A catalogue of 136 microbial draft genomes from Red Sea metagenomes
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Philip Hugenholtz | Donovan H. Parks | Luke R. Thompson | U. Stingl | P. Hugenholtz | M. Haroon | Ulrich Stingl | Mohamed F. Haroon
[1] S. Giovannoni,et al. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing , 1991, Applied and environmental microbiology.
[2] Shihu Hu,et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage , 2013, Nature.
[3] Peer Bork,et al. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..
[4] K. Schleifer,et al. ARB: a software environment for sequence data. , 2004, Nucleic acids research.
[5] V. Bajic,et al. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA) , 2014, Front. Microbiol..
[6] P. Qian,et al. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing , 2011, The ISME Journal.
[7] Peter Williams,et al. IMG: the integrated microbial genomes database and comparative analysis system , 2011, Nucleic Acids Res..
[8] G. Gloor,et al. Human milk microbiota profiles in relation to birthing method, gestation and infant gender , 2016, Microbiome.
[9] David Bryant,et al. Genome Networks Root the Tree of Life between Prokaryotic Domains , 2010, Genome biology and evolution.
[10] Robert A. Edwards,et al. Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..
[11] Nihar Ranjan Biswas,et al. Evaluation of pharmacological activities and assessment of intraocular penetration of an ayurvedic polyherbal eye drop (Itone™) in experimental models , 2013, BMC Complementary and Alternative Medicine.
[12] A. Halpern,et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.
[13] Luke R. Thompson,et al. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome , 2016, Genome Announcements.
[14] Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea , 2016, Genome Announcements.
[15] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[16] Donovan H. Parks,et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics , 2015, Science.
[17] Connor T. Skennerton,et al. An Expanded Genomic Representation of the Phylum Cyanobacteria , 2014, Genome biology and evolution.
[18] Lisa R. Moore,et al. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes , 1998, Nature.
[19] 田中 俊典. National Center for Biotechnology Information (NCBI) , 2012 .
[20] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[21] M. Saito,et al. Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean , 2015, Proceedings of the National Academy of Sciences.
[22] V. Bajic,et al. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. , 2014, FEMS microbiology ecology.
[23] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[24] Dongwan D. Kang,et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities , 2015, PeerJ.
[25] Luke R. Thompson,et al. Metagenomic covariation along densely sampled environmental gradients in the Red Sea , 2016, The ISME Journal.
[26] R. Friedman,et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter , 2008, The ISME Journal.
[27] Natalia N. Ivanova,et al. Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.
[28] Sallie W. Chisholm,et al. Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties , 1995 .
[29] J. Gilbert,et al. Recovering complete and draft population genomes from metagenome datasets , 2016, Microbiome.
[30] U. Stingl,et al. Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea , 2012, PloS one.
[31] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[32] Connor T. Skennerton,et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.
[33] E. Delong. Archaea in coastal marine environments. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[34] Brian C. Thomas,et al. Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.
[35] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[36] A. Bull,et al. Marine actinobacteria: new opportunities for natural product search and discovery. , 2007, Trends in microbiology.
[37] Amy S. Bower,et al. The transport of nutrient-rich Indian Ocean water through the Red Sea and into coastal reef systems , 2014 .
[38] Tyas I. Hikmawan,et al. Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea , 2013, BMC Complementary and Alternative Medicine.
[39] Jens Roat Kultima,et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes , 2014, Nature Biotechnology.
[40] Andrew C. Tolonen,et al. The genome of a motile marine Synechococcus , 2003, Nature.
[41] P. Hugenholtz,et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes , 2013, Nature Biotechnology.
[42] Luis Pedro Coelho,et al. Structure and function of the global ocean microbiome , 2015, Science.
[43] S. Giovannoni,et al. Genetic diversity in Sargasso Sea bacterioplankton , 1990, Nature.
[44] W. Koh,et al. Single-cell genome sequencing: current state of the science , 2016, Nature Reviews Genetics.
[45] D. Vaulot,et al. Clade-Specific 16S Ribosomal DNA Oligonucleotides Reveal the Predominance of a Single Marine Synechococcus Clade throughout a Stratified Water Column in the Red Sea , 2003, Applied and Environmental Microbiology.
[46] J. Felsenstein. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.
[47] D. Vaulot,et al. Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance , 1999, Microbiology and Molecular Biology Reviews.
[48] Tanja Woyke,et al. Reconstructing each cell's genome within complex microbial communities—dream or reality? , 2014, Front. Microbiol..