The Genome Sequence of “Candidatus Fokinia solitaria”: Insights on Reductive Evolution in Rickettsiales

Wholly Rickettsia ! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells

(2017) Timothy P. Driscoll et al.   mBio

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

(2017) Benjamin J. Tully et al.   PeerJ

Disentangling the Taxonomy of Rickettsiales and Description of Two Novel Symbionts (“Candidatus Bealeia paramacronuclearis” and “Candidatus Fokinia cryptica”) Sharing the Cytoplasm of the Ciliate Protist Paramecium biaurelia

(2016) Franziska Szokoli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fitness Impact of Obligate Intranuclear Bacterial Symbionts Depends on Host Growth Phase

(2016) Chiara Bella et al.   Frontiers in Microbiology

“Candidatus Fokinia solitaria”, a Novel “Stand-Alone” Symbiotic Lineage of Midichloriaceae (Rickettsiales)

(2016) Franziska Szokoli et al.   PLoS One

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

A R ickettsiales symbiont of amoebae with ancient features

(2015) Frederik Schulz et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution

(2015) Joran Martijn et al.   ISME Journal

A House for Two—Double Bacterial Infection in Euplotes woodruffi Sq1 (Ciliophora, Euplotia) Sampled in Southeastern Brazil

(2015) Marcus V. X. Senra et al.   MICROBIAL ECOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Draft genome sequences of threeHolosporaspecies (Holospora obtusa,Holospora undulata, andHolospora elegans), endonuclear symbiotic bacteria of the ciliateParamecium caudatum

(2014) Hideo Dohra et al.   FEMS MICROBIOLOGY LETTERS

Evolution, phylogeny, and molecular epidemiology of Chlamydia

(2014) Alexandra Nunes et al.   INFECTION GENETICS AND EVOLUTION

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

(2014) Zhang Wang et al.   PLoS One

Evolutionary origin of insect-Wolbachia nutritional mutualism

(2014) N. Nikoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria

(2013) Matteo Montagna et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes

(2013) Francesco Comandatore et al.   Genome Biology and Evolution

Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont

(2013) Timothy Driscoll et al.   Genome Biology and Evolution

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

Host Specificity of Bacterial Pathogens

(2013) A. Baumler et al.   Cold Spring Harbor Perspectives in Medicine

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association

(2012) Claudia Vannini et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Phylogenomic Evidence for the Presence of a Flagellum and cbb3 Oxidase in the Free-Living Mitochondrial Ancestor

(2011) D. Sassera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme genome reduction in symbiotic bacteria

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

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Functional diversity of ankyrin repeats in microbial proteins

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

Genome-Based Construction of the Metabolic Pathways ofOrientia tsutsugamushiand Comparative Analysis within the Rickettsiales Order

(2008) Chan-Ki Min et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Midichloria mitochondrii is widespread in hard ticks (Ixodidae) and resides in the mitochondria of phylogenetically diverse species

(2008) S. EPIS et al.   PARASITOLOGY