2. Fraser 2000

3. Metzker 2010

4. Metzker 2010

5. Boller and Felix 2009

6. Jones and Dangl 2006

7. Jones and Dangl 2006

8. Problems in pathogenic microbiology in pre-genomics era:
Genes associated with deployment of virulence factors have strong but pleiotropic phenotypes
Genes interacting with host and its immune system
are typically redundant and have weak phenotypes
Raskin et al. 2006
Lindeberg et al. 2006

9. Medini et al. 2008

10. Brown et al. 2001

11. Harris et al. 2010

12. Medini et al. 2008

13. Hacker and Kaper 2000

14. Hacker and Kaper 2000

15. Fraser 2000

17. Bumann 2009

18. Falkow 2004

19. Pallen and Wren 2007

21. Torto-Alalibo et al. 2009

22. Falkow 2004

23. Schneider and Collmer 2010

24. Biology is an Informational Science
"The Human Genome Project has propelled us toward the view that biological systems are fundamentally composed of two types of information: genes, encoding the molecular machines that execute the functions of life, and networks of regulatory interactions, specifying how genes are expressed. All of this information is hierarchical in nature: DNA  mRNA  protein  protein interactions  informational pathways  informational networks  cells  tissues or networks of cells  an organism  populations  ecologies. Of course, other macro-moleculesand small molecules also participate in these information hierarchies, but the process is driven by genes and interactions between genes and their environments. The central task of systems biology is (a) to comprehensively gather information from each of these distinct levels for individual biological systems and (b) to integrate these data to generate predictive mathematical models of the system".
Biological information has several important features:
It operates on multiple hierarchical levels of organization.
It is processed in complex networks.
These information networks are typically robust, such that many single perturbations will not greatly effect them.
There are key nodes in the network where perturbations may have profound effects; these offer powerful targets for the understanding and manipulation of the system."
From: Ideker, T., T. Galitski, and L. Hood A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:

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