007) Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. Plos One 2(8). ARTN e770 DOI 10.1371/journal.pone.0000770
Bailey, Joseph M. et al. (2007) Confederate guerrilla : the Civil War memoir of Joseph M. Bailey. The Civil War in the West , xix, 148 p..
Barns, S. M. et al. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73(9), 3113-6. 10.1128/AEM.02012-06
Beckstrom-Sternberg, S. M. et al. (2007) Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One 2(9), e947. 10.1371/journal.pone.0000947
Challacombe, J. F. et al. (2007) The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol 189(9), 3680-1. 10.1128/JB.00241-07
Chistoserdova, L. et al. (2007) Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol 189(11), 4020-7. 10.1128/JB.00045-07
Dalevi, D. et al. (2007) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. Bmc Bioinformatics 8. Artn 402 Doi 10.1186/1471-2105-8-402
Field, D. et al. (2007) The positive role of the ecological community in the genomic revolution. Microb Ecol 53(3), 507-11. 10.1007/s00248-007-9206-5
Fong, J. J. et al. (2007) A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals. Animal Conservation 10(4), 452-460. DOI 10.1111/j.1469-1795.2007.00131.x
Fujita, M. K. et al. (2007) Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; squamata, gekkonidae). Molecular Biology and Evolution 24(12), 2775-2786. DOI 10.1093/molbev/msm212
Giraud, E. et al. (2007) Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316(5829), 1307-12. 10.1126/science.1139548
Gordon, L. et al. (2007) Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res 17(11), 1603-13. 10.1101/gr.6775107
Gowda, M. et al. (2007) Interrogation of the RNA species in Magnaporthe grisea. Phytopathology 97(7), S42-S42.
Grossman, A. R. et al. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10(2), 190-198. Doi 10.1016/J.Pbi.2007.01.012
Gu, S. Y. et al. (2007) TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23(6), 764-766. Doi 10.1093/Bioinformatics/Btl643
Horner-Devine, M. C. et al. (2007) A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88(6), 1345-1353. Doi 10.1890/06-0286
Housman, D. C. et al. (2007) Heterogeneity of soil nutrients and subsurface biota in a dryland ecosystem. Soil Biology & Biochemistry 39(8), 2138-2149. Doi 10.1016/J.Soilbio.2007.03.015
Hristova, K. R. et al. (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and Environmental Microbiology 73(22), 7347-7357. Doi 10.1128/Aem.01604-07
Hugenholtz, P. et al. (2007) Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology 18(3), 235-236. Doi 10.1016/J.Copbio.2007.05.004
Hugenholtz, P. et al. (2007) Riding giants. Environmental Microbiology 9(1), 5-5. Doi 10.1111/J.1462-2920.2006.01222_4.X
Jansen, R. K. et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America 104(49), 19369-19374. DOI 10.1073/pnas.0709121104
Jeffries, T. W. et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25(3), 319-26. 10.1038/nbt1290
Johnson, S. L. et al. (2007) Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands. Environmental Microbiology 9(3), 680-689. Doi 10.1111/J.1462-2920.2006.01187.X
Kalluri, U. C. et al. (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. Bmc Plant Biology 7. Artn 59Doi 10.1186/1471-2229-7-59
Kamburov, A. et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. Bmc Genomics 8. Artn 460 Doi 10.1186/1471-2164-8-460
Kane, S. R. et al. (2007) Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 189(5), 1931-45. 10.1128/JB.01259-06
Kane, S. R. et al. (2007) Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of Bacteriology 189(5), 1931-1945. Doi 10.1128/Jb.01259-06
Kazakov, A. E. et al. (2007) RegTransBase – a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research 35, D407-D412. Doi 10.1093/Nar/Gkl865
Kelleher, C. T. et al. (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal 50(6), 1063-1078. Doi 10.1111/J.1365-313x.2007.03112.X
Larroux, C. et al. (2007) The NK homeobox gene cluster predates the origin of Hox genes. Current Biology 17(8), 706-710. Doi 10.1016/J.Cub.2007.03.008
Leonardi, R. et al. (2007) Localization and regulation of mouse pantothenate kinase 2. FEBS Lett 581(24), 4639-44. 10.1016/j.febslet.2007.08.056
Lo, I. et al. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135), 537-541. Doi 10.1038/Nature05624
Lykidis, A. et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of Bacteriology 189(6), 2477-2486. Doi 10.1128/Jb.01899-06
Lykidis, A. et al. (2007) Genomics and evolution of eukaryotic phospholipid biosynthesis. Faseb Journal 21(6), A976-A976.
Lykidis, A. et al. (2007) Comparative genomics and evolution of eukaryotic phospholipid biosynthesis. Progress in Lipid Research 46(3-4), 171-199. Doi 10.1016/J.Plipres.2007.03.003
Makarova, K. S. et al. (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2(9), e955. 10.1371/journal.pone.0000955
Marcy, Y. et al. (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America 104(29), 11889-11894. Doi 10.1073/Pnas.0704662104
Markowitz, V. M. et al. (2007) Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol 395, 35-56.
Markowitz, V. M. et al. (2007) Microbial genome data resources. Curr Opin Biotechnol 18(3), 267-72. 10.1016/j.copbio.2007.04.005
Martin, F. N. et al. (2007) Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P-sojae. Current Genetics 51(5), 285-296. Doi 10.1007/S00294-007-0121-6
Mavromatis, K. et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4(6), 495-500. Doi 10.1038/Nmeth1043
McHardy, A. C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods 4(1), 63-72. Doi 10.1038/Nmeth976
McMahon, K. D. et al. (2007) Integrating ecology into biotechnology. Current Opinion in Biotechnology 18(3), 287-292. Doi 10.1016/J.Copbio.2007.04.007
McNeal, J. R. et al. (2007) Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. Bmc Plant Biology 7. Artn 57 Doi 10.1186/1471-2229-7-57
McNeal, J. R. et al. (2007) Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology 5. Artn 55 Doi 10.1186/1741-7007-5-55
Meier, S. et al. (2007) Continuous molecular evolution of protein-domain structures by single amino acid changes. Current Biology 17(2), 173-178. Doi 10.1016/J.Cub.2006.10.063
Merchant, S. et al. (2007) Establishing potential chloroplast function through phylogenomics. Photosynthesis Research 91(2-3), 271-272.
Merchant, S. S. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848), 245-251. Doi 10.1126/Science.1143609
Minovitsky, S. et al. (2007) Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. Bmc Genomics 8. Artn 378 Doi 10.1186/1471-2164-8-378
Montsant, A. et al. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43(3), 585-604. Doi 10.1111/J.1529-8817.2007.00342.X
Moran, M. A. et al. (2007) Ecological genomics of marine roseobacters. Applied and Environmental Microbiology 73(14), 4559-4569. Doi 10.1128/Aem.02580-06
Newton, I. L. G. et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315(5814), 998-1000. Doi 10.1126/Science.1138438
Normand, P. et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp strains reflect host range and host plant biogeography. Genome Research 17(1), 7-15. Doi 10.1101/Gr.5798407
Oudot-Le Secq, M. P. et al. (2007) Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Molecular Genetics and Genomics 277(4), 427-439. Doi 10.1007/S00438-006-0199-4
Palenik, B. et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America 104(18), 7705-7710. Doi 10.1073/Pnas.0611046104
Pel, H. J. et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2), 221-31. 10.1038/nbt1282
Putnam, N. H. et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317(5834), 86-94. 10.1126/science.1139158
Raubeson, L. A. et al. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. Bmc Genomics 8. Artn 174 Doi 10.1186/1471-2164-8-174
Romeo, S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nature Genetics 39(4), 513-516. Doi 10.1038/Ng1984
Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
Sorek, R. et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318(5855), 1449-52. 10.1126/science.1147112
Sorek, R. et al. (2007) The birth of new exons: mechanisms and evolutionary consequences. RNA 13(10), 1603-8. 10.1261/rna.682507
Stein, L. Y. et al. (2007) Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol 9(12), 2993-3007. 10.1111/j.1462-2920.2007.01409.x
Tanaka, S. et al. (2007) Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr D Biol Crystallogr 63(Pt 10), 1109-12. 10.1107/S090744490704228X
Tang, Y. J. et al. (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73(12), 3859-64. 10.1128/AEM.02986-06
Timme, R. E. et al. (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94(3), 302-12. 10.3732/ajb.94.3.302
Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
Udwary, D. W. et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences of the United States of America 104(25), 10376-10381. Doi 10.1073/Pnas.0700962104
Vannini, C. et al. (2007) Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environmental Microbiology 9(2), 347-359. Doi 10.1111/J.1462-2920.2006.01144.X
Visel, A. et al. (2007) Enhancer identification through comparative genomics. Seminars in Cell & Developmental Biology 18(1), 140-152. Doi 10.1016/J.Semcdb.2006.12.014
von Mering, C. et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126-1130. Doi 10.1126/Science.1133420
Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
Warnecke, F. et al. (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8(12), 231. 10.1186/gb-2007-8-12-231
Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
Wong, R. et al. (2007) The story told by 100 shotgun sequenced microbial genomes – Why the clonability for genomes are different.. Plasmid 57(2), 239-239.
Xie, G. et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Applied and Environmental Microbiology 73(11), 3536-3546. Doi 10.1128/Aem.00225-07
Yamada, T. et al. (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. Isme Journal 1(3), 246-255. Doi 10.1038/Ismej.2007.28
Yeager, C. M. et al. (2007) Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N-2-fixing members of biological soil crusts of the Colorado Plateau, USA. Fems Microbiology Ecology 60(1), 85-97. Doi 10.1111/J.1574-6941.2006.00265.X