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Christopher S. Oehmen et al.
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Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
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Itai Sharon et al.
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Mads Albertsen et al.
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Toni Gabaldon et al.
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Rogan Carr et al.
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Todd J. Treangen et al.
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The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
Andreas Wilke et al.
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Ultrafast clustering algorithms for metagenomic sequence analysis
Weizhong Li et al.
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Barbara A. Methe et al.
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Junjie Qin et al.
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Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
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Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
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eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Sean Powell et al.
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Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
David R. Kelley et al.
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IMG: the integrated microbial genomes database and comparative analysis system
Victor M. Markowitz et al.
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
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KEGG for integration and interpretation of large-scale molecular data sets
Minoru Kanehisa et al.
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The Pfam protein families database
Marco Punta et al.
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MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Jens Roat Kultima et al.
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Sharon Greenblum et al.
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Bioinformatics for the Human Microbiome Project
Dirk Gevers et al.
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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Sahar Abubucker et al.
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Integrative analysis of environmental sequences using MEGAN4
Daniel H. Huson et al.
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Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees
Dongying Wu et al.
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PyNAST: a flexible tool for aligning sequences to a template alignment
J. Gregory Caporaso et al.
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A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin et al.
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Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
Jesse R. Zaneveld et al.
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Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
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A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
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Dongying Wu et al.
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Peter J. Turnbaugh et al.
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Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Martin Kircher et al.
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Metagenomics: Read length matters
K. Eric Wommack et al.
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Annotation of metagenome short reads using proxygenes
Daniel Dalevi et al.
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The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer et al.
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Evolution of mammals and their gut microbes
Ruth E. Ley et al.
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The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific
Douglas B. Rusch et al.
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Toward automatic reconstruction of a highly resolved tree of life
FD Ciccarelli et al.
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Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method
J Evans et al.
JOURNAL OF MOLECULAR EVOLUTION (2006)
Community structure and metabolism through reconstruction of microbial genomes from the environment
GW Tyson et al.
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The COG database: an updated version includes eukaryotes
RL Tatusov et al.
BMC BIOINFORMATICS (2003)