Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

Pseudovibrio hongkongensis sp. nov., isolated from a marine flatworm

(2015) Ying Xu et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Phosphate Limitation Induces Drastic Physiological Changes, Virulence-Related Gene Expression, and Secondary Metabolite Production in Pseudovibrio sp. Strain FO-BEG1

(2015) Stefano Romano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts

(2015) Young-Su Seo et al.   BMC GENOMICS

A novel sponge disease caused by a consortium of micro-organisms

(2015) Michael Sweet et al.   CORAL REEFS

SecReT6: a web-based resource for type VI secretion systems found in bacteria

(2015) Jun Li et al.   ENVIRONMENTAL MICROBIOLOGY

Whole Genome Sequencing of the SymbiontPseudovibriosp. from the Intertidal Marine SpongePolymastia penicillusRevealed a Gene Repertoire for Host-Switching Permissive Lifestyle

(2015) Anoop Alex et al.   Genome Biology and Evolution

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis

(2015) Cléa Bauvais et al.   MARINE ENVIRONMENTAL RESEARCH

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

(2015) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

Substrate Use of Pseudovibrio sp. Growing in Ultra-Oligotrophic Seawater

(2015) Anne Schwedt et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Type VI Secretion System Helps Find a Niche

(2014) Nicole Kapitein et al.   Cell Host & Microbe

Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta

(2014) Lay-Sun Ma et al.   Cell Host & Microbe

Serratia marcescensSuppresses Host Cellular Immunity via the Production of an Adhesion-inhibitory Factor against Immunosurveillance Cells

(2014) Kenichi Ishii et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of Tc toxin action revealed in molecular detail

(2014) Dominic Meusch et al.   NATURE

Type VI secretion system effectors: poisons with a purpose

(2014) Alistair B. Russell et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Exo-Metabolome of Pseudovibrio sp. FO-BEG1 Analyzed by Ultra-High Resolution Mass Spectrometry and the Effect of Phosphate Limitation

(2014) Stefano Romano et al.   PLoS One

Tle distribution and diversity in metagenomic datasets reveal niche specialization

(2014) Frank Egan et al.   Environmental Microbiology Reports

Correction: Sequence-Based Prediction of Type III Secreted Proteins

(2014) Roland Arnold et al.   PLoS Pathogens

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Type V secretion: From biogenesis to biotechnology

(2013) Peter van Ulsen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Culturable Heterotrophic Bacteria Associated with Healthy and Bleached Scleractinian Madracis decactis and the Fireworm Hermodice carunculata from the Remote St. Peter and St. Paul Archipelago, Brazil

(2013) Ana Paula B. Moreira et al.   CURRENT MICROBIOLOGY

The genusPseudovibriocontains metabolically versatile bacteria adapted for symbiosis

(2013) Vladimir Bondarev et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms

(2013) Shana K Goffredi et al.   ISME Journal

Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair

(2013) John C. Whitney et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors

(2013) Alistair B. Russell et al.   NATURE

Pfam: the protein families database

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

T3_MM: A Markov Model Effectively Classifies Bacterial Type III Secretion Signals

(2013) Yejun Wang et al.   PLoS One

The expanding bacterial type IV secretion lexicon

(2013) Minny Bhatty et al.   RESEARCH IN MICROBIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains

(2012) Anastasia D Gazi et al.   BMC MICROBIOLOGY

A Widespread Bacterial Type VI Secretion Effector Superfamily Identified Using a Heuristic Approach

(2012) Alistair B. Russell et al.   Cell Host & Microbe

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

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

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

An rhs gene of Pseudomonas aeruginosa encodes a virulence protein that activates the inflammasome

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

High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles

(2011) Yejun Wang et al.   BIOINFORMATICS

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

(2011) Diego Darriba et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

(2011) M. C. Schatz et al.   BRIEFINGS IN BIOINFORMATICS

Diversity and antimicrobial activity of Pseudovibrio spp. from Irish marine sponges

(2011) J.A. O’ Halloran et al.   JOURNAL OF APPLIED MICROBIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Extreme genome reduction in symbiotic bacteria

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

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

(2011) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Targeting effectors: the molecular recognition of Type III secreted proteins

(2010) Roland Arnold et al.   MICROBES AND INFECTION

The Evolution of Extracellular Matrix

(2010) Suat Özbek et al.   MOLECULAR BIOLOGY OF THE CELL

A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria

(2010) Stephanie K. Aoki et al.   NATURE

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?

(2009) Frédéric Boyer et al.   BMC GENOMICS

High abundance of virulence gene homologues in marine bacteria

(2009) Olof P. Persson et al.   ENVIRONMENTAL MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology