Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

(2017) Alyse A. Larkin et al.   Environmental Microbiology Reports

Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

(2016) Grace Pold et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

(2016) Alexander B. Chase et al.   Frontiers in Microbiology

Avoiding Pandemic Fears in the Subway and Conquering the Platypus: TABLE 1 

(2016) A. Gonzalez et al.   mSystems

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Temporal variation overshadows the response of leaf litter microbial communities to simulated global change

(2015) Kristin L Matulich et al.   ISME Journal

Microbial species delineation using whole genome sequences

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

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Global biogeography ofStreptomycesantibiotic inhibition, resistance, and resource use

(2014) Daniel C. Schlatter et al.   FEMS MICROBIOLOGY ECOLOGY

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

A single genus in the gut microbiome reflects host preference and specificity

(2014) A Murat Eren et al.   ISME Journal

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Transcriptome Sequencing Reveals the Virulence and Environmental Genetic Programs of Vibrio vulnificus Exposed to Host and Estuarine Conditions

(2014) Tiffany C. Williams et al.   PLoS One

Cellulolytic potential under environmental changes in microbial communities from grassland litter

(2014) Renaud Berlemont et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Microbial enzymatic responses to drought and to nitrogen addition in a southern California grassland

(2013) Charlotte J. Alster et al.   SOIL BIOLOGY & BIOCHEMISTRY

Phylogenetic Distribution of Potential Cellulases in Bacteria

(2012) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial abundance and composition influence litter decomposition response to environmental change

(2012) Steven D. Allison et al.   ECOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Ecological effects of experimental drought and prescribed fire in a southern California coastal grassland

(2012) D.L. Potts et al.   JOURNAL OF ARID ENVIRONMENTS

Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates

(2012) Shatavia S. Morrison et al.   PLoS One

Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park

(2011) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ecological Significance of Microdiversity: Coexistence Among Casing Soil Bacterial Strains Through Allocation of Nutritional Resource

(2011) Devendra Kumar Choudhary et al.   INDIAN JOURNAL OF MICROBIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

A Rapid and Easy Method for the Detection of Microbial Cellulases on Agar Plates Using Gram’s Iodine

(2008) Ramesh Chand Kasana et al.   CURRENT MICROBIOLOGY

Taxonomic resolution, ecotypes and the biogeography ofProchlorococcus

(2008) Adam C. Martiny et al.   ENVIRONMENTAL MICROBIOLOGY

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