1.   Ran Zhang*, Menghua Wu*, Dan Xiang*, Jieying Zhu*, Qi Zhang*, Hui Zhong*, Yuling Peng, Zhenhua Wang, Gang Ma, Guihuan Li, Fengping Liu, Weipeng Ye, Ruona Shi, Xuemeng Zhou, Isaac A. Babarinde, Huanxing Su, Jiekai Chen,Xiaofei Zhang^＃, Dajiang Qin^＃, Andrew P. Hutchins^＃, Duanqing Pei^＃, Dongwei Li^＃. A primate-specific endogenous retroviral envelope protein sequesters SFRP2 to regulate human cardiomyocyte development. Cell Stem Cell., 10.1016/j.stem.2024.07.006

2.   Yufei Wang*, Wanlin Zhang*, Ruona Shi*, Yanran Luo, Zhenhuan Feng, Yanhong Chen, Qiuting Zhang, Yan Zhou, Jingtong Liang, Xiaoping Ye, Qisheng Feng, Xiaofei Zhang^＃, Miao Xu^＃. Identification of HLA-A*11:01 and A*02:01-Restricted EBV Peptides Using HLA Peptidomics. Viruses., 2024 Apr; 10.3390/v16050669

3. Xue Shi, Xiaofei Zhang^＃. Control of ATG14 solubility and autophagy by MARCHF7/MARCH7-mediated ubiquitination. Autophagy., 2023 Nov; 10.1080/15548627.2023.2278414

4.   Zhenhuan Feng*, Peiyang Fang*, Hui Zheng, Xiaofei Zhang^＃. DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data. Bioinformatics., 2023 Aug 1;39(8):btad526

5.   Xue Shi, Wenfeng Wu, Zhenhuan Feng, Peiyang Fan, Ruona Shi, Xiaofei Zhang^＃. MARCH7-Mediated Ubiquitination Decreases the Solubility of ATG14 to Inhibit Autophagy. Cell Reports., 2023 Aug 25;42(9):113045

6.   Mingwei Sun*, Qing Zhang*, Baofeng Zhao, Qiuling Huang, Wenfeng Wu, Peiyang Fan, Lihua Zhang^＃, Xiaofei Zhang^＃. Antibody-free approach for ubiquitination profiling by selectively clicking the ubiquitination sites. Analytica Chimica Acta., 2023, Mar 15; 1246:340877

7.   Xiaotong Cen, Qing Chen, Bin Wang, Hongjie Xu, Xu Wang, Yixia Ling, Xiaofei Zhang^＃ and Dajing Qin^＃. UBE2O ubiquitinates PTRF/CAVIN1 and inhibits the secretion of exosome-related PTRF/CAVIN1. Cell Communication and Signaling., 2022, Nov 28;20(1):191

8.   Yaping Chen, Xiaofei Zhang^＃. TRABID targets DDB2 for deubiquitination to promote proliferation   of hepatocellular carcinoma cells. Biochemical and Biophysical Research Communications., 2022, Oct 15;625:23-30

9.   Mingwei Sun, Xiaofei Zhang^＃. Current Methodologies in Protein Ubiquitination Characterization: from Ubiquitinated Protein to Ubiquitin Chain Architecture. 2022, Cell & Bioscience., Aug;12(1):126

10.  Qiuling Huang, Dajiang Qin, Duanqing Pei, Michiel Vermeulen, Xiaofei Zhang^＃. UBE2O and USP7 co-regulate RECQL4 ubiquitination and homologous recombination-mediated DNA repair. FASEB J., 2022 Jan;36(1):e22112

11.  Yuling Qi, Zhenhuan Feng, Xu Wang, Yaping Chen, Xiaofei Zhang^＃. Characterization of the USP10 protein interactome idenfies UPF1 as a USP10-associated protein. Chinese Journal of Biochemistry and Molecular Biology., 2021 Dec 37(12):1638-1647

12.  Ruona Shi*, Zhenhuan Feng*, Xiaofei Zhang^＃. Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses. Genomics, Proteomics & Bioinformatics., 2021; Nov 10;S1672-0229(21)00241-2

13.  Ruona Shi, Xue Shi, Dajiang Qin, Shibing Tang, Michiel Vermeulen, Xiaofei Zhang^＃. SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation. Cell & Bioscience., 2021 Jul 27;11(1):146

14.  Pingping Chen*, Hexige Saiyin*, Ruona Shi, Bin Liu, Xu Han, Yuping Gao, Xiantao Ye, Xiaofei Zhang^＃, Yu Sun^＃.  Loss of SPACA1 function causes autosomal recessive globozoospermia by damaging the acrosome-acroplaxome complex. Human reproduction., 2021 Aug 18;36(9):2587-2596

15.  Qiuling Huang, Xiaofei Zhang^＃. Emerging Roles and Research Tools of Atypical Ubiquitination. Proteomics., 2020 May; 20 (9)

16.  Xiaofei Zhang*^＃, Arne H. Smits*^＃, Gabrielle B.A. van Tilburg*, Huib Ovaa, Wolfgang Huber, Michiel Vermeulen^＃. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nature Protocols., 13, 530-550 (2018)

17.  Xiaofei Zhang*^＃, Arne H. Smits*, Gabrielle B.A. van Tilburg*, Pascal W.T.C. Jansen, Matthew M. Makowski, Huib Ovaa^＃, Michiel Vermeulen^＃. An Interaction Landscape of Ubiquitin Signaling. Molecular Cell., 65, 941–955 (2017)

18.  Xiaofei Zhang, Juan Zhang, Andreas Bauer, Long Zhang, Douglas W Selinger, Chris X. Lu, and Peter ten Dijke. Fine-tuning BMP7 signalling in adipogenesis by UBE2O/E2-230K-mediated monoubiquitination of SMAD6. EMBO. J., 2013 Apr 3;32(7):996-1007

19.  Xiaofei Zhang*, Juan Zhang*, Hans van Dam, Peter ten Dijke. UBE2O negatively regulates TRAF6-mediated NF-κB activation by inhibiting TRAF6 polyubiquitination.  Cell Research., 2013 Mar; 23(3):366-77

20.  Juan Zhang*, Xiaofei Zhang*, Long Zhang, Fangfang Zhou, Maarten van Dinther, Peter ten Dijke. LRP8 mediates Wnt/β-catenin signaling and controls osteoblast differentiation. J Bone Miner Res., 2012 Oct;27(10):2065-74

21.  Juan Zhang*, Xiaofei Zhang*, Yunqian Guo*, Liangliang Xu* and Duanqing Pei. Sorting nexin 33 induces mammalian cell micronucleated phenotype and actin polymerization by interacting with wiskott-aldrich syndrome protein. J. Biol. Chem., 2009; 284(32):21659-69

22.  Juan Zhang*, Xiaofei Zhang*, and Duanqing Pei. Mutations of Nuclear Localization Signals in mNANOG generate Dominant Negative Mutants. Chinese Science Bulletin., 2009, Vol. 54 (8): 1361-1368

23.  Xiaofei Zhang*, Juan Zhang*, Tao Wang, Miguel A. Esteban, and Duanqing Pei. Esrrb activates oct4 transcription and sustains self renewal and pluripotency in embryonic stem cells. J. Biol. Chem., 2008; 283(51):35825-33