Publications

Found 3 results
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2012
F. - B. Guo, Wei, W., Wang, X. L., Lin, H., Ding, H., Huang, J., and Rao, N., Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands, vol. 11, pp. 3735-3743, 2012.
Chu KH, Qi J, Yu Z-G and Anh V (2004). Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol. Biol. Evol. 21: 200-206. http://dx.doi.org/10.1093/molbev/msh002 PMid:14595102   Dobrindt U, Hochhut B, Hentschel U and Hacker J (2004). Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2: 414-424. http://dx.doi.org/10.1038/nrmicro884 PMid:15100694   Doolittle WF (1999). Phylogenetic classification and the universal tree. Science 284: 2124-2129. http://dx.doi.org/10.1126/science.284.5423.2124 PMid:10381871   Gao L, Qi J, Wei H, Sun Y, et al. (2003). Molecular phylogeny of coronaviruses including human SARS-CoV. Chin. Sci. Bull. 48: 1170-1174.   Garcia-Vallvé S, Romeu A and Palau J (2000). Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10: 1719-1725. http://dx.doi.org/10.1101/gr.130000 PMid:11076857 PMCid:310969   Garcia-Vallvé S, Guzman E, Montero MA and Romeu A (2003). HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31: 187-189. http://dx.doi.org/10.1093/nar/gkg004 PMid:12519978 PMCid:165451   Gascuel O (1997). BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14: 685-695. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025808 PMid:9254330   Gogarten JP and Townsend JP (2005). Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3: 679-687. http://dx.doi.org/10.1038/nrmicro1204 PMid:16138096   Hacker J and Kaper JB (2000). Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54: 641-679. http://dx.doi.org/10.1146/annurev.micro.54.1.641 PMid:11018140   Hacker J and Carniel E (2001). Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2: 376-381. PMid:11375927 PMCid:1083891   Hentschel U and Hacker J (2001). Pathogenicity islands: the tip of the iceberg. Microbes Infect. 3: 545-548. http://dx.doi.org/10.1016/S1286-4579(01)01410-1   Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, et al. (2009). The association of virulence factors with genomic islands. PLoS One 4: e8094. http://dx.doi.org/10.1371/journal.pone.0008094 PMid:19956607 PMCid:2779486   Juhas M, van der Meer JR, Gaillard M, Harding RM, et al. (2009). Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33: 376-393. http://dx.doi.org/10.1111/j.1574-6976.2008.00136.x PMid:19178566 PMCid:2704930   Jun SR, Sims GE, Wu GA and Kim SH (2010). Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proc. Natl. Acad. Sci. U. S. A. 107: 133-138. http://dx.doi.org/10.1073/pnas.0913033107 PMid:20018669 PMCid:2806744   Keeling PJ and Palmer JD (2008). Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9: 605-618. http://dx.doi.org/10.1038/nrg2386 PMid:18591983   Langille MG, Hsiao WW and Brinkman FS (2008). Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 9: 329. http://dx.doi.org/10.1186/1471-2105-9-329 PMid:18680607 PMCid:2518932   Langille MG, Hsiao WW and Brinkman FS (2010). Detecting genomic islands using bioinformatics approaches. Nat. Rev. Microbiol. 8: 373-382. http://dx.doi.org/10.1038/nrmicro2350 PMid:20395967   Lawrence JG (1999). Gene transfer, speciation, and the evolution of bacterial genomes. Curr. Opin. Microbiol. 2: 519-523. http://dx.doi.org/10.1016/S1369-5274(99)00010-7   Lawrence JG and Ochman H (1997). Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44: 383-397. http://dx.doi.org/10.1007/PL00006158 PMid:9089078   Nakamura Y, Itoh T, Matsuda H and Gojobori T (2004). Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36: 760-766. http://dx.doi.org/10.1038/ng1381 PMid:15208628   Ochman H, Lawrence JG and Groisman EA (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. http://dx.doi.org/10.1038/35012500 PMid:10830951   Pennisi E (1998). Genome data shake tree of life. Science 280: 672-674. http://dx.doi.org/10.1126/science.280.5364.672 PMid:9599142   Qi J, Wang B and Hao BI (2004). Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol. 58: 1-11. http://dx.doi.org/10.1007/s00239-003-2493-7 PMid:14743310   Sims GE and Kim SH (2011). Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Natl. Acad. Sci. U. S. A. 108: 8329-8334. http://dx.doi.org/10.1073/pnas.1105168108 PMid:21536867 PMCid:3100984   Sims GE, Jun SR, Wu GA and Kim SH (2009a). Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc. Natl. Acad. Sci. U. S. A. 106: 2677-2682. http://dx.doi.org/10.1073/pnas.0813249106 PMid:19188606 PMCid:2634796   Sims GE, Jun SR, Wu GA and Kim SH (2009b). Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc. Natl. Acad. Sci. U. S. A. 106: 17077-17082. http://dx.doi.org/10.1073/pnas.0909377106 PMid:19805074 PMCid:2761373   Tamura K, Dudley J, Nei M and Kumar S (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599. http://dx.doi.org/10.1093/molbev/msm092 PMid:17488738   Touzain F, Denamur E, Medigue C, Barbe V, et al. (2010). Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome Biol. 11: R45. http://dx.doi.org/10.1186/gb-2010-11-4-r45 PMid:20433696 PMCid:2884548   Vernikos GS and Parkhill J (2006). Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196-2203. http://dx.doi.org/10.1093/bioinformatics/btl369 PMid:16837528   Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, et al. (2001). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1: 8. http://dx.doi.org/10.1186/1471-2148-1-8 PMid:11734060 PMCid:60490   Wolf YI, Rogozin IB, Grishin NV and Koonin EV (2002). Genome trees and the tree of life. Trends Genet. 18: 472-479. http://dx.doi.org/10.1016/S0168-9525(02)02744-0   Wu GA, Jun SR, Sims GE and Kim SH (2009). Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc. Natl. Acad. Sci. U. S. A. 106: 12826-12831. http://dx.doi.org/10.1073/pnas.0905115106 PMid:19553209 PMCid:2722272   Xu Z and Hao B (2009). CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res. 37: W174-W178. http://dx.doi.org/10.1093/nar/gkp278 PMid:19398429 PMCid:2703908   Yoon SH, Hur CG, Kang HY, Kim YH, et al. (2005). A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics 6: 184. http://dx.doi.org/10.1186/1471-2105-6-184 PMid:16033657 PMCid:1188055   Yoon SH, Park YK, Lee S, Choi D, et al. (2007). Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 35: D395-D400. http://dx.doi.org/10.1093/nar/gkl790 PMid:17090594 PMCid:1669727
2011
W. Wei and Guo, F. - B., Prediction of genomic islands in seven human pathogens using the Z-Island method, vol. 10, pp. 2307-2315, 2011.
Charkowski AO (2004). Making sense of an alphabet soup: the use of a new bioinformatics tool for identification of novel gene islands. Focus on “identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis”. Physiol. Genomics 16: 180-181. http://dx.doi.org/10.1152/physiolgenomics.00199.2003 PMid:14726601 Do JH and Miyano S (2008). The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome. Appl. Microbiol. Biotechnol. 80: 841-847. http://dx.doi.org/10.1007/s00253-008-1638-4 PMid:18719902 Gogarten JP, Doolittle WF and Lawrence JG (2002). Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19: 2226-2238. http://dx.doi.org/10.1093/oxfordjournals.molbev.a004046 PMid:12446813 Greub G, Collyn F, Guy L and Roten CA (2004). A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiol. 4: 48. http://dx.doi.org/10.1186/1471-2180-4-48 PMid:15615594    PMCid:548262 Hentschel U and Hacker J (2001). Pathogenicity islands: the tip of the iceberg. Microb. Infect. 3: 545-548. http://dx.doi.org/10.1016/S1286-4579(01)01410-1 Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, et al. (2009). The association of virulence factors with genomic islands. PLoS One 4: e8094. http://dx.doi.org/10.1371/journal.pone.0008094 PMid:19956607    PMCid:2779486 Hsiao WW, Ung K, Aeschliman D, Bryan J, et al. (2005). Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet. 1: e62. http://dx.doi.org/10.1371/journal.pgen.0010062 PMid:16299586    PMCid:1285063 Kanhere A and Vingron M (2009): Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol. Biol. 9: 9. http://dx.doi.org/10.1186/1471-2148-9-9 PMid:19134215    PMCid:2651853 Langille MG, Hsiao WW and Brinkman FS (2008). Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 9: 329. http://dx.doi.org/10.1186/1471-2105-9-329 PMid:18680607    PMCid:2518932 Langille MG, Hsiao WW and Brinkman FS (2010). Detecting genomic islands using bioinformatics approaches. Nat. Rev. Microbiol. 8: 373-382. http://dx.doi.org/10.1038/nrmicro2350 PMid:20395967 Monier A, Pagarete A, de Vargas C, Allen MJ, et al. (2009). Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res. 19: 1441-1449. http://dx.doi.org/10.1101/gr.091686.109 PMid:19451591    PMCid:2720186 Ochman H, Lawrence JG and Groisman EA (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. http://dx.doi.org/10.1038/35012500 PMid:10830951 Ou HY, Chen LL, Lonnen J, Chaudhuri RR, et al. (2006). A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 34: e3. http://dx.doi.org/10.1093/nar/gnj005 PMid:16414954    PMCid:1326021 Sridhar J and Rafi ZA (2007). Identification of novel genomic islands associated with small RNAs. In Silico Biol. 7: 601- 611. PMid:18467773 Vernikos GS and Parkhill J (2008). Resolving the structural features of genomic islands: a machine learning approach. Genome Res. 18: 331-342. http://dx.doi.org/10.1101/gr.7004508 PMid:18071028    PMCid:2203631 Waack S, Keller O, Asper R, Brodag T, et al. (2006). Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7: 142. http://dx.doi.org/10.1186/1471-2105-7-142 PMid:16542435    PMCid:1489950 Yang J, Chen LH, Sun LL, Yu J, et al. (2008). VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res. 36: D539-D542. http://dx.doi.org/10.1093/nar/gkm951 PMid:17984080    PMCid:2238871 Yoon SH, Park YK, Lee S, Choi D, et al. (2007). Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 35: D395-D400. http://dx.doi.org/10.1093/nar/gkl790 PMid:17090594    PMCid:1669727 Zhang R and Zhang CT (2004). A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I. Bioinformatics 20: 612-622. http://dx.doi.org/10.1093/bioinformatics/btg453 PMid:15033867 Zhang R and Zhang CT (2005). Genomic islands in the Corynebacterium efficiens genome. Appl. Environ. Microbiol. 71: 3126-3130. http://dx.doi.org/10.1128/AEM.71.6.3126-3130.2005 PMid:15933011    PMCid:1151870