Yan Fu

Address: No.55 Zhongguancun East Road,
Haidian District, Beijing, 100190, China

[Chinese version]

Research Interests

Data mining and Bioinformatics. Currently focus on computational proteomics and mass spectrometry: algorithms and software tools for protein identification from LC-MS/MS data, post-translational modification discovery, search results reranking, multiple hypothesis testing, etc.

Positions and Education

Associate Professor (2011 - ), Academy of Mathematics and Systems Science, Chinese Academy of Sciences

Associate Professor (2009 - 2011) and Assistant Professor (2007 - 2009), Institute of Computing Technology, Chinese Academy of Sciences

Ph.D. (2000 - 2007), Institute of Computing Technology, Chinese Academy of Sciences

Selected publications

Yan Fu and Xiaohong Qian. Transferred Subgroup False Discovery Rate for Rare >Post-translational Modifications Detected by Mass Spectrometry. Molecular & Cellular Proteomics, 13(5):1359-1368, 2014.(pdf)

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.(pdf)

Yan Fu. Bayesian false discovery rates for post-translational modification proteomics. Statistics and Its Interface, 5:4759, 2012.(pdf)

Zuo-Fei Yuan, Chao Liu, Hai-Peng Wang, Rui-Xiang Sun, Yan Fu, Jing-Fen Zhang, Le-Heng Wang, Hao Chi, You Li, Li-Yun Xiu, Wen-Ping Wang, Si-Min He. pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics, 12(2): 226–235, 2012. (pdf)

Yan Fu, Liyun Xiu, Wei Jia, Ding Ye, Ruixiang Sun, Xiaohong Qian, Si-min He. DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Molecular & Cellular Proteomics, 10(5):M110.000455, 2011. (pdf)

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. (pdf)

Yan Fu, Ding Ye. Towards Fully Identifying a Benchmark Dataset of Tandem mass Spectra with an Integrated Modification Discovery Pipeline. 59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011.

Ding Ye, Yan Fu, Ruixiang Sun, Haipeng Wang, Zuofei Yuan, Hao Chi and Simin 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. (pdf)

Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, 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. The Seventh Asia-Pacific Bioinformatics Conference (APBC 2009). BMC Bioinformatics. 10(Suppl 1):S50, 2009. (pdf)

Wei Jia, Zhuang Lu, Yan Fu(co-first author), Hai-Peng Wang, Le-Heng Wang, 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, and Xiao-Hong Qian. A strategy for precise and large-scale identification of core fucosylated glycoproteins. Molecular & Cellular Proteomics. 8:913-923, 2009. (pdf)

Yan Fu, Wen Gao, Simin He, Ruixiang Sun, Hu Zhou, Rong Zeng. Mining Tandem Mass Spectral Data to Develop a More Accurate Mass Error Model for Peptide Identification. Pacific Symposium on Biocomputing (PSB) 12:421-432, 2007. (pdf/Supplementary information)

Le-Heng Wang, De-Quan Li, Yan Fu, Hai-Peng Wang, Jing-Fen Zhang, Zuo-Fei Yuan,Rui-Xiang Sun, Rong Zeng, Si-Min He, Wen Gao, pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 21,2985-2991,2007. (pdf)

Haipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, and Wen Gao. An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry. Pacific Symposium on Biocomputing (PSB) 11:303-314, 2006. (pdf)

Dequan Li, Yan Fu, Ruixiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Simin He and Wen Gao. pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics, 21(13), pp3049-3050, 2005. (pdf)

Yan Fu, Ruixiang Sun, Qiang Yang, Simin He, Chunli Wang, Haipeng Wang, Shiguang Shan, Junfa Liu, Wen Gao. A Block-Based Support Vector Machine Approach to the Protein Homology Prediction Task in KDD Cup 2004. ACM SIGKDD Explorations. Vol.6, No.2, pp120-124, 2004.(pdf)

Yan Fu, Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, Wen Gao. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics. Vol.20, pp1948-1954, 2004. (pdf/Supplementary information)

Yan Fu, Qiang Yang, Charles X. Ling, Haipeng Wang, Dequan Li, Ruixiang Sun, Hu Zhou, Rong Zeng, Yiqiang Chen, Simin He, Wen Gao. A Kernel-based Case Retrieval Algorithm with Application to Bioinformatics. In Proceedings of the 8th Pacific Rim International Conference on Artificial Intelligence (PRICAI 2004), Auckland, New Zealand, August 9-13, 2004, LNAI 3157, pp. 544–553. (pdf)

Yan Fu, Simin He, Ruixiang Sun, Leheng Wang. A review of Key computational problems in tandem mass spectrometry-based protein identification. Information Technology Letter, 8(1):16-32, 2010. (in Chinese) (pdf)

Yan Fu. Machine Learning Based Bioinformation Retrieval. Doctoral dissertation, Chinese Academy of Sciences, 2007. (in Chinese) (abstract/pdf)

Ruixiang Sun, Yan Fu, Dequan Li, Jingfen Zhang, Xiaobiao Wang, Quanhu Sheng, Rong Zeng, Yiqiang Chen, Simin He, Wen Gao. Mass Spectrometry-Based Computational Proteomics Research. SCIENCE IN CHINA Ser. E Information Sciences. 36(2), 222-234, 2006. (in Chinese) (pdf)

Yiqiang Chen, Wen Gao, Yan Fu, Dequan Li, Xiang Chen. Research on Protein Recognition base on Information Technology. Chinese Bulletin of Life Sciences, Vol.15, No.2, pp70-78, 2003. (in Chinese) (pdf)

Yan Fu, Yaowei Wang, Weiqiang Wang, Wen Gao. Content-Based Natural Image Classification and Retrieval Using SVM. Chinese Journal of Computers, Vol.26, No.10, pp.1261-1265, 2003. (in Chinese) (pdf)

Yan Fu, Tiejun Huang, Ke Yu, Tao Li, Hao Zhang. Overview of Interactive Model of Computing. Chinese Journal of Computer Research and Development, vol.39, no.6, pp701-706, 2002. (in Chinese) (pdf)

Software tools

pFind: a database-searching engine for peptide & protein identification via tandem mass spectrometry

pCluster: a clustering tool for modification detection using LC, MS or MS/MS information

pMatch: an open MS/MS library search tool for identification of peptides and their modifications

Professional activities

Referee for Proteomics, BMC Bioinformatics, Plos ONE, Journal of Computer Science and Technology, Statistics and Its Interface, International Journal of Machine Learning and Cybernetics, Data Mining and Knowledge Discovery, IEEE Transactions on Computational Biology and Bioinformatics, etc.

Honors

President Scholarship 2007, Chinese Academy of Sciences

Microsoft Fellowship 2004, Microsoft Research Asia

Winner of ACM KDD Cup 2004's Bioinformatics Task