Publications
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“Characterization of a novel Cry8Ea3-binding V-ATPase Subunit A in Holotrichia parallela”, vol. 15, p. -, 2016.
, “Characterization of a novel Cry8Ea3-binding V-ATPase Subunit A in Holotrichia parallela”, vol. 15, p. -, 2016.
, , , “Anti-osteoporosis activity of red yeast rice extract on ovariectomy-induced bone loss in rats”, vol. 14, pp. 8137-8146, 2015.
, “Characterization of abnormal epithelium after laser-assisted subepithelial keratectomy using in vivo confocal microscopy”, vol. 14, pp. 4749-4756, 2015.
, “Intracranial aneurysm risk factor genes: relationship with intracranial aneurysm risk in a Chinese Han population”, vol. 14, pp. 6865-6878, 2015.
, , , “Statistical analyses of conserved features of genomic islands in bacteria”, vol. 13, pp. 1782-1793, 2014.
, , “Colorectal cancer susceptibility variants alter risk of breast cancer in a Chinese Han population”, vol. 12, pp. 6268-6274, 2013.
, “Association of MHC class-III gene polymorphisms with ER-positive breast cancer in Chinese Han population”, vol. 11, pp. 4299-4306, 2012.
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PMid:11134191
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http://dx.doi.org/10.1007/BF02893448
Bhutia SK, Mallick SK and Maiti TK (2010). Tumour escape mechanisms and their therapeutic implications in combination tumour therapy. Cell Biol. Int. 34: 553-563.
http://dx.doi.org/10.1042/CBI20090206
PMid:20384587
Cantú de León D, Perez-Montiel D, Villavicencio V, Garcia CA, et al. (2009). High resolution human leukocyte antigen (HLA) class I and class II allele typing in Mexican mestizo women with sporadic breast cancer: case-control study. BMC Cancer 9: 48.
http://dx.doi.org/10.1186/1471-2407-9-48
PMid:19196481 PMCid:2653544
de Jong MM, Nolte IM, de Vries EG, Schaapveld M, et al. (2003). The HLA class III subregion is responsible for an increased breast cancer risk. Hum. Mol. Genet. 12: 2311-2319.
http://dx.doi.org/10.1093/hmg/ddg245
PMid:12915440
Dunn GP, Bruce AT, Ikeda H, Old LJ, et al. (2002). Cancer immunoediting: from immunosurveillance to tumor escape. Nat. Immunol. 3: 991-998.
http://dx.doi.org/10.1038/ni1102-991
PMid:12407406
Dunnwald LK, Rossing MA and Li CI (2007). Hormone receptor status, tumor characteristics, and prognosis: a prospective cohort of breast cancer patients. Breast Cancer Res. 9: R6.
http://dx.doi.org/10.1186/bcr1639
PMid:17239243 PMCid:1851385
Ghaderi A, Talei A, Gharesi-Fard B, Farjadian SH, et al. (2001). HLA-DBR 1 alleles and the susceptibility of Iranian patients with breast cancer. Pathol. Oncol. Res. 7: 39-41.
http://dx.doi.org/10.1007/BF03032603
PMid:11349219
Gruen JR and Weissman SM (2001). Human MHC class III and IV genes and disease associations. Front Biosci. 6: D960-D972.
http://dx.doi.org/10.2741/Gruen
PMid:11487469
Gun FD, Ozturk OG, Polat A and Polat G (2012). HLA class-II allele frequencies in Turkish breast cancer patients. Med. Oncol. 29: 466-471.
http://dx.doi.org/10.1007/s12032-011-9873-4
PMid:21373933
Hashimoto M, Nakamura N, Obayashi H, Kimura F, et al. (1999). Genetic contribution of the BAT2 gene microsatellite polymorphism to the age-at-onset of insulin-dependent diabetes mellitus. Hum. Genet. 105: 197-199.
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http://dx.doi.org/10.1038/ng0293-137
PMid:8499947
Jemal A, Bray F, Center MM, Ferlay J, et al. (2011). Global cancer statistics. CA Cancer J. Clin. 61: 69-90.
http://dx.doi.org/10.3322/caac.20107
PMid:21296855
Lavado R, Benavides M, Villar E, Ales I, et al. (2005). The HLA-B7 allele confers susceptibility to breast cancer in Spanish women. Immunol. Lett. 101: 223-225.
http://dx.doi.org/10.1016/j.imlet.2005.03.006
PMid:16188571
Linos E, Spanos D, Rosner BA, Linos K, et al. (2008). Effects of reproductive and demographic changes on breast cancer incidence in China: a modeling analysis. J. Natl. Cancer Inst. 100: 1352-1360.
http://dx.doi.org/10.1093/jnci/djn305
PMid:18812552 PMCid:2556703
Mahmoodi M, Nahvi H, Mahmoudi M, Kasaian A, et al. (2012). HLA-DRB1, -DQA1 and -DQB1 allele and haplotype frequencies in female patients with early onset breast cancer. Pathol. Oncol. Res. 18: 49-55.
http://dx.doi.org/10.1007/s12253-011-9415-6
PMid:21720852
Mestiri S, Bouaouina N, Ahmed SB, Khedhaier A, et al. (2001). Genetic variation in the tumor necrosis factor-alpha promoter region and in the stress protein hsp70-2: susceptibility and prognostic implications in breast carcinoma. Cancer 91: 672-678.
http://dx.doi.org/10.1002/1097-0142(20010215)91:4<672::AID-CNCR1050>3.0.CO;2-J
Milner CM and Campbell RD (2001). Genetic organization of the human MHC class III region. Front Biosci. 6: D914-D926.
http://dx.doi.org/10.2741/Milner
PMid:11487476
Shiina T, Inoko H and Kulski JK (2004). An update of the HLA genomic region, locus information and disease associations: 2004. Tissue Antigens 64: 631-649.
http://dx.doi.org/10.1111/j.1399-0039.2004.00327.x
PMid:15546336
Singal DP, Li J and Zhu Y (2000). HLA class III region and susceptibility to rheumatoid arthritis. Clin. Exp. Rheumatol. 18: 485-491.
PMid:10949724
Spies T, Blanck G, Bresnahan M, Sands J, et al. (1989). A new cluster of genes within the human major histocompatibility complex. Science 243: 214-217.
http://dx.doi.org/10.1126/science.2911734
PMid:2911734
Xie T, Rowen L, Aguado B, Ahearn ME, et al. (2003). Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res. 13: 2621-2636.
http://dx.doi.org/10.1101/gr.1736803
PMid:14656967 PMCid:403804
Yu CY (1998). Molecular genetics of the human MHC complement gene cluster. Exp. Clin. Immunogenet. 15: 213-230.
http://dx.doi.org/10.1159/000019075
PMid:10072631
Ziegler RG, Anderson WF and Gail MH (2008). Increasing breast cancer incidence in China: the numbers add up. J. Natl. Cancer Inst. 100: 1339-1341.
http://dx.doi.org/10.1093/jnci/djn330
PMid:18812546
“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.
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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.
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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.
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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
“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.
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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
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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.
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Zhang R and Zhang CT (2005). Genomic islands in the Corynebacterium efficiens genome. Appl. Environ. Microbiol. 71: 3126-3130.
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