BIBLIOGRAPHY J. Rogers, P. F. Stadler, T. M. Lowe, C.-L. Wei, Y. Ruan, K. Struhl, M. Gerste<strong>in</strong>, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaoz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstr<strong>and</strong>, P. J. Good, E. A. Fe<strong>in</strong>gold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Loytynoja, S. Whelan, F. Pardi, T. Mass<strong>in</strong>gham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullik<strong>in</strong>, A. Ureta- Vidal, B. Paten, M. Ser<strong>in</strong>ghaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Tr<strong>in</strong>kle<strong>in</strong>, Z. D. Zhang, L. Barrera, R. Stuart, D. C. K<strong>in</strong>g, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bh<strong>in</strong>ge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. H. Lee, P. Ng, A. Shahab, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. S<strong>in</strong>ger, T. A. Richmond, K. J. Munn, A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van Calcar, N. He<strong>in</strong>tzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. L<strong>in</strong>, H. P. Shulha, X. Zhang, M. Xu, J. N. S. Haidar, Y. Yu, Y. Ruan, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. H<strong>in</strong>richs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. W. de Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Mart<strong>in</strong>, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrimsdottir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. B. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. We<strong>in</strong>stock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. L<strong>in</strong>dblad-Toh, E. S. L<strong>and</strong>er, M. Koriab<strong>in</strong>e, M. Nefedov, K. Osoegawa, Y. Yosh<strong>in</strong>aga, B. Zhu, & P. J. de Jong (2007). ‘Identification <strong>and</strong> analysis of functional elements <strong>in</strong> 1of the human genome by the encode pilot project.’ Nature 447:799–816. F. R. Blattner, G. r. Plunkett, C. A. Bloch, N. T. Perna, V. Burl<strong>and</strong>, M. Riley, J. Collado- Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, & Y. Shao (1997). ‘The complete genome sequence of Escherichia coli k–12.’ Science 277:1453–62. A. J. t. Bokal, W. Ross, & R. L. Gourse (1995). ‘The transcriptional activator prote<strong>in</strong> fis: Dna <strong>in</strong>teractions <strong>and</strong>cooperative <strong>in</strong>teractions with rna polymerase at the Escherichia coli rrnbp1 promoter.’ J Mol Biol 245:197–207. A. Bolshoy, P. McNamara, R. E. Harr<strong>in</strong>gton, & E. N. Trifonov (1991). ‘Curved dna without a–a: experimental estimation of all 16 dna wedgeangles.’ Proc Natl Acad Sci U S A 88:2312–6. P. J. Brett, D. DeShazer, & D. E. Woods (1998). ‘Burkholderia thail<strong>and</strong>ensis sp. nov., a Burkholderia pseudomallei–likespecies.’ Int J Syst Bacteriol 48:317–20. E. Brzuszkiewicz, H. Bruggemann, H. Liesegang, M. Emmerth, T. Olschlager, G. Nagy, K. Albermann, C. Wagner, C. Buchrieser, L. Emody, G. Gottschalk, J. Hacker, & U. Dobr<strong>in</strong>dt (2006). ‘How to become a uropathogen: comparative genomic analysis ofextra<strong>in</strong>test<strong>in</strong>al pathogenic Escherichia coli stra<strong>in</strong>s.’ Proc Natl Acad Sci U S A 103:12879–84. S. L. Chen, C.-S. Hung, J. Xu, C. S. Reigstad, V. Magr<strong>in</strong>i, A. Sabo, D. Blasiar, T. Bieri, R. R. Meyer, P. Ozersky, J. R. Armstrong, R. S. Fulton, J. P. Latreille, J. Spieth, T. M. 175
BIBLIOGRAPHY Hooton, E. R. Mardis, S. J. Hultgren, & J. I. Gordon (2006). ‘Identification of genes subject to positive selection <strong>in</strong> uropathogenicstra<strong>in</strong>s of Escherichia coli: a comparative genomics approach.’ Proc Natl Acad Sci U S A 103:5977–82. A. L. Delcher, D. Harmon, S. Kasif, O. White, & S. L. Salzberg (1999). ‘Improved microbial gene identification with glimmer.’ Nucleic Acids Res 27:4636–41. J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dew<strong>in</strong>ter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. He<strong>in</strong>er, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. L<strong>in</strong>, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccar<strong>in</strong>, P. Zhao, F. Zhong, J. Korlach, & S. Turner (2009). ‘Real–time dna sequenc<strong>in</strong>g from s<strong>in</strong>gle polymerase molecules.’ Science 323:133–8. M. Ender, B. Berger-Bachi, & N. McCallum (2009). ‘A novel dna–b<strong>in</strong>d<strong>in</strong>g prote<strong>in</strong> modulat<strong>in</strong>g methicill<strong>in</strong> resistance <strong>in</strong> Staphylococcus aureus.’ BMC Microbiol 9:15. S. T. Estrem, T. Gaal, W. Ross, & R. L. Gourse (1998). ‘Identification of an up element consensus sequence for bacterialpromoters.’ Proc Natl Acad Sci U S A 95:9761–6. P. F. Hall<strong>in</strong> & D. W. Ussery (2004). ‘Cbs Genome Atlas Database: a dynamic storage for bio<strong>in</strong>formatic results <strong>and</strong> sequence data.’ Bio<strong>in</strong>formatics 20:3682–6. K. Hayashi, N. Morooka, Y. Yamamoto, K. Fujita, K. Isono, S. Choi, E. Ohtsubo, T. Baba, B. L. Wanner, H. Mori, & T. Horiuchi (2006). ‘Highly accurate genome sequences of Escherichia coli k–12 stra<strong>in</strong>s mg1655<strong>and</strong> w3110.’ Mol Syst Biol 2:2006.0007. T. Hayashi, K. Mak<strong>in</strong>o, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C. G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T. Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, & H. Sh<strong>in</strong>agawa (2001). ‘Complete genome sequence of enterohemorrhagic Escherichia coli o157:h7 <strong>and</strong>genomic comparison with a laboratory stra<strong>in</strong> k–12.’ DNA Res 8:11–22. P. N. Hengen, S. L. Bartram, L. E. Stewart, & T. D. Schneider (1997). ‘Information analysis of Fis b<strong>in</strong>d<strong>in</strong>g sites.’ Nucleic Acids Res 25:4994–5002. C. A. Hirvonen, W. Ross, C. E. Wozniak, E. Marasco, J. R. Anthony, S. E. Aiyar, V. H. Newburn, & R. L. Gourse (2001). ‘Contributions of up elements <strong>and</strong> the transcription factor fis toexpression from the seven rrn p1 promoters <strong>in</strong> Escherichia coli.’ J Bacteriol 183:6305–14. A. M. Huerta & J. Collado-Vides (2003). ‘Sigma70 promoters <strong>in</strong> Escherichia coli: specific transcription <strong>in</strong> denseregions of overlapp<strong>in</strong>g promoter–like signals.’ J Mol Biol 333:261– 78. L. J. Jensen, C. Friis, & D. W. Ussery (1999). ‘Three views of microbial genomes.’ Res Microbiol 150:773–7. L. J. Jensen, M. Skovgaard, T. Sicheritz-Ponten, N. T. Hansen, H. Johansson, M. K. Joergensen, K. Kiil, P. F. Hall<strong>in</strong>, & D. Ussery (2005). THE PSEUDOMONADS VOL I. GENOMICS, LIFE STYLE AND MOLECULAR ARCHITECTURE, vol. 1, chap. Chapter 5: <strong>Comparative</strong> genomics of four Pseudomonas species, pp. 139–164. Kluwer Academic / Plenum Publishers, New York. 176
- Page 1 and 2:
Peter Fischer Hallin | 2009 Peter F
- Page 4:
Preface This Ph.D. thesis is writte
- Page 7 and 8:
thesis, the work is just being publ
- Page 9 and 10:
ved at blive publiceret i Standards
- Page 11 and 12:
viii
- Page 13 and 14:
Paper VI [Lagesen K, Hallin P] 1 ,
- Page 15 and 16:
xii
- Page 17 and 18:
3.3.3 Refining E. coli and Shigella
- Page 19 and 20:
xvi
- Page 21 and 22:
xviii 2.17 Pan- and core-genome plo
- Page 24 and 25:
Chapter 1 Introduction Introduction
- Page 26 and 27:
Chapter 2 Comparative Genomics 2.1
- Page 28 and 29:
Comparative Genomics the publicly a
- Page 30 and 31:
Comparative Genomics source CDS tot
- Page 32 and 33:
Comparative Genomics 1 mysql -N -B
- Page 34 and 35:
Listing 2.8: R code to generate a 2
- Page 36 and 37:
1st U C A G U 2nd position C A G 3r
- Page 38 and 39:
1st U C A G U 2nd position C A G 3r
- Page 40 and 41:
Escherichia coli strain K-12, subst
- Page 42 and 43:
Comparative Genomics
- Page 44 and 45:
3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
- Page 46 and 47:
Streptococcus Escherichia Bacillus
- Page 48 and 49:
2.4 Summary Comparative Genomics Th
- Page 50 and 51:
Comparative Genomics 2.5 Instant in
- Page 52 and 53:
‘ReSourCe is he best online submi
- Page 54 and 55:
up to a total of 41 different E. co
- Page 56 and 57:
Fig. 2 Genes (or segments) from eac
- Page 58 and 59:
Fig. 5 BLASTatlas of Clostridium bo
- Page 60 and 61:
different applications, such as ide
- Page 62 and 63:
1 Comparative Genomics 2.7 Paper II
- Page 64 and 65:
166 literally millions of bacterial
- Page 66 and 67:
168
- Page 68 and 69:
170 resistance genes on mobile gene
- Page 70 and 71:
172 involved in generating diversit
- Page 72 and 73:
174 recipient DNA. A feature observ
- Page 74 and 75:
176 Fig. 5 Genome length distributi
- Page 76 and 77:
178
- Page 78 and 79:
180 reasons why organisms remain un
- Page 80 and 81:
182 A final problem has to do with
- Page 82 and 83:
184 Middendorf B, Hochhut B, Leipol
- Page 84 and 85:
1 Comparative Genomics 2.8 Paper II
- Page 86 and 87:
2 O. N. Reva et al. Fig. 1. Genome
- Page 88 and 89:
4 O. N. Reva et al. decrease of the
- Page 90 and 91:
6 O. N. Reva et al. of which are kn
- Page 92 and 93:
8 O. N. Reva et al. compiled into a
- Page 94 and 95:
10 O. N. Reva et al. encoded by a c
- Page 96 and 97:
12 O. N. Reva et al. systems and ef
- Page 98 and 99:
1 2.9 Paper IV: The origins of Vibr
- Page 100 and 101:
phylogenies based on alternative ho
- Page 102 and 103:
Figure 1 Phylogenetic tree of the 1
- Page 104 and 105:
25000 20000 15000 10000 5000 0 Pan
- Page 106 and 107:
Gap F 2M 2.5M Gap E 875k 750k 625k
- Page 108 and 109:
Table 2 A selection of genes locate
- Page 110 and 111:
Open Access This article is distrib
- Page 112 and 113:
1 Comparative Genomics 2.10 Paper V
- Page 114 and 115:
4314 74 Tools Abstract: Of the plet
- Page 116 and 117:
4316 74 Tools Size distribution of
- Page 118 and 119:
4318 74 Tools Genome atlas Intrinsi
- Page 120 and 121:
4320 74 Tools Genome atlas Intrinsi
- Page 122 and 123:
4322 74 Tools for Comparison of Bac
- Page 124 and 125:
4324 74 Tools for Comparison of Bac
- Page 126 and 127:
4326 74 Tools information, as genet
- Page 128 and 129:
Chapter 3 rRNA operons and promoter
- Page 130 and 131:
tuB murI Fis III Fis II Fis I UP -3
- Page 132 and 133:
Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
- Page 134 and 135:
RNA operons and promoter analysis O
- Page 136 and 137:
Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
- Page 138 and 139:
Code Meaning Example C Coding CCCCC
- Page 140 and 141:
RNA operons and promoter analysis 3
- Page 142 and 143:
P2 -10 -35 UP P1 -10 -35 UP FIS FIS
- Page 144 and 145:
1 rRNA operons and promoter analysi
- Page 146 and 147:
Using HMMs also simplifies the use
- Page 148 and 149: Information content Information con
- Page 150 and 151: of the annotation. Some of the majo
- Page 152 and 153: where match states stop around 10 c
- Page 154 and 155: 1 rRNA operons and promoter analysi
- Page 156 and 157: synthesis in flow cells to simultan
- Page 158 and 159: Read absence. A boolean where ‘on
- Page 160 and 161: Hallin, et al. Figure 4 | The dataf
- Page 162 and 163: Genome homology: Comparing multiple
- Page 164 and 165: ing platform-‐independent Java
- Page 166 and 167: 34. Wang H, Noordewier M, Benham CJ
- Page 168 and 169: Chapter 4 Web Services and Interope
- Page 170 and 171: Web Services and Interoperability i
- Page 172 and 173: Web Services and Interoperability i
- Page 174 and 175: Web Services and Interoperability i
- Page 176 and 177: Web Services and Interoperability i
- Page 178 and 179: Chapter 5 Conclusion and perspectiv
- Page 180 and 181: Appendix A Appendix: Workshops, tea
- Page 182 and 183: Appendix B Appendix: Ph.D. study pl
- Page 184 and 185: Danmarks Tekniske Universitet AFI,
- Page 186 and 187: Danmarks Tekniske Universitet AFI,
- Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
- Page 190 and 191: D.2 Sample output from queryGenomes
- Page 192 and 193: Appendix: Software 13 w a r n " $ o
- Page 194 and 195: Appendix: Software 109 m y ( $ m i
- Page 196 and 197: Appendix: Software 25 [ ] A l t e r
- Page 200 and 201: BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
- Page 202 and 203: BIBLIOGRAPHY Velicer, F.-J. Vorholt