Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

(2020) Daniel J Wilson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia

(2019) Carolina Alejandra Martinez-Gutierrez et al.   Genome Biology and Evolution

Novel model‐based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient

(2019) Anna K. Simonsen et al.   ECOLOGY LETTERS

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Factors driving effective population size and pan-genome evolution in bacteria

(2018) Louis-Marie Bobay et al.   BMC EVOLUTIONARY BIOLOGY

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Metabolic adaptations underlying genome flexibility in prokaryotes

(2018) Akshit Goyal   PLoS Genetics

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Beyond Paralogs: The Multiple Layers of Redundancy in Bacterial Pathogenesis

(2017) Soma Ghosh et al.   Frontiers in Cellular and Infection Microbiology

The Evolution of Bacterial Genome Architecture

(2017) Louis-Marie Bobay et al.   Frontiers in Genetics

The population genetics of pangenomes

(2017) B. Jesse Shapiro   Nature Microbiology

Are pangenomes adaptive or not?

(2017) Michiel Vos et al.   Nature Microbiology

Why prokaryotes have pangenomes

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

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium

(2016) Stephanie S Porter et al.   ISME Journal

Theory of prokaryotic genome evolution

(2016) Itamar Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

(2016) Tess E. Brewer et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Migration and horizontal gene transfer divide microbial genomes into multiple niches

(2015) Rene Niehus et al.   Nature Communications

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

(2013) Niv Sabath et al.   Genome Biology and Evolution

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Response to temperature stress in rhizobia

(2012) Ana Alexandre et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

(2012) C. F. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mvabund- anRpackage for model-based analysis of multivariate abundance data

(2012) Yi Wang et al.   Methods in Ecology and Evolution

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Selection-Driven Gene Loss in Bacteria

(2012) Sanna Koskiniemi et al.   PLoS Genetics

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

The significance of nitrogen cost minimization in proteomes of marine microorganisms

(2011) Joseph J Grzymski et al.   ISME Journal

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Essence of life: essential genes of minimal genomes

(2011) Mario Juhas et al.   TRENDS IN CELL BIOLOGY

Loss of Genetic Redundancy in Reductive Genome Evolution

(2011) André G. Mendonça et al.   PLoS Computational Biology

Statistical Inference on the Mechanisms of Genome Evolution

(2011) Michael Lynch   PLoS Genetics

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

(2009) Håvard Rue et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Looking for Darwin's footprints in the microbial world

(2009) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Rhizobial mediation ofAcaciaadaptation to soil salinity: evidence of underlying trade-offs and tests of expected patterns

(2008) Peter H. Thrall et al.   JOURNAL OF ECOLOGY