dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

(2016) Tali Raveh-Sadka et al.   ISME Journal

Patient-Specific Bacteroides Genome Variants in Pouchitis

(2016) Joseph H. Vineis et al.   mBio

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

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

(2015) Tali Raveh-Sadka et al.   eLife

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

(2015) A. Murat Eren et al.   PeerJ

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

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA