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

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

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

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

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

(2015) Dongwan D. Kang et al.   PeerJ

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Population Genomics: How Bacterial Species Form and Why They Don't Exist

(2012) W. Ford Doolittle   CURRENT BIOLOGY

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

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Patterns of Gene Flow Define Species of Thermophilic Archaea

(2012) Hinsby Cadillo-Quiroz et al.   PLOS BIOLOGY

The multiplicity of divergence mechanisms in a single evolving population

(2012) Ram P Maharjan et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metastats: an improved statistical method for analysis of metagenomic data

(2011) Joseph N Paulson et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

THE SPECIES AND THE VARIETY AS ECOLOGICAL UNITS

(2010) GÖTE TURESSON   HEREDITAS

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans

(2010) Rex R Malmstrom et al.   ISME Journal

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

(2010) Alejandro Caro-Quintero et al.   ISME Journal

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

(2008) Konstantinos T Konstantinidis et al.   ISME Journal

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

(2008) Sheri L Simmons et al.   PLOS BIOLOGY