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1. Jihua Ouyang, Guangkun Han, Jinsong Chen, Jiaxuan Hu, Lei Luo, Hao Zhang, Chunliu Lan, Qianyu Lu, Yin Gou, Hanjie Gu, Yonghua Hu, Peng Zhang, Anlong Xu, Shengfeng Huang *. Identification and characterization of a novel ApeC-containing transmembrane protein family in parasitic flatworms. International Journal of Biological Macromolecules . 2025 May; 309: 142866. https://doi.org/10.1016/j.ijbiomac.2025.142866
2. Panwei Weng#, Mengjiao Lan#, Hao Zhang, Huiping Fan, Xiao Wang, Chenrui Ran, Zirui Yue, Jiaxuan Hu, Anlong Xu and Shengfeng Huang* . Both IRAK3 and IRAK1 Activate the MyD88-TRAF6 Pathway in Zebrafish. Journal of Immunology . 2024. https://doi.org/10.4049/jimmunol.2400054
3. Shenghui Chen, Huiping Fan, Chenrui Ran, Yun Hong, Huixiong Feng, Zirui Yue, Hao Zhang, Pierre Pontarotti, Anlong Xu* and Shengfeng Huang* . The IL-17 Pathway Intertwines with Neurotrophin and TLR/IL-1R Pathways Since Its Domain Shuffling Origin. Proc Natl Acad Sci U S A . 2024 May 7; 121(19): e2400903121. https://doi.org/10.1073/pnas.2400903121
4. Zirui Yue, Zhaoyu Fan, Hao Zhang, Buhan Feng, Chengyi Wu, Shenghui Chen, Jihua Ouyang, Huiping Fan, Panwei Weng, Huixiong Feng, Shangwu Chen, Meiling Dong, Anlong Xu* and Shengfeng Huang* . Differential roles of the fish chitinous membrane in gut barrier immunity and digestive compartments. EMBO Reports . 2023 Feb 28; 24(4): e56645. https://doi.org/10.15252/embr.202256645
5. Jin Li, Shumin Liu, Yang Zhang, Qiuyun Huang, Hao Zhang, Jihua OuYang, Fan Mao, Huiping Fan, Wenjie Yi, Meiling Dong, Anlong Xu* and Shengfeng Huang* . Two Novel Mollusk Short-form ApeC-containing Proteins Act as Pattern Recognition Proteins for Peptidoglycan. Frontiers in Immunology . 2022 Oct 7; 13:971883. https://doi.org/10.3389/fimmu.2022.971883
6. Jin Li, Yuhui Li, Zhaoyu Fan, Shenghui Chen, Xinyu Yan, Zirui Yue, Guangrui Huang, Shumin Liu, Hao Zhang, Meiling Dong, Anlong Xu* and Shengfeng Huang* . Two amphioxus ApeC-containing proteins bind to microbes and inhibit the TRAF6 Pathway. Frontiers in Immunology . 2021 Jul 30;12:715245. https://doi.org/10.3389/fimmu.2021.715245
7. Yuhui Li, Jin Li, Xinyu Yan, Shenghui Chen, Chengyi Wu, Huiqing Huang, Yi Shi, Guangrui Huang, Meiling Dong, Anlong Xu* and Shengfeng Huang* . Broad distribution, high diversity and ancient origin of the ApeC-containing proteins. Molecular Phylogenetics and Evolution . 2021 Feb; 155:107009. https://doi.org/10.1016/j.ympev.2020.107009
8. Yi Shi, Zhaoyu Fan, Guang Li, Lei Zhang, Zirui Yue, Xinyu Yan, Anlong Xu and Shengfeng Huang* . The family of amphioxus chitin synthases offers insight into the evolution of chitin formation in chordates. Molecular Phylogenetics and Evolution . 2020 Feb; 143: 106691. https://doi.org/10.1016/j.ympev.2019.106691
9. Xinyu Yan, Shenghui Chen, Huiqing Huang, Ting Peng, Mengjiao Lan, Xia Yang, Meiling Dong, Shangwu Chen, Anlong Xu*, and Shengfeng Huang* . Functional variation of IL-1R associated kinases in the conserved MyD88-TRAF6 pathway during evolution. Journal of Immunology . 2020 Feb 15; 204(4):832-843. https://doi.org/10.4049/jimmunol.1900222
10. Shengfeng Huang# , Xin Tao#, Shaochun Yuan#, Yuhang Zhang, Peiyi Li, Helen A. Beilinson, Ya Zhang, Wenjuan Yu, Pierre Pontarotti, Hector Escriva, Yann Le Petillon, Xiaolong Liu, Shangwu Chen, David G. Schatz, Anlong Xu. Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination. Cell . 2016 Jun 30;166(1):102-14. http://dx.doi.org/10.1016/j.cell.2016.05.032
11. Shengfeng Huang , Zelin Chen, Xinyu Yan, Ting Yu, Guangrui Huang, Pierre Antoine Pontarotti, Qingyu Yan, Hongchen Zhao, Jie Li, Ping Yang, Ruihua Wang, Rui Li, Xin Tao, Ting Deng, Yiquan Wang, Guang Li, Qiujin Zhang, Sisi Zhou, Leiming You, Shaochun Yuan, Yonggui Fu, Fenfang Wu, Meiling Dong, Shangwu Chen, Anlong Xu. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nature communications . 2014 Dec 19; 5:5896. http://dx.doi.org/10.1038/ncomms6896
12. Guangrui Huang#, Shengfeng Huang# , Xinyu Yan, Ping Yang, Jun Lia, Weiya Xua, Lingling Zhang, Ruihua Wang, Yingcai Yu, Shaochun Yuan, Shangwu Chen, Guangbin Luo and Anlong Xu. Two apextrin-like proteins mediate extracellular and intracellular bacterial recognition in amphioxus. Proc Natl Acad Sci U S A . 2014 Sep 16;111(37):13469-74. http://dx.doi.org/10.1073/pnas.1405414111
13. Shengfeng Huang# , Zelin Chen#, Guangrui Huang, Ting Yu, Jie Li, Yonggui Fu, Shaochun Yuan, Shangwu Chen, Anlong Xu. HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Research . 2012 May; 22(8): 1581-1588. http://dx.doi.org/10.1101/gr.133652.111
14. Shengfeng Huang# , Xin Wang#, Qingyu Yan, Lei Guo, Shaochun Yuan, Meiling Dong, Shangwu Chen, Anlong Xu. The evolution and regulation of the mucosal immune complexity in the basal chordate amphioxus. Journal of Immunology . 2011 Feb 15;186(4):2042-55. http://dx.doi.org/10.4049/jimmunol.1001824
15. Shengfeng Huang# , Shaochun Yuan, Lei Guo, Yanhong Yu, Jun Li, Tao Wu, Tong Liu, Manyi Yang, Kui Wu, Huiling Liu, Jin Ge, Yingcai Yu, Huiqing Huang, Meiling dong, Cuiling Yu, Shangwu Chen, Anlong Xu. Genomic Analysis of the Immune Gene Repertoire of Amphioxus Reveals Extraordinary Innate Complexity and Diversity. Genome Research . 2008 Jul;18(7):1112-26. http://dx.doi.org/10.1101/gr.069674.107
16. Shenghui Chen, Xianan Fu, Ruihua Wang, Mingshi Li, Xinyu Yan, Zirui Yue, Shang-Wu Chen, Meiling Dong, Anlong Xu, Shengfeng Huang*. SUMO and PIAS repress NF-κB activation in a basal chordate. Fish and Shellfish Immunology . 2023 Jun;137: 108754. https://doi.org/10.1016/j.fsi.2023.108754
17. Xianan Fu, Ruihua Wang, Mingshi Li, Xinyu Yan, Huiqing Huang, Jin Li, Shenghui Chen, Zirui Yue, Shangwu Chen, Yingqiu Li, Meiling Dong, Anlong Xu*, Shengfeng Huang* . Chordate PIAS proteins act as conserved repressors of the TRAF6 self-polyubiquitination. Developmental & Comparative Immunology . 2020 Mar; 104:103554. https://doi.org/10.1016/j.dci.2019.103554
18. Muniba Faiza, Dongming Lan, Shengfeng Huang* , Yonghua Wang*. UPObase: An online database of unspecific peroxygenases. Database . 2019: baz122. https://doi.org/10.1093/database/baz122
19. Muniba Faiza, Shengfeng Huang* , Dongming Lan and Yonghua Wang*. New insights on unspecific peroxygenases: superfamily reclassification and evolution. BMC Evolutionary Biology . 2019 Mar 13; 19(1):76. https://doi.org/10.1186/s12862-019-1394-3
20. 严信宇 #, 黄盛丰 #, 徐安龙 , 人类抗体重排机制的起源 , 科技导报 , 2018;36(7):43-47. [ 北大中文核心期刊 ]
21. Shengfeng Huang*, Mingjin Kang and Anlong Xu. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics . 2017 Aug 15;33(16):2577-2579. https://doi.org/10.1093/bioinformatics/btx220 .
22. Ruihua Wang#, Shengfeng Huang# , Xianan Fu, Guangrui Huang, Xinyu Yan, Zirui Yue, Shangwu Chen, Yingqiu Li and Anlong Xu. The conserved ancient role of chordate PIAS as a multilevel repressor of the NF-κB pathway. Scientific Reports. Scientific Reports . 2017 Dec 6;7(1):17063. https://doi.org/10.1038/s41598-017-16624-7 . #co-first author
23. Jose Ricardo Poole # , ShengFeng Huang# , Anlong Xu, Justine Bayet and Pontarotti Pierre. The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates. Immunogenetics . 2017 Jun;69(6):391-400. https://doi.org/10.1007/s00251-017-0979-5 .
24. Xinyu Yan, Wenbin Meng, Fenfang Wu, Anlong Xu and Shengfeng Huang* . The Nuclear DNA Content and Genetic Diversity of Lampetra morii. PLoS ONE . 2016 Jul 7;11(7):e0157494. http://dx.doi.org/10.1371/journal.pone.0157494
25. Jie Li, Rui Li, Leiming You, Yonggui Fu, Anlong Xu* and Shengfeng Huang *. Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching. PLoS ONE . 2015 Apr 14; 10(4):e0124324. http://dx.doi.org/10.1371/journal.pone.0124324
26. Ping Yang#, Shengfeng Huang# , Xinyu Yan, Guangrui Huang, Xiangru Dong, Tingting Zheng, Dongjuan Yuan, Ruihuan Wang, Rui Li, Ying Tan and Anlong Xu. Origin of the phagocytic respiratory burst and its role in gut epithelial phagocytosis in a basal chordate. Free radical biology & medicine . 2014 May; 70C: 54-67. http://dx.doi.org/10.1016/j.freeradbiomed.2014.02.007
27. Shengfeng Huang* , Jie Li, Anlong Xu, Guangrui Huang, Leiming You. Small insertions are more deleterious than small deletions in human genomes. Human Mutation . 2013 Sep 18; 34(12): 1642-1649. http://dx.doi.org/10.1002/humu.22435
28. Zelin Chen#, Shengfeng Huang# , Yuxin Li, Anlong Xu. AliquotG: an improved heuristic algorithm for genome aliquoting. PLoS ONE . 2013 May 14; 8(5): e64279. http://dx.doi.org/10.1371/journal.pone.0064279
29. Shengfeng Huang# , Ting Yu#, Zelin Chen, Shaochun Yuan, Shangwu Chen, Anlong Xu. More single-nucleotide mutations surround small insertions than small deletions in primates. Human Mutation . 2012 April 9; 33(7): 1099-1106. http://dx.doi.org/10.1002/humu.22085
30. Huiqing Huang#, Shengfeng Huang# , Yanhong Yu, Shaochun Yuan, Rui Li, Xin Wang, Hongchen Zhao, Jun Li, Manyi Yang, Liqun Xu, Shangwu Chen, Anlong Xu. Functional characterization of a ficolin-mediated complement pathway in amphioxus. Journal of Biological Chemistry . 2011 Oct 21; 286(42):36739-48. http://dx.doi.org/10.1074/jbc.M111.245944
31. Shengfeng Huang# , Haozheng Tian, Zelin Chen, Ting Yu, Anlong Xu. The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications. BMC Evolutionary Biology . 2010;10:306. http://dx.doi.org/10.1186/1471-2148-10-306
32. Shaochun Yuan#, Shengfeng Huang# , Wei Zhang, Tao Wu, Meiling Dong, Yanhong Yu, Tong Liu, Kui Wu, Huiling Liu, Manyi Yang, Hongwei Zhang, Anlong Xu. An amphioxus TLR with dynamic embryonic expression pattern responses to pathogens and activates NF-kappaB pathway via MyD88. Molecular Immunology . 2009 Jul;46(11-12):2348-56. http://dx.doi.org/10.1016/j.molimm.2009.03.022
33. Shengfeng Huang# , Shaochun Yuan, Meiling Dong, Jing Su, Cuiling Yu, Xiaojin Xie, Yang Shen, xuesong Yu, Yanhong Yu, Shangwu Chen , Shicui Zhang, Pierre Pontarotti, Anlong Xu. The phylogenetic analysis of tetraspanins projects the evolution of cell-cell interactions from unicellular to multicellular organisms. Genomics . 2005 Dec; 86(6):674-684. https://doi.org/10.1016/j.ygeno.2005.08.004
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