Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Activities at the Universal Protein Resource (UniProt)

(2014)   NUCLEIC ACIDS RESEARCH

The chlamydial OTU domain-containing proteinChlaOTU is an early type III secretion effector targeting ubiquitin and NDP52

(2013) Ana Rita Furtado et al.   CELLULAR MICROBIOLOGY

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

(2013) Ilias Lagkouvardos et al.   ISME Journal

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

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

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

DIALIGN at GOBICS—multiple sequence alignment using various sources of external information

(2013) Layal Al Ait et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves

(2013) Aura Navarro-Quezada et al.   PLoS One

Tracing the primordial Chlamydiae: extinct parasites of plants?

(2013) Agathe Subtil et al.   TRENDS IN PLANT SCIENCE

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle

(2012) Olga K. Kamneva et al.   Genome Biology and Evolution

Rapid Evolution of the Sequences and Gene Repertoires of Secreted Proteins in Bacteria

(2012) Teresa Nogueira et al.   PLoS One

Unity in Variety--The Pan-Genome of the Chlamydiae

(2011) A. Collingro et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Host Proteasomal Degradation Generates Amino Acids Essential for Intracellular Bacterial Growth

(2011) C. T. D. Price et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

(2011) David A. Baltrus et al.   PLoS Pathogens

Hijacking of the Host SCF Ubiquitin Ligase Machinery by Plant Pathogens

(2011) Shimpei Magori et al.   Frontiers in Plant Science

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Gene duplications in prokaryotes can be associated with environmental adaptation

(2010) Marit S Bratlie et al.   BMC GENOMICS

The Legionella pneumophila F-box protein Lpp2082 (AnkB) modulates ubiquitination of the host protein parvin B and promotes intracellular replication

(2010) M. Lomma et al.   CELLULAR MICROBIOLOGY

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

E3 Ubiquitin Ligase Activity and Targeting of BAT3 by Multiple Legionella pneumophila Translocated Substrates

(2010) A. W. Ensminger et al.   INFECTION AND IMMUNITY

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effective--a database of predicted secreted bacterial proteins

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Waddlia Genome: A Window into Chlamydial Biology

(2010) Claire Bertelli et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

Effector protein modulation of host cells: examples in the Chlamydia spp. arsenal

(2009) Helen J Betts et al.   CURRENT OPINION IN MICROBIOLOGY

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

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

Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification

(2009) Guixia Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Mimicry by an F-Box Effector of Legionella pneumophila Hijacks a Conserved Polyubiquitination Machinery within Macrophages and Protozoa

(2009) Christopher T. Price et al.   PLoS Pathogens

Sequence-Based Prediction of Type III Secreted Proteins

(2009) Roland Arnold et al.   PLoS Pathogens

Chlamydiae as Symbionts in Eukaryotes

(2008) Matthias Horn   Annual Review of Microbiology

Diversity of Bacterial Endosymbionts of Environmental Acanthamoeba Isolates

(2008) S. Schmitz-Esser et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Birth-and-death evolution of the internalin multigene family in Listeria

(2008) Alejandro P. Rooney et al.   GENE

The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity

(2008) Masatoshi Nei et al.   NATURE REVIEWS GENETICS