Updated to February 2025, * Corresponding author, # Co-first authors

1. Desheng Zeng, Junqing Lv, Xu Li, Hongtao Liu*. (2025) The Arabidopsis blue-light photoreceptor CRY2 is active in darkness to inhibit root growth, Cell, 188(1), 60-76.

2. Yuhan Hao#, Zexian Zeng#, Minhang Yuan, Hui Li, Shisong Guo, Yu Yang, Shushu Jiang, Eva Hawara, Jianxu Li, Peng Zhang, Jiawei Wang, Xiufang Xin, Wenbo Ma, Hongtao Liu*. (2025) The blue-light receptor CRY1 serves as a switch to balance photosynthesis and plant defense, Cell Host & Microbe, 33(1), 137-150.

3. Zhiwei Zhao#, Fan Feng#, Yaqi Liu#, Yawen Liu#, Fei Wang, Yifan Ni, Huafeng Liang, Wenli Hu, Shanshan Wang, Yuhan Hao, Xu Li, Jigang Li, Jia-wei Wang, Peng Zhang & Hongtao Liu*. Blue-light-enhanced interaction between ZmCRY1s and GL2 modulates epidermal wax composition in Zea mays. Nat Commun (2025).

4. Yaqi Liu#, Zhiwei Zhao#, Xue Zhang, Yahui Hao, Fan Feng, Yuan Chen, Ji Wang, Miaolian Ma, Jianxu Li Fang Yu, Hongtao Liu*, and Peng Zhang*. Structural assembly of maize CRY-GL2 photosignaling complex provides insights into its regulatory role in cuticular wax biosynthesis. Sci. Adv(2025).

5. Chen Shi#, Xisen Yuan#, Libang Ma, Tangtao Wen, Xiaoyu Jia, Xu Li, Hongtao Liu*. (2025) "CRY2 interacts with PRR5 in a blue light-dependent manner to mediate blue light-regulated circadian period."Journal of Integrative Plant Biology.

6. Li Jigang*, and Hongtao Liu*. "Rhizosphere microbes attenuate plant response to shade." Cell Host & Microbe 33.6 (2025): 936-938.

7. Zhang Nan, and Liu HongTao*. (2025). "Switch on and off: Phospho-events in light signaling pathways". Journal of Integrative Plant Biology. 00: 1–15.

8. Pan Geng, Changxuan Li, Xuebo Quan, Jiaxuan Peng, Zhiying Yao, Yunhe Wang, Ming Yang, Yanning Wang, Yunfan Jin, Yan Xiong, Hongtao Liu, Yijun Qi, Peiguo Yang, Kai Huang* & Xiaofeng Fang*. "A thermosensor FUST1 primes heat-induced stress granule formation via biomolecular condensation in Arabidopsis." Cell research (2025): 1-14.

9. Hongtao Liu*, Jigang Li. "Plant photobiology: From basic theoretical research to crop production improvement." Journal of Integrative Plant Biology 66.5 (2024): 847-848.

10. Sridevi Sureshkumar, Champa Bandaranayake, Junqing Lv, Craig I. Dent, Prakash Kumar Bhagat, Sourav Mukherjee, Rucha Sarwade, Chhaya Atri, Harrison M. York, Prashanth Tamizhselvan, Nawar Shamaya, Giulia Folini, Benjamin G. Bergey, Avilash Singh Yadav, Subhasree Kumar, Oliver S. Grummisch, Prince Saini, Ram K. Yadav, Senthil Arumugam, Emanuel Rosonina, Ari Sadanandom, Hongtao Liu & Sureshkumar Balasubramanian*. (2024) SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana. Nature Plants, 10, 749–759.

11. Hongtao Liu*. (2023) Plant biology: Putting a break on stomatal opening, Current Biology, 33(6):R236-R237.

12. Xin Liu, Wei Jiang, Yali Li, Haozhen Nie, Lina Cui, Rongxia Li, Li Tan, Li Peng, Chao Li, Jinyan Luo, Ming Li, Hongxia Wang, Jun Yang, Bing Zhou, Pengcheng Wang, Hongtao Liu, Jian-Kang Zhu* & Chunzhao Zhao*. "FERONIA coordinates plant growth and salt tolerance via the phosphorylation of phyB." Nature Plants 9.4 (2023): 645-660.

13. Yuhan Hao, Zexian Zeng, Xiaolin Zhang, Dixiang Xie, Xu Li, Libang Ma, Muqing Liu and Hongtao Liu*. (2023) Green means go: Green light promotes hypocotyl elongation via Brassinoteroid signaling, Plant Cell, 35(5), 1304-1317.

14. Ling-Zi Li, Zhou-Geng Xu, Tian-Gen Chang, Long Wang, Heng Kang, Dong Zhai, Lu-Yi Zhang, Peng Zhang, Hongtao Liu, Xin-Guang Zhu & Jia-Wei Wang. "Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds." Nature Communications 14.1 (2023): 290.

15. Zhao Zhiwei, Dent Craig, Liang Huafeng, Lv Junqing, Shang Guandong, Liu Yawen, Feng Fan, Wang Fei, Pang Junhong, Li Xu, Ma Libang, Li Bing, Sureshkumar Sridevi, Wan Jia-Weig, Balasubramanian Sureshkumar, and Liu Hongtao*. (2022) CRY2 interacts with CIS1 to regulate thermosensory flowering via FLM alternative splicing, Nature Communications, Nov 17;13(1):7045.

16. Zhenhua Zhang, Chenjie Xu, Shiyu Zhang, Chen Shi, Hong Cheng, Hongtao Liu, Bojian Zhong*（2022） Origin and adaptive evolution of UV RESISTANCE LOCUS 8-mediated signaling during plant terrestrialization. Plant Physiology. 188(1):332-346.

17. Li X, Liang T, Liu H*. (2022) How plants coordinate their development in response to light and temperature signals. The Plant Cell. (invited review) 34:955-966.

18. Fang Luo, Qian Zhang, Hu Xin, Hongtao Liu, Hongquan Yang, Monika S. Doblin, Antony Bacic, Laigeng Li. "A Phytochrome B-PIF4-MYC2/MYC4 module inhibits secondary cell wall thickening in response to shaded light." Plant Communications 3.6 (2022).

19. Ma Libang, Li Xu, Zhao Zhiwei, Hao Yuhao, Shang Ruixin, Zeng Desheng, Liu Hongtao*. (2021) Light-Response Bric-A-Brack/Tramtrack/Broad proteins mediate cryptochrome 2 degradation in response to low ambient temperature. The Plant Cell. 33：3610-3620.

20. Shi, C., & Liu, H*. (2021). How plants protect themselves from ultraviolet-B radiation stress. Plant Physiology, 187(3), 1096-1103. (invited review)

21. Youping Li, Yiting Shi, Minze Li, Diyi Fu, Shifeng Wu, Jigang Li, Zhizhong Gong, Hongtao Liu, Shuhua Yang*. "The CRY2–COP1–HY5–BBX7/8 module regulates blue light-dependent cold acclimation in Arabidopsis." The Plant Cell 33.11 (2021): 3555-3573.

22. Liang T^#, Shi C^#, Peng Y, Tan H, Xin P, Yang Y, Wang F, Li X, Chu J, Huang J, Yin Y, Liu H*. (2020) Brassinosteroid-Activated BRI1-EMS-SUPPRESSOR 1 Inhibits Flavonoid Biosynthesis and Coordinates Growth and UV-B Stress Responses in Plants. The Plant Cell.

23. Xu Li^#, Cuicui Liu^#, Zhiwei Zhao, Dingbang Ma, Jinyu Zhang, Yu Yang, Yawen Liu, Hongtao Liu^*. (2020) COR27 and COR28 are Novel Regulators of the COP1–HY5 Regulatory Hub and Photomorphogenesis in Arabidopsis. The Plant Cell.

24. Shao K^#, Zhang X^#, Li X^#, Hao Y, Huang X, Ma M, Zhang M, Yu F, Liu H*, Zhang P*. (2020) The oligomeric structures of plant cryptochromes. Nature Structural & Molecular Biology. 27: 472–479

25. Yang Y, Liu H*. (2020) Coordinated shoot and root responses to light signaling in Arabidopsis. Plant Communications.

26. Yang Y, Zhang L, Chen P, Liang T, Li X, Liu H*. (2020) UVR8 interacts with MYB73/MYB77 in a UV-B-dependent manner, regulating auxin responses and lateral root development. EMBO Journal.

27. Yan-Qiu Tan, Yang Yang, An Zhang, Cui-Fang Fei, Li-Li Gu, Shu-Jing Sun, Wei Xu, Lingling Wang, Hongtao Liu, Yong-Fei Wang*. "Three CNGC family members, CNGC5, CNGC6, and CNGC9, are required for constitutive growth of Arabidopsis root hairs as Ca2+-permeable channels." Plant Communications 1.1 (2020).

28. Liu Hongtao, Rongcheng Lin, and Xing Wang Deng. "Photobiology: Light signal transduction and photomorphogenesis." Journal of Integrative Plant Biology 62.9 (2020): 1267.

29. Zhang N, Meng Y, Li X, Zhou Y, Ma L, Fu L, Schwarzlander M, Liu H, Xiong Y. (2019) Metabolite-mediated TOR signaling regulates the circadian clock in Arabidopsis. Proc Natl Acad Sci U S A.

30. Wang F, Yuan Z, Zhao Z, Li C, Zhang X, Liang H, Liu Y, Xu Q, Liu H*. (2019) Tasselseed5 encodes a cytochrome C oxidase that functions in sex determination by affecting jasmonate catabolism in maize. Journal of Integrative Plant Biology.

31. Wang F^#, Gao Y#, Liu Y#, Zhang X, Gu X, Ma D, Zhao Z, Yuan Z, Xue H and Liu H*. (2019) BES1 regulated BEE1 controls photoperiodic flowering downstream of blue light signaling pathway in Arabidopsis New Phytologist.

32. Wang J, Chen S, Jiang N, Li N, Wang X, Li Z, Li X, Liu H, Li L, Yang Y, Ni T, Yu C, Ma J, Zheng B, Ren G*.  (2019) Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana. Nucleic Acids Res. 47(15):7886-7900.

33. Tan Y, Yang Y, Zhang A, Fei CF, Gu L, Sun S, Xu W, Wang L, Liu H, Wang YF*. (2019) Three CNGC Family Members, CNGC5, CNGC6, and CNGC9, Are Required for Constitutive Growth of Arabidopsis Root Hairs as Ca2+-Permeable Channels. Plant Communications.

34. Liang T, Yang Y, Liu H*. (2018) Signal transduction mediated by the plant UV-B photoreceptor UVR8. New Phytologist. 221(3):1247-1252.

35. Liu Y, Li X, Ma D, Chen Z, Wang JW, Liu H*. (2018) CIB1 and CO interact to mediate CRY2 regulation of flowering. EMBO Reports. 19(10). pii: e45762.

36. Liang T, Mei S, Shi C, Yang Y, Peng Y, Ma L, Wang F, Li X, Huang X, Yin Y, Liu H*. (2018) UVR8 interacts with BES1 and BIM1 to regulate transcription and photomorphogenesis in Arabidopsis. Developmental Cell. 44:1-12.

37. Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H*.(2018)  UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nature Plants. 4:98-107.

38. Li X, Cai W, Liu Y, Li H, Fu L, Liu Z, Xu L, Liu H, Xu T, Xiong Y* (2017) Differential TOR activation and cell proliferation in Arabidopsis root and shoot apexes. Proc Natl Acad Sci U S A. 114(10):2765-2770.

39. He R#, Li X#, Zhong M#, Yan J, Ji R, Li X, Wang Q, Wu D, Sun M, Tang J, Lin J, Li H, Liu B, Liu H, Liu X*, Zhao X*, Chentao Lin, A photo-responsive F-box protein FOF2 regulates floral initiation by promoting FLC expression in Arabidopsis. The Plant Journal, 2017, 91, 788-801.

40. Li X^#, Ma D^#, Lu S#, Hu X, Huang R, Liang T, Xu T, Tobin E, Liu H*. (2016) Blue Light- and Low Temperature-Regulated COR27 and COR28 Play Roles in the Arabidopsis Circadian Clock. The Plant Cell. 28(11):2755-2769.

41. Ma D^#, Li X^#, Guo Y, Chu J, Fang S, Yan C, Noel J, Liu H*. (2016) Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light. Proc Natl Acad Sci U S A. 113(1):224-9.

42. Li L, Li X, Liu Y, Liu H*. (2016) Flowering responses to light and temperature. Sci China Life Science.

43. Gao QF, Gu LL, Wang HQ, Fei CF, Fang X, Hussain J, Sun SJ, Dong JY, Liu H, Wang YF*. (2016) Cyclic nucleotide-gated channel 18 is an essential Ca2+ channel in pollen tube tips for pollen tube guidance to ovules in Arabidopsis. Proc Natl Acad Sci U S A. 113(11):3096-101.

44. Zhang TQ, Lian H, Tang H, Dolezal K, Zhou CM, Yu S, Chen JH, Chen Q, Liu H, Ljung K, and Wang JW*. (2015) An intrinsic microRNA timer regulates progressive decline in shoot regenerative capacity in plants. Plant Cell.  27(2):349-60. 

45. Tan ST, Dai C, Liu HT, and Xue HW*. (2013) Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome 2 to regulate blue light signaling. Plant Cell. 25: 2618-2632.

46. Liu Y, Li X, Li K, Liu H*, Lin C (2013) Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in Arabidopsis, PLoS Genetics. 9(10): e1003861 (Corresponding author)

47. Liu H*, Wang Q, Liu Y, Zhao X, Lin C* (2013) The Arabidopsis photoreceptors CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms. Proc Natl Acad Sci U S A. 43：17582-17587 (Co-corresponding author)

48. Liu H*, GomezG, Lin S, Lin S, Lin C (2012) Optogenetic control of transcription in zebrafish. PLoS One. 2012;7(11):e50738.

49. Wang Q, Fristedt R, Yu X, Chen Z, Liu H et al (2012). The γ-carbonic anhydrase subcomplex of mitochondrial complex I is essential for development and important for photomorphogenesis of Arabidopsis. Plant Physiology.

50. Li X, Wang Q, Yu X, Liu H, Yang H et al (2011) Arabidopsis cryptochrome 2 (CRY2) functions by the photoactivation mechanism distinct from the tryptophan (trp) triad-dependent photoreduction. Proc Natl Acad Sci U S A. 108(51):20844-20849.

51. Liu H, Liu B. Zhao C, Pepper M and Lin C (2011). The action mechanisms of plant cryptochromes, Trends in Plant Sciences,16:684-691.

52. Lu S*, Liu H*, Knowles S, Li J, Ma L, Tobin E, Lin C. (2011). A role for protein kinase CK2 alpha subunits in the Arabidopsis circadian clock.  (co-first author) Plant Physiology. 157: 1537-1545.

53. Zuo Z^#, Liu H^#, Liu B^#, Liu X, Lin C.(2011) Blue Light-Dependent Interaction of CRY2 with SPA1 Regulates COP1 activity and Floral Initiation in Arabidopsis. (co-first author) Current Biology. 21:841-847.

54. Liu B, Zuo Z, Liu H, Lin C. (2011). Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light. Gene & Development. 25:1004-1009.

55. Liu B, Liu H, Zhong D, and Lin C. (2010). Searching for a photocycle of the Cryptochrome photoreceptors. Current Opinion in Plant Biology. 13:1-9.

56. Liu H, Yu X, Li K, Klejnot J, Yang H, Lisiero D, Lin C. (2008). Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science. 322:1535-1539.

57. Liu HT, Gao F, Li GL, Han JL, Liu DL, Sun DY, Zhou RG. (2008). The calmodulin-binding protein kinase 3 is part of heat-shock signal transduction in Arabidopsis thaliana. The Plant Journal. 55(5):760-73.

58. Liu HT, Li GL, Chang H, Sun DY, Zhou RG, Li B. (2007). Calmodulin-binding protein phosphatase PP7 is involved in thermotolerance in Arabidopsis. Plant Cell & Enviroment. 30(2):156-64.

59. Liu HT, Gao F, Sun DY, Zhou RG. (2006). Primary evidence for involvement of IP₃ in heat-shock signal transduction in Arabidopsis. Cell Research. 16(4):394-400.

60. Liu HT, Sun DY, Zhou RG. (2005). Ca²⁺ and AtCaM3 are Involved in the Expression of Heat Shock Protein Gene in Arabidopsis. Plant Cell & Environment. 28:1276-1284.

61. Li B, Liu HT，Sun DY, Zhou RG. (2004). Ca²⁺ and Calmodulin modulate DNA-binding activity of maize heat shock transcription factor in vitro. Plant Cell Physiology. 45(5): 627-634.

62. Liu HT，Li B, Shang ZL, Mu RL Sun DY, Zhou RG. (2003). Calmodulin is involved in heat shock signal transduction in wheat. Plant Physiology. 132(7): 1186-1195.