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Found 15 results
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2012
Q. Pan, Ning, Y., Chen, L. Z., Zhang, S., Liu, Z. Z., Yang, X. X., Wei, W., Wei, H., Li, Q. G., Yue, H. N., and Wang, J. X., Association of MHC class-III gene polymorphisms with ER-positive breast cancer in Chinese Han population, vol. 11, pp. 4299-4306, 2012.
Anderson WF, Chu KC, Chatterjee N, Brawley O, et al. (2001). Tumor variants by hormone receptor expression in white patients with node-negative breast cancer from the surveillance, epidemiology, and end results database. J. Clin. Oncol. 19: 18-27. PMid:11134191   Baccar HA, Yacoubi LB, Troudi W, Hmida S, et al. (2006). HLA class II polymorphism: protective or risk factors to breast cancer in Tunisia? Pathol. Oncol. Res. 12: 79-81. 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. http://dx.doi.org/10.1007/s004390051089 PMid:10987645   Iris FJ, Bougueleret L, Prieur S, Caterina D, et al. (1993). Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment. Nat. Genet. 3: 137-145. 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
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