Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

Morphology and Phylogeny of a New Species of Anaerobic Ciliate, Trimyema finlayi n. sp., with Endosymbiotic Methanogens

(2018) William H. Lewis et al.   Frontiers in Microbiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Identification of Pelomyxa palustris Endosymbionts

(2017) Gabriel Gutiérrez et al.   PROTIST

Comparison of Intracellular “Ca.Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA

(2016) Kazuki Izawa et al.   Genome Biology and Evolution

Mitochondria in the second act

(2016) Thijs J. G. Ettema   NATURE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

(2015) Jimmy H. Saw et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ankyrin domains across the Tree of Life

(2014) Kristin K. Jernigan et al.   PeerJ

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria

(2013) V. Boscaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Genomics of Wolbachia and the Bacterial Species Concept

(2013) Kirsten Maren Ellegaard et al.   PLoS Genetics

Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris

(2012) G. Gutierrez   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

(2012) S. L. Jorgensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extreme genome reduction in symbiotic bacteria

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

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

(2009) S. Schmitz-Esser et al.   JOURNAL OF BACTERIOLOGY

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

The Complete Genome of Teredinibacter turnerae T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

(2009) Joyce C. Yang et al.   PLoS One

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional diversity of ankyrin repeats in microbial proteins

(2009) Souhaila Al-Khodor et al.   TRENDS IN MICROBIOLOGY

Analysis of the Methanobrevibacter ruminantium draft genome: understanding methanogen biology to inhibit their action in the rumen

(2008) G. T. Attwood et al.   Australian journal of experimental agriculture

Prediction of signal peptides in archaea

(2008) P.G. Bagos et al.   PROTEIN ENGINEERING DESIGN & SELECTION