2012 Pubs - DOE Joint Genome Institute

Abraham, P. et al. (2012) Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics. Journal of Proteome Research 11(1), 449-460. Doi 10.1021/Pr200851y
Abt, B. et al. (2012) Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 6(2), 194-209. 10.4056/sigs.2796069
Aklujkar, M. et al. (2012) The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. BMC Genomics 13, 690. 10.1186/1471-2164-13-690
Anderson, I. et al. (2012) Genomics of aerobic cellulose utilization systems in actinobacteria. PLoS One 7(6), e39331. 10.1371/journal.pone.0039331
Anderson, I. et al. (2012) Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci 6(3), 1-13. 10.4056/sigs.2736042
Anderson, I. et al. (2012) Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Stand Genomic Sci 6(2), 174-84. 10.4056/sigs.2746047
Anderson, I. et al. (2012) Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Stand Genomic Sci 6(2), 155-64. 10.4056/sigs.2665915
Anderson, I. et al. (2012) Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)). Stand Genomic Sci 6(1), 31-42. 10.4056/sigs.2505605
Anderson, I. et al. (2012) Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Stand Genomic Sci 7(2), 210-20. 10.4056/sigs.3117229
Aylward, F. O. et al. (2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J 6(9), 1688-701. 10.1038/ismej.2012.10
Baelum, J. et al. (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9), 2405-16. 10.1111/j.1462-2920.2012.02780.x
Baker, S. E. et al. (2012) Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma. Microbiology 158(Pt 1), 147-54. 10.1099/mic.0.053462-0
Bayer, T. et al. (2012) Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals. Plos One 7(4). ARTN e35269 DOI 10.1371/journal.pone.0035269
Beckham, G. T. et al. (2012) Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol 23(3), 338-45. 10.1016/j.copbio.2011.11.030
Beckloff, N. et al. (2012) Bacterial genome annotation. Methods Mol Biol 881, 471-503. 10.1007/978-1-61779-827-6_16
Bennetzen, J. L. et al. (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6), 555-61. 10.1038/nbt.2196
Berg Miller, M. E. et al. (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14(1), 207-27. 10.1111/j.1462-2920.2011.02593.x
Blanc, G. et al. (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol 13(5), R39. 10.1186/gb-2012-13-5-r39
Brisson, V. L. et al. (2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6(9), 1702-14. 10.1038/ismej.2012.15
Burow, L. C. et al. (2012) Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J 6(4), 863-74. 10.1038/ismej.2011.142
Challacombe, J. et al. (2012) Mobile genetic elements in the bacterial phylum Acidobacteria. Mob Genet Elements 2(4), 179-183. 10.4161/mge.21943
Chan, C. X. et al. (2012) Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism. Journal of Phycology 48(6), 1328-1342. DOI 10.1111/j.1529-8817.2012.01229.x
Chan, C. X. et al. (2012) Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems. Plant Physiology 158(4), 2001-2012. DOI 10.1104/pp.112.193896
Cho, Y. et al. (2012) Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola. PLoS Pathog 8(10), e1002974. 10.1371/journal.ppat.1002974
Chow, V. et al. (2012) Complete genome sequence of Paenibacillus sp. strain JDR-2. Stand Genomic Sci 6(1), 1-10. 10.4056/sigs.2374349
Copeland, A. et al. (2012) Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences 6(1), 21-30. Doi 10.4056/Sigs.2435521
Copeland, A. et al. (2012) Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Stand Genomic Sci 6(2), 240-50. 10.4056/sigs.2756060
Copeland, A. et al. (2012) Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 6(2), 145-54. 10.4056/sigs.2475579
Cui, Y. et al. (2012) Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 7(6), e38333. 10.1371/journal.pone.0038333
Curtis, B. A. et al. (2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492(7427), 59-65. 10.1038/nature11681
Davis, J. R. et al. (2012) Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. J Bacteriol 194(9), 2396-7. 10.1128/JB.00186-12
de Wit, P. J. G. M. et al. (2012) The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLoS Genet 8(11). Artn E1003088Doi 10.1371/Journal.Pgen.1003088
DeAngelis, K. M. et al. (2012) Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. MBio 3(1). 10.1128/mBio.00249-11
Deng, L. et al. (2012) Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. MBio 3(6). 10.1128/mBio.00373-12
Desiniotis, A. et al. (2012) Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacteriol 194(21), 5966-7. 10.1128/JB.01398-12
Dichosa, A. E. et al. (2012) Artificial polyploidy improves bacterial single cell genome recovery. PLoS One 7(5), e37387. 10.1371/journal.pone.0037387
Dilly, G. F. et al. (2012) Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes. Proc Biol Sci 279(1741), 3347-56. 10.1098/rspb.2012.0098
Dunbar, J. et al. (2012) Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ Microbiol 14(5), 1145-58. 10.1111/j.1462-2920.2011.02695.x
Eichorst, S. A. et al. (2012) Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing. Applied and Environmental Microbiology 78(7), 2316-2327. Doi 10.1128/Aem.07313-11
Fernandez-Fueyo, E. et al. (2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proceedings of the National Academy of Sciences of the United States of America 109(14), 5458-5463. DOI 10.1073/pnas.1119912109
Floudas, D. et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089), 1715-9. 10.1126/science.1221748
Fodor, A. A. et al. (2012) The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing. Plos One 7(7). ARTN e41294 DOI 10.1371/journal.pone.0041294
Garcia-Amado, M. A. et al. (2012) Bacterial diversity in the cecum of the world’s largest living rodent (Hydrochoerus hydrochaeris). Microb Ecol 63(4), 719-25. 10.1007/s00248-011-9963-z
Giovannelli, D. et al. (2012) Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent. Stand Genomic Sci 7(1), 82-90. 10.4056/sigs.2856770
Gladden, J. M. et al. (2012) Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng 109(5), 1140-5. 10.1002/bit.24388
Godoy-Vitorino, F. et al. (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6(3), 531-41. 10.1038/ismej.2011.131
Godoy-Vitorino, F. et al. (2012) Differences in crop bacterial community structure between hoatzins from different geographical locations. Research in Microbiology 163(3), 211-220. DOI 10.1016/j.resmic.2012.01.001
Goker, M. et al. (2012) Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Stand Genomic Sci 6(2), 230-9. 10.4056/sigs.2726028
Goodstein, D. M. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40(D1), D1178-D1186. Doi 10.1093/Nar/Gkr944
Graham, D. E. et al. (2012) Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J 6(4), 709-12. 10.1038/ismej.2011.163
Grigoriev, I. V. et al. (2012) The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 40(Database issue), D26-32. 10.1093/nar/gkr947
Han, C. et al. (2012) Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Stand Genomic Sci 6(1), 94-103. 10.4056/sigs.2456004
Harhangi, H. R. et al. (2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol 78(3), 752-8. 10.1128/AEM.07113-11
Hollister, E. B. et al. (2012) Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One 7(6), e39689. 10.1371/journal.pone.0039689
Human Microbiome Project, Consortium et al. (2012) A framework for human microbiome research. Nature 486(7402), 215-21. 10.1038/nature11209
Human Microbiome Project, Consortium et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207-14. 10.1038/nature11234
Huntemann, M. et al. (2012) Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Stand Genomic Sci 6(2), 185-93. 10.4056/sigs.2786069
Isanapong, J. et al. (2012) High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J Bacteriol 194(10), 2744-5. 10.1128/JB.00264-12
Izquierdo, J. A. et al. (2012) Complete Genome Sequence of Clostridium clariflavum DSM 19732. Stand Genomic Sci 6(1), 104-15. 10.4056/sigs.2535732
Jiang, K. et al. (2012) Complete genome sequence of Thauera aminoaromatica strain MZ1T. Stand Genomic Sci 6(3), 325-35. 10.4056/sigs.2696029
Jones, F. C. et al. (2012) A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr Biol 22(1), 83-90. 10.1016/j.cub.2011.11.045
Joshi, H. J. et al. (2012) 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. Bioinformatics 28(10), 1303-6. 10.1093/bioinformatics/bts133
Jung, S. et al. (2012) Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. Bmc Genomics 13. Artn 129 Doi 10.1186/1471-2164-13-129
Kamke, J. et al. (2012) Exploring symbioses by single-cell genomics. Biol Bull 223(1), 30-43.
Kappler, U. et al. (2012) Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)). Stand Genomic Sci 7(1), 44-58. 10.4056/sigs.3006378
Khudyakov, J. I. et al. (2012) Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci U S A 109(32), E2173-82. 10.1073/pnas.1112750109
Kimelman, A. et al. (2012) A vast collection of microbial genes that are toxic to bacteria. Genome Research 22(4), 802-809. DOI 10.1101/gr.133850.111
Kinney, J. N. et al. (2012) Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly. J Biol Chem 287(21), 17729-36. 10.1074/jbc.M112.355305
Klenk, H. P. et al. (2012) Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Stand Genomic Sci 6(2), 220-9. 10.4056/sigs.2635833
Klenk, H. P. et al. (2012) Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Stand Genomic Sci 6(2), 265-75. 10.4056/sigs.2655905
Knight, R. et al. (2012) Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology 30(6), 513-520. Doi 10.1038/Nbt.2235
Kontur, W. S. et al. (2012) Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. J Bacteriol 194(24), 7016-7. 10.1128/JB.01214-12
Koren, S. et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30(7), 693-700. 10.1038/nbt.2280
Kostka, J. E. et al. (2012) Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol 194(16), 4461-2. 10.1128/JB.00871-12
Lamour, K. H. et al. (2012) Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact 25(10), 1350-60. 10.1094/MPMI-02-12-0028-R
Leung, K. et al. (2012) A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc Natl Acad Sci U S A 109(20), 7665-70. 10.1073/pnas.1106752109
Liolios, K. et al. (2012) The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Stand Genomic Sci 6(3), 438-47. 10.4056/sigs.2675953
Lorenz, W. W. et al. (2012) Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genetics & Genomes 8(6), 1477-1485. Doi 10.1007/S11295-012-0547-Y
Lucas-Elio, P. et al. (2012) Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)). Stand Genomic Sci 7(1), 31-43. 10.4056/sigs.2976373
Lucas-Elio, P. et al. (2012) Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)). Stand Genomic Sci 6(1), 63-73. 10.4056/sigs.2545743
Lucas, S. et al. (2012) Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3. J Bacteriol 194(21), 5974-5. 10.1128/JB.01430-12
Lundberg, D. S. et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488(7409), 86-90. 10.1038/nature11237
Luo, C. et al. (2012) Individual genome assembly from complex community short-read metagenomic datasets. ISME J 6(4), 898-901. 10.1038/ismej.2011.147
Luo, C. et al. (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7(2), e30087. 10.1371/journal.pone.0030087
Luo, C. et al. (2012) Individual genome assembly from complex community short-read metagenomic datasets. ISME J 6(4), 898-901. 10.1038/ismej.2011.147
Markowitz, V. M. et al. (2012) IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 40(Database issue), D123-9. 10.1093/nar/gkr975
Markowitz, V. M. et al. (2012) IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One 7(7), e40151. 10.1371/journal.pone.0040151
Markowitz, V. M. et al. (2012) IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 40(Database issue), D115-22. 10.1093/nar/gkr1044
Martinez-Garcia, M. et al. (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 7(4), e35314. 10.1371/journal.pone.0035314
Martinez, R. J. et al. (2012) Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil. J Bacteriol 194(8), 2113-4. 10.1128/JB.00095-12
Martinez, R. J. et al. (2012) Complete genome sequence of Rahnella aquatilis CIP 78.65. J Bacteriol 194(11), 3020-1. 10.1128/JB.00380-12
Marx, C. J. et al. (2012) Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol 194(17), 4746-8. 10.1128/JB.01009-12
Mason, O. U. et al. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6(9), 1715-27. 10.1038/ismej.2012.59
Mavromatis, K. et al. (2012) Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Stand Genomic Sci 6(2), 210-9. 10.4056/sigs.2816096
Mavromatis, K. et al. (2012) The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One 7(12), e48837. 10.1371/journal.pone.0048837
Mead, D. A. et al. (2012) Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci 6(3), 381-400. 10.4056/sigs.2605792
Meincke, L. et al. (2012) Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)). Stand Genomic Sci 6(1), 74-83. 10.4056/sigs.2395367
Monier, A. et al. (2012) Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14(1), 162-176. DOI 10.1111/j.1462-2920.2011.02576.x
Morin, E. et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A 109(43), 17501-6. 10.1073/pnas.1206847109
Neupane, S. et al. (2012) Complete genome sequence of Serratia plymuthica strain AS12. Stand Genomic Sci 6(2), 165-73. 10.4056/sigs.2705996
Neupane, S. et al. (2012) Complete genome sequence of the plant-associated Serratia plymuthica strain AS13. Stand Genomic Sci 7(1), 22-30. 10.4056/sigs.2966299
Neupane, S. et al. (2012) Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9. Stand Genomic Sci 6(1), 54-62. 10.4056/sigs.2595762
Novichkov, P. S. et al. (2012) RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res 40(Web Server issue), W604-8. 10.1093/nar/gks562
Ohm, R. A. et al. (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog 8(12), e1003037. 10.1371/journal.ppat.1003037
Olson, A. et al. (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytologist 194(4), 1001-1013. DOI 10.1111/j.1469-8137.2012.04128.x
Orsi, W. et al. (2012) Effect of oxygen minimum zone formation on communities of marine protists. ISME J 6(8), 1586-601. 10.1038/ismej.2012.7
Padamsee, M. et al. (2012) The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol 49(3), 217-26. 10.1016/j.fgb.2012.01.007
Pagani, I. et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 40(D1), D571-D579. Doi 10.1093/Nar/Gkr1100
Pagani, I. et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 40(D1), D571-D579. Doi 10.1093/Nar/Gkr1100
Park, J. I. et al. (2012) A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One 7(5), e37010. 10.1371/journal.pone.0037010
Paterson, A. H. et al. (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429), 423-7. 10.1038/nature11798
Pell, J. et al. (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A 109(33), 13272-7. 10.1073/pnas.1121464109
Peng, Z. et al. (2012) Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach. Plos One 7(1). ARTN e29437 DOI 10.1371/journal.pone.0029437
Penz, T. et al. (2012) Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genet 8(10), e1003012. 10.1371/journal.pgen.1003012
Pester, M. et al. (2012) Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. J Bacteriol 194(22), 6300-1. 10.1128/JB.01392-12
Piskur, J. et al. (2012) The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. International Journal of Food Microbiology 157(2), 202-209. DOI 10.1016/j.ijfoodmicro.2012.05.008
Plett, J. M. et al. (2012) Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor. Fungal Genetics and Biology 49(3), 199-209. DOI 10.1016/j.fgb.2012.01.002
Prochnik, S. et al. (2012) The Cassava Genome: Current Progress, Future Directions. Trop Plant Biol 5(1), 88-94. 10.1007/s12042-011-9088-z
Queiroux, C. et al. (2012) A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules. Bmc Microbiology 12. Artn 74 Doi 10.1186/1471-2180-12-74
Rawat, S. R. et al. (2012) Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil. Standards in Genomic Sciences 7(1), 59-69. Doi 10.4056/Sigs.3036810
Riedel, T. et al. (2012) Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Stand Genomic Sci 7(1), 107-19. 10.4056/sigs.3216895
Riedel, T. et al. (2012) Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Stand Genomic Sci 7(1), 120-30. 10.4056/sigs.3296896
Rineau, F. et al. (2012) The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. Environmental Microbiology 14(6), 1477-1487. DOI 10.1111/j.1462-2920.2012.02736.x
Roberts, E. W. et al. (2012) Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D. J Bacteriol 194(4), 787-95. 10.1128/JB.06444-11
Roberts, E. W. et al. (2012) Isolation and Characterization of the Prochlorococcus Carboxysome Reveal the Presence of the Novel Shell Protein CsoS1D. Journal of Bacteriology 194(4), 787-795. Doi 10.1128/Jb.06444-11
Scholz, M. B. et al. (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23(1), 9-15. 10.1016/j.copbio.2011.11.013
Schuster, A. et al. (2012) A versatile toolkit for high throughput functional genomics with Trichoderma reesei. Biotechnol Biofuels 5(1), 1. 10.1186/1754-6834-5-1
Sessitsch, A. et al. (2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions 25(1), 28-36. Doi 10.1094/Mpmi-08-11-0204
Sessitsch, A. et al. (2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions 25(1), 28-36. Doi 10.1094/Mpmi-08-11-0204
Sharma, M. K. et al. (2012) A genome-wide survey of switchgrass genome structure and organization. PLoS One 7(4), e33892. 10.1371/journal.pone.0033892
Siddaramappa, S. et al. (2012) A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 13, 165. 10.1186/1471-2164-13-165
Siddaramappa, S. et al. (2012) Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to “Dehalococcoides” strains. Stand Genomic Sci 6(2), 251-64. 10.4056/sigs.2806097
Slavov, G. T. et al. (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196(3), 713-25. 10.1111/j.1469-8137.2012.04258.x
Spring, S. et al. (2012) Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)). Stand Genomic Sci 7(2), 304-19. 10.4056/sigs.3226659
Srivastava, A. et al. (2012) A Zinc-Finger-Family Transcription Factor, AbVf19, Is Required for the Induction of a Gene Subset Important for Virulence in Alternaria brassicicola. Molecular Plant-Microbe Interactions 25(4), 443-452. Doi 10.1094/Mpmi-10-11-0275
Steven, B. et al. (2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ Microbiol Rep 4(2), 248-56. 10.1111/j.1758-2229.2012.00328.x
Susanti, D. et al. (2012) Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. J Bacteriol 194(20), 5703-4. 10.1128/JB.01314-12
Suzuki, H. et al. (2012) Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. Bmc Genomics 13. Artn 444 Doi 10.1186/1471-2164-13-444
Swaminathan, K. et al. (2012) A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. Bmc Genomics 13. Artn 142Doi 10.1186/1471-2164-13-142
Swingley, W. D. et al. (2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem. Plos One 7(6). ARTN e38108 DOI 10.1371/journal.pone.0038108
Tisserant, E. et al. (2012) The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. New Phytol 193(3), 755-69. 10.1111/j.1469-8137.2011.03948.x
van der Lelie, D. et al. (2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 7(5), e36740. 10.1371/journal.pone.0036740
Vandera, E. et al. (2012) Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans. Appl Environ Microbiol 78(3), 621-7. 10.1128/AEM.07137-11
Wang, L. et al. (2012) Mapping N-Linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry. Journal of Proteome Research 11(1), 143-156. Doi 10.1021/Pr200916k
Wilson, A. et al. (2012) The essential role of the N-terminal domain of the orange carotenoid protein in cyanobacterial photoprotection: importance of a positive charge for phycobilisome binding. Plant Cell 24(5), 1972-83. 10.1105/tpc.112.096909
Woebken, D. et al. (2012) Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. Isme Journal 6(7), 1427-1439. DOI 10.1038/ismej.2011.200
Worden, A. Z. et al. (2012) Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol 22(17), R675-7. 10.1016/j.cub.2012.07.054
Zeytun, A. et al. (2012) Complete genome sequence of Francisella philomiragia ATCC 25017. J Bacteriol 194(12), 3266. 10.1128/JB.00413-12
Zhang, X. et al. (2012) Improving genome assemblies by sequencing PCR products with PacBio. Biotechniques 53(1), 61-2. 10.2144/0000113891
Zhaxybayeva, O. et al. (2012) Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date. Genome Biol Evol 4(8), 700-8. 10.1093/gbe/evs059