Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA

(2015) Olivia U. Mason et al.   MICROBIAL ECOLOGY

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association

(2015) Gloria Torres-Cortés et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

(2015) Mizue Naito et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

(2014) Onur Erbilgin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Origin and Evolution of the Sodium -Pumping NADH: Ubiquinone Oxidoreductase

(2014) Adrian Reyes-Prieto et al.   PLoS One

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes

(2013) J. J. Davis et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi

(2013) Alessandro Desirò et al.   ISME Journal

Evidence that a Metabolic Microcompartment Contains and Recycles Private Cofactor Pools

(2013) D. L. Huseby et al.   JOURNAL OF BACTERIOLOGY

Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ‘Candidatus Phytoplasma'

(2013) Michael Kube et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

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

The cytochrome bd respiratory oxygen reductases

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

FACIL: Fast and Accurate Genetic Code Inference and Logo

(2011) Bas E. Dutilh et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Genome Sequence of Haloplasma contractile, an Unusual Contractile Bacterium from a Deep-Sea Anoxic Brine Lake

(2011) A. Antunes et al.   JOURNAL OF BACTERIOLOGY

Complete Genome and Proteome of Acholeplasma laidlawii

(2011) V. N. Lazarev et al.   JOURNAL OF BACTERIOLOGY

The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism's Intracellular Adaptations

(2011) Y. Ogawa et al.   JOURNAL OF BACTERIOLOGY

The Evolution of Respiratory Chain Complex I from a Smaller Last Common Ancestor Consisting of 11 Protein Subunits

(2011) Vamsi K. Moparthi et al.   JOURNAL OF MOLECULAR EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Bacterial Microcompartments

(2010) Cheryl A. Kerfeld et al.   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Draft Genome Sequence of Turicibacter sanguinis PC909, Isolated from Human Feces

(2010) P. O. Cuiv et al.   JOURNAL OF BACTERIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A New Lineage of Halophilic, Wall-Less, Contractile Bacteria from a Brine-Filled Deep of the Red Sea

(2008) A. Antunes et al.   JOURNAL OF BACTERIOLOGY

An Improved Cryogen for Plunge Freezing

(2008) William F. Tivol et al.   MICROSCOPY AND MICROANALYSIS

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features

(2008) H. Seedorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA