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