(#Equal contribution, *Correspondence)

Selected recent publications

  1. 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, 2019, 91, 8705−8711.
  2. 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, 2019, 18 (2) 391-405.
  3. 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, 2019, 91, 1335−1343.
  4. 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, 2019 04 12;29(4):682-696.
  5. 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.
  6. 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.
  7. 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.
  8. 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,2015.06.14,3249~3253
  9. 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,2015.01.01,12:329~331
  10. Yan Fu*,Xiaohong Qian,Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry,Molecular & Cellular Proteomics,2014.01.01,13(5):1359~1368
  11. 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.
  12. Yan Fu*,Bayesian false discovery rates for post-translational modification proteomics,Statistics and Its Interface,2012.01.01,5(1):47~59
  13. Yan Fu*,Li-Yun Xiu,Wei Jia,Ding Ye,Rui-Xiang Sun,Xiao-Hong Qian,Si-Min He,DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data,Molecular & Cellular Proteomics,2011.5.01,10(5):1~15
  14. Yan Fu#*, Rong Pan, Qiang Yang, Wen Gao. Query-Adaptive Ranking with Support Vector Machines for Protein Homology Prediction. In Proceedings of the 7th International Symposium on Bioinformatics Research and Applications (ISBRA2011). Lecture Notes in Bioinformatics, 6674:320–331, 2011
  15. Ding Ye#,Yan Fu*,Rui-Xiang Sun*,Hai-Peng Wang,Zuo-Fei Yuan,Hao Chi, Si-Min He,Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. In Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). Bioinformatics, 26(12):i399-i406, 2010
  16. Jia Wei#,Lu Zhuang#,Yan Fu#,Hai-Peng Wang,Wang Le-Heng,Hao Chi,Zuo-Fei Yuan,Zhao-Bin Zheng,Li-Na Song,Huan-Huan Han, Yi-Min Liang,Jing-Lan Wang,Yun Cai,Yu-Kui Zhang,Yu-Lin Deng,Wan-Tao Ying*,Si-Min He*,Xiao-Hong Qian*,A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins,MOLEC ULAR & CELLULAR PROTEOMICS,2009.5.01,8(5):913~923
  17. Yan Fu#*,Wei Jia,Zhuang Lu,Haipeng Wang,Zuofei Yuan,Zuofei Yuan,Hao Chi,You Li,Liyun Xiu,Wenping Wang,Chao Liu,Leheng Wang,Ruixiang Sun,Wen Gao,Xiaohong Qian,Si-Min He,Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences. In Proceedings of the 7th Asia-Pacific Bioinformatics Conference (APBC 2009),BMC Bioinformatics,2009.01.01,10:S50~S50
  18. 安志武#,付岩*,基于质谱的蛋白质修饰定位算法,生命的化学2017.2.01,37(1):104~112

Manuscripts in submission & preprints

  1. Xinpei Yi#, Fuzhou Gong, Yan Fu*. Grouped local false discovery rate estimation for peptide identification. 2019
  2. Feng Xu#*, Li Yu#, Xuehui Peng#, Junling Zhang, Suzhen Li, Shu Liu, Yanan Yi, Zhiwu An, Fuqiang Wang, Yan Fu*, Ping Xu*. The use of LysargiNase complementary to trypsin in large scale phosphoproteome study for unambiguous phosphosite localization. 2019
  3. 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. 2019
  4. Kun He#, Mengjie Li, Yan Fu*, Fuzhou Gong, Xiaoming Sun. Null-free False Discovery Rate Control Using Decoy Permutations for Multiple Testing. arXiv:1804.08222. 2018.
  5. 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.

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