2016 Pubs - DOE Joint Genome Institute

Aizenberg-Gershtein, Y. et al. (2016) High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. Stand Genomic Sci 11, 4. 10.1186/s40793-015-0127-5
Alfaro, M. et al. (2016) Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus. Environ Microbiol . 10.1111/1462-2920.13360
Anderson, I. J. et al. (2016) Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 11(1), 70. 10.1186/s40793-016-0194-2
Arango Isaza, R. E. et al. (2016) Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control. PLoS Genet 12(8), e1005876. 10.1371/journal.pgen.1005876
Bashir, M. et al. (2016) Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Frontiers in Microbiology 7. 10.3389/fmicb.2016.01321
Beall, B. F. et al. (2016) Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate. Environ Microbiol 18(6), 1704-19. 10.1111/1462-2920.12819
Beam, J. P. et al. (2016) Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Frontiers in Microbiology 7, 25. 10.3389/fmicb.2016.00025
Bendall, M. L. et al. (2016) Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J . 10.1038/ismej.2015.241
Bewick, A. J. et al. (2016) On the origin and evolutionary consequences of gene body DNA methylation. Proc Natl Acad Sci U S A 113(32), 9111-6. 10.1073/pnas.1604666113
Blow, M. J. et al. (2016) The Epigenomic Landscape of Prokaryotes. PLoS Genet 12(2), e1005854. 10.1371/journal.pgen.1005854
Boden, R. et al. (2016) Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. Stand Genomic Sci 11, 74. 10.1186/s40793-016-0188-0
Bredeson, J. V. et al. (2016) Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat Biotechnol 34(5), 562-70. 10.1038/nbt.3535
Bremges, A. et al. (2016) MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics . 10.1093/bioinformatics/btw144
Brown, C. T. et al. (2016) Measurement of bacterial replication rates in microbial communities. Nat Biotechnol 34(12), 1256-1263. 10.1038/nbt.3704
Browne, P. et al. (2016) Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. ISME J . 10.1038/ismej.2016.104
Brumm, P. J. et al. (2016) Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost. Stand Genomic Sci 11, 33. 10.1186/s40793-016-0153-y
Buels, R. et al. (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17(1), 66. 10.1186/s13059-016-0924-1
Butterfield, C. N. et al. (2016) Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 4, e2687. 10.7717/peerj.2687
Castanera, R. et al. (2016) Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet 12(6), e1006108. 10.1371/journal.pgen.1006108
Chen, I. M. et al. (2016) Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics 17(1), 307. 10.1186/s12864-016-2629-y
Chin, C. S. et al. (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13(12), 1050-1054. 10.1038/nmeth.4035
Coleman-Derr, D. et al. (2016) Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol . 10.1111/nph.13697
Collier, R. et al. (2016) Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum. Front Plant Sci 7, 716. 10.3389/fpls.2016.00716
Corrochano, L. M. et al. (2016) Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol . 10.1016/j.cub.2016.04.038
Daly, R. A. et al. (2016) Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol 1, 16146. 10.1038/nmicrobiol.2016.146
David, A. S. et al. (2016) Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass. Genome Announc 4(2). 10.1128/genomeA.00270-16
De Meyer, S. E. et al. (2016) Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes. Mol Plant Microbe Interact 29(8), 609-619. 10.1094/MPMI-05-16-0091-R
Denef, V. J. et al. (2016) Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria. Front Microbiol 7, 606. 10.3389/fmicb.2016.00606
Denef, V. J. et al. (2016) Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation. Appl Environ Microbiol 82(5), 1423-32. 10.1128/AEM.03014-15
Dinh Thi, V. H. et al. (2016) Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PLoS One 11(12), e0167171. 10.1371/journal.pone.0167171
Duncan, D. S. et al. (2016) Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods. Soil Biology & Biochemistry 96, 160-168. 10.1016/j.soilbio.2016.02.002
Eiler, A. et al. (2016) Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME J . 10.1038/ismej.2015.260
Eloe-Fadrosh, E. A. et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun 7, 10476. 10.1038/ncomms10476
Eloe-Fadrosh, Emiley A. et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nature Microbiology , 15032. 10.1038/nmicrobiol.2015.32
Eudes, A. et al. (2016) Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microb Cell Fact 15(1), 198. 10.1186/s12934-016-0593-5
Flynn, J. D. et al. (2016) Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems. Genome Announc 4(1). 10.1128/genomeA.01629-15
Fonseca-Garcia, C. et al. (2016) The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity. Frontiers in Microbiology 7, 150. 10.3389/fmicb.2016.00150
Frazier, T. P. et al. (2016) Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. BMC Genomics 17(1), 892. 10.1186/s12864-016-3201-5
Frei, C. S. et al. (2016) Analysis of Amino Acid Substitutions in AraC Variants that Respond to Triacetic Acid Lactone. Protein Sci . 10.1002/pro.2873
Fujimoto, Masanori et al. (2016) Spatiotemporal distribution of bacterioplankton functional groups along a freshwater estuary to pelagic gradient in Lake Michigan. Journal of Great Lakes Research -(-), -. 10.1016/j.jglr.2016.07.029
Gach, P. C. et al. (2016) A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synth Biol . 10.1021/acssynbio.6b00011
Ganji, R. et al. (2016) High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada. Genome Announc 4(5). 10.1128/genomeA.01112-16
Gazis, R. et al. (2016) The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol 120(1), 26-42. 10.1016/j.funbio.2015.10.002
Gehlot, H. S. et al. (2016) High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. Stand Genomic Sci 11, 43. 10.1186/s40793-016-0157-7
Ghodhbane-Gtari, F. et al. (2016) Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca. Genome Announc 4(4). 10.1128/genomeA.00770-16
Ghodhbane-Gtari, F. et al. (2016) Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca. Genome Announc 4(4). 10.1128/genomeA.00799-16
Goodwin, S. B. et al. (2016) The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete. Fungal Biol 120(8), 961-74. 10.1016/j.funbio.2016.05.003
Goordial, J. et al. (2016) Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol . 10.1093/femsec/fiv154
Goordial, J. et al. (2016) Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica. Genome Announc 4(2). 10.1128/genomeA.00069-16
Grabowski, P. P. et al. (2016) Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data. New Phytol . 10.1111/nph.14101
Gregory, A. C. et al. (2016) Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17(1), 930. 10.1186/s12864-016-3286-x
Guibert, L. M. et al. (2016) Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments. Microb Ecol 71(1), 100-12. 10.1007/s00248-015-0698-0
Gunsalus, R. P. et al. (2016) Complete genome sequence of Methanospirillum hungatei type strain JF1. Stand Genomic Sci 11, 2. 10.1186/s40793-015-0124-8
Gupta, V. K. et al. (2016) Biotechnological Innovations through Fungi. Mycosphere 7(10), 1490-1490. 10.5943/mycosphere/si/3b/11
Gutierrez, T. et al. (2016) Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 4(4). 10.1128/genomeA.00765-16
Gutierrez, T. et al. (2016) Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum. Genome Announc 4(5). 10.1128/genomeA.00937-16
Hahnke, R. L. et al. (2016) Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 7, 2003. 10.3389/fmicb.2016.02003
Hatzenpichler, R. et al. (2016) Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A . 10.1073/pnas.1603757113
Hausmann, B. et al. (2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J . 10.1038/ismej.2016.42
Hausmann, B. et al. (2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J 10(10), 2365-75. 10.1038/ismej.2016.42
Hillson, N. J. et al. (2016) Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs. ACS Synth Biol 5(6), 449-51. 10.1021/acssynbio.6b00146
Hirschman, L. et al. (2016) Crowdsourcing and curation: perspectives from biology and natural language processing. Database (Oxford) 2016. 10.1093/database/baw115
Holmfeldt, K. et al. (2016) Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol . 10.1111/1462-2920.13392
Holmfeldt, K. et al. (2016) Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 18(11), 3949-3961. 10.1111/1462-2920.13392
Huntemann, M. et al. (2016) The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci 11, 17. 10.1186/s40793-016-0138-x
Hutchinson, M. I. et al. (2016) Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica. Fungal Genet Biol 86, 9-19. 10.1016/j.fgb.2015.11.007
Hwang, C. et al. (2016) Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds. Genome Announc 4(6). 10.1128/genomeA.01226-16
Ikeda-Ohtsubo, W. et al. (2016) ‘Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environ Microbiol . 10.1111/1462-2920.13234
Javidpour, P. et al. (2016) Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli. PLoS One 11(3), e0151087. 10.1371/journal.pone.0151087
Jay, Z. J. et al. (2016) The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park. Environ Microbiol 18(12), 4755-4769. 10.1111/1462-2920.13366
Kamke, J. et al. (2016) Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4(1), 56. 10.1186/s40168-016-0201-2
Kan, J. et al. (2016) Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake. Frontiers in Microbiology 7, 210. 10.3389/fmicb.2016.00210
Kanukollu, S. et al. (2016) Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. Stand Genomic Sci 11, 25. 10.1186/s40793-016-0143-0
Kappler, U. et al. (2016) Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing gamma-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 11, 38. 10.1186/s40793-016-0162-x
Kelly, W. J. et al. (2016) Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract. Sci Rep 6, 30768. 10.1038/srep30768
Kim, J. W. et al. (2016) Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis. PLoS One 11(3), e0151883. 10.1371/journal.pone.0151883
Kyrpides, N. C. et al. (2016) Microbiome Data Science: Understanding Our Microbial Planet. Trends Microbiol 24(6), 425-7. 10.1016/j.tim.2016.02.011
Lam, K. K. et al. (2016) BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly. BMC Bioinformatics 17(1), 435. 10.1186/s12859-016-1288-y
Lastovetsky, O. A. et al. (2016) Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria. Proc Natl Acad Sci U S A 113(52), 15102-15107. 10.1073/pnas.1615148113
Li, G. et al. (2016) Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation. Mol Plant . 10.1016/j.molp.2016.03.009
Linshiz, G. et al. (2016) End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. J Biol Eng 10, 3. 10.1186/s13036-016-0024-5
Louca, S. et al. (2016) Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proc Natl Acad Sci U S A 113(40), E5925-E5933. 10.1073/pnas.1602897113
Louie, T. S. et al. (2016) High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment. Stand Genomic Sci 11, 66. 10.1186/s40793-016-0191-5
Lovell, J. T. et al. (2016) Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res 26(4), 510-8. 10.1101/gr.198135.115
Lux, M. et al. (2016) acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics 17(1), 543. 10.1186/s12859-016-1397-7
Mamidi, S. et al. (2016) Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean. Plant Genome 9(2). 10.3835/plantgenome2015.09.0092
Mefferd, C. C. et al. (2016) High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China. Genome Announc 4(2). 10.1128/genomeA.00312-16
Melton, E. D. et al. (2016) Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes. Stand Genomic Sci 11(1), 67. 10.1186/s40793-016-0184-4
Miettinen, O. et al. (2016) Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2. Genome Announc 4(5). 10.1128/genomeA.00976-16
Miyauchi, S. et al. (2016) Visual Comparative Omics of Fungi for Plant Biomass Deconstruction. Front Microbiol 7, 1335. 10.3389/fmicb.2016.01335
Moghaddam, S. M. et al. (2016) Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean. Plant Genome 9(3). 10.3835/plantgenome2016.02.0012
Morales, J. et al. (2016) Development of a toolbox to dissect host-endosymbiont interactions and protein trafficking in the trypanosomatid Angomonas deanei. BMC Evol Biol 16(1), 247. 10.1186/s12862-016-0820-z
Mosier, A. C. et al. (2016) Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Frontiers in Microbiology 7, 238. 10.3389/fmicb.2016.00238
Mukai, T. et al. (2016) Facile Recoding of Selenocysteine in Nature. Angew Chem Int Ed Engl 55(17), 5337-41. 10.1002/anie.201511657
Mukai, T. et al. (2016) Transfer RNAs with novel cloverleaf structures. Nucleic Acids Res . 10.1093/nar/gkw898
Nguyen, H. D. et al. (2016) Ochratoxin A production by Penicillium thymicola. Fungal Biol 120(8), 1041-9. 10.1016/j.funbio.2016.04.002
Nicholson, W. L. et al. (2016) An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T). Stand Genomic Sci 11(1), 65. 10.1186/s40793-016-0193-3
Niederhuth, C. E. et al. (2016) Widespread natural variation of DNA methylation within angiosperms. Genome Biol 17(1), 194. 10.1186/s13059-016-1059-0
Nouioui, I. et al. (2016) Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales. Genome Announc 4(3). 10.1128/genomeA.00437-16
Olsen, J. L. et al. (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530(7590), 331-5. 10.1038/nature16548
Paez-Espino, D. et al. (2016) Uncovering Earth’s virome. Nature . 10.1038/nature19094
Panschin, I. et al. (2016) Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. Stand Genomic Sci 11, 37. 10.1186/s40793-016-0163-9
Pena, A. et al. (2016) High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains. Stand Genomic Sci 11(1), 55. 10.1186/s40793-016-0178-2
Peter, M. et al. (2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun 7, 12662. 10.1038/ncomms12662
Petrik, D. L. et al. (2016) BdCESA7, BdCESA8, and BdPMT Utility Promoter Constructs for Targeted Expression to Secondary Cell-Wall-Forming Cells of Grasses. Front Plant Sci 7, 55. 10.3389/fpls.2016.00055
Piche-Choquette, S. et al. (2016) H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups. PeerJ 4, e1782. 10.7717/peerj.1782
Putnam, N. H. et al. (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26(3), 342-50. 10.1101/gr.193474.115
Rabe, F. et al. (2016) A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. Elife 5. 10.7554/eLife.20522
Raissig, M. T. et al. (2016) Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity. Proc Natl Acad Sci U S A . 10.1073/pnas.1606728113
Rice, M. C. et al. (2016) Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Stand Genomic Sci 11, 46. 10.1186/s40793-016-0168-4
Riley, R. et al. (2016) Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A . 10.1073/pnas.1603941113
Rivers, A. R. et al. (2016) Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. Front Microbiol 7, 380. 10.3389/fmicb.2016.00380
Roehner, N. et al. (2016) Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synth Biol 5(6), 498-506. 10.1021/acssynbio.5b00215
Rojas-Rojas, F. U. et al. (2016) Draft Genome Sequence of Heavy Metal-Resistant Cupriavidus alkaliphilus ASC-732T, Isolated from Agave Rhizosphere in the Northeast of Mexico. Genome Announc 4(5). 10.1128/genomeA.01013-16
Salman, V. et al. (2016) Insights into the single cell draft genome of “Candidatus Achromatium palustre”. Stand Genomic Sci 11, 28. 10.1186/s40793-016-0146-x
Schneebeli, K. et al. (2016) Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8. Functional Plant Biology 43(2), 189-198. 10.1071/Fp15244
Schwander, T. et al. (2016) A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354(6314), 900-904. 10.1126/science.aah5237
Session, A. M. et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538(7625), 336-343. 10.1038/nature19840
Shaw, A. J. et al. (2016) The Sphagnum Genome Project: A New Model for Ecological and Evolutionary Genomics. Genomes and Evolution of Charophytes, Bryophytes, Lycophytes and Ferns 78, 167-187. 10.1016/bs.abr.2016.01.003
Shih, P. M. et al. (2016) A robust gene-stacking method utilizing yeast assembly for plant synthetic biology. Nat Commun 7, 13215. 10.1038/ncomms13215
Singer, E. et al. (2016) High-resolution phylogenetic microbial community profiling. ISME J . 10.1038/ismej.2015.249
Singer, E. et al. (2016) Next generation sequencing data of a defined microbial mock community. Sci Data 3, 160081. 10.1038/sdata.2016.81
Small, G. E. et al. (2016) Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes. Biogeochemistry 128(3), 353-368. 10.1007/s10533-016-0212-x
Solomon, K. V. et al. (2016) Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science . 10.1126/science.aad1431
Solomon, K. V. et al. (2016) Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi. Anaerobe 38, 39-46. 10.1016/j.anaerobe.2015.11.008
Song, Q. et al. (2016) Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics 17(1), 33. 10.1186/s12864-015-2344-0
Spatafora, J. W. et al. (2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108(5), 1028-1046. 10.3852/16-042
Spatafora, J. W. et al. (2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108(5), 1028-1046. 10.3852/16-042
Stevenson, S. R. et al. (2016) Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance. Plant Cell . 10.1105/tpc.16.00091
Strassert, J. F. et al. (2016) Genome analysis of ‘Candidatus Ancillula trichonymphae’, first representative of a deep-branching clade of Bifidobacteriales, strengthens evidence for convergent evolution in flagellate endosymbionts. Environ Microbiol Rep . 10.1111/1758-2229.12451
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