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1. Wang K, He SP, Zhu YX (2025) Cotton2035: From genomics research to optimized breeding. Mol. Plant., 18, 298–312.
2. Zhang L, Wen XP, Chen X, Zhou YF, Wang K, Zhu YX (2024) GhCASPL1 regulates secondary cell wall thickening in cotton fibers by stabilizing the cellulose synthase complex on the plasma membrane. Journal of Integrative Plant Biology, 66 (12) , 2632-2647.
3. Huang G, Bao ZG, Feng L, Zhai JX, Wendel JF, Cao XF, Zhu YX (2024) A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nature Genetics,56, 1953-1963.
4. Li X, Huang G, Zhou YF, Wang K, Zhu YX (2024) GhATL68b Regulates Cotton Fiber Cell Development by Ubiquitinating the Enzyme Required for β-oxidation of Polyunsaturated Fatty Acids. Plant Communications. 5, 101003.
5. Li WW, Chen X, Yu JN, Zhu YX (2024) Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. Sci. China Life Sci. 67 (6), 1266-1279.
6. Chen X, Li WW, Gao J, Wu ZG, Du J, Zhang XM, Zhu YX (2024) Arabidopsis PDLP7 modulated plasmodesmata function is related to BG10-dependent glucosidase activity required for callose degradation. Science Bulletin, 69 (19), 3075-3088.
7. Guo BY, Eun-Ji Kim, Zhu YX, Wang K, Russinova E (2024) Shaping Brassinosteroid Signaling through Scaffold Proteins. Plant and Cell Physiology, 65, 1608-1617.
8. Eun-Ji Kim, Zhang Ch, Guo BY, Thomas Eekhout, Anaxi Houbaert, Jos R. Wendrich, Niels Vandamme, Manish Tiwari, Claire Simon-Vezo, Isabelle Vanhoutte, Yvan Saeys, Wang K, Zhu YX, Bert De Rybel and Eugenia Russinova (2023) Cell type–specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division. PNAS, 120, e2303758120.
9. Guo JP, Wang HY, Guan W, Guo Q, Wang J, Yang J, Peng YX, Shan JH, Gao MY, Shi SJ, Shangguan XX, Liu BF, Jing SL, Zhang J, Xu CX, Huang J, Rao WW, Zheng XH, Wu D, Zhou C, Du B, Chen RZ, Zhu LL, Zhu YX, Linda L. Walling, Zhang QF and He GC (2023) A tripartite rheostat controls self-regulated host plant resistance to insects. Nature 618, 799–807.
10. Li Yang, Xi W, Hao JF, Zhang L, Wen XP, Wu ZG and Zhu YX (2023) A Novel Tandem Zinc Finger Protein in Gossypium hirsutum, GhTZF2, Interacts with GhMORF8 to Regulate Cotton Fiber Cell Development. Agronomy-Basel, 13, 519.
11. Yang Y, Wen XP, Wu ZG, Wang K and Zhu YX (2023) Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton. Sci. China Life Sci. 66, 1711-1724.
12. Wen XP, Chen ZW, Yang ZR, Wang MJ, Jin SX, Wang GD, Li Z, Wang LJ, Li JY, Saeed S, He SP, Wang Z, Wang K, Kong ZS, Li FG, Zhang XL, Chen XY and Zhu YX (2023) A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. Sci. China Life Sci 66, 2214-2256.
13. Zhang, L., Yang, Y., Mu, C., Liu, M., Ishida, T., Sawa, S., Zhu, Y., and Pi, L. (2022) Control of Root Stem Cell Differentiation and Lateral Root Emergence by CLE16/17 Peptides in Arabidopsis. Front Plant Sci 13, 869888.
14. Gao J, Huang G, Chen X and Zhu YX (2022) PROTEIN S-ACYL TRANSFERASE 13/16 (PAT13/PAT16) modulate disease resistance by S-acylation of the NB-LRR protein R5L1 in Arabidopsis. Journal of Integrative Plant Biology, 64 (9), 1789-1802.
15. Wu ZG, Xi W, Han ZX, Wu YH, Guan YZ and Zhu YX (2022) Genome-Wide Comparative Analysis of Transposable Elements by Matrix-TE Method Revealed Indica and Japonica Rice Evolution. Agronomy-Basel, 12 (7), 1490.
16. Wen XP, Zhai YF, Zhang L, Chen YJ, Zhu ZY, Chen G, Wang K and Zhu YX (2022) Molecular studies of cellulose synthase supercomplex from cotton fiber reveals its unique biochemical properties. Sci. China Life Sci. 65, 1776–1793.
17. Liu W, Sun J, Li J, Liu C, Si F, Yan B, Wang Z, Song X, Yang Y, Zhu YX and Cao XF (2022). Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line. J. Genet. Genomics. 49(7) , 624-635.
18. Li S, Li L, Fan W, Ma S, Zhang C, Kim JC, Wang K, Russinova E, Zhu YX, and Zhou Y (2022). LeafNet: A tool for segmenting and quantifying stomata and pavement cells. Plant Cell. 34, 1171-1188.
19. 朱玉贤（2021）富阳籍中科院院士朱玉贤：我与即将成为“90后”的父亲。富阳日报。
20. Huang G, Huang JQ, Chen XY, Zhu YX (2021) Recent Advances and Future Perspectives in Cotton Research. Annual Review of Plant Biology, 72: 437–462.
21. Huang G, Wu Z, Percy RG, Bai M, Li Y, Frelichowski JE, Hu J, Wang K, Yu, JZ, Zhu YX (2020) Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics., 52:515-524.
22. Wang ZH，Li Y, Hou B，Pronobis, MI, Wang MQ, Wang YM, Cheng GC, Weng WN, Wang YQ, Tang YF, Xu XF, Pan R, Lin F, Wang N, Chen ZQ, Wang SW, Ma LZ, Li YR, Huang DL, Jiang L, Wang ZQ, Zeng WF, Zhang Y, Du XM, Lin Y, Li ZQ, Xia QY, Geng J, Dai HP, Yu Y, Zhao XD, Yuan Z, Yan J, Nie QH, Zhang XQ, Wang K, Chen FL, Zhang Q, Zhu YX, Zheng S, Poss KD, Tao SC, Meng S (2020) An array of 60,000 antibodies for proteome-scale antibody generation and target discovery. Sci. Adv. 6: eaax2271.
23. Liu NJ, Zhang T, Liu ZH, Chen X, Guo HS, Ju BH, Zhang YY, Li GZ, Zhou QH, Qin YM, Zhu YX (2020) Phytosphinganine affects plasmodesmata permeability via facilitating PDLP5-stimulated callose accumulation in Arabidopsis. Mol. Plant., 13: 128-143.
24. Wang, K., Wang, D., Zheng, X., Qin, A., Zhou, J., Guo, B., Chen, Y., Wen, X., Ye, W., Zhou, Y., Zhu, YX (2019). Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nature Communications, 10: 4714.
25. Xia, Y.Y., Huang, G., Zhu, YX (2019). Sustainable plant diseases control: biotic information flow and behavior manipulation. SCIENCE CHINA Life Sciences. 62: 1710-1713.
26. Du XM, Gai H, He SP, Yang ZE, Sun GF, Ma XF, Li N, Zhang XY, Sun JL, Liu M, Jia YH, Pan ZE, Gong WF, Liu ZH, Zhu HQ, Ma L, Liu FY, Yang DG, Wang F, Fan W, Gong Q, Peng Z, Wang LR, Wang XY, Xu SJ, Shang HH, Lu CR, Zheng HK, Huang SW, Lin T, Zhu YX, Li FG. (2018) Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature Genetics, 50: 796-802.
27. Wu ZG; Yang Y; Huang G; Lin J, Xia YY, Zhu YX (2017) Cotton functional genomics reveals global insight into genome evolution and fiber development, J Genet Genomics, 44：511-518.
28. Zhang YZ, Jiao Y, Jiao HY, Zhao HB, Zhu YX. (2017) Two-step functional innovation of the stem-cell factors WUS/WOX5 during plant evolution. Mol. Biol. Evol. 34: 640-653.
29. Zhu YX. (2016) The post-genomics era of cotton. Science China-Life Sciences, 59: 109-111.
30. Jiao Y, Zhang YZ, Zhu YX (2016). Recent advances in the research for the homolog of breast cancer associated gene AtROW1 in higher plants. Science China Life Sciences, 59, 8:825-831
31. Wang k, Hang G, Zhu YX. (2016) Transposable elements play an important role during cotton genome evolution and fiber cell development. Science China-Life Sciences, 59: 112-121.
32. Xiao GH, Wang K, Huang G, Zhu YX. (2016) Genome-scale analysis of the cotton KCS gene family revealed a binary mode of action for gibberellin A regulated fiber growth. Journal of Integrative Plant Biology, 58: 577-589.
33. Xiao GH, Wang K, Huang G, Zhu YX. (2015) Genome-scale analysis and characterization of KCS gene family in cottons revealed a new mode of action for GA regulated fiber growth. Journal of Integrative Plant Biology, DOI: 10.1111/jipb.12429.
34. Liu GJ, Xiao GH, Liu NJ, Liu D, Chen PS, Qin YM, Zhu YX. (2015) Targeted lipidomics studies reveal that linolenic acid promote cotton fiber elongation by activating phosphatidylinositol and phosphatidylinositol monophosphate biosynthesis. Mol Plant, 8: 911-921.
35. Li, F.G., Fan, G.Y., Lu, C.R., Xiao, G.H., Zou, C.S., Kohel, R.J., Ma, Z.Y., Shang, H.H., Ma, X.F., Wu, J.Y., Liang, X.M., Huang, G., Percy, R.G., Liu, K., Yang, W.H., Chen, W.B., Du, X.M., Shi, C.C., Yuan, Y.L., Ye, W.W., Liu, X., Zhang, X.Y., Liu, W.Q., Wei, H.L., Wei, S.J., Huang, G.D., Zhang, X.L., Zhu, S.J., Zhang, H., Sun, F.M., Wang, X.F., Liang, J., Wang, J.H., He, Q., Huang, L.H., Wang, J., Cui, J.J., Song, G.L., Wang, K.B., Xu, X., Yu, J.Z., Zhu, Y.X., Yu S.X.. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat. Biotechnol, 33 (2015),524-530.
36. Zhang, Y.Z., Jiao, Y., Liu, Z.H., Zhu, Y.X. ROW1 maintains quiescent centre identity by confining WOX5 expression to specific cells. Nature communications 2015 doi: 10.1038/ncomms6003.
37. Li, F. G., Zhu, Y. X., Wang, J. Yu, S. X et al , Genome sequence of the cultivated cotton Gossypium arboretum , Nature Genetics , 2014 , 46: 567-572
38. Li, Q., Xiao, G. H., and Zhu, Y. X , Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns , Molecular Plant , 2014 , 7: 829-840
39. Zhu, Y. X , Regulation of cotton lint growth. In: McGraw-Hill , Yearbook of Science & Technology , 2014 , 319-322
40. Jin, X., Pang, Y., Jia, F. X., Xiao, G. H., Li, Q., Zhu, Y. X , A potential role for CHH DNA methylation in cotton fiber growth patterns , PLOS ONE , 2013 , 8: e60547
41. Zhu, Y. X. and Li, F. G , The Gossypium raimondii genome, a huge leap forward in cotton genomics , J. Integrative Plant Biology , 2013 , 55: 570-571
42. Jin, X., Li, Q., Xiao, G. H., Zhu, Y. X , Using genome-referenced expressed sequence tag assembly to analyze the origin and expression patterns of Gossypium hirsutum transcripts , J. Integrative Plant Biology , 2013 , 55: 576-585
43. Wang, K. B., Zhu, Y. X. , Wang, J., Yu, S. X. et al , The draft genome of a diploid cotton Gossypium raimondii , Nature Genetics , 2012 , 44: 1098-1103
44. Li, Q., Jin, X., Zhu, Y. X , Identification and analyses of miRNA genes in allotetraploid Gossypium hirsutum fiber cells based on the sequenced diploid G. raimondii genome , Journal of Genetics and Genomics , 2012 , 39: 351-360
45. Qin, Y. M. and Zhu Y. X , How cotton fibers elongate: a tale of linear cell-growth mode , Curr. Opin. Plant Biol , 2011 , 14 : 106-111
46. Wang, H., Mei, W. Q., Qin, Y. M. and Zhu, Y. X , 1-Aminocyclopropane-1-carboxylic acid synthase 2 is phosphorylated by calcium-dependent protein kinase 1 during cotton fiber elongation , Acta Biochim. et Bioph. Sin , 2011 , 43: 654-661
47. Pang, C.Y., Wang, H., Pang, Y., Xu, C., Jiao, Y., Qin, Y.M., Western, T.L., Yu, S.X. and Zhu, Y.X. , Comparative proteomics indicate that biosynthesis of pectic precursors is important for cotton fiber and Arabidopsis root hair elongation , Molecular Cellular Proteomics , 2010 , 9: 2019-2033
48. Pang, Y., Wang, H., Song, W. Q. and Zhu, Y. X , The cotton ATP synthase δ1 subunit is required to maintain a higher ATP⁄ADP ratio that facilitates rapid fibre cell elongation , Plant Biology , 2010 , 12: 903-909
49. Zhu, Y. X , The epigenetic involvement in plant hormone signaling , Chinese Science Bulletin , 2010 , 55: 2198-2203
50. Mei, W. Q., Qin, Y. M., Song, W. Q., Li, J. and Zhu, Y. X , Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation , J. Genet. Genomics , 2009 , 36: 141-150
51. Song, W.Q., Qin, Y.M., Saito, M., Shirai, T., Pujol, F.M., Kastaniotis, A.J., Hiltunen, J.K. and Zhu, Y.X , Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif , Journal of Experimental Botany , 2009 , 60: 1839–1848
52. Han, P. and Zhu, Y. X , BARD1 may be renamed ROW1 because it functions mainly as a REPRESSOR OF WUSCHEL1 , Plant Signaling & Behavior , 2009 , 4: 52-54
53. Han P, Li Q, Zhu YX , Mutation in the Arabidopsis BARD1 BRCT Domain Releases WUSCHEL Expression from the Organizing Center , The Plant Cell , 2008 , 20:1482-1493
54. Qu, L. J. and Zhu, Y. X , Transcription factor families in Arabidopsis: major progress and outstanding issues for future research , Curr. Opin. Plant Biol , 2007 , 9: 544-549
55. Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, Zhu YX , Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis , The Plant Cell , 2007 , 19: 3692-3704
56. Shi YH, Zhu SW, Mao X, Feng JX, Qin YM, Zhang L, Cheng J, Wei L, Wang ZY, Zhu YX , Transcriptome profiling, molecular biological and physiological studies reveal a major role for ethylene in cotton fiber cell elongation , The Plant Cell , 2006 , 18: 651-664
57. Gong, W et al. , Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes , Plant Physiol , 2004 , 135: 773-782
58. Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC and Zhu YX , Isolation and Analyses of Genes Preferentially Expressed During Early Cotton Fiber Development by Subtractive PCR and cDNA Array , Nucleic Acids Res. , 2003 , 31: 2534-2543
59. Zhu, Y. X., Tepperman, J. M., Fairchild, C. and Quail, P. H , Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3 , Proc. Natl. Acad. Sci. USA , 2000 , 97: 13419-13424
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