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PUBLICATIONS

*equal contribution, §corresponding author

  1. Bai, Y., Shabbir, S., Chen, Y., Morgante, F., Ludwig, M., Park, S.-Y., Acharya, M., Li, Y., Ali, S., Trudnak, A., Rajesh, M., Kreitman, M., & Zhuang, X.§ 2026. Outbred Drosophila populations reveal diet-dependent genetic effects on development time. bioRxiv. doi.org/10.64898/2026.06.05.730474

  2. Lamba, V., Alverson, A., Danne, J., & Zhuang, X.§ 2026. Gene loss under constant cold reveals "natural knockout" loci in Antarctic notothenioid fishes. bioRxiv. doi.org/10.64898/2026.06.06.730616

  3. Rives, N., Bajpai, P., & Zhuang, X.§ 2026. Transposable elements facilitate the de novo origin of antifreeze protein and the diversification of its gene family in snailfishes. bioRxiv. doi.org/10.64898/2026.04.28.721326

  4. Stewart, M., Pradhan, H., Zhuang, X., & Wang, Y. 2026. Disruption of Drosophila melanogaster larval locomotion caused by silver ions. bioRxiv. doi.org/10.64898/2026.04.03.716380

  5. Cao X, Miyamoto MM, Yuan J, Bajpai P, Zhuang X§, & Ding S§. (2025). An amino acid polymorphism in the membrane progesterone receptor alpha protein is tied to female sexual maturity in the large yellow croaker (Larimichthys crocea). Gene, 149409.

  6. Alatawi I, Xiong H, Chiwina K, Alkabkabi H, Luo Q, Joshi, NK, Sun X, Zhuang X, Ling K, & Shi A. (2025). Identification of Salt Tolerance and Stress Response in US Department of Agriculture Tomato Germplasm at the Seedling Stage. HortScience, 60(1), 56-65.

  7. Rives N*, Lamba V*, Cheng C.-H.C., Zhuang X§. (2024). Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence. Mol. Biol. Evol. DOI: 10.1093/molbev/msae182.

  8. Yuan J*, Zhuang X*, Wu L, Lin H, Li Y, Wu L, Yao J, Liu J, Ding S. (2024). Assessing the population genetic structure of yellow croaker in China: Insights into the ecological and genetic consequences of artificial breeding on natural populations. Aquaculture, 30:741026.

  9. Cao X, Deng S, Liu Q, Wu L, Zhuang X, Ding S. (2023). Important role of the Ihh signaling pathway in initiating early cranial remodeling and morphological specialization in Cromileptes altivelis. Animals, 13(24), 3840.

  10. Bilyk K, Zhuang X, Papetti C (2023). Positive and relaxed selective pressures have both strongly influenced the evolution of cryonotothenioid fishes during their radiation in the freezing Southern Ocean. Genome Biol. Evol. 15(4).

  11. Li Y, Lou F, Liu S, Hai L, Xiang J, Shan B, Lin L§, Zhuang X§. (2022). Differentiation and temperature adaptation of Pampus echinogaster based on genome-wide SNPs. Front. Mar. Sci. 1194. DOI: 10.3389/fmars.2022.936217

  12. Zhuang X, Cheng C.-H.C. (2021). Propagation of a de novo gene under natural selection:  anti-freeze glycoprotein genes and their evolutionary history in codfishes. Genes. 12(11):1777.

  13. Yuan J, Lin H, Wu L, Zhuang X, Ma J, Kang B, Ding S. (2021). Resource Status and Effect of Long-term Stock Enhancement of Large Yellow Croaker in China. Front. Mar. Sci. 1218.

  14. Bilyk K, Zhuang X, Vargas-Chacoff L, and Cheng CH-C. (2021). Evolution of chaperome gene expression and regulatory elements in the Antarctic Notothenioid fishes. Heredity. 1-17.

  15. Cheng C.-H.C., Zhuang X. (2020). Molecular Origins and Mechanisms of Fish Antifreeze Evolution. In: Ramløv H., Friis D. (eds) Antifreeze Proteins Volume 1. Springer, Cham. https://doi.org/10.1007/978-3-030-41929-5_9

  16. Zhuang X, Yang C, Murphy KR, Cheng C.-H.C. (2019). Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proc Natl Acad Sci USA. 116(10):4400-4405

  17. Bilyk KT*, Zhuang X*, Cheng C.-H.C. (2019). A Tale of Two Genes: Divergent Evolutionary Fate of Haptoglobin and Hemopexin in the Hemoglobin Lacking Antarctic Icefishes. J Exp Biol. 222(6)

  18. Chen L, Lu Y, Li W, Ren Y, Yu M, Jiang S, Fu Y, Wang J, Peng S, Bilyk KT, Murphy KR, Zhuang X, Hune M, Zhai W, Wang W, Xu Q, Cheng C.-H.C. (2019). The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonia robalo genomes. Gigascience. 8(4), giz016

  19. Zhuang X, Murphy KR, Ghigliottic L, Pisanoc E, Cheng C.-H.C. (2018). Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. Marine Genomics. 39: 73-84

  20. Zhuang X. (2014). Creating sense from non-sense DNA: de novo genesis and evolutionary history of antifreeze glycoprotein gene in northern cod fishes (Gadidae). Ph.D. Dissertation, University of Illinois at Urbana-Champaign

  21. Zhuang X*, Qu M*, Zhang X, Ding S. (2013). A comprehensive description and evolutionary analysis of 22 grouper (Perciformes, Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS ONE. 8(8): e73561.

  22. Welsh D, Zhou M, Mussmann SM, Fields LG, Thomas CL, Pearish SP, Kilburn SL, Parker JL, Stein LR, Bartlett JA, Bertram CR, Bland TJ, Laskowski KL, Mommer BC, Zhuang X, Fuller RC. (2013). The effects of age, sex, and habitat on body size and shape of the blackstripe topminnow, Fundulus notatus (Cyprinodontiformes: Fundulidae) (Rafinesque 1820). Biol J Linnean Soc. 108(4):784-789

  23. Zhuang X, Yang C, Fevolden S, Cheng C.-H.C. (2012). Protein genes in repetitive sequence — antifreeze glycoproteins in Atlantic cod genome. BMC Genomics. 13(1):293

  24. Zhuang X, Cheng C.-H.C. (2010). ND6 gene “lost” and found: evolution of mitochondrial gene rearrangement in Antarctic notothenioids. Mol Biol Evol. 27(6):1391–1403

  25. Zhuang X, Ding S, Wang J, Wang Y, and Su Y. (2009). A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara). Mol Ecol Res. 9(6):1551–1553

  26. Zhuang X, Qin Y, Su Y, Wang J, Ding S. (2007). Cloning and sequencing of FlaA gene of Vibrio harveyi and construction of its eukaryotic expression recombinant plasmid. Acta Oceanol Sin. 29(6):74–79

  27. Qin Y, Su Y, Wang S, Wang J, Zhuang X. (2007). Study on the expression of recombinant plasmid pcFlaA in Epinephelus awoara. High Technology Letters. 17(6):14–17

  28. Zhuang X*, Ding S*, Guo F, Wang J, Su Y, Zhang Q, Li Q. (2006). Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences. Science in China Ser C– life Science. 36(1):27–34 [English Version: 49(3):235–242]

  29. Ding S, Wang Y, Wang J, Zhuang X, Su Y, You Y, Li QF. (2006). Molecular phylogenetic relationships of 30 groupers species in China Seas based on 16S rDNA fragment sequences. Acta Zool Sin. 52(3):504–513

  30. Du J, Ding S, Wang J, Wang S, Zhuang X, You Y. (2006). The identification of Epinephelus malabaricus and E. coioides based on DNA markers. Acta Oceanol Sin. 28(6):94–99

  31. Wang Y, Ding S, Wang J, Zhuang X, Su Y. (2006). A review on molecular phylogenetic studies of groupers. J Xiamen Univ (Natural Science). 45(2):132–135

Contact Email: xz036(at)uark(dot)edu

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