EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

[1]  Susan M. Huse,et al.  24. Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere” , 2011 .

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

[3]  Fei Zou,et al.  BIPES, a cost-effective high-throughput method for assessing microbial diversity , 2011, The ISME Journal.

[4]  P. D’haeseleer,et al.  Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria , 2010, Science.

[5]  Jean M. Macklaim,et al.  Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products , 2010, PLoS ONE.

[6]  Susan M. Huse,et al.  Ironing out the wrinkles in the rare biosphere through improved OTU clustering , 2010, Environmental microbiology.

[7]  Matthew Berriman,et al.  Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology , 2010, Bioinform..

[8]  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.

[9]  Vincent J. Denef,et al.  AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature , 2010, The ISME Journal.

[10]  F. Chen,et al.  Experimental factors affecting PCR-based estimates of microbial species richness and evenness , 2010, The ISME Journal.

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

[12]  J. Eisen,et al.  Metagenomic Sequencing of an In Vitro-Simulated Microbial Community , 2010, PloS one.

[13]  Bernard Henrissat,et al.  Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins , 2010, Proceedings of the National Academy of Sciences.

[14]  R. Knight,et al.  Forensic identification using skin bacterial communities , 2010, Proceedings of the National Academy of Sciences.

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

[16]  Susan M. Huse,et al.  Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. , 2009, Journal of microbiological methods.

[17]  V. Kunin,et al.  Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. , 2009, Environmental microbiology.

[18]  Brian C. Thomas,et al.  Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.

[19]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[20]  Bas E. Dutilh,et al.  Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly , 2009, Bioinform..

[21]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[22]  Christine L. Sun,et al.  Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms , 2009, Applied and Environmental Microbiology.

[23]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[24]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[25]  J. Banfield,et al.  Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities , 2009, Applied and Environmental Microbiology.

[26]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[27]  Susan M. Huse,et al.  Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing , 2008, PLoS genetics.

[28]  Les Dethlefsen,et al.  The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing , 2008, PLoS biology.

[29]  Philip Hugenholtz,et al.  A renaissance for the pioneering 16S rRNA gene. , 2008, Current opinion in microbiology.

[30]  Joel Dudley,et al.  MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences , 2008, Briefings Bioinform..

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

[32]  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.

[33]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[34]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[35]  R. Knight,et al.  Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities , 2007, Applied and Environmental Microbiology.

[36]  Eoin L. Brodie,et al.  Urban aerosols harbor diverse and dynamic bacterial populations , 2007, Proceedings of the National Academy of Sciences.

[37]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[38]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[39]  Eoin L. Brodie,et al.  Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB , 2006 .

[40]  Michael B. Eisen,et al.  Rapid quantitative profiling of complex microbial populations , 2006, Nucleic acids research.

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

[42]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[43]  J. Banfield,et al.  Comparison of Acid Mine Drainage Microbial Communities in Physically and Geochemically Distinct Ecosystems , 2000, Applied and Environmental Microbiology.

[44]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[45]  N. Pace A molecular view of microbial diversity and the biosphere. , 1997, Science.

[46]  T. Moon The expectation-maximization algorithm , 1996, IEEE Signal Process. Mag..

[47]  S. Giovannoni,et al.  Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.

[48]  E. Stackebrandt,et al.  Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species , 1995, Applied and environmental microbiology.

[49]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[50]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010 .

[51]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[52]  Frank Dellaert,et al.  The Expectation Maximization Algorithm , 2002 .