Profiling microbial strains in urban environments using metagenomic sequencing data

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

(2016) Marta Nascimento et al.   BIOINFORMATICS

Human extraintestinal pathogenic Escherichia coli strains differ in prevalence of virulence factors, phylogroups, and bacteriocin determinants

(2016) Lenka Micenková et al.   BMC MICROBIOLOGY

High-level resistance to meropenem in clinical isolates of Pseudomonas aeruginosa in the absence of carbapenemases: role of active efflux and porin alterations

(2016) Hussein Chalhoub et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Improved multilocus sequence typing of Burkholderia pseudomallei and closely related species

(2016) Erin P. Price et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Health Disparities and the Microbiome

(2016) Keisha Findley et al.   TRENDS IN MICROBIOLOGY

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens

(2016) Sirijan Santajit et al.   Biomed Research International

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Humans differ in their personal microbial cloud

(2015) James F. Meadow et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Sources of airborne microorganisms in the built environment

(2015) Aaron J. Prussin et al.   Microbiome

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities?

(2014) Gary M. King   JOURNAL OF MICROBIOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Evolution of a Pathogen: A Comparative Genomics Analysis Identifies a Genetic Pathway to Pathogenesis in Acinetobacter

(2013) Jason W. Sahl et al.   PLoS One

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Clonal Composition and Community Clustering of Drug-Susceptible and -Resistant Escherichia coli Isolates from Bloodstream Infections

(2012) Sheila Adams-Sapper et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Diversity, distribution and sources of bacteria in residential kitchens

(2012) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Human Occupancy as a Source of Indoor Airborne Bacteria

(2012) Denina Hospodsky et al.   PLoS One

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

(2010) Laure Diancourt et al.   PLoS One

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

(2009) Alexandre P Francisco et al.   BMC BIOINFORMATICS

Halomonas, a Newly Recognized Human Pathogen Causing Infections and Contamination in a Dialysis Center

(2009) David A. Stevens et al.   MEDICINE

Role of the MexAB-OprM Efflux Pump of Pseudomonas aeruginosa in Tolerance to Tea Tree (Melaleuca alternifolia) Oil and Its Monoterpene Components Terpinen-4-ol, 1,8-Cineole, and  -Terpineol

(2008) C. J. Papadopoulos et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hymenobacter soli sp. nov., isolated from grass soil

(2008) K.-H. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY