Part 1: Bioinformatics 1. Galaxy as a Platform for Identifying Candidate Pathogen Effectors Peter J. A. Cock and Leighton Pritchard 2. Bioinformatic analysis of expression data to identify effector candidates Adam J. Reid and John T. Jones 3. Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes Diane G.O. Saunders, Joe Win, Sophien Kamoun, and Sylvain Raffaele 4. On The Statistics Of Identifying Candidate Pathogen Effectors Leighton Pritchard amd David Broadhurst Part 2: Cell Biology 5. High-throughput imaging of plant immune responses Martina Beck, Ji Zhou, Christine Faulkner, and Silke Robatzek 6. In vivo protein-protein interaction studies with BiFC: conditions, cautions and caveats Petra Boevink, Hazel McLellan, Tatyana Bukharova, Stefan Engelhardt, and Paul R.J. Birch 7. Particle bombardment-mediated transient expression to identify localization signals in plant disease resistance proteins and target sites for the proteolytic activity of pathogen effectors Daigo Takemoto and David Jones 8. Purification of fungal haustoria from infected plant tissue by flow cytometry Diana P. Garnica and John P. Rathjen Part 3: From assays of pathogen virulence to effector function 9. Functional Characterisation of Nematode Effectors in Plants Axel A. Elling and John T. Jones 10. Silencing of aphid genes by feeding on stable transgenic Arabidopsis thaliana Alexander D. Coleman, Marco Pitino, and Saskia A. Hogenhout 11. Leaf-disc assay based on transient over-expression in Nicotiana benthamiana to allow functional screening of candidate effectors from aphids Patricia A. Rodriguez, Saskia A. Hogenhout, and Jorunn I.B. Bos 12. A growth quantification assay for Hyaloperonospora arabidopsidis isolates in Arabidopsis thaliana Daniel F.A. Tomé, Jens Steinbrenner, and Jim L. Beynon 13. Simple quantification of in planta fungal biomass Michael Ayliffe, Sambasivam K Periyannan, Angela Feechan, Ian Dry, Ulrike Schumann, Evans Lagudah, and Anthony Pryor 14. Virus-induced Gene Silencing and Agrobacterium Tumefaciens-Mediated Transient Expression in Nicotiana Tabacum Zhao Zhang and Bart P.H.J. Thomma 15. DIGE-ABPP by click chemistry: Pairwise comparison of serine hydrolase activities from the apoplast of infected plants Tram Ngoc Hong and Renier A.L. van der Hoorn 16. A Simple and Fast Protocol for Protein Complex Immunoprecipitation (Co-IP) of Effector-Host Protein Complexes Jens Steinbrenner, Matthew Eldridge, Daniel F.A. Tomé, and Jim L. Beynon 17. An Arabidopsis and Tomato Mesophyll Protoplast System for fast Identification of early MAMP-triggered Immunity-Suppressing Effectors Malou Fraiture, Xiangzi Zheng, and Frédéric Brunner 18. Production of RXLR effector proteins for structural analysis by X-ray crystallography Richard K. Hughes and Mark J. Banfield Part 4: Methods to identify Resistance genes and avirulence genes 19. The Do's and Don'ts of effectoromics Juan Du and Vivianne G.A.A. Vleeshouwers 20. Protoplast cell death assay to study Magnaporthe oryzae AVR gene function in rice Hiroyuki Kanzaki, Kentaro Yoshida, Hiromasa Saitoh, Muluneh Tamiru, and Ryohei Terauchi 21. A Bacterial Type III Secretion Based Delivery System for Functional Assays of Fungal Effectors in Cereals Narayana M. Upadhyaya, Jeffery G. Ellis, and Peter N. Dodds 22. Capture arrays to annotate resistance genes in plant genomes and to accelerate plant resistance gene discovery Florian Jupe, Xinwei Chen, Walter Verweij, Kamil Witek, Jonathan D.G. Jones, and Ingo Hein sakriti opis