Computational tools and Interoperability in Comparative ... - CBS

BIBLIOGRAPHY
Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang,
X. Zhang, J. Zhang, G. Yang, H. Wu, D. Qu, J. Dong, L. Sun, Y. Xue, A. Zhao, Y. Gao,
J. Zhu, B. Kan, K. Ding, S. Chen, H. Cheng, Z. Yao, B. He, R. Chen, D. Ma, B. Qiang,
Y. Wen, Y. Hou, & J. Yu (2002). ‘Genome sequence of Shigella flexneri 2a: insights
into pathogenicitythrough comparison with genomes of Escherichia coli k12 and o157.’
Nucleic Acids Res 30:4432–41.
T. J. Johnson, S. Kariyawasam, Y. Wannemuehler, P. Mangiamele, S. J. Johnson,
C. Doetkott, J. A. Skyberg, A. M. Lynne, J. R. Johnson, & L. K. Nolan (2007). ‘The
genome sequence of avian pathogenic Escherichia coli strain o1:k1:h7shares strong similarities
with human extraintestinal pathogenic e. coligenomes.’ J Bacteriol 189:3228–36.
J. Kyte & R. F. Doolittle (1982). ‘A simple method for displaying the hydropathic character
of a protein.’ J Mol Biol 157:105–32.
K. Lagesen, P. Hallin, E. A. Rodland, H.-H. Staerfeldt, T. Rognes, & D. W. Ussery (2007).
‘RNAmmer: consistent and rapid annotation of ribosomal rna genes.’ Nucleic Acids Res
35:3100–8.
T. S. Larsen & A. Krogh (2003). ‘EasyGene–a prokaryotic gene finder that ranks ORFs
by statistical significance.’ BMC Bioinformatics 4:21.
T. Lefebure & M. J. Stanhope (2007). ‘Evolution of the core and pan–genome of Streptococcus:
positive selection, recombination, and genome composition.’ Genome Biol
8:R71.
X. Liao, T. Ying, H. Wang, J. Wang, Z. Shi, E. Feng, K. Wei, Y. Wang, X. Zhang,
L. Huang, G. Su, & P. Huang (2003). ‘A two–dimensional proteome map of Shigella
flexneri.’ Electrophoresis 24:2864–82.
B. Liebig & R. Wagner (1995). ‘Effects of different growth conditions on the in vivo
activity of thetandem Escherichia coli ribosomal rna promoters p1 and p2.’ Mol Gen
Genet 249:328–35.
D. Lim & N. C. J. Strynadka (2002). ‘Structural basis for the beta lactam resistance of
pbp2a from methicillin–resistant Staphylococcus aureus.’ Nat Struct Biol 9:870–6.
T. M. Lowe & S. R. Eddy (1997). ‘tRNAscan–se: a program for improved detection of
transfer rna genes ingenomic sequence.’ Nucleic Acids Res 25:955–64.
J. P. McCutcheon, B. R. McDonald, & N. A. Moran (2009). ‘Origin of an alternative
genetic code in the extremely small and gc–rich genome of a bacterial symbiont.’ PLoS
Genet 5:e1000565.
C. E. McEwan, D. Gatherer, & N. R. McEwan (1998). ‘Nitrogen–fixing aerobic bacteria
have higher genomic gc content than non–fixing species within the same genus.’
Hereditas 128:173–8.
W. G. Miller, C. T. Parker, M. Rubenfield, G. L. Mendz, M. M. S. M. Wosten, D. W.
Ussery, J. F. Stolz, T. T. Binnewies, P. F. Hallin, G. Wang, J. A. Malek, A. Rogosin,
L. H. Stanker, & R. E. Mandrell (2007). ‘The complete genome sequence and analysis
of the epsilonproteobacteriumArcobacter butzleri.’ PLoS One 2:e1358.
H. D. Murray & R. L. Gourse (2004). ‘Unique roles of the rrn p2 rrna promoters in
Escherichia coli.’ Mol Microbiol 52:1375–87.
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