Publications
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, “A novel method for identifying SNP disease association based on maximal information coefficient”, vol. 13, pp. 10863-10877, 2014.
, “Predicting bacterial essential genes using only sequence composition information”, vol. 13, pp. 4564-4572, 2014.
, “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