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For: Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420-8. [PMID: 22495754 DOI: 10.1093/bioinformatics/bts174] [Citation(s) in RCA: 2083] [Impact Index Per Article: 160.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1901
Bolaños LM, Rosenblueth M, Castillo-Ramírez S, Figuier-Huttin G, Martínez-Romero E. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota. Environ Microbiol 2015;18:1364-78. [PMID: 26058415 DOI: 10.1111/1462-2920.12939] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/31/2015] [Indexed: 01/20/2023]
1902
Mitochondrial Genome Sequence of the Glass Sponge Oopsacas minuta. GENOME ANNOUNCEMENTS 2015;3:3/4/e00823-15. [PMID: 26227597 PMCID: PMC4520895 DOI: 10.1128/genomea.00823-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
1903
Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL, Banfield JF. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015;17:4929-41. [DOI: 10.1111/1462-2920.12936] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 01/25/2023]
1904
Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, Banfield JF. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol 2015;18:159-73. [DOI: 10.1111/1462-2920.12930] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/29/2022]
1905
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife 2015. [PMID: 26200428 PMCID: PMC4533152 DOI: 10.7554/elife.08490] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
1906
Nelson WC, Stegen JC. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Front Microbiol 2015;6:713. [PMID: 26257709 PMCID: PMC4508563 DOI: 10.3389/fmicb.2015.00713] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/29/2015] [Indexed: 11/21/2022]  Open
1907
Kim Y, Aw TG, Teal TK, Rose JB. Metagenomic Investigation of Viral Communities in Ballast Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015;49:8396-407. [PMID: 26107908 DOI: 10.1021/acs.est.5b01633] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
1908
Aguado MT, Glasby CJ, Schroeder PC, Weigert A, Bleidorn C. The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata. Sci Rep 2015;5:12072. [PMID: 26183383 PMCID: PMC4505326 DOI: 10.1038/srep12072] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/12/2015] [Indexed: 12/13/2022]  Open
1909
Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L. Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children. EBioMedicine 2015;2:968-84. [PMID: 26425705 PMCID: PMC4563136 DOI: 10.1016/j.ebiom.2015.07.007] [Citation(s) in RCA: 287] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022]  Open
1910
Metagenomic Assembly and Draft Genome Sequence of an Uncharacterized Prevotella sp. from Nelore Rumen. GENOME ANNOUNCEMENTS 2015;3:3/4/e00723-15. [PMID: 26159527 PMCID: PMC4498113 DOI: 10.1128/genomea.00723-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
1911
Kinjo Y, Saitoh S, Tokuda G. An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. Microbes Environ 2015;30:208-20. [PMID: 26156552 PMCID: PMC4567559 DOI: 10.1264/jsme2.me14153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
1912
Bolduc B, Wirth JF, Mazurie A, Young MJ. Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis. ISME JOURNAL 2015;9:2162-77. [PMID: 26125684 DOI: 10.1038/ismej.2015.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 12/29/2014] [Accepted: 01/12/2015] [Indexed: 01/31/2023]
1913
Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJC, Chiu KP. Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy. PLoS One 2015;10:e0130673. [PMID: 26125617 PMCID: PMC4488429 DOI: 10.1371/journal.pone.0130673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/24/2015] [Indexed: 11/18/2022]  Open
1914
Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015;24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
1915
Alkema W, Boekhorst J, Wels M, van Hijum SAFT. Microbial bioinformatics for food safety and production. Brief Bioinform 2015;17:283-92. [PMID: 26082168 PMCID: PMC4793891 DOI: 10.1093/bib/bbv034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022]  Open
1916
Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 2015;523:208-11. [PMID: 26083755 DOI: 10.1038/nature14486] [Citation(s) in RCA: 727] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/10/2015] [Indexed: 02/04/2023]
1917
Bikel S, Valdez-Lara A, Cornejo-Granados F, Rico K, Canizales-Quinteros S, Soberón X, Del Pozo-Yauner L, Ochoa-Leyva A. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J 2015;13:390-401. [PMID: 26137199 PMCID: PMC4484546 DOI: 10.1016/j.csbj.2015.06.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/07/2023]  Open
1918
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Curr Microbiol 2015;71:296-302. [PMID: 26044993 PMCID: PMC4486115 DOI: 10.1007/s00284-015-0846-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022]
1919
Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME JOURNAL 2015;10:225-39. [PMID: 26046257 DOI: 10.1038/ismej.2015.81] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/05/2015] [Accepted: 04/09/2015] [Indexed: 11/08/2022]
1920
Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments. GENOME ANNOUNCEMENTS 2015;3:3/3/e00585-15. [PMID: 26044431 PMCID: PMC4457068 DOI: 10.1128/genomea.00585-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
1921
Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. Lifestyle evolution in cyanobacterial symbionts of sponges. mBio 2015;6:e00391-15. [PMID: 26037118 PMCID: PMC4453008 DOI: 10.1128/mbio.00391-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/30/2015] [Indexed: 01/04/2023]  Open
1922
Al Rwahnih M, Daubert S, Golino D, Islas C, Rowhani A. Comparison of Next-Generation Sequencing Versus Biological Indexing for the Optimal Detection of Viral Pathogens in Grapevine. PHYTOPATHOLOGY 2015;105:758-63. [PMID: 25689518 DOI: 10.1094/phyto-06-14-0165-r] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
1923
Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PSG, Huang LN, Shu WS. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. THE ISME JOURNAL 2015;9:1280-94. [PMID: 25361395 PMCID: PMC4438317 DOI: 10.1038/ismej.2014.212] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 07/21/2014] [Accepted: 09/21/2014] [Indexed: 12/22/2022]
1924
Aguirre de Cárcer D, López-Bueno A, Pearce DA, Alcamí A. Biodiversity and distribution of polar freshwater DNA viruses. SCIENCE ADVANCES 2015;1:e1400127. [PMID: 26601189 PMCID: PMC4640604 DOI: 10.1126/sciadv.1400127] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 05/05/2015] [Indexed: 05/29/2023]
1925
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ 2015;3:e985. [PMID: 26038737 PMCID: PMC4451026 DOI: 10.7717/peerj.985] [Citation(s) in RCA: 729] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023]  Open
1926
Wang Y, Navin NE. Advances and applications of single-cell sequencing technologies. Mol Cell 2015;58:598-609. [PMID: 26000845 PMCID: PMC4441954 DOI: 10.1016/j.molcel.2015.05.005] [Citation(s) in RCA: 425] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
1927
Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy. GENOME ANNOUNCEMENTS 2015;3:3/3/e00490-15. [PMID: 25999577 PMCID: PMC4440957 DOI: 10.1128/genomea.00490-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
1928
Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. Bioinformatics 2015;31:2972-80. [PMID: 25995232 DOI: 10.1093/bioinformatics/btv311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/13/2015] [Indexed: 11/14/2022]  Open
1929
Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium. GENOME ANNOUNCEMENTS 2015;3:3/3/e00457-15. [PMID: 25977433 PMCID: PMC4432339 DOI: 10.1128/genomea.00457-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
1930
Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015;32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
1931
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights 2015;9:75-88. [PMID: 25983555 PMCID: PMC4426941 DOI: 10.4137/bbi.s12462] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 12/14/2022]  Open
1932
Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res 2015;43:5331-9. [PMID: 25940625 PMCID: PMC4477656 DOI: 10.1093/nar/gkv424] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/17/2015] [Indexed: 11/16/2022]  Open
1933
Metagenome sequencing of a coastal marine microbial community from monterey bay, california. GENOME ANNOUNCEMENTS 2015;3:3/2/e00341-15. [PMID: 25931598 PMCID: PMC4417694 DOI: 10.1128/genomea.00341-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
1934
Flot JF, Marie-Nelly H, Koszul R. Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Lett 2015;589:2966-74. [PMID: 25935414 DOI: 10.1016/j.febslet.2015.04.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 12/12/2022]
1935
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME JOURNAL 2015;9:2697-711. [PMID: 25918833 DOI: 10.1038/ismej.2015.66] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
1936
Urbieta MS, Donati ER, Chan KG, Shahar S, Sin LL, Goh KM. Thermophiles in the genomic era: Biodiversity, science, and applications. Biotechnol Adv 2015;33:633-47. [PMID: 25911946 DOI: 10.1016/j.biotechadv.2015.04.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/18/2014] [Accepted: 04/14/2015] [Indexed: 01/30/2023]
1937
Simpson JT, Pop M. The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum Genet 2015;16:153-72. [PMID: 25939056 DOI: 10.1146/annurev-genom-090314-050032] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
1938
CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. mBio 2015;6:mBio.00262-15. [PMID: 25900652 PMCID: PMC4453577 DOI: 10.1128/mbio.00262-15] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
1939
Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 2015;6:mBio.00231-15. [PMID: 25873374 PMCID: PMC4453556 DOI: 10.1128/mbio.00231-15] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
1940
Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol 2015;18:1686-703. [DOI: 10.1111/1462-2920.12817] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 11/28/2022]
1941
Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 2015;25:534-43. [PMID: 25665577 PMCID: PMC4381525 DOI: 10.1101/gr.183012.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/06/2015] [Indexed: 01/18/2023]
1942
Chandler JA, Liu RM, Bennett SN. RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi. Front Microbiol 2015;6:185. [PMID: 25852655 PMCID: PMC4371751 DOI: 10.3389/fmicb.2015.00185] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/19/2015] [Indexed: 01/09/2023]  Open
1943
Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets. GENOME ANNOUNCEMENTS 2015;3:3/2/e00132-15. [PMID: 25792053 PMCID: PMC4395064 DOI: 10.1128/genomea.00132-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
1944
Roux S, Enault F, Ravet V, Pereira O, Sullivan MB. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Front Microbiol 2015;6:199. [PMID: 25852662 PMCID: PMC4360716 DOI: 10.3389/fmicb.2015.00199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022]  Open
1945
McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015;4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/20/2022]  Open
1946
McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015;4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 03/26/2024]  Open
1947
Chan CS, Chan KG, Tay YL, Chua YH, Goh KM. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front Microbiol 2015;6:177. [PMID: 25798135 PMCID: PMC4350410 DOI: 10.3389/fmicb.2015.00177] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 02/04/2023]  Open
1948
Grandjean F, Tan MH, Gan HY, Gan HM, Austin CM. The complete mitogenome of the endangered white-clawed freshwater crayfish Austropotamobius pallipes (Lereboullet, 1858) (Crustacea: Decapoda: Astacidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015;27:3329-30. [DOI: 10.3109/19401736.2015.1018207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
1949
Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 2015;4. [PMID: 25735037 PMCID: PMC4384745 DOI: 10.7554/elife.05477] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 12/11/2022]  Open
1950
Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism. Appl Environ Microbiol 2015;81:3142-56. [PMID: 25724961 DOI: 10.1128/aem.00039-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/23/2015] [Indexed: 11/20/2022]  Open
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