Publications

(#Equal contribution, *Correspondence)

Selected recent publications

  1. Xiaoya Sun, Yan Fu*. Local false discovery rate estimation with competition-based procedures for variable selection. Statistics in Medicine, 43(1):61-88, 2024.
  2. Jinghan Yang, Zhiyuan Cheng, Fuzhou Gong, and Yan Fu*. DeepDetect: Deep Learning of Peptide Detectability Enhanced by Peptide Digestibility and Its Application to DIA Library Reduction. Analytical Chemistry, 95(15), 6235-6243, 2023.
  3. Zhiyuan Cheng#, Ge Song#, Yan Fu*. A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra. Biophysics Reports, 8(5-6): 269-281, 2022.
  4. Kun He, Meng-jie Li, Yan Fu*, Fu-zhou Gong, Xiao-ming Sun. Null-free False Discovery Rate Control Using Decoy Permutations. Acta Mathematicae Applicatae Sinica, English Series, 38(2):235-253, 2022. [pdf]
  5. Jinghan Yang#, Zhiqiang Gao#, Xiuhan Ren, Jie Sheng, Ping Xu, Cheng Chang*, Yan Fu*. DeepDigest: prediction of protein proteolytic digestion with deep learning. Analytical Chemistry, 93(15):6094-6103, 2021.
  6. Xinpei Yi, Fuzhou Gong*, Yan Fu*. Transfer posterior error probability estimation for peptide identification. BMC Bioinformatics, 21:173, 2020.
  7. Feng Xu#*, Li Yu#, Xuehui Peng#, Junling Zhang, Suzhen Li, Shu Liu, Yanan Yi, Zhiwu An, Fuqiang Wang, Yan Fu*, Ping Xu*. Unambiguous Phosphosite Localization through the Combination of Trypsin and LysargiNase Mirror Spectra in a Large-Scale Phosphoproteome Study. Journal of Proteome Research, 19(6):2185-2194, 2020.
  8. Qingbo Shu#, Mengjie Li#, Lian Shu#, Zhiwu An, Jifeng Wang, Hao Lv, Ming Yang, Tanxi Cai, Tony Hu, Yan Fu* and Fuquan Yang*. Large-scale Identification of N-linked Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search. Molecular & Cellular Proteomics, 19:672–689, 2020.
  9. Zhiqiang Gao#, Cheng Chang#, Jinghan Yang, Yunping Zhu*, Yan Fu*. AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility. Analytical Chemistry, 91, 8705−8711, 2019.
  10. Zhiwu An#, Linhui Zhai#, Wantao Ying, Xiaohong Qian, Fuzhou Gong*, Minjia Tan* and Yan Fu*. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome. Molecular & Cellular Proteomics, 18(2) 391-405, 2019.
  11. Cheng Chang#, Zhiqiang Gao#, Wantao Ying#, Yan Fu*, Yan Zhao, Songfeng Wu, Mengjie Li, Guibin Wang, Xiaohong Qian*, Yunping Zhu*, Fuchu He*. LFAQ: towards unbiased label-free absolute protein quantification by predicting peptide quantitative factors. Analytical Chemistry, 91, 1335−1343, 2019.
  12. Yi Shao, Chunyan, Chen Hao, Shen, Bin Z He, Daqi Yu, Shuai Jiang, Shilei Zhao, Zhiqiang Gao, Zhenglin Zhu, Xi Chen, Yan Fu, Hua Chen, Ge Gao, Manyuan Long, Yong E Zhang. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research, 29(4):682-696, 2019.
  13. Xinpei Yi#, Bo Wang#, Zhiwu An, Fuzhou Gong*, Jing Li*, Yan Fu*, Quality control of single amino acid variations detected by tandem mass spectrometry, Journal of Proteomics, 187:144–151, 2018.
  14. Zhiwu An#, Qingbo Shu#, Hao Lv, Lian Shu, Jifeng Wang, Fuquan Yang*, Yan Fu*, N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search, BioMed Research International, doi.org/10.1155/2018/1564136, 2018.
  15. 安志武, 付岩*, 基于质谱的蛋白质修饰定位算法. 生命的化学, 37(1):104-112, 2017.
  16. Yan Fu, Data Analysis Strategies for Protein Modification Identification, In Klaus Jung (Ed.): Statistical Analysis in Proteomics, Humana Press, New York, NY,pp1362:265-75, 2016.
  17. Kun Zhang, Yan Fu*, Wen-Feng Zeng, Kun He, Hao Chi, Chao Liu, Yan-Chang Li, Yuan Gao, Ping Xu*, Si-Min He*, A note on the false discovery rate of novel peptides in proteogenomic. Bioinformatics, 31(20):3249-3253, 2015.
  18. Shan Lu, Sheng-Bo Fan, Bing Yang, Yu-Xin Li, Jia-Ming Meng, Long Wu, Pin Li, Kun Zhang, Mei-Jun Zhang, Yan Fu, Jin-Cai Luo, Rui-Xiang Sun, Si-Min He, Meng-Qiu Dong, Mapping native disulfide bonds at a proteome scale. Nature Methods, 12:329-331, 2015.
  19. Yan Fu*, Xiaohong Qian, Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry, Molecular & Cellular Proteomics, 13(5):1359-1368, 2014.
  20. Yan Fu, Kernel Methods and Applications in Bioinformatics. In Kasabov, Nikola K. (Ed.): Handbook of Bio-/Neuro-Informatics, Springer-Verlag Berlin and Heidelberg GmbH & Co. K, pp275-285, 2013.
  21. Yan Fu, Bayesian false discovery rates for post-translational modification proteomics, Statistics and Its Interface, 59(1):47-59, 2012.

Manuscripts

  1. Kun He, Mengjie Li, Yan Fu*, Fuzhou Gong, Xiaoming Sun. A direct approach to false discovery rates by decoy permutations. arXiv:1804.08222. 2018.
  2. Kun He, Yan Fu*, Wen-Feng Zeng, Lan Luo, Hao Chi, Chao Liu, Lai-Yun Qing, Rui-Xiang Sun, and Si-Min He. A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics. arXiv:1501.00537. 2015.