Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

(2017) Yi An et al.   Scientific Reports

Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes

(2016) Christopher K. Hobbs et al.   BMC GENOMICS

Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires

(2016) David Burstein et al.   NATURE GENETICS

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

Phylogenetic Profiling: How Much Input Data Is Enough?

(2015) Nives Škunca et al.   PLoS One

Prediction of bacterial type IV secreted effectors by C-terminal features

(2014) Yejun Wang et al.   BMC GENOMICS

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff 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

Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles

(2013) Lingyun Zou et al.   BIOINFORMATICS

Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal

(2013) Z. Lifshitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

(2013) Jeffrey A. Kimbrel et al.   PLoS Pathogens

Dual effect of Mesorhizobium loti T3SS functionality on the symbiotic process

(2012) Cintia Sánchez et al.   FEMS MICROBIOLOGY LETTERS

Functional and Computational Analysis of Amino Acid Patterns Predictive of Type III Secretion System Substrates in Pseudomonas syringae

(2012) Lisa M. Schechter et al.   PLoS One

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

(2012) Teresa Nogueira et al.   PLoS One

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

(2011) Yejun Wang et al.   BIOINFORMATICS

The Type VI Secretion System: A Multipurpose Delivery System with a Phage-Like Machinery

(2011) Angela R. Records   MOLECULAR PLANT-MICROBE INTERACTIONS

Bacterial Contact-Dependent Delivery Systems

(2010) Christopher S. Hayes et al.   Annual Review of Genetics

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Computational prediction of type III secreted proteins from gram-negative bacteria

(2010) Yang Yang et al.   BMC BIOINFORMATICS

Targeting effectors: the molecular recognition of Type III secreted proteins

(2010) Roland Arnold et al.   MICROBES AND INFECTION

Genome-Wide Identification of a Large Repertoire ofRalstonia solanacearumType III Effector Proteins by a New Functional Screen

(2010) Takafumi Mukaihara et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Effective--a database of predicted secreted bacterial proteins

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

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

(2009) Teresa Nogueira et al.   CURRENT BIOLOGY

Biological Diversity of Prokaryotic Type IV Secretion Systems

(2009) C. E. Alvarez-Martinez et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Characterization of theMesorhizobium lotiMAFF303099 Type-Three Protein Secretion System

(2009) Cintia Sánchez et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genome-Scale Identification of Legionella pneumophila Effectors Using a Machine Learning Approach

(2009) David Burstein et al.   PLoS Pathogens

Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems

(2009) Ram Samudrala et al.   PLoS Pathogens

Sequence-Based Prediction of Type III Secreted Proteins

(2009) Roland Arnold et al.   PLoS Pathogens

Rhizobial secreted proteins as determinants of host specificity in the rhizobium–legume symbiosis

(2008) Maarten Fauvart et al.   FEMS MICROBIOLOGY LETTERS

Analysis of the secretome of the soybean symbiont Bradyrhizobium japonicum

(2008) Jana Hempel et al.   JOURNAL OF BIOTECHNOLOGY