Publications
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| 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001 & Earlier | Ha, M., Kim, E.-D., and Chen, Z. J. (2009) Duplicate genes increase expression diversity in related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106:2295-2300. PubMed Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J. (2009) Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457:327-331. PubMed Ha, M., Pang, M., Agarwal, V., Chen, Z. J. (2008) Interspecies regulation of microRNAs and their targets. Biochim. Biophy. Acta 1779:735-742. PubMed Chen, M., Ha, M., Lackey, E., Wang, J., and Chen, Z. J. (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178:1845-1858. PubMed Chen, Z. J., Scheffler, B. E., Dennis, E., Triplett, B. A., Zhang, T., Chen, X., Stelly, D. M., Rabinowicz, P. D., Town, C. D., Arioli, T., Brubaker, C., Cantrell, R. G., Lacape, J. M., Ulloa, M., Chee, P., Gingle, A. R., Haigler, C. H., Percy, R., Saha, S., Wilkins, T., Wright, R. J., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ananda-Kumar, P., Rahman, M., Yusuf Zafar, Y., Yu, J. Z., Kohel, R. J., Wendel, J. F., and Paterson, A. H. (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145:1303-1310. PubMed Lee, J., Woodward, A. W., and Chen, Z. J. (2007) Gene expression changes and early events in cotton fiber development. Annals of Botany 100:1391-1401. PubMed Ha, M., Li, W.-H., and Z. J. Chen (2007). External factors accelerate expression divergence between duplicate genes. Trends in Genet. 23:162-166. PubMed Chen, Z. J. (2007). Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Ann Rev. Plant Biol. 58:377-406. PubMed Chen, Z. J., Ha, M., and Soltis, D. E. (2007). Polyploidy: Genome obesity and its consequences. New Phytologist 174: 717-720. PubMed Chen, Z. J. and Tian, L. (2007). Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophy. Acta 1769:295-307. PubMed Zhao, J., Wang, J., An, L., Doerge, R. W., Chen, Z. J., Grau, C. R., Meng, J., and Osborn, T. C. (2007). Arabidopsis microarray combined with comparative mapping identify candidate resistance genes in Brassica napus. Planta 227:13-24. PubMed Udall, J. A., Cheung, F., Woodward, A. W., Swanson, J. M., Flagel, L., Hovav, R., Ryan A. Rapp, R. A., Nettleton, D., Lee, J. J., Gingle, A. R., Town, C., Chen, Z. J., Wendel, J. F. (2007). Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8:81. PubMed Chen, Z. J. and Z. Ni (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252. PubMed Wang, J., L Tian, H.-S. Lee, N. E. Wei, H. Jiang, B. Watson, A. Madlung, T. C. Osborn, R.W. Doerge, L. Comai, and Z. J. Chen (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507-517. PubMed Wang, J., Tian, L., Lee, H.-S., and Chen, Z. J. (2006). Nonadditive regulation of FRI and FLC mediates flowering-time variation in Arabidopsis allopolyploids. Genetics 173:965-974. PubMed Yang, S. S., Foo Cheung, J. J. Lee, Misook Ha, N. E. Wei, S.-H. Sze, D. M. Stelly, P. Thaxton, B. Triplett, C. D. Town, Z. J. Chen (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant Journal 47:761-775. PubMed Lee, J. J., O. S. Hassan, W. Gao, J. J. Wang, N. E. Wei, R. J. Kohel, P. Payton, X.-Y. Chen, D. M. Stelly, and Z. J. Chen (2006) Developmental and gene expression analyses of a cotton naked seed mutant using cotton oligo-gene microarrays. Planta 223: 418-432. PubMed Gao, W., Z. J. Chen, J. Z. Yu, R. J. Kohel, J. E. Womack, D. M. Stelly (2006) Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome, Mol. Genet. & Genomics 275:105-113. PubMed Fong, P. M., L. Tian, and Z. J. Chen (2006) Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro. Cell Research 16: 479-488. PubMed Tate, J. A., Z. Ni, A.-C. Scheen, J. Koh, C. A. Gilbert, Z. J. Chen, P. S. Soltis, and D. E. Soltis (2006) Evolution and expression of homoeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173:1599-1611. PubMed Wang, N., Lu, S.E., Wang. J., Chen, Z. J., Gross, D. C. (2006) The expression of genes encoding lipodepsipeptide phytotoxins by Pseudomonas syringae pv. syringae is coordinated in response to plant signal molecules. Mol. Plant Microbe Interact. 19:257-69. PubMed Wang J, Lee JJ, Tian L, Lee HS, Chen M, Rao S, Wei EN, Doerge RW, Comai L, Chen ZJ (2005) Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol. 395:570-596. PubMed Pikaard, C. S., Preuss, S. Earley, K., Lewis, M. S., Lawrence, R. J., and Chen, Z. J. (2005). Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids. Methods Enzymol. 395:554-569. PubMed Tian, L., M. P. Fong, J. J. Wang, N. E. Wei, H. Jiang, R. W. Doerge, and Z. J. Chen (2005). Reversible histone acetylation and deacetylation mediate dynamic changes in plant gene regulation and development. Genetics 169:337-345. PubMed Syed, N. H. and Z. J. Chen (2005). Molecular marker genotypes, hetrozygosity and genetic interactions explain heterosis in Arabidopsis thaliana . Heredity 94(3):295-304. PubMed Lu, S.-E., Wang, N., Wang, J., Chen, Z. J., and Gross, D. C. (2005). Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae. Mol. Plant Microbe Interact. 18:324-333. PubMed Johnston, J. S., A. Pepper, A. E. Hall, Z. J. Chen, G. Hodnett, J. Drabek, R. Lopez, and H. J. Price (2005). Evolution of genome size in the Brassicaceae. Ann. Bot. 95: 229-235. PubMed Wang, J., H.-S. Lee, L. Tian, M. Chen, J. J. Lee, A. Madlung, L. Comai, and Z. J. Chen (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-1973. PubMed Chen, Z. J., J. Wang, L. Tian, H.-S. Lee, J. J. Wang, M. Chen, J. J. Lee, C. Josefsson, A. Madlung, B. Watson, J. C. Pires, Z. Lippman, M. Vaughn, V. Colot, R.W. Doerge, R. A. Martienssen, L. Comai, and T. C. Osborn (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol. J. Linn. Soc. 82:689-700. PubMed Lawrence, R. J., K. Earley, M. Silva, O. Pontes, Z. J. Chen, N. Neves, W. Viegas and C. S. Pikaard (2004) A concerted DNA methylation/histone methylation switch regulating rRNA gene dosage control and nucleolar dominance requires nucleolar histone deacetylase, HDT1 . Mol. Cell 13:599-609. PubMed Lee, H.-S., J. Wang, L. Tian, M. Black, H. Jiang, A. Madlung, B. Watson, L. Lukens, J.C. Pires, J. J. Wang, L. Comai, T. Osborn, R. W. Doerge, and Z. J. Chen (2004) Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and Brassica . Plant Biotechnology J. 2:45-57. PubMed Syed, N. H., H.S. Pooni, M. Mei, Z. J. Chen, and M. J. Kearsey (2004). Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations. Molecular Breeding 13:59-68. PubMed Mei, M., N. H. Syed, W. Gao, P.M. Thaxton, D. M. Stelly, and Z. J. Chen (2004) Genetic mapping and QTL analysis of fiber related traits in cotton (Gossypium). Theor. Appl. Genet. 108:280-291. PubMed Gao, W. Z. J. Chen, J. Yu, D. Raska, R. J. Kohel, C. W. Smith, J. E. Womack, and D. M. Stelly (2004) Wide-cross whole genome radiation hybrid (WWRH) mapping of cotton ( Gossypium hirsutum L.). Genetics 167: 1317-1329. PubMed Tian, L., J. Wang, M. K. Fong, M. Chen, H. Cao, S. B. Gelvin, and Z. J. Chen (2003) Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 ( AtHD1 ) expression. Genetics 165:399-409. PubMed Osborn, T. C., J. C. Pires, J. A. Birchler, D. L. Auger, Z. J. Chen, H.-S. Lee, L. Comai, A. Madlung, R.W. Doerge, V. Colot, R. A. Martienssen (2003) Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19:141-147. PubMed Pontes, O., Lawrence, R. J., Neve, N., Silva, M., Lee, J.-H., Chen, Z. J, Viegas, W., and Pikaard, C. S. (2003). Nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis allopolyploids displaying natural variation in nucleolar dominance. Proc. Natl. Acad. Sci. USA 100:11418-11423. PubMed Lee, H.-S. and Z. J. Chen (2001). Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98:6753-6758. PubMed Tian, L. and Z. J. Chen (2001). Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA 98:200-205. PubMed . Frieman, M. B., Z. J. Chen, A. L. Shen, J. Saez-Vasquez, and C. S. Pikaard (1999) RNA polymerase I transcription in an interspecific hybrid and its progenitors: tests of transcription factor involvement in uniparental rRNA gene silencing. Genetics 152:451-460. PubMed . Chen, Z. J., L. Comai, and C. S. Pikaard (1998) Gene dosage and stochastic effects determine direction and severity of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. USA 95:14891-14896. PubMed . Chen, Z. J., R. L. Phillips and H. W. Rines (1998) Maize DNA enrichment by representational difference analysis in a maize chromosome addition line of oat. Theor. Appl. Genet. 97:337-344. Abstract Chen, Z. J. and C. S. Pikaard (1997a) Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes & Development 11:2124-2136. PubMed . Chen, Z. J. and C. S. Pikaard (1997b) Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. USA 94:3442-3447. PubMed . Chen, Z., K. F. Schertz, J. Mullet, A. DuBell, and G. E. Hart (1995) Characterization and expression of rpoC2 in CMS and fertile lines of sorghum. Plant Mol. Biol. 28:799-80912. Abstract Chen, Z., M. Devey, N. A. Tuleen, and G. E. Hart (1994) Use of recombinant substitution lines in construction of RFLP-based genetic maps of chromosomes 6A and 6B of tetraploid wheat ( Triticum turgidum L.). Theor. Appl. Genet. 89:703-712. Abstract Chen, Z., G. H. Liang, S. Muthukrishnan, K. F. Schertz, and G. E. Hart (1993). A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum. Mol. Gen. Genet. 236:251-259. Abstract Chen, Z., G. H. Liang, S. Muthukrishnan, K. D. Kofoid (1990) Chloroplast DNA polymorphism in fertile and male-sterile cytoplasms of sorghum [ Sorghum bicolor (L.) Moench]. Theor. Appl. Genet. 80:4435-4439. Abstract |
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