Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Comparison of transcript profiles in different life stages of the nematodeGlobodera pallidaunder different host potato genotypes

(2012) Juan E. Palomares-Rius et al.   MOLECULAR PLANT PATHOLOGY

Big data in small places

(2012) Daniel MacLean et al.   NATURE BIOTECHNOLOGY

NGS analyses by visualization with Trackster

(2012) Jeremy Goecks et al.   NATURE BIOTECHNOLOGY

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

(2011) Yejun Wang et al.   BIOINFORMATICS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins

(2011) Michelle S Scott et al.   BMC BIOINFORMATICS

The metabolic interface between Pseudomonas syringae and plant cells

(2011) Arantza Rico et al.   CURRENT OPINION IN MICROBIOLOGY

Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors

(2011) R. RYAN MCNALLY et al.   MOLECULAR PLANT PATHOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

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

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

Studying Plant-Pathogen Interactions in the Genomics Era: Beyond Molecular Koch's Postulates to Systems Biology

(2010) David J. Schneider et al.   Annual Review of Phytopathology

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

Bacterial virulence effectors and their activities

(2010) Dagmar R Hann et al.   CURRENT OPINION IN PLANT BIOLOGY

TAL effectors: finding plant genes for disease and defense

(2010) Adam J Bogdanove et al.   CURRENT OPINION IN PLANT BIOLOGY

Plant immunity: towards an integrated view of plant–pathogen interactions

(2010) Peter N. Dodds et al.   NATURE REVIEWS GENETICS

Characterization and prediction of protein nucleolar localization sequences

(2010) Michelle S. Scott et al.   NUCLEIC ACIDS RESEARCH

Effective--a database of predicted secreted bacterial proteins

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

A systems biology perspective on plant–microbe interactions: Biochemical and structural targets of pathogen effectors

(2010) Leighton Pritchard et al.   PLANT SCIENCE

Genome-Wide Identification of HrpL-Regulated Genes in the Necrotrophic Phytopathogen Dickeya dadantii 3937

(2010) Shihui Yang et al.   PLoS One

Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions

(2010) Adrian C. Newton et al.   TRENDS IN MICROBIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

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

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

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

(2009) Alex N Nguyen Ba et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Pseudomonas syringae type III secretion system effectors: repertoires in search of functions

(2009) Sébastien Cunnac et al.   CURRENT OPINION IN MICROBIOLOGY

Host–pathogen warfare at the plant cell wall

(2009) Kian Hématy et al.   CURRENT OPINION IN PLANT BIOLOGY

Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans

(2009) P. R. J. Birch et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematodeGlobodera pallida

(2009) JOHN T. JONES et al.   MOLECULAR PLANT PATHOLOGY

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Sequence-Based Prediction of Type III Secreted Proteins

(2009) Roland Arnold et al.   PLoS Pathogens

Phytopathogen type III effector weaponry and their plant targets

(2008) Anna Block et al.   CURRENT OPINION IN PLANT BIOLOGY

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

(2008) Marco Punta et al.   PLoS Computational Biology