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

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

(2015) Zhang Wang et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Flagellar Movement in Two Bacteria of the Family Rickettsiaceae: A Re-Evaluation of Motility in an Evolutionary Perspective

(2014) Claudia Vannini et al.   PLoS One

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

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

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

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

(2013) Ilias Lagkouvardos et al.   ISME Journal

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

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

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

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

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

‘Candidatus Megaira polyxenophila’ gen. nov., sp. nov.: Considerations on Evolutionary History, Host Range and Shift of Early Divergent Rickettsiae

(2013) Martina Schrallhammer et al.   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Rediscovering the genus Lyticum, multiflagellated symbionts of the order Rickettsiales

(2013) Vittorio Boscaro et al.   Scientific Reports

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

(2013) Katarzyna Zaremba-Niedzwiedzka et al.   GENOME BIOLOGY

Ehrlichia type IV secretion effector ECH0825 is translocated to mitochondria and curbs ROS and apoptosis by upregulating host MnSOD

(2012) Hongyan Liu et al.   CELLULAR MICROBIOLOGY

A study on the presence of flagella in the order Rickettsiales: the case of 'Candidatus Midichloria mitochondrii'

(2012) M. Mariconti et al.   MICROBIOLOGY-SGM

SecReT4: a web-based bacterial type IV secretion system resource

(2012) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

(2012) Naiara Rodríguez-Ezpeleta et al.   PLoS One

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

(2012) J. Grote et al.   mBio

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

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

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

The sequence read archive: explosive growth of sequencing data

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

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

(2011) Björn Brindefalk et al.   PLoS One

Phylogenomic Analysis of Odyssella thessalonicensis Fortifies the Common Origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana Mitochondrion

(2011) Kalliopi Georgiades et al.   PLoS One

Identification of Anaplasma marginale Type IV Secretion System Effector Proteins

(2011) Svetlana Lockwood et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Effective--a database of predicted secreted bacterial proteins

(2010) M.-A. Jehl et al.   NUCLEIC ACIDS RESEARCH

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

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

Characterization of an ATP Translocase Identified in the Destructive Plant Pathogen "Candidatus Liberibacter asiaticus"

(2009) C. M. Vahling et al.   JOURNAL OF BACTERIOLOGY

Lawsonia intracellularis Contains a Gene Encoding a Functional Rickettsia-Like ATP/ADP Translocase for Host Exploitation

(2008) S. Schmitz-Esser et al.   JOURNAL OF BACTERIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION