Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

(2017) Sarahi L. Garcia et al.   ISME Journal

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics

(2016) Alexandra Meziti et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Matthew L Bendall et al.   ISME Journal

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs

(2016) Qiang Zheng et al.   Frontiers in Microbiology

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

(2016) Eric R. Johnston et al.   Frontiers in Microbiology

Bacterial diversity along a 2600 km river continuum

(2015) Domenico Savio et al.   ENVIRONMENTAL 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

Phylogenomic Analysis and Predicted Physiological Role of the Proton-Translocating NADH:Quinone Oxidoreductase (Complex I) Across Bacteria

(2015) Melanie A. Spero et al.   mBio

Catchment-scale biogeography of riverine bacterioplankton

(2014) Daniel S Read et al.   ISME Journal

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

(2014) Despina Tsementzi et al.   Environmental Microbiology Reports

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Temporal variability in the diversity and composition of stream bacterioplankton communities

(2012) Maria C. Portillo et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

(2012) Byron C Crump et al.   ISME Journal

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

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

Bacterial species may exist, metagenomics reveal

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

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

(2011) Rohit Ghai et al.   PLoS One

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Konstantinos T Konstantinidis et al.   ISME Journal