付岩

地址:北京市海淀区中关村东路55号,100190

[English version]

招收计算机、概率统计、生物信息学或相关方向免试/统考研究生、以及实习生和博士后,请发简历至邮箱!

研究方向

数据挖掘、生物信息学。目前专注于计算蛋白质组学研究,包括蛋白质鉴定、翻译后修饰发现、搜索引擎重排序和统计评估等问题的算法研究和软件开发。

工作和教育经历

副研究员(2011—), 中国科学院数学与系统科学研究院

副研究员(20092011)、助理研究员(20072009),中国科学院计算技术研究所

博士学位(20002007, 中国科学院计算技术研究所

部分学术论文

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, 6674:320331, 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. 544553. (pdf)

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. (摘要/pdf)

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. (pdf)\

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. (pdf)

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. (pdf)

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. (pdf)

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. (pdf)

软件工具

pFind: 利用串联质谱数据鉴定肽和蛋白质及其修饰的数据库搜索引擎

pCluster: 用于翻译后修饰检测的液谱质谱数据聚类软件

pMatch: 用于蛋白质修饰鉴定的开放式质谱库搜索软件

学术活动

期刊审稿人: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, 中国科学,生命的化学, 生物化学与生物物理进展, 等等。

学术荣誉

中科院院长奖学金优秀奖(2007

微软学者(2004, 微软亚洲研究院)

ACM KDD Cup 2004数据挖掘竞赛生物信息学任务全球并列第一名