2014 Pubs - DOE Joint Genome Institute

Ardley, J. et al. (2014) Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598. Stand Genomic Sci 9, 5. 10.1186/1944-3277-9-5
Axen, S. D. et al. (2014) A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 10(10), e1003898. 10.1371/journal.pcbi.1003898
Aylward, F. O. et al. (2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6). 10.1128/mBio.02077-14
Bartholome, J. et al. (2014) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol . 10.1111/nph.13150
Beck, D. A. et al. (2014) The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes. PLoS One 9(7), e102458. 10.1371/journal.pone.0102458
Becker, E. A. et al. (2014) Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet 10(11), e1004784. 10.1371/journal.pgen.1004784
Beissinger, T. M. et al. (2014) A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics 196(3), 829-40. 10.1534/genetics.113.160655
Biddle, A. S. et al. (2014) The complete genome sequence of Clostridium indolis DSM 755(T.). Stand Genomic Sci 9(3), 1089-104. 10.4056/sigs.5281010
Billis, K. et al. (2014) Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation. PLoS One 9(10), e109738. 10.1371/journal.pone.0109738
Blaby, I. K. et al. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci . 10.1016/j.tplants.2014.05.008
Blanc-Mathieu, R. et al. (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 15, 1103. 10.1186/1471-2164-15-1103
Breider, S. et al. (2014) Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 9(3), 687-703. 10.4056/sigs.3828824
Byrne, R. T. et al. (2014) Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife 3, e01322. 10.7554/eLife.01322
Campbell, A. G. et al. (2014) Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environ Microbiol . 10.1111/1462-2920.12461
Chaib De Mares, M. et al. (2014) Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita. New Phytol . 10.1111/nph.13140
Chang, P. J. et al. (2014) Force measurements of a magnetic micro actuator proposed for a microvalve array. Journal of Micromechanics and Microengineering 24(3). 10.1088/0960-1317/24/3/034005
Childs, K. L. et al. (2014) Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass. Plant Genome 7(2). Doi 10.3835/Plantgenome2013.12.0041
Cho, Y. et al. (2014) Transcriptional responses of the Bdtf1-deletion mutant to the phytoalexin brassinin in the necrotrophic fungus Alternaria brassicicola. Molecules 19(8), 10717-32. 10.3390/molecules190810717
Cimermancic, P. et al. (2014) Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters. Cell 158(2), 412-421. Doi 10.1016/J.Cell.2014.06.034
Clingenpeel, S. et al. (2014) Effects of sample treatments on genome recovery via single-cell genomics. ISME J . 10.1038/ismej.2014.92
Clingenpeel, S. et al. (2014) Reconstructing each cell’s genome within complex microbial communities-dream or reality?. Front Microbiol 5, 771. 10.3389/fmicb.2014.00771
Coleman-Derr, D. et al. (2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5(283), 283. 10.3389/fmicb.2014.00283
Collavino, M. M. et al. (2014) nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2 -fixing community dynamics. Environ Microbiol 16(10), 3211-23. 10.1111/1462-2920.12423
Deng, K. et al. (2014) Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol 9(7), 1470-9. 10.1021/cb5000289
Dmytrenko, O. et al. (2014) The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15(1), 924. 10.1186/1471-2164-15-924
Duanmu, D. et al. (2014) Marine algae and land plants share conserved phytochrome signaling systems. Proc Natl Acad Sci U S A . 10.1073/pnas.1416751111
Dubchak, I. et al. (2014) An integrative computational approach for prioritization of genomic variants. PLoS One 9(12), e114903. 10.1371/journal.pone.0114903
Durham, B. P. et al. (2014) Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genomic Sci 9(3), 632-45. 10.4056/sigs.4998989
Earl, D. et al. (2014) Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res 24(12), 2077-89. 10.1101/gr.174920.114
Erbilgin, O. et al. (2014) Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides. Applied and Environmental Microbiology 80(7), 2193-2205. Doi 10.1128/Aem.03887-13
Evans, L. M. et al. (2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46(10), 1089-96. 10.1038/ng.3075
Field, D. et al. (2014) Genomic standards consortium projects. Stand Genomic Sci 9(3), 599-601. 10.4056/sigs.5559680
Field, E. K. et al. (2014) Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J . 10.1038/ismej.2014.183
Gallo, A. et al. (2014) Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius. Int J Food Microbiol 179, 10-7. 10.1016/j.ijfoodmicro.2014.03.013
Gan, F. et al. (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science 345(6202), 1312-7. 10.1126/science.1256963
Gao, D. et al. (2014) Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris). Front Plant Sci 5, 339. 10.3389/fpls.2014.00339
Garau, G. et al. (2014) Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of Medicago murex and M. polymorpha. Stand Genomic Sci 9, 4. 10.1186/1944-3277-9-4
Gaudana, S. B. et al. (2014) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase C uptake by cyanobacteria. Photosynth Res . 10.1007/s11120-014-0059-8
Ghylin, T. W. et al. (2014) Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J . 10.1038/ismej.2014.135
Goker, M. et al. (2014) Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 9(3), 1076-88. 10.4056/sigs.5138968
Goker, M. et al. (2014) Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci 9(3), 1105-17. 10.4056/sigs.3016383
Golberg, A. et al. (2014) Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water. PLoS One 9(1), e86341. 10.1371/journal.pone.0086341
Golberg, A. et al. (2014) Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications for developing economies. Biofuels Bioproducts & Biorefining-Biofpr 8(1), 67-82. Doi 10.1002/Bbb.1438
Gordon, S. P. et al. (2014) Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines. Plant J . 10.1111/tpj.12569
Gostincar, C. et al. (2014) Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. BMC Genomics 15, 549. 10.1186/1471-2164-15-549
Grigoriev, I. V. et al. (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42(Database issue), D699-704. 10.1093/nar/gkt1183
Haider, B. et al. (2014) Omega: an Overlap-graph de novo Assembler for Metagenomics. Bioinformatics . 10.1093/bioinformatics/btu395
Hawley, E. R. et al. (2014) Metagenomic sequencing of two salton sea microbiomes. Genome Announc 2(1). 10.1128/genomeA.01208-13
Hawley, E. R. et al. (2014) Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics . 10.1016/j.margen.2014.06.003
Hawley, E. R. et al. (2014) Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 9(3), 1259-74. 10.4056/sigs.5029016
Hedlund, B. P. et al. (2014) Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles 18(5), 865-75. 10.1007/s00792-014-0664-7
Heins, R. A. et al. (2014) Phylogenomically Guided Identification of Industrially Relevant GH1 beta-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. Acs Chemical Biology 9(9), 2082-2091. 10.1021/Cb500244v
Heller, P. et al. (2014) ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. Bioinformatics . 10.1093/bioinformatics/btu417
Hess, J. et al. (2014) Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi. Genome Biol Evol 6(7), 1564-78. 10.1093/gbe/evu121
Hillson, NathanJ et al. (2014) j5 DNA Assembly Design Automation. DNA Cloning and Assembly Methods 1116, 245-269. 10.1007/978-1-62703-764-8_17
Hirsch, C. N. et al. (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26(1), 121-35. 10.1105/tpc.113.119982
Hori, C. et al. (2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood. PLoS Genet 10(12), e1004759. 10.1371/journal.pgen.1004759
Howe, A. C. et al. (2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13), 4904-9. 10.1073/pnas.1402564111
Hurley, J. M. et al. (2014) Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A 111(48), 16995-7002. 10.1073/pnas.1418963111
International Wheat Genome Sequencing, Consortium et al. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194), 1251788. 10.1126/science.1251788
Ivanova, N. N. et al. (2014) Stop codon reassignments in the wild. Science 344(6186), 909-13. 10.1126/science.1250691
Jansson, J. K. et al. (2014) The microbial ecology of permafrost. Nat Rev Microbiol 12(6), 414-25. 10.1038/nrmicro3262
Jay, Z. J. et al. (2014) Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 80(1), 294-305. 10.1128/AEM.02860-13
Kamke, J. et al. (2014) The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 9(1), e87353. 10.1371/journal.pone.0087353
Kashtan, N. et al. (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344(6182), 416-20. 10.1126/science.1248575
Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Stand Genomic Sci 9, 7. 10.1186/1944-3277-9-7
Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. Stand Genomic Sci 9, 6. 10.1186/1944-3277-9-6
Kis-Papo, T. et al. (2014) Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum. Nat Commun 5, 3745. 10.1038/ncomms4745
Kouvelis, V. N. et al. (2014) Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer. Genome Announc 2(1). 10.1128/genomeA.00845-13
Kruse, T. et al. (2014) Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. J Bacteriol . 10.1128/JB.02370-14
Kuever, J. et al. (2014) Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 9(3), 821-39. 10.4056/sigs.5209235
Kuo, A. et al. (2014) Expanding genomics of mycorrhizal symbiosis. Front Microbiol 5, 582. 10.3389/fmicb.2014.00582
Kyrpides, N. C. et al. (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 12(8), e1001920. 10.1371/journal.pbio.1001920
Kyrpides, N. C. et al. (2014) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci 9(3), 1278-84. 10.4056/sigs.5068949
Lamendella, R. et al. (2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 5, 130. 10.3389/fmicb.2014.00130
Lassila, J. K. et al. (2014) Assembly of robust bacterial microcompartment shells using building blocks from an organelle of unknown function. J Mol Biol 426(11), 2217-28. 10.1016/j.jmb.2014.02.025
Leverenz, R. L. et al. (2014) Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection. Plant Cell 26(1), 426-37. 10.1105/tpc.113.118588
Lewis, S. M., Gross, S., Visel, A., Kelly, M. and Morrow, W. et al. (2014) Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock. GCB Bioenergy . 10.1111/gcbb.12116
Lim, Y. W. et al. (2014) Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J Vis Exp (94). 10.3791/52117
Linshiz, G. et al. (2014) PR-PR: cross-platform laboratory automation system. ACS Synth Biol 3(8), 515-24. 10.1021/sb4001728
Lowry, D. B. et al. (2014) The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. New Phytol . 10.1111/nph.13027
Marcussen, T. et al. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345(6194), 1250092. 10.1126/science.1250092
Markowitz, V. M. et al. (2014) IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res 42(Database issue), D568-73. 10.1093/nar/gkt919
Markowitz, V. M. et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42(Database issue), D560-7. 10.1093/nar/gkt963
Martin, J. A. et al. (2014) A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 4, 4519. 10.1038/srep04519
Mason, O. U. et al. (2014) Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Front Microbiol 5, 332. 10.3389/fmicb.2014.00332
Matzke, N. J. et al. (2014) Bayesian analysis of congruence of core genes in prochlorococcus and synechococcus and implications on horizontal gene transfer. PLoS One 9(1), e85103. 10.1371/journal.pone.0085103
Meier-Kolthoff, J.P. et al. (2014) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9, 2. 10.1186/1944-3277-9-2
Moulin, L. et al. (2014) Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Stand Genomic Sci 9(3), 763-74. 10.4056/sigs.4861021
Mukherjee, S. et al. (2014) Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One 9(1), e86731. 10.1371/journal.pone.0086731
Myburg, A. A. et al. (2014) The genome of Eucalyptus grandis. Nature 509(7505), 356-62. 10.1038/nature13308
Nagy, L. G. et al. (2014) Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Commun 5, 4471. 10.1038/ncomms5471
Nandasena, K. et al. (2014) Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)). Stand Genomic Sci 9(3), 462-72. 10.4056/sigs.4458283
Nobu, M. K. et al. (2014) The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol . 10.1111/1462-2920.12444
Nobu, M. K. et al. (2014) Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph. Genome Announc 2(1). 10.1128/genomeA.01064-13
Nordberg, H. et al. (2014) The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res 42(Database issue), D26-31. 10.1093/nar/gkt1069
Ntougias, S. et al. (2014) High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway. Stand Genomic Sci 9(3), 783-93. 10.4056/sigs.5088950
O’Connor, R. M. et al. (2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A 111(47), E5096-104. 10.1073/pnas.1413110111
Ohm, R. A. et al. (2014) Genomics of wood-degrading fungi. Fungal Genet Biol . 10.1016/j.fgb.2014.05.001
Pedersen, K. et al. (2014) Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announc 2(3). 10.1128/genomeA.00509-14
Pedras, M. S. et al. (2014) The phytoalexin camalexin induces fundamental changes in the proteome of Alternaria brassicicola different from those caused by brassinin. Fungal Biol 118(1), 83-93. 10.1016/j.funbio.2013.11.005
Pendleton, A. L. et al. (2014) Duplications and losses in gene families of rust pathogens highlight putative effectors. Front Plant Sci 5, 299. 10.3389/fpls.2014.00299
Pfeifer, M. et al. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345(6194), 1250091. 10.1126/science.1250091
Piao, H. et al. (2014) Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng 111(8), 1550-65. 10.1002/bit.25250
Plett, J. M. et al. (2014) The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses. Mol Plant Microbe Interact . 10.1094/MPMI-05-14-0129-FI
Podell, S. et al. (2014) Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J 8(5), 979-90. 10.1038/ismej.2013.221
Poliakov, A. et al. (2014) GenomeVISTA-an integrated software package for whole-genome alignment and visualization. Bioinformatics . 10.1093/bioinformatics/btu355
Prestat, E. et al. (2014) FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res . 10.1093/nar/gku702
Ramirez, M. S. et al. (2014) Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates. Genome Announc 2(3). 10.1128/genomeA.00558-14
Reddy, T. B. et al. (2014) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res . 10.1093/nar/gku950
Reeve, W. et al. (2014) Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). Stand Genomic Sci 9(3), 540-50. 10.4056/sigs.4548266
Reeve, W. et al. (2014) Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128. Stand Genomic Sci 9(3), 602-13. 10.4056/sigs.4929626
Reeve, W. et al. (2014) Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. Stand Genomic Sci 9(3), 514-26. 10.4056/sigs.4938652
Reeve, W. et al. (2014) Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas. Stand Genomic Sci 9(3), 1159-67. 10.4056/sigs.5249382
Reeve, W. et al. (2014) Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. Stand Genomic Sci 9(3), 473-83. 10.4056/sigs.4828625
Reeve, W. et al. (2014 ) Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. Stand Genomic Sci 9, 3. 10.1186/1944-3277-9-3
Riedel, T. et al. (2014) Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments. Stand Genomic Sci 9(3), 855-65. 10.4056/sigs.5601028
Riedel, T. et al. (2014) Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9(3), 1333-45. 10.4056/sigs.4909790
Riley, R. et al. (2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A 111(27), 9923-8. 10.1073/pnas.1400592111
Rinke, C. et al. (2014) Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9(5), 1038-48. 10.1038/nprot.2014.067
Roux, S. et al. (2014) Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. Elife 3, e03125. 10.7554/eLife.03125
Sato, T. K. et al. (2014) Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. Appl Environ Microbiol 80(2), 540-54. 10.1128/AEM.01885-13
Satoh, N. et al. (2014) Chordate evolution and the three-phylum system. Proc Biol Sci 281(1794), 20141729. 10.1098/rspb.2014.1729
Scheuner, C. et al. (2014) Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 9, 10. 10.1186/1944-3277-9-10
Schmutz, J. et al. (2014) A reference genome for common bean and genome-wide analysis of dual domestications.. Nature 46(7), 707-713. 10.1038/ng.3008
Scholz, M. et al. (2014) Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Sci Rep 4, 6480. 10.1038/srep06480
Shi, W. et al. (2014) Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res . 10.1101/gr.168245.113
Shilova, I. N. et al. (2014) A microarray for assessing transcription from pelagic marine microbial taxa. ISME J . 10.1038/ismej.2014.1
Simmons, C. W. et al. (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7(1), 495. 10.1186/s13068-014-0180-0
Singan, V. R. et al. (2014) Precision Drug Targeting: Understanding the Intracellular Transport Mechanism. Journal of Investigative Genomics 2(1). 10.15406/jig.2015.02.00011
Singh, G. et al. (2014) Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia. J Clin Microbiol 52(7), 2430-8. 10.1128/JCM.01626-13
Sulakhe, D. et al. (2014) High-throughput translational medicine: challenges and solutions. Adv Exp Med Biol 799, 39-67. 10.1007/978-1-4614-8778-4_3
Swan, B. K. et al. (2014) Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One 9(4), e95380. 10.1371/journal.pone.0095380
Tas, N. et al. (2014) Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J . 10.1038/ismej.2014.36
Terpolilli, J. et al. (2014) Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. Stand Genomic Sci 9(3), 527-39. 10.4056/sigs.4988693
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