1. Genome sequencing and annotation Comprehensive identification of virulence gene candidates by various means Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors Experimental determination of functions of individual virulence factors Integrate knowledge of factors for use in: -eco-evo-systems biology study of pathogen -comparative genomics “Characterization bottleneck” Pathogenomics research overview StepsLimitations (Conserved) hypotheticals and misannotation next-gen sequencing problems with “mobilome” Ongoing curation Protein structure/function prediction Bioinformatic and experimental screens

2. Andrews-Polymenis et al. 2009 Vivo

3. Sassetti and Rubin 2002

4. Wolfgang et al. 2003 Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa

5. rpoS was downregulated in biofilm Whiteley et al. 2001 Gene expression in Pseudomonas aeruginosa biofilms

6. Rediers et al. 2005

7. Valdivia and Falkow 1997 Fluorescence-based isolation of bacterial genes expressed within host cells

8. Valdivia and Falkow 1997

9. Chang et al. 2005 A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae

10. Lindeberg et al. 2006 Collmer et al. 2002

11. Tobe et al. 2006 An extensive repertoire of type III secretion effectors in Escherichia coli O157

12. Mazurkiewicz et al. 2006 Signature-tagged mutagenesis

13. Mazurkiewicz et al. 2006 TraSH = Transposon site hybridization 

14. Mazurkiewicz et al. 2006

15. Jacobs et al. 2003 Comprehensive transposon mutant library of Pseudomonas aeruginosa

16. Jacobs et al. 2003

17. Comprehensive transposon mutant library of Pseudomonas aeruginosa

18. Medini et al. 2008

20. Metzker 2010

21. Langridge et al. 2009

23. Sorek and Cossart 2010

26. Chain et al. 2009

28. Howe et al. 2008