The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

(2014) Kelly C Wrighton et al.   ISME Journal

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Role of Type IV Pili in Predation by Bdellovibrio bacteriovorus

(2014) Ryan M. Chanyi et al.   PLoS One

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

(2014) Ying Zhang et al.   Frontiers in Microbiology

Signal Recognition Particle: An Essential Protein-Targeting Machine

(2013) David Akopian et al.   Annual Review of Biochemistry

The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome bd Oxidase Complex and Is Required for Cytochrome bd Oxidase Activity

(2013) C. E. VanOrsdel et al.   JOURNAL OF BACTERIOLOGY

Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater–river interaction zone

(2013) John M. Zachara et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Type IV Pili in Gram-Positive Bacteria

(2013) S. Melville et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The C-terminal regions of YidC fromRhodopirellula balticaandOceanicaulis alexandriibind to ribosomes and partially substitute for SRP receptor function inEscherichia coli

(2013) Ines Seitl et al.   MOLECULAR MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

“Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea)

(2013) Jun Gong et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium “Chlorochromatium aggregatum”

(2013) Zhenfeng Liu et al.   GENOME BIOLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov 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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

(2012) Xueju Lin et al.   ISME Journal

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

(2012) Sari Peura et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

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

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

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

(2012) Roman Häuser et al.   PLoS Genetics

Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis

(2011) Sharon Y. Wong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

(2011) Xueju Lin et al.   ENVIRONMENTAL MICROBIOLOGY

Extreme genome reduction in symbiotic bacteria

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

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome

(2011) Maria W. Górna et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France)

(2010) Guillaume Borrel et al.   ARCHIVES OF MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The type IV pilin, PilA, is required for full virulence of Francisella tularensis subspecies tularensis

(2010) Anna-Lena Forslund et al.   BMC MICROBIOLOGY

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Type IV Pili Are Required for Virulence, Twitching Motility, and Biofilm Formation ofAcidovorax avenaesubsp.citrulli

(2009) Ofir Bahar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Ultrastructural Characterization of the Prokaryotic Symbiosis in "Chlorochromatium aggregatum"

(2008) G. Wanner et al.   JOURNAL OF BACTERIOLOGY

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH