A computational study of bacterial gene regulation and adaptation ...

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Statement of lengthThis thesis does not exceed the length limit specified by the Degree Committee for Biology, whichis 300, single-sided, pages of double spaced text, not including the bibliography and appendices.
Page 4 and 5: A computational study of bacterial
Page 6 and 7: AcknowledgmentsI would like to than
Page 8 and 9: List of FiguresTitlePageSummary fig
Page 10 and 11: List of TablesTitlePage(s)Table 2.1
Page 12 and 13: IntroductionI.1. IntroductionBacter
Page 14 and 15: IntroductionI.2. Basal players for
Page 16 and 17: Introductionelement. Both the -10 a
Page 18 and 19: Introductionrelative abundance of t
Page 20 and 21: IntroductionAutomated searches of T
Page 22 and 23: Introductionmetabolic functional ca
Page 24 and 25: IntroductionI.4.3. Subnetwork archi
Page 26 and 27: Introductionfor which comes from th
Page 28 and 29: IntroductionI.4.6. Evolution of tra
Page 30 and 31: Introductioncontrast to enzymes syn
Page 32 and 33: IntroductionI.6. Signal transductio
Page 34 and 35: Introductioncode for several hundre
Page 36 and 37: Chapter 1: Global regulators of bac
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Chapter 1: Global regulators of bac
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Chapter 2: Transcriptional control
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Chapter 3: Transcriptional and post
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Chapter 4: Comparative genomics of
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immune system, at least in the case
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to a combination of developmental p
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Discussion and conclusionsD1. Key f
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Discussion and conclusionsD1.1.5. C
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BibliographyBibliographyAchtman, M.
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BibliographyBabu, M.M., Priya, M.L.
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BibliographyCadoret, J.C., Rousseau
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BibliographyDaniel, P.B., Walker, W
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BibliographyFrye, J., Karlinsey, J.
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BibliographyGutteridge, A., Kanehis
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BibliographyIsalan, M., Lemerle, C.
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BibliographyKalir, S., Mangan, S.,
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BibliographyKrupa, A., and Srinivas
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BibliographyMacek, B., Gnad, F., So
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BibliographyMoran, N.A. 2002. Micro
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BibliographyPei, J., and Grishin, N
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BibliographyRomling, U., and Amikam
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BibliographyShlomi, T., Eisenberg,
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BibliographyTischler, A.D., Lee, S.
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BibliographyWayne, P.K., and Rosen,
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Appendix 1Appendix 1Supplementary m
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Appendix 1Appendix 1.2: List of gen
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Appendix 1Appendix 1.4: AT-content
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Appendix 2Appendix 2.2: Anabolic pa
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Appendix 2Appendix 2.4: Overlapping
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Appendix 2Appendix 2.6: Divergent p
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Appendix 2Appendix 2.8A: Evaluation
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Appendix 2Appendix 2.9: Differences
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Appendix 2Appendix 2.11: Role of op
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Appendix 2Appendix 2.12B: Robustnes
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Appendix 3Appendix 3.1: Specificity
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Appendix 3Appendix 3.3A: Direct reg
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Appendix 3Appendix 3.4A: Direct reg
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Appendix 3Appendix 3.5: Anabolic re
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Appendix 4Appendix 4.1: Occurrence
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Appendix 4Habitat Pathogenicity Mot
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Appendix 5Appendix 5.1B: PFAMs for
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Appendix 5Appendix 5.2A: Transcript
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Appendix 5Appendix 5.2C: Histidine
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Appendix 5Appendix 5.4: HK content
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Appendix 5Appendix 5.6A: Some confo
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Appendix 5Appendix 5.6B: Complexity
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Appendix 5Appendix 5.7: List of org
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Appendix 5Appendix 5.9: Small-molec
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Appendix 6(Organism names derived f
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Appendix 696. Corynebacterium gluta
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Appendix 6192. Mycoplasma hyopneumo
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Appendix 6288. Anaplasma phagocytop
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Appendix 6384. Mycobacterium smegma
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Appendix 6480. Lactobacillus reuter
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Appendix 6576. Acholeplasma laidlaw
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Appendix 6672. Burkholderia cenocep
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Appendix 7(Organism names derived f
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Appendix 796. Dehalococcoides CBDB1
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Appendix 7192. Mycoplasma penetrans
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Appendix 7288. Saccharophagus degra
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Appendix 8Appendix 8Reprints of pap
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Downloaded from genome.cshlp.org on
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4028 PEARSON ET AL. J. BACTERIOL.fi
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4030 PEARSON ET AL. J. BACTERIOL.Do
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4032 PEARSON ET AL. J. BACTERIOL.FI
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4034 PEARSON ET AL. J. BACTERIOL.TA
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4036 PEARSON ET AL. J. BACTERIOL.Th
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Nucleic Acids Research Advance Acce
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Nucleic Acids Research, 2008 3Figur
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Nucleic Acids Research, 2008 5sulfu
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Nucleic Acids Research, 2008 7Figur
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Mol Genet Genomics (2008) 279:523-5
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Activation of Candida rugosa lipase
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J.J. James et al. / FEBS Letters 58
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DAM and Transcriptionalternative sc
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DAM and TranscriptionTable S2 Exper
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