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Song, Q., Ando, A., Jiang, N., Ikeda, Y., Chen, Z. J. (2020) Single-cell analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biology 21:178. PubMed

Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., Plott, C., Lovell, J., Lin, Y.-M., Vaughn, R., Liu, B., Wen, L., Simpson, S., Scheffler, B. E., Saski, C. A., Grover, C. E., Hu, G., Conover, J., Carlson, J. W., Shu, S., Boston, L. B., Williams, M., Peterson, D. G., McGee, K., Jones, D. C., Wendel, J. F., Stelly, D. M., Grimwood, J., Schmutz, J. (2020) Genomic diversifications of five allopolyploid Gossypium species and their impact on cotton improvement. Nature Genetics 52:525-533. PubMed Press Release


Yin, D., Ji, C., Song, Q.*, Zhang, W., Zhang, X., Zhao, K., Chen, C. Y., Wang, C., He, G., Liang, Z., Ma, X., Li, Z., Tang, Y., Wang, Y., Li, K., Ning, L., Zhang, H., Zhu, W., Li, X., Yu, H., Lei, Y., Wang, M., Ma, L., Zheng, H., Zhang, Y., Zhang, J., Hu, W., Chen, Z. J. (2019) Comparison of Arachis monticola with diploid and cultivated tetraploid genomes reveals asymmetric subgenome evolution and improvement of peanut. Advanced Science 7:1901672. PubMed


Ding, M., Chen, Z. J. (2018) Epigenetic perspectives on the evolution and domestication of polyploid plants and crops. Current Opinions in Plant Biology 42:37-48. PubMed Press Release


Song, Q., Zhang, T., Stelly, D. M., and Chen, Z. J. (2017) Epigenomic and functional analyses reveal roles for epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology 18:99. PubMed

Fang, L., Gong, H., Hu, Y., Liu, C., Zhou, B., Huang, T., Wang, Y., Chen, S., Fang, D. D., Du, X., Chen, H., Chen, J., Wang, S., Wang, Q., Wan, Q., Liu, B., Pan, M., Chang, L., Wu, H., Mei, G., Xiang, D., Li, X., Cai, C., Zhu, X., Chen, Z. J., Han, H., Chen, X., Guo, W., Zhang, T., and Huang, X. (2017) Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biology 18:33. PubMed

Saski, C. A., Scheffler, B. E., Hulse-Kemp, A. M., Liu, B., Song, Q., Ando, A., Stelly, D. M., Scheffler, J. A., Grimwood, J., Jones, D. C., Peterson, D. G., Schmutz, J., and Chen, Z. J. (2017) Subgenome anchored physical frameworks and an approach toward reference-grade assemblies of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome. Scientific Reports 7(1):15274. PubMed


Zheng, D., Ye, W., Song, Q., Han, F., Zhang, T., and Chen, Z. J. (2016) Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton. Plant Physiology 172:1760-1771. PubMed.


Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., Hulse-Kemp, A. M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R. C., Chen, X., Dennis, E., Llewellyn, D. J., Peterson, D. G., Thaxton, P., Jones, D. C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., and Chen, Z. J. (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33:531-537. Pubmed.

Liu, X., Zhao, B., Zheng, H.-J., Hu, Y., Lu, G., Yang, C.-Q., Chen, J.-D., Chen, J.-J., Chen, D.-Y., Zhang, L., Zhou, Y., Wang, L.-J., Guo, W.-Z., Bai, Y.-L.; Ruan, J.-X., Shangguan, X.-X., Mao, Y.-B., Shan, C.-M., Jiang, J.-P., Zhu, Y.-Q., Jin, L., Kang, H., Chen, S.-T., He, X.-L., Wang, R., Wang, Y.-Z., Chen, J., Wang, L.-J., Yu, S.-T., Wang, B.-Y., Wei, J., Song, S.-C., Lu, X.-Y., Gao, Z.-C., Gu, W.-Y., Deng, X., Ma, D., Wang, S., Liang, W.-H., Fang, L., Cai, C.-P., Zhu, X.-F., Zhou, B.-L., Chen, Z. J., Xu, S.-H., Xu, S.-H., Zhang, Y.-G., Wang, S.-Y., Zhang, T.-Z., Zhao, G.-P., and Chen, X.-Y. (2015)Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Scientific Reports 5:14139. Pubmed.

Song, Q., Guan, X., and Chen, Z. J. (2015) Dynamic roles for small RNAs and DNA methylation during ovule and fiber development in allotetraploid cotton. PLoS Genetics 11(12):e1005724. Pubmed.

Song, Q. and Chen, Z. J. (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinions in Plant Biology 24:101–109. Pubmed.

Tuttle, J. R., Nah, G., Duke, M. V., Alexander, D. C., Guan, X., Song, Q., Chen, Z. J., Scheffler, B. E., and Haigler, C. H. (2015) Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 16:477. Pubmed.

Hulse-Kemp, A. M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C., Scheffler, B. E., Fang, D. D., Chen, Z. J., Van Deynze, A., and Stelly D. M. (2015) BAC-end sequence-based SNP mining in allotetraploid cotton (Gossypium) utilizing resequencing data, phylogenetic inferences and perspectives for genetic mapping. G3 5:1095-1105. Pubmed.

Kim, H. J., Hinchliffe, D. J., Barbara A. Triplett, B. A., Chen, Z. J., Stelly, D. M., Yeater, K. M., Moon, H., Gilbert, M. K., Thyssen, G., Turley, R. B., Fang, D. D. (2015) Phytohormonal networks promote differentiation of fiber initials on preanthesis cotton ovules grown in culture and in planta. PLoS One10:e0125046. PubMed.

Ashrafi, H., Hulse-Kemp, A. M, Wang, F., Yang, S. S., Guan, X., Jones, D. C., Matvienko, M., Mockaitis, K., Chen, Z. J., Stelly, D. M., and Van Deynze, A. (2015) A long-read transcriptome assembly of cotton (Gossypium hirsutum L.) and intraspecific single nucleotide polymorphism discovery. Plant Genome8(2) 1-14. Article.

Shi, X., Zhang, C., Ko, D.-K., and Chen, Z. J. (2015) Genome-wide dosage-dependent and -independent regulation contributes to gene expression and evolutionary novelty in plant polyploids. Molecular Biology and Evolution 32:2351-2366. Pubmed.

Miller, M., Song, Q., Shi, X., Juenger, T. E., and Chen, Z. J. (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of ArabidopsisNature Communications 6:7453. Pubmed


Shan, C.-M., Shangguan X.-X., Zhao, B., Zhang, X.-F., Chao, L.-M., Yang, C.-Q., Wang, L.-J., Zhu, H.-Y., Zeng, Y.-D., Guo, W.-Z., Zhou, B.-L., Hu, G.-J., Guan, X.-Y., Chen, Z. J., Wendel, J. F., Zhang, T.-Z., and Chen, X.-Y. (2014) Control of cotton fiber elongation by a homeodomian transcription factor GhHOX3.Nature Communications 5:5519. PubMed

Guan, X., Nah, G., Song, Q., Udall, J. A., Stelly, D. M., Chen, Z. J. (2014) Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. BMC Research Notes 7:493. PubMed

Guan, X., Song, Q., Chen, Z. J. (2014) Polyploidy and small RNA regulation of cotton fiber development. Trends in Plant Science 19:516-528. PubMed

Guan, X., Pang, M., Nah, G., Shi, X., Ye, W., Stelly, D. M., and Chen, Z. J. (2014) miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development.Nature Communications 5:3050. PubMed


Chen, Z. J. (2013) Genomic and epigenetic insights into the molecular bases of heterosis. Nature Reviews Genetics 14:471-482. Pubmed

Chen, Z. J. and Birchler, J. A. (2013) Polyploid and Hybrid Genomics. Wiley-Blackwell, New York. pp. 363 (ISBN 978-0-470-96037-0)

Guan, X. and Chen, Z. J. (2013) Chapter 11. Cotton fiber genomics. In Becraft, P. W. (ed.) Seed Genomics. p203-216. Wiley-Blackwell, New York. (DOI: 10.1002/9781118525524.ch11)


Tuttle JR, Haigler CH, Robertson D (2012) Low-cost delivery of the cotton leaf crumple virus-induced gene silencing system. Plant Methods 8:27. PubMed

Haigler CH, Betancur L, Stiff MR, Tuttle JR (2012) Cotton fiber: a powerful single-cell model for cell wall and cellulose research. Frontiers in Plant Science 3:104. PubMed

Shi, X., Ng, D. W-K., Zhang, C., Comai, L. Ye, W., and Chen, Z. J. (2012) Cis- and trans-regulatroy divergence between progenitor species determines gene expression novelty in Arabidopsisallopolyploids. Nature Communications 3:950. PubMed

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo M-J, Byers R, W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee T-H, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, Rahman M-ur, Rainville LN , Rambani A, Reddy UK, Rong J-K, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Deynze AV, Vaslin MFS, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KFX, Peterson DG, Rokhsar DS, Wang X, & Schmutz J (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423–427. PubMed


Guan X., Lee, J.J., Pang, M., Shi, X., Stelly, D.M., and Chen, Z.J. (2011) Activation of Arabidopsis seed hair development by cotton fiber-related genes. PLoS ONE 6(7): e21301. PubMed

Chen, Z. J. and Guan, X. (2011) Auxin boost for cotton. Nature Biotechnology 29:407-409. 


Hinchliffe, D. J., Meredith, W. R., Yeater, K. M., Kim, H. J., Woodward, A. W., Chen, Z. J., and Triplett, B. A. (2010) Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression pattern as revealed by comparative high-throughput profiling.Theor. Appl. Genet. PubMed

Wang, K., Guo, W, Yang, Z., Hu, Y., Zhang, W., Zhou, B., Stelly, D. M., Chen, Z. J., and Zhang, T. (2010) Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma PubMed

Chen, Z. J. (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends in Plant Science15:57-71. PubMed

Jackson, S. and Chen, Z. J. (2010) Genomic and expression plasticity of polyploidy. Current Opinions in Plant Biology 13:153-159. PubMed

Clark, G., Torres, J., Finlayson, S., Guan, X., Handley, C., Lee, J., Kays, J. E., Chen, Z. J., and Roux, S. J.(2010) Apyrase (NTPDase) and extracellular nucleotides regulate cotton fiber elongation in cultured ovules. Plant Physiology 152:1073-1083. PubMed


Pang, M., Woodward, A. W., Agarwal, V., Ha, M., Guan, X., Vanitharani Ramachandran, V., Chen, X., Triplett, B. A., Stelly, D. M., and Chen, Z. J. (2009). Genome-wide analysis revealed rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.) Genome Biology 10:R122. PDF

Lu, Y., and Sze, S.H. (2009) Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res. 37, 463-472. PubMed


Guo, Y.F., Saha, S., Yu, J.Z., Jenkins, J.N., Kohel, R.J., Scheffler, B.E., and Stelly, D.M. (2008) BAC-derived SSR markers chromosome locations in cotton. Euphytica 161, 361-370. PDF

Kim, H.J., and Triplett, B. (2008) Involvement of extracellular Cu/Zn superoxide dismutase in cotton fiber primary and secondary cell wall biosynthesis. Plant Signal Behav 3, 1119-1121. PubMed

Kim, H.J., Kato, N., Kim, S., and Triplett, B. (2008) Cu/Zn superoxide dismutases in developing cotton fibers: evidence for an extracellular form. Planta 228, 281-292. PubMed

Lu, Y., and Sze, S.H. (2008) Multiple sequence alignment based on profile alignment of intermediate sequences. J. Comput. Biol. 15, 767-777.

Zhong, H., Lau, W.S., Sze, W.F., and Hung, Y.S. (2008) Shape recovery from turntable sequence using rim reconstruction. Pattern Recogn 41, 3295-3301.

Sze, S.C.W., Song, J.X., Wong, R.N.S., Feng, Y.B., Ng, T.B., Tong, Y., and Zhang, K.Y.B. (2008) Application of SCAR (sequence characterized amplified region) analysis to authenticate Lycium barbarum (wolfberry) and its adulterants. Biotechnol Appl Bioc. 51, 15-21.


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

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

Lu S., Zhang F., Chen J. and Sze S.-H. (2007) Finding Pathway Structures in Protein Interaction Networks. Algorithmica 48: 363-374.

Yang Q. and Sze S.-H. (2007) Path Matching and Graph Matching in Biological Networks. Journal of Computational Biology 14:56-67.

Yi G., Sze S.-H. and Thon M.R. (2007) Identifying Clusters of Functionally Related Genes in Genomes.Bioinformatics 23:1053-1060.

Chen J., Lu S., Sze S.-H. and Zhang F. (2007) Improved Algorithms for Path, Matching, and Packing Problems. Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms(SODA'2007):298-307.

Lu Y. and Sze S.-H. (2007) Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB'2007).Lecture Notes in Bioinformatics 4453:283-295.

An, C.F., Saha, S., Jenkins, J.N., Scheffler, B.E., Wilkins, T.A., and Stelly, D.M. (2007) Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278, 539-553.

Zhong, H., Lau, W.S., Sze, W.F., and Hung, Y.S. (2007) Shape recovery from turntable image sequence. Lect Notes Comput. Sc. 4844, 186-195.


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

Sze, S.H., Lu, Y., and Yang, Q.W. (2006). A polynomial time solvable formulation of multiple sequence alignment. J Comput Biol.13, 309-319.

Triplett, B.A., Kim, H.J., Hinchliffe, D., Sze, S.H., Thaxton, P., Stelly, D., and Chen, Z.J. (2007) Phytohormone regulation of cotton fiber development in vitroBiotechnology and Sustainable Agriculture 2006 and Beyond 153-156 (495).