4.8 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Microbiology

Explaining microbial genomic diversity in light of evolutionary ecology

Otto X. Cordero et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Review Biochemistry & Molecular Biology

Ordering microbial diversity into ecologically and genetically cohesive units

B. Jesse Shapiro et al.

TRENDS IN MICROBIOLOGY (2014)

Article Multidisciplinary Sciences

PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E. Darling et al.

PEERJ (2014)

Article Multidisciplinary Sciences

Insights into the phylogeny and coding potential of microbial dark matter

Christian Rinke et al.

NATURE (2013)

Article Biotechnology & Applied Microbiology

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

Mads Albertsen et al.

NATURE BIOTECHNOLOGY (2013)

Review Ecology

Population genomics of rapid adaptation by soft selective sweeps

Philipp W. Messer et al.

TRENDS IN ECOLOGY & EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

Matthew D. Herron et al.

PLOS BIOLOGY (2013)

Editorial Material Biochemistry & Molecular Biology

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

W. Ford Doolittle

CURRENT BIOLOGY (2012)

Review Microbiology

Bacterial species may exist, metagenomics reveal

Alejandro Caro-Quintero et al.

ENVIRONMENTAL MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

IMG: the integrated microbial genomes database and comparative analysis system

Victor M. Markowitz et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

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

Heewook Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

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

Kelly C. Wrighton et al.

SCIENCE (2012)

Article Multidisciplinary Sciences

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

Vaughn Iverson et al.

SCIENCE (2012)

Article Multidisciplinary Sciences

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

B. Jesse Shapiro et al.

SCIENCE (2012)

Article Biochemistry & Molecular Biology

Patterns of Gene Flow Define Species of Thermophilic Archaea

Hinsby Cadillo-Quiroz et al.

PLOS BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

The multiplicity of divergence mechanisms in a single evolving population

Ram P. Maharjan et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

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

Tanja Magoc et al.

BIOINFORMATICS (2011)

Article Genetics & Heredity

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

Mark A. DePristo et al.

NATURE GENETICS (2011)

Meeting Abstract Biotechnology & Applied Microbiology

Metastats: an improved statistical method for analysis of metagenomic data

Joseph N. Paulson et al.

GENOME BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Genetics & Heredity

THE SPECIES AND THE VARIETY AS ECOLOGICAL UNITS

GÖTE TURESSON

HEREDITAS (2010)

Article Ecology

Viral and microbial community dynamics in four aquatic environments

Beltran Rodriguez-Brito et al.

ISME JOURNAL (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

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

Jeffrey E. Barrick et al.

NATURE (2009)

Review Multidisciplinary Sciences

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

Christophe Fraser et al.

SCIENCE (2009)

Proceedings Paper Biochemistry & Molecular Biology

Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli

J. E. Barrick et al.

EVOLUTION: THE MOLECULAR LANDSCAPE (2009)

Review Biochemistry & Molecular Biology

A systematics for discovering the fundamental units of bacterial diversity

Frederick M. Cohan et al.

CURRENT BIOLOGY (2007)

Article Biochemical Research Methods

Minimus: a fast, lightweight genome assembler

Daniel D. Sommer et al.

BMC BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Genome dynamics in a natural archaeal population

Eric E. Allen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Multidisciplinary Sciences

Recombination and the nature of bacterial speciation

Christophe Fraser et al.

SCIENCE (2007)

Review Biochemistry & Molecular Biology

Code and context: Prochlorococcus as a model for cross-scale biology

Maureen L. Coleman et al.

TRENDS IN MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus

RJ Whitaker et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Multidisciplinary Sciences

Genomic insights that advance the species definition for prokaryotes

KT Konstantinidis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Recombination and mutation during long-term gastric colonization by Helicobacter pylori:: Estimates of clock rates, recombination size, and minimal age

D Falush et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biotechnology & Applied Microbiology

rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity

I Dahllöf et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)