 |
付岩 博士，研究员，博士生导师 地址：北京市海淀区中关村东路55号，100190 电邮: yfu(at)amss(dot)ac(dot)cn |
招收数学、统计学、计算机、生物信息学或相关专业免试/统考硕士生、博士生、博士后以及实习生和科研助理，请发简历至邮箱！
视频课程：《蛋白质及其修饰鉴定的质量控制》
研究方向
生物信息学、生物医学统计、机器学习与数据科学
工作和教育经历
2021.04—现在 中国科学院数学与系统科学研究院，研究员
2011.12—2021.04 中国科学院数学与系统科学研究院，副研究员
2009.09—2011.12 中国科学院计算技术研究所，副研究员
2007.03—2009.09 中国科学院计算技术研究所，助理研究员
2000.09—2007.03 中国科学院计算技术研究所，博士学位
部分学术论文
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]
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.
Xinpei Yi, Fuzhou Gong*, Yan Fu*. Transfer posterior error probability estimation for peptide identification. BMC Bioinformatics, 21:173, 2020.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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
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.
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.
Yan Fu. Bayesian false discovery rates for post-translational modification proteomics. Statistics and Its Interface, 5:47–59, 2012.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
付岩. 基于机器学习技术的生物信息检索研究. 博士学位论文, 中国科学院, 2007.
付岩, 贺思敏, 孙瑞祥, 王乐珩. 串联质谱蛋白质鉴定的关键计算问题. 信息技术快报, 8(1):16-32, 2010.
孙瑞祥, 付岩, 李德泉, 张京芬, 王晓彪, 盛泉虎, 曾嵘, 陈益强, 贺思敏, 高文. 基于质谱技术的计算蛋白质组学研究. 中国科学 E 辑 信息科学. 36(2), 222-234, 2006.
陈益强, 高文, 付岩,李德泉, 陈翔. 基于信息技术的蛋白质识别研究. 生命科学, 15(2): 70-78, 2003.
付岩, 王耀巍, 王伟强, 高文. SVM用于基于内容的自然图像检索和分类. 计算机学报, 26(10): 1261-1265, 2003.
付岩, 黄铁军, 余珂, 李涛, 张浩. 交互计算模型概述.计算机研究与发展, 39(6): 701-706, 2002.
软件工具
TransferPEP: 肽鉴定的分组PEP/fdr估计软件
PTMiner: 蛋白质修饰位点定位和质控软件
SAVControl: 氨基酸突变质量控制软件
LFAQ: 肽段定量效率预测和无偏非标蛋白质定量软件
AP3: 肽段可检测性预测软件
DeepDigest: 肽段酶切概率预测软件
pMatchGlyco: 基于谱库搜索的Ｎ糖鉴定软件
pMatch: 用于蛋白质修饰鉴定的开放式质谱库搜索软件
pCluster: 用于翻译后修饰检测的质谱数据聚类软件
pFind: 基于串联质谱数据的肽和蛋白质鉴定软件
学术荣誉
微软学者（2004, 微软亚洲研究院）
ACM KDD Cup 2004数据挖掘竞赛冠军