The Phylogeny ofRickettsiaUsing Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

(2015) G. W. C. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

(2015) Alastair Crisp et al.   GENOME BIOLOGY

Genomic Diversification in Strains of Rickettsia felis Isolated from Different Arthropods

(2014) Joseph J. Gillespie et al.   Genome Biology and Evolution

Genotyping, evolution and epidemiological findings of Rickettsia species

(2014) Vicky Merhej et al.   INFECTION GENETICS AND EVOLUTION

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria

(2013) Antonio Hernández-López 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

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Conserved Genes, Sampling Error, and Phylogenomic Inference

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ

(2012) R. Hilker et al.   BIOINFORMATICS

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

(2012) Phuong Le et al.   BMC EVOLUTIONARY BIOLOGY

Phylo-MCOA: A Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics Using Multiple Co-inertia Analysis

(2012) D. M. de Vienne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

Gene gain and loss events in Rickettsia and Orientia species

(2011) Kalliopi Georgiades et al.   Biology Direct

Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids

(2011) Min Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Purifying Selection, Sequence Composition, and Context-Specific Indel Mutations Shape Intraspecific Variation in a Bacterial Endosymbiont

(2011) Laura E. Williams et al.   Genome Biology and Evolution

A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

(2011) J. J. Gillespie et al.   JOURNAL OF BACTERIOLOGY

The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences

(2011) V. Merhej et al.   MOLECULAR BIOLOGY AND EVOLUTION

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

Extreme genome reduction in symbiotic bacteria

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

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

The post-Darwinist rhizome of life

(2010) Didier Raoult   LANCET

Watching the clock: Studying variation in rates of molecular evolution between species

(2010) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Endosymbiotic Bacteria in the Parasitic Ciliate Ichthyophthirius multifiliis

(2009) H. Y. Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

(2009) Vicky Merhej et al.   Biology Direct

Evolution and diversity of Rickettsia bacteria

(2009) Lucy A Weinert et al.   BMC BIOLOGY

Whole genome-based phylogenetic analysis of Rickettsiae

(2009) V. Merhej et al.   CLINICAL MICROBIOLOGY AND INFECTION

Reconstructing ancestral gene content by coevolution

(2009) T. Tuller et al.   GENOME RESEARCH

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Darwinian evolution in the light of genomics

(2009) E. V. Koonin   NUCLEIC ACIDS RESEARCH

Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally

(2009) L. A. Weinert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

(2008) Matthew J. Phillips   GENE

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

(2008) Joseph J. Gillespie et al.   PLoS One

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE

The Impact of Reticulate Evolution on Genome Phylogeny

(2008) Robert G. Beiko et al.   SYSTEMATIC BIOLOGY

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics

Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction

(2008) Hans-Henrik Fuxelius et al.   GENOME BIOLOGY