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Genome sequencing and annotation

Pathogenomics research overview. Steps. Limitations. Genome sequencing and annotation. (Conserved) hypotheticals and misannotation next-gen sequencing problems with “ mobilome ”. Comprehensive identification of virulence gene candidates by various means.

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Genome sequencing and annotation

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  1. Pathogenomics research overview Steps Limitations Genome sequencing and annotation (Conserved) hypotheticals and misannotation next-gen sequencing problems with “mobilome” Comprehensive identification of virulence gene candidates by various means Bioinformatic and experimental screens 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

  2. Vivo Andrews-Polymenis et al. 2009

  3. Sassetti and Rubin 2002

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

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

  6. Rediers et al. 2005

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

  8. Valdivia and Falkow 1997

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

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

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

  12. Signature-tagged mutagenesis Mazurkiewicz et al. 2006

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

  14. Mazurkiewicz et al. 2006

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

  16. Jacobs et al. 2003

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

  18. Medini et al. 2008

  19. Medini et al. 2008

  20. Metzker 2010

  21. Langridge et al. 2009

  22. Langridge et al. 2009

  23. Sorek and Cossart 2010

  24. Sorek and Cossart 2010

  25. Sorek and Cossart 2010

  26. Chain et al. 2009

  27. Chain et al. 2009

  28. Howe et al. 2008

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