EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

Mitochondria: A target for bacteria

(2015) Elodie Lobet et al.   BIOCHEMICAL PHARMACOLOGY

Prediction of microbial phenotypes based on comparative genomics

(2015) Roman Feldbauer et al.   BMC BIOINFORMATICS

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

(2015) Jun Li et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

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

BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors

(2015) Xiaobao Dong et al.   Database-The Journal of Biological Databases and Curation

From next-generation sequencing to systematic modeling of the gut microbiome

(2015) Boyang Ji et al.   Frontiers in Genetics

T346Hunter: A Novel Web-Based Tool for the Prediction of Type III, Type IV and Type VI Secretion Systems in Bacterial Genomes

(2015) Pedro Manuel Martínez-García et al.   PLoS One

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

(2014) Yejun Wang et al.   BMC GENOMICS

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

(2013) Lingyun Zou et al.   BIOINFORMATICS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

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

AtlasT4SS: A curated database for type IV secretion systems

(2012) Rangel C Souza et al.   BMC MICROBIOLOGY

Expanded Roles for Multicargo and Class 1B Effector Chaperones in Type III Secretion

(2012) N. A. Thomas et al.   JOURNAL OF BACTERIOLOGY

The International Nucleotide Sequence Database Collaboration

(2012) Y. Nakamura et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

A New Means To Identify Type 3 Secreted Effectors: Functionally Interchangeable Class IB Chaperones Recognize a Conserved Sequence

(2012) S. C. P. Costa et al.   mBio

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Efficient learning of microbial genotype–phenotype association rules

(2010) Norman J. MacDonald et al.   BIOINFORMATICS

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

(2010) David M. Kristensen et al.   BIOINFORMATICS

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays

(2010) Hong Fang et al.   BMC BIOINFORMATICS

Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria

(2010) Jason E. McDermott et al.   INFECTION AND IMMUNITY

Effective--a database of predicted secreted bacterial proteins

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Sequence-Based Prediction of Type III Secreted Proteins

(2009) Roland Arnold et al.   PLoS Pathogens