Alterations of the human gut microbiome in liver cirrhosis
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journal
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July 2014 |
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
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June 2011 |
Genomic GC level, optimal growth temperature, and genome size in prokaryotes
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journal
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August 2006 |
Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect
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journal
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August 2013 |
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
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January 2012 |
An Approach to the Measurement of Genetic Relatedness Among Organisms
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July 1963 |
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
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March 1998 |
De novo assembly of human genomes with massively parallel short read sequencing
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December 2009 |
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome"
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September 2005 |
Constraint-based models predict metabolic and associated cellular functions
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January 2014 |
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
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December 2007 |
Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont
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November 2011 |
The RAST Server: Rapid Annotations using Subsystems Technology
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January 2008 |
The Complete Genome Sequence of Escherichia coli K-12
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Supersize me: how whole-genome sequencing and big data are transforming epidemiology
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May 2014 |
Normal gut microbiota modulates brain development and behavior
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January 2011 |
Impact of Small Repeat Sequences on Bacterial Genome Evolution
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January 2011 |
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
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June 2013 |
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
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May 1975 |
The quest for a unified view of bacterial land colonization
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January 2014 |
Reconstructing the metabolic network of a bacterium from its genome
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November 2005 |
Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria: Bacterial Microcompartments
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January 2013 |
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
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April 2000 |
Genomic variation in Salmonella enterica core genes for epidemiological typing
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January 2012 |
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
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November 2013 |
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
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May 2006 |
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms
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August 2014 |
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
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journal
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December 2012 |
Gemina: A Web-Based Epidemiology and Genomic Metadata System Designed to Identify Infectious Agents
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book
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January 2007 |
Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes
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July 2005 |
Bacterial genomes in epidemiology—present and future
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March 2013 |
Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium
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July 2010 |
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data
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May 2014 |
ISfinder: the reference centre for bacterial insertion sequences
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January 2006 |
Genome Project Standards in a New Era of Sequencing
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October 2009 |
Comparative genomics of defense systems in archaea and bacteria
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journal
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March 2013 |
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution
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December 2009 |
Efficiently gap-filling reaction networks
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June 2014 |
Marine metaproteomics: Current status and future directions
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January 2014 |
The formation of hybrid DNA molecules and their use in studies of DNA homologies
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October 1961 |
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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December 2009 |
Comparison of 61 Sequenced Escherichia coli Genomes
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July 2010 |
Comparative Genomic Structure of Prokaryotes
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journal
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December 2004 |
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
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July 1995 |
Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response
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journal
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November 2012 |
CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea
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March 2008 |
IMG 4 version of the integrated microbial genomes comparative analysis system
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October 2013 |
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
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August 2013 |
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
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May 2000 |
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies
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October 2006 |
Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology
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September 2014 |
Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
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February 2014 |
Dual RNA-seq of pathogen and host
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August 2012 |
In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
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October 2010 |
Analyzing large biological datasets with association networks
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May 2012 |
Bistability in Atomic-Scale Antiferromagnets
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January 2012 |
A metagenome-wide association study of gut microbiota in type 2 diabetes
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September 2012 |
Environmental Genome Shotgun Sequencing of the Sargasso Sea
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April 2004 |
Get the most out of your metagenome: computational analysis of environmental sequence data
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October 2007 |
Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites
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March 2010 |
CRISPR/Cas, the Immune System of Bacteria and Archaea
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January 2010 |
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
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July 2014 |
Pathoscope: Species identification and strain attribution with unassembled sequencing data
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July 2013 |
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
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March 2013 |
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
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January 2011 |
Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches
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journal
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October 2012 |
Diverse Bacterial Microcompartment Organelles
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journal
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September 2014 |
First Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain ATCC 13311 (NCTC 74), a Reference Strain of Multidrug Resistance, as Achieved by Use of PacBio Single-Molecule Real-Time Technology
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journal
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September 2014 |
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
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journal
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January 2013 |
The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries
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journal
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January 2014 |
Predicting microbial growth
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journal
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June 2014 |
Genomic insights that advance the species definition for prokaryotes
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journal
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February 2005 |
An integrated catalog of reference genes in the human gut microbiome
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journal
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July 2014 |
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
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journal
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January 2012 |
What is flux balance analysis?
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journal
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March 2010 |
A Genomic Redefinition of Pseudomonas avellanae species
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journal
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September 2013 |
Next-Generation Digital Information Storage in DNA
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journal
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August 2012 |
Extreme genome reduction in symbiotic bacteria
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journal
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November 2011 |
A first look at the Oxford Nanopore MinION sequencer
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September 2014 |
The Minimal Gene Complement of Mycoplasma genitalium
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October 1995 |
MetaRef: a pan-genomic database for comparative and community microbial genomics
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journal
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November 2013 |
Using MLST to study bacterial variation: prospects in the genomic era
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May 2014 |
A human gut microbial gene catalogue established by metagenomic sequencing
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journal
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March 2010 |
Sigma factors in a thousand E. coli genomes : Genomics update
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journal
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August 2013 |
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
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journal
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July 2014 |
Gut microbiota composition correlates with diet and health in the elderly
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journal
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July 2012 |
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
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journal
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November 2013 |
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
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journal
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December 2012 |
Environmental Diversity of Bacteria and Archaea
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journal
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August 2001 |
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
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journal
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May 2014 |
Genomic approaches to studying the human microbiota
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journal
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September 2012 |
Identification of acquired antimicrobial resistance genes
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journal
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July 2012 |
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
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journal
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January 2007 |
Intracellular Concentrations of 65 Species of Transcription Factors with Known Regulatory Functions in Escherichia coli
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journal
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May 2014 |
Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria
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journal
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April 2000 |
The future is now: single-cell genomics of bacteria and archaea
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journal
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May 2013 |
Genome assembly reborn: recent computational challenges
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journal
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May 2009 |
Construction and completion of flux balance models from pathway databases
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journal
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January 2012 |
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
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journal
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December 2007 |
The Whole Set of Constitutive Promoters Recognized by RNA Polymerase RpoD Holoenzyme of Escherichia coli
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journal
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March 2014 |
Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu
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journal
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July 2013 |
Veillonella, Firmicutes: Microbes disguised as Gram negatives
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journal
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December 2013 |
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
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journal
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December 2011 |
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
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journal
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January 2009 |
Gut metagenome in European women with normal, impaired and diabetic glucose control
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journal
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May 2013 |
Large Variations in Bacterial Ribosomal RNA Genes
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journal
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March 2012 |
The Uncultured Microbial Majority
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journal
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October 2003 |
Robustness Analysis of the Escherichia coli Metabolic Network
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journal
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December 2000 |
TerraGenome: a consortium for the sequencing of a soil metagenome
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journal
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April 2009 |
Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
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journal
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December 2013 |
High-throughput generation, optimization and analysis of genome-scale metabolic models
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journal
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August 2010 |
Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
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journal
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February 2014 |
Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs
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journal
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January 2013 |
Software platforms to facilitate reconstructing genome-scale metabolic networks: Software platforms for network reconstruction
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journal
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November 2013 |
Quality scores for 32,000 genomes
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journal
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December 2014 |
Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads
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journal
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December 2013 |
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
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journal
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February 2013 |
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data
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journal
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October 2013 |
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
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journal
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February 2012 |
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
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journal
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August 2014 |
Reconstruction of biochemical networks in microorganisms
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journal
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December 2008 |
A protocol for generating a high-quality genome-scale metabolic reconstruction
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January 2010 |
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
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Evolution and classification of the CRISPR–Cas systems
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journal
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May 2011 |
Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells
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journal
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January 2014 |
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
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journal
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January 2012 |
Genome update: the 1000th genome - a cautionary tale
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journal
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January 2010 |
Development and Evaluation of a Panel of Filovirus Sequence Capture Probes for Pathogen Detection by Next-Generation Sequencing
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journal
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September 2014 |
Community structure and metabolism through reconstruction of microbial genomes from the environment
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journal
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February 2004 |
The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101
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journal
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August 2014 |
Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming
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April 2014 |
The transcription unit architecture of the Escherichia coli genome
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November 2009 |
Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing
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July 2014 |
Next-generation DNA sequencing
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October 2008 |
Holographic optical data storage
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
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March 2012 |
Analysis of intra-genomic GC content homogeneity within prokaryotes
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January 2010 |
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
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journal
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October 2014 |
The Formation of Hybrid DNA Molecules and their use in Studies of DNA Homologies
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book
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Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response
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journal
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November 2012 |
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
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Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
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Integrated pathway–genome databases and their role in drug discovery
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July 1999 |
From Infection to Colonization: The Role of Microbiota in Transplantation
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April 2013 |
Life With 482 Genes
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Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments.
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Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems
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September 2011 |
Benchmarking of Methods for Genomic Taxonomy
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February 2014 |
The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria
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March 2014 |
To DNA, all information is equal
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journal
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July 2012 |