Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

[1]  Monzoorul Haque Mohammed,et al.  Classification of metagenomic sequences: methods and challenges , 2012, Briefings Bioinform..

[2]  Bud Mishra,et al.  Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons , 2012, PloS one.

[3]  Brian C. Thomas,et al.  Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.

[4]  R. Lasken Genomic sequencing of uncultured microorganisms from single cells , 2012, Nature Reviews Microbiology.

[5]  Edward C. Uberbacher,et al.  Gene and translation initiation site prediction in metagenomic sequences , 2012, Bioinform..

[6]  Aaron Marc Saunders,et al.  Microbial communities involved in enhanced biological phosphorus removal from wastewater--a model system in environmental biotechnology. , 2012, Current opinion in biotechnology.

[7]  Elmar Pruesse,et al.  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..

[8]  D. Missiakas,et al.  Protein secretion and surface display in Gram-positive bacteria , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[9]  N. Kyrpides,et al.  Individual genome assembly from complex community short-read metagenomic datasets , 2011, The ISME Journal.

[10]  Ruben E. Valas,et al.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage , 2011, The ISME Journal.

[11]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[12]  N. Moran,et al.  Extreme genome reduction in symbiotic bacteria , 2011, Nature Reviews Microbiology.

[13]  Daniel G. Brown,et al.  PANDAseq: paired-end assembler for illumina sequences , 2012, BMC Bioinformatics.

[14]  M. Wagner,et al.  Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification , 2011, Applied and Environmental Microbiology.

[15]  S. Schuster,et al.  Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.

[16]  Radhey S. Gupta Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes , 2011, Antonie van Leeuwenhoek.

[17]  Richard A. Flavell,et al.  NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis , 2011, Cell.

[18]  Harald Meier,et al.  46. ARB: A Software Environment for Sequence Data , 2011 .

[19]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..

[20]  I. Sutcliffe Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war. , 2011, Environmental microbiology.

[21]  S. Tringe,et al.  Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen , 2011, Science.

[22]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[23]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[24]  J. Einasto Dark Matter , 2011, Brazilian Journal of Physics.

[25]  Iain C Sutcliffe,et al.  A phylum level perspective on bacterial cell envelope architecture. , 2010, Trends in microbiology.

[26]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[27]  Aaron Marc Saunders,et al.  A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. , 2010, Water research.

[28]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[29]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[30]  Doug Hyatt,et al.  Enigmatic, ultrasmall, uncultivated Archaea , 2010, Proceedings of the National Academy of Sciences.

[31]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[32]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[33]  K. Knittel,et al.  Anaerobic oxidation of methane: progress with an unknown process. , 2009, Annual review of microbiology.

[34]  Sallie W. Chisholm,et al.  Whole Genome Amplification and De novo Assembly of Single Bacterial Cells , 2009, PloS one.

[35]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[36]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[37]  Alison M. Cupples,et al.  Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing , 2009, Applied and Environmental Microbiology.

[38]  S. Hedges,et al.  A major clade of prokaryotes with ancient adaptations to life on land. , 2009, Molecular biology and evolution.

[39]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[40]  P. Lepage,et al.  Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. , 2008, Journal of medical microbiology.

[41]  Alla Lapidus,et al.  A Bioinformatician's Guide to Metagenomics , 2008, Microbiology and Molecular Biology Reviews.

[42]  M. Wagner,et al.  Microbial diversity and the genetic nature of microbial species , 2008, Nature Reviews Microbiology.

[43]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[44]  C. Weidenmaier,et al.  Teichoic acids and related cell-wall glycopolymers in Gram-positive physiology and host interactions , 2008, Nature Reviews Microbiology.

[45]  Anjali Mandlik,et al.  Pili in Gram-positive bacteria: assembly, involvement in colonization and biofilm development. , 2008, Trends in microbiology.

[46]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[47]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[48]  S. Quake,et al.  Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth , 2007, Proceedings of the National Academy of Sciences.

[49]  Karsten Zengler,et al.  Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities , 2007, Applied and Environmental Microbiology.

[50]  Marcy Yann,et al.  ヒト口腔からの微量の培養されないTM7微生物の単一細胞遺伝分析による生物学的「不明な物体」の詳細な分析 , 2007 .

[51]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[52]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[53]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[54]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[55]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[56]  D. Relman,et al.  Prevalence of Bacteria of Division TM7 in Human Subgingival Plaque and Their Association with Disease , 2003, Applied and Environmental Microbiology.

[57]  P. Hugenholtz,et al.  In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. , 2002, Environmental microbiology.

[58]  P. Hugenholtz Exploring prokaryotic diversity in the genomic era , 2002, Genome Biology.

[59]  P. Hugenholtz,et al.  Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives , 2001, Applied and Environmental Microbiology.

[60]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[61]  E. Hoiczyk,et al.  Cyanobacterial Cell Walls: News from an Unusual Prokaryotic Envelope , 2000, Journal of bacteriology.