Computational tools and Interoperability in Comparative ... - CBS
Computational tools and Interoperability in Comparative ... - CBS
Computational tools and Interoperability in Comparative ... - CBS
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Schmidt H, Hensel M (2004) Pathogenicity isl<strong>and</strong>s <strong>in</strong> bacterial<br />
pathogenesis. Cl<strong>in</strong> Microbiol Rev 17(1):14–56<br />
Schneider G, Dobr<strong>in</strong>dt U, Bruggemann H, Nagy G, Janke B, Blum-<br />
Oehler G, Buchrieser C, Gottschalk G, Emody L, Hacker J<br />
(2004) The pathogenicity isl<strong>and</strong>-associated K15 capsule determ<strong>in</strong>ant<br />
exhibits a novel genetic structure <strong>and</strong> correlates with<br />
virulence <strong>in</strong> uropathogenic Escherichia coli stra<strong>in</strong> 536. Infect<br />
Immun 72(10):5993–6001<br />
Serruto D, Adu-Bobie J, Capecchi B, Rappuoli R, Pizza M,<br />
Masignani V (2004) Biotechnology <strong>and</strong> vacc<strong>in</strong>es: application<br />
of functional genomics to Neisseria men<strong>in</strong>gitidis <strong>and</strong> other<br />
bacterial pathogens. J Biotechnol 113:15–32<br />
Sharp PM, Li WH (1987) The codon adaptation <strong>in</strong>dex—a measure<br />
of directional synonymous codon usage bias, <strong>and</strong> its potential<br />
applications. Nucleic Acids Res 15(3):1281–1295<br />
Shendure J, Porreca GJ, Reppas NB, L<strong>in</strong> X, McCutcheon JP,<br />
Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM<br />
(2005) Accurate multiplex polony sequenc<strong>in</strong>g of an evolved<br />
bacterial genome. Science 309(5741):1728–1732<br />
Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba<br />
T, Ogasawara N, Hattori M, Kuhara, Hayashi H (2002)<br />
Complete genome sequence of Clostridium perfr<strong>in</strong>gens, an<br />
anaerobic flesh-eater. Proc Natl Acad Sci U S A 99(2):996–1001<br />
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A (2001) On<br />
the total number of genes <strong>and</strong> their length distribution <strong>in</strong><br />
complete microbial genomes. Trends Genet 17(8):425–428<br />
Stahl FW, Murray NE (1966) The evolution of gene clusters <strong>and</strong><br />
genetic circularity <strong>in</strong> microorganisms. Genetics 53(3):569–576<br />
Starl<strong>in</strong>ger P, Saedler H (1976) IS-elements <strong>in</strong> microorganisms. Curr<br />
Top Microbiol Immunol 75:111–152<br />
Talarico S, Cave MD, Marrs CF, Foxman B, Zhang L, Yang Z (2005)<br />
Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene<br />
among cl<strong>in</strong>ical isolates. J Cl<strong>in</strong> Microbiol 43(10):4954–4960<br />
Taoka M, Yamauchi Y, Sh<strong>in</strong>kawa T, Kaji H, Motohashi W,<br />
Nakayama H, Takahashi N, Isobe T (2004) Only a small<br />
subset of the horizontally transferred chromosomal genes <strong>in</strong><br />
Escherichia coli are translated <strong>in</strong>to prote<strong>in</strong>s. Mol Cell<br />
Proteomics 3(8):780–787<br />
Tobes R, Ramos JL (2005) REP code: def<strong>in</strong><strong>in</strong>g bacterial identity <strong>in</strong><br />
extragenic space. Environ Microbiol 7(2):225–228<br />
Toh H, Weiss BL, Perk<strong>in</strong> SA, Yamashita A, Oshima K, Hattori M,<br />
Aksoy S (2006) Massive genome erosion <strong>and</strong> functional<br />
adaptations provide <strong>in</strong>sights <strong>in</strong>to the symbiotic lifestyle of<br />
Sodalis gloss<strong>in</strong>idius <strong>in</strong> the tsetse host. Genome Res 16:149–156<br />
Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG,<br />
Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty<br />
BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson<br />
S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A,<br />
McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK,<br />
Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM,<br />
Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L,<br />
Wall<strong>in</strong> E, Hayes WS, Borodovsky M, Karp PD, Smith HO,<br />
Fraser CM, Venter JC (1997) The complete genome sequence<br />
of the gastric pathogen Helicobacter pylori. Nature 388<br />
(6642):539–547<br />
Torsvik V, Salte K, Sorheim R, Goksoyr J (1990) Comparison of<br />
phenotypic diversity <strong>and</strong> DNA heterogeneity <strong>in</strong> a population of<br />
soil bacteria. Appl Environ Microbiol 56:776–781<br />
Tr<strong>in</strong>ge SG, Rub<strong>in</strong> EM (2005) Metagenomics: DNA sequenc<strong>in</strong>g of<br />
environmental samples. Nat Rev Genet 6(11):805–814<br />
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ,<br />
Richardson PM, Solovyev VV, Rub<strong>in</strong> EM, Rokhsar DS,<br />
Banfield JF (2004) Community structure <strong>and</strong> metabolism<br />
through reconstruction of microbial genomes from the environment.<br />
Nature 428(6978):37–43<br />
185<br />
Ussery DW, Hall<strong>in</strong> PF (2004a) Genome update: AT content <strong>in</strong><br />
sequenced prokaryotic genomes. Microbiology 150(Pt 4):749–752<br />
Ussery DW, Hall<strong>in</strong> PF (2004b) Genome update: length distributions of<br />
sequenced prokaryotic genomes. Microbiology 150(Pt 3):513–516<br />
Ussery DW, B<strong>in</strong>newies TT, Gouveia-Oliveira R, Jarmer H, Hall<strong>in</strong><br />
PF (2004a) Genome update: DNA repeats <strong>in</strong> bacterial genomes.<br />
Microbiology 150(Pt 11):3519–3521<br />
Ussery DW, Hall<strong>in</strong> PF, Lagesen K, Coenye T (2004b) Genome<br />
update: rRNAs <strong>in</strong> sequenced microbial genomes. Microbiology<br />
150(Pt 5):1113–1115<br />
Ussery DW, Hall<strong>in</strong> PF, Lagesen K, Wassenaar TM (2004c) Genome<br />
update: tRNAs <strong>in</strong> sequenced microbial genomes. Microbiology<br />
150(Pt 6):1603–1606<br />
Ussery DW, T<strong>in</strong>dbaek N, Hall<strong>in</strong> PF (2004d) Genome update:<br />
promoter profiles. Microbiology 150(Pt 9):2791–2793<br />
Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus<br />
A, Pascal G, Scarpelli C, Medigue C (2006) MaGe: a microbial<br />
genome annotation system supported by synteny results.<br />
Nucleic Acids Res 34(1):53–65<br />
van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short<br />
sequence DNA repeats <strong>in</strong> prokaryotic genomes. Microbiol Mol<br />
Biol Rev 62(2):275–293<br />
van der Meer JR, Sentchilo V (2003) Genomic isl<strong>and</strong>s <strong>and</strong> the<br />
evolution of catabolic pathways <strong>in</strong> bacteria. Curr Op<strong>in</strong><br />
Biotechnol 14:248–254<br />
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong<br />
X, Lu P, Szafron D, Gre<strong>in</strong>er R, Wishart DS (2005) BASys: a web<br />
server for automated bacterial genome annotation. Nucleic<br />
Acids Res 33(Web Server issue):W455–W459<br />
Venter JC, Rem<strong>in</strong>gton K, Heidelberg JF, Halpern AL, Rusch D,<br />
Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE,<br />
Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson<br />
J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C,<br />
Rogers YH, Smith HO (2004) Environmental genome shotgun<br />
sequenc<strong>in</strong>g of the Sargasso Sea. Science 304(5667):66–74<br />
Vezzi A, Campanaro S, D’Angelo M, Simonato F, Vitulo N, Lauro<br />
FM, Cestaro A, Malacrida G, Simionati B, Cannata N,<br />
Romualdi C, Bartlett DH, Valle G (2005) Life at depth:<br />
Photobacterium profundum genome sequence <strong>and</strong> expression<br />
analysis. Science 307(5714):1459–1461<br />
Willenbrock H, B<strong>in</strong>newies TT, Hall<strong>in</strong> PF, Ussery DW (2005) Genome<br />
update: 2D cluster<strong>in</strong>g of bacterial genomes. Microbiology 151<br />
(Pt 2):333–336<br />
Worn<strong>in</strong>g P, Jensen LJ, Nelson KE, Brunak S, Ussery DW (2000)<br />
Structural analysis of DNA sequence: evidence for lateral gene<br />
transfer <strong>in</strong> Thermotoga maritima. Nucleic Acids Res 28<br />
(3):706–709<br />
Worn<strong>in</strong>g P, Jensen LJ, Hall<strong>in</strong> PF, Stærfeldt H-H, Ussery DW (2006)<br />
Orig<strong>in</strong> of replication <strong>in</strong> circular prokaryotic chromosomes.<br />
Environ Microbiol (In press)<br />
Yan F, Polk DB (2004) Commensal bacteria <strong>in</strong> the gut: learn<strong>in</strong>g who<br />
our friends are. Curr Op<strong>in</strong> Gastroenterol 20(6):565–571<br />
Zagursky RJ, Russell D (2001) Bio<strong>in</strong>formatics: use <strong>in</strong> bacterial<br />
vacc<strong>in</strong>e discovery. Biotechniques 31:636–659<br />
Zhang R, Zhang CT (2004) A systematic method to identify<br />
genomic isl<strong>and</strong>s <strong>and</strong> its applications <strong>in</strong> analyz<strong>in</strong>g the genomes<br />
of Corynebacterium glutamicum <strong>and</strong> Vibrio vulnificus CMCP6<br />
chromosome I. Bio<strong>in</strong>formatics 20(5):612–622<br />
Zheng Y, Anton BP, Roberts RJ, Kasif S (2005) Phylogenetic<br />
detection of conserved gene clusters <strong>in</strong> microbial genomes.<br />
BMC Bio<strong>in</strong>formatics 6:243<br />
Zubrzycki IZ (2004) Analysis of the products of genes encompassed<br />
by the theoretically predicted pathogenicity isl<strong>and</strong>s of Mycobacterium<br />
tuberculosis <strong>and</strong> Mycobacterium bovis. Prote<strong>in</strong>s:<br />
Struct, Funct, Bio<strong>in</strong>f 54:563–568