| 2007 | 2006 | 2005 | 2004 | 2003 | 2001 & Earlier |
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. Full Text
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. Full Text
Chen, Z. J. (2007). Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Ann Rev. Plant Biol. 58:377-406. Full Text
Chen, Z. J., Ha, M., and Soltis, D. E. (2007). Polyploidy: Genome obesity and its consequences. New Phytologist 174: 717-720. Full Text
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. Full Text
Ha, M., Li, W.-H., and Z. J. Chen (2007). External factors accelerate expression divergence between duplicate genes. Trends in Genet. 23:162-166. Full Text
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. Full Text
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. Full Text
Chen, Z. J. and Z. Ni (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text
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. Full Text .
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. Full Text .
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. Full Text .
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. Full Text .
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. Full Text .
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
Copyright 2006 @ The Chen Lab at the University of Texas at Austin. All Rights Reserved