生物信息学、生物医学统计、机器学习和数据科学

详见个人主页：http://fugroup.amss.ac.cn/People/fuyan/index_ch.htm

招收概率统计、计算机、生物信息学或相关方向免试/统考研究生

071400-统计学
081203-计算机应用技术
070103-概率论与数理统计

生物与医学统计
生物信息与计算生物学
机器学习与人工智能

2000-09--2006-12   中国科学院计算技术研究所   博士学位

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
2007-01~2011-12,中国科学院计算技术研究所, 助理研究员、副研究员

   

（1） KDD Cup数据挖掘竞赛冠军, , 其他, 2004
（2） 微软学者, 其他, 2004

[1] 付岩, 杨婧涵. 肽段可检测性预测方法. CN: CN114093415A, 2022-02-25.
[2] 常乘, 付岩, 高志强, 朱云平. 一种蛋白质无标绝对定量方法. CN: CN110310706A, 2019-10-08.
[3] 常乘, 付岩, 高志强, 朱云平. 一种酶切概率辅助的肽段可检测性预测方法. CN: CN109243527A, 2019-01-18.
[4] 付岩, 常乘, 高志强, 朱云平. 一种蛋白质组学中肽段的肽段定量效率预测方法. CN: CN108491690A, 2018-09-04.
[5] 付岩. 一种基于子集错误率估计的肽鉴定方法. CN: CN103439441A, 2013-12-11.

   

[1] Jinghan Yang, Zhiyuan Cheng, Fuzhou Gong, Yan Fu. DeepDetect: Deep Learning of Peptide Detectability Enhanced by Peptide Digestibility and Its Application to DIA Library Reduction. Analytical Chemistry[J]. 2023, 95(15): 6235-6243, [2] He, Kun, Li, Mengjie, Fu, Yan, Gong, Fuzhou, Sun, Xiaoming. Null-free False Discovery Rate Control Using Decoy Permutations. ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES[J]. 2022, 38(2): 235-253, http://dx.doi.org/10.1007/s10255-022-1077-5.
[3] Zhiyuan, 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[J]. 2022, 8(5-6): 269-281, http://www.biophysics-reports.org/en/article/doi/10.52601/bpr.2022.220024.
[4] Yang, Jinghan, Gao, Zhiqiang, Ren, Xiuhan, Sheng, Jie, Xu, Ping, Chang, Cheng, Fu, Yan. DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning. ANALYTICAL CHEMISTRY[J]. 2021, 93(15): 6094-6103, http://dx.doi.org/10.1021/acs.analchem.0c04704.
[5] Yi, Xinpei, Gong, Fuzhou, Fu, Yan. Transfer posterior error probability estimation for peptide identification. BMC BIOINFORMATICS[J]. 2020, 21(1): https://doaj.org/article/b72063daeae440b1a1d3fb6a27900210.
[6] Xu, Feng, Yu, Li, Peng, Xuehui, Zhang, Junling, Li, Suzhen, Liu, Shu, Yin, Yanan, An, Zhiwu, Wang, Fuqiang, Fu, Yan, Xu, Ping. Unambiguous Phosphosite Localization through the Combination of Trypsin and LysargiNase Mirror Spectra in a Large-Scale Phosphoproteome Study. JOURNAL OF PROTEOME RESEARCH[J]. 2020, 19(6): 2185-2194, [7] Shu, Qingbo, Li, Mengjie, Shu, Lian, An, Zhiwu, Wang, Jifeng, Lv, Hao, Yang, Ming, Cai, Tanxi, Hu, Tony, Fu, Yan, Yang, Fuquan. Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search. MOLECULAR & CELLULAR PROTEOMICS[J]. 2020, 19(4): 672-689, http://dx.doi.org/10.1074/mcp.RA119.001791.
[8] Shao, Yi, Chen, Chunyan, Shen, Hao, He, Bin Z, Yu, Daqi, Jiang, Shuai, Zhao, Shilei, Gao, Zhiqiang, Zhu, Zhenglin, Chen, Xi, Fu, Yan, Chen, Hua, Gao, Ge, Long, Manyuan, Zhang, Yong E. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. GENOME RESEARCH[J]. 2019, 29(4): 682-696, http://ir.amss.ac.cn/handle/2S8OKBNM/34321, http://www.irgrid.ac.cn/handle/1471x/6869267, http://ir.amss.ac.cn/handle/2S8OKBNM/34322, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000462858600015&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[9] Chang, Cheng, Gao, Zhiqiang, Ying, Wantao, Fu, Yan, Zhao, Yan, Wu, Songfeng, Li, Mengjie, Wang, Guibin, Qian, Xiaohong, Zhu, Yunping, He, Fuchu. LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors. ANALYTICAL CHEMISTRY[J]. 2019, 91(2): 1335-1343, http://ir.amss.ac.cn/handle/2S8OKBNM/32190.
[10] An, Zhiwu, Zhai, Linhui, Ying, Wantao, Qian, Xiaohong, Gong, Fuzhou, Tan, Minjia, Fu, Yan. 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. MOLECULARCELLULARPROTEOMICS[J]. 2019, 18(2): 391-405, http://ir.amss.ac.cn/handle/2S8OKBNM/32417.
[11] Gao, Zhiqiang, Chang, Cheng, Yang, Jinghan, Zhu, Yunping, Fu, Yan. AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility. ANALYTICAL CHEMISTRY[J]. 2019, 91(13): 8705-8711, http://ir.amss.ac.cn/handle/2S8OKBNM/35175, http://www.irgrid.ac.cn/handle/1471x/6869286, http://ir.amss.ac.cn/handle/2S8OKBNM/35176, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000474477900098&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[12] Yi, Xinpei, Wang, Bo, An, Zhiwu, Gong, Fuzhou, Li, Jing, Fu, Yan. Quality control of single amino acid variations detected by tandem mass spectrometry. JOURNAL OF PROTEOMICS[J]. 2018, 187: 144-151, http://dx.doi.org/10.1016/j.jprot.2018.07.004.
[13] An, Zhiwu, Shu, Qingbo, Lv, Hao, Shu, Lian, Wang, Jifeng, Yang, Fuquan, Fu, Yan. N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search. BIOMED RESEARCH INTERNATIONAL[J]. 2018, 2018: https://doaj.org/article/9367f3fc4458411bb04869919850e5de.
[14] 安志武, 付岩. 基于质谱的蛋白质修饰定位算法. 生命的化学[J]. 2017, 37(1): 104-, http://ir.amss.ac.cn/handle/2S8OKBNM/46253, http://www.irgrid.ac.cn/handle/1471x/6869599, http://ir.amss.ac.cn/handle/2S8OKBNM/46254.
[15] 许海玉, 刘振明, 付岩, 张彦琼, 于建军, 郭非非, 唐仕欢, 吕传宇, 苏瑾, 崔如意, 杨洪军. 中药整合药理学计算平台的开发与应用. 中国中药杂志[J]. 2017, 42(18): 3633-, https://kns.cnki.net/KCMS/detail/detail.aspx?dbcode=CJFQ&dbname=CJFDLAST2017&filename=ZGZY201718030&v=Mjc5NzdJUjhlWDFMdXhZUzdEaDFUM3FUcldNMUZyQ1VSN3FmYnVadEZDamhVTHpLUHlyUmQ3RzRIOWJOcDQ5R1o=.
[16] Yan Fu. Data Analysis Strategies for Protein Modification Identification. Methods in Molecular Biology. 2016, [17] 丁磊, 于建军, 付岩, 许海玉, 刘振明, 张彦琼, 杨洪军. 基于分子指纹的中药分子作用网络分析系统的研究与实现. 科研信息化技术与应用. 2016, 59-66, https://kns.cnki.net/KCMS/detail/detail.aspx?dbcode=CJFQ&dbname=CJFDLAST2017&filename=KYXH201605008&v=MDM3MDdmYnVadEZDdm1WTHpNTGpUVFpyRzRIOWZNcW85RmJJUjhlWDFMdXhZUzdEaDFUM3FUcldNMUZyQ1VSN3E=.
[18] Zhang, Kun, Fu, Yan, Zeng, WenFeng, He, Kun, Chi, Hao, Liu, Chao, Li, YanChang, Gao, Yuan, Xu, Ping, He, SiMin. A note on the false discovery rate of novel peptides in proteogenomics. BIOINFORMATICS[J]. 2015, 31(20): 3249-3253, https://www.webofscience.com/wos/woscc/full-record/WOS:000362846600002.
[19] 赵立, 李慧, 刘一帆, 付岩, 刘宇灵, 张晓莉. 支持向量机法优化复方威灵仙喷雾剂的水提工艺研究. 中国中药杂志[J]. 2015, 40(7): 1291-, http://lib.cqvip.com/Qikan/Article/Detail?id=664540528.
[20] Lu, Shan, Fan, ShengBo, Yang, Bing, Li, YuXin, Meng, JiaMing, Wu, Long, Li, Pin, Zhang, Kun, Zhang, MeiJun, Fu, Yan, Luo, Jincai, Sun, RuiXiang, He, SiMin, Dong, MengQiu. Mapping native disulfide bonds at a proteome scale. NATURE METHODS[J]. 2015, 12(4): 329-U73, http://dx.doi.org/10.1038/NMETH.3283.
[21] Liu, Chao, Song, ChunQing, Yuan, ZuoFei, Fu, Yan, Chi, Hao, Wang, LeHeng, Fan, ShengBo, Zhang, Kun, Zeng, WenFeng, He, SiMin, Dong, MengQiu, Sun, RuiXiang. pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios. ANALYTICAL CHEMISTRY[J]. 2014, 86(11): 5286-5294, https://www.webofscience.com/wos/woscc/full-record/WOS:000336953100015.
[22] Fu, Yan, Qian, Xiaohong. Transferred Subgroup False Discovery Rate for Rare Post-translational Modifications Detected by Mass Spectrometry. MOLECULAR & CELLULAR PROTEOMICS[J]. 2014, 13(5): 1359-1368, http://dx.doi.org/10.1074/mcp.O113.030189.
[23] Yan Fu. Kernel Methods and Applications in Bioinformatics. Handbook of Bio-/Neuro-Informatic. 2013, [24] Fu, Yan. Bayesian false discovery rates for post-translational modification proteomics. STATISTICS AND ITS INTERFACE[J]. 2012, 5(1): 47-59, https://www.webofscience.com/wos/woscc/full-record/WOS:000301056700005.
[25] Fu, Yan, Xiu, LiYun, Jia, Wei, Ye, Ding, Sun, RuiXiang, Qian, XiaoHong, He, SiMin. DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data. MOLECULAR & CELLULAR PROTEOMICS[J]. 2011, 10(5): http://dx.doi.org/10.1074/mcp.M110.000455.
[26] Fu Yan, Pan Rong, Yang Qiang, Gao Wen, Chen J, Wang JX, Zelikovsky A. Query-Adaptive Ranking with Support Vector Machines for Protein Homology Prediction. BIOINFORMATICS RESEARCH AND APPLICATIONS[J]. 2011, 6674: 320-331, [27] Ye, Ding, Fu, Yan, Sun, RuiXiang, Wang, HaiPeng, Yuan, ZuoFei, Chi, Hao, He, SiMin. Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. BIOINFORMATICS[J]. 2010, 26(12): i399-i406, http://www.corc.org.cn/handle/1471x/2410669.
[28] Fu, Yan, Jia, Wei, Lu, Zhuang, Wang, Haipeng, Yuan, Zuofei, Chi, Hao, Li, You, Xiu, Liyun, Wang, Wenping, Liu, Chao, Wang, Leheng, Sun, Ruixiang, Gao, Wen, Qian, Xiaohong, He, SiMin. Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences. BMC BIOINFORMATICS[J]. 2009, 10(Suppl 1): S50-S50, https://www.webofscience.com/wos/woscc/full-record/WOS:000265601900050.
[29] Jia, Wei, Lu, Zhuang, Fu, Yan, Wang, HaiPeng, Wang, LeHeng, Chi, Hao, Yuan, ZuoFei, Zheng, ZhaoBin, Song, LiNa, Han, HuanHuan, Liang, YiMin, Wang, JingLan, Cai, Yun, Zhang, YuKui, Deng, YuLin, Ying, WanTao, He, SiMin, Qian, XiaoHong. A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins. MOLECULAR & CELLULAR PROTEOMICS[J]. 2009, 8(5): 913-923, http://dx.doi.org/10.1074/mcp.M800504-MCP200.
[30] Fu Yan, Gao Wen, He Simin, Sun Ruixiang, Zhou Hu, Zeng Rong, Altman RB, Dunker AK, Hunter L, Murray T, Klein TE. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2007[J]. 2007, 421-+, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000245296300040.
[31] Yan Fu, Yang, Q, Sun, RX, Li, DQ, Zeng, R, Ling, CX, Gao, W. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. BIOINFORMATICS[J]. 2004, 20(12): 1948-1954, https://www.webofscience.com/wos/woscc/full-record/WOS:000223588300014.
[32] Yan Fu, et al. A Block-Based Support Vector Machine Approach to the Protein Homology Prediction Task in KDD Cup 2004. SIGKDD Explorations[J]. 2004, 6(2): 120-124, 

   

（ 1 ） 蛋白质组信息学关键技术及分析系统研发, 参与, 国家任务, 2014-04--2018-04
（ 2 ） 基于质谱数据的非限制性翻译后修饰检测算法研究, 负责人, 国家任务, 2010-01--2012-12
（ 3 ） 基于质谱数据的大规模蛋白质鉴定算法与软件研究, 负责人, 国家任务, 2007-06--2010-11
（ 4 ） 非完整、异构材料数据关联统计分析与挖掘技术, 参与, 国家任务, 2018-07--2022-06
（ 5 ） 质谱和序列多源信息的翻译后修饰位点精确测定研究, 负责人, 国家任务, 2021-01--2024-12
（ 6 ） 基于信息技术的蛋白质组研究, 参与, 国家任务, 2002-12--2008-08
（ 7 ） 高通量生物大数据测量的数学模型和算法, 参与, 中国科学院计划, 2014-07--2018-12

1. pFind: 基于串联质谱数据的肽和蛋白质鉴定软件
2. pMatch: 用于蛋白质修饰鉴定的开放式质谱库搜索软件
3. pCluster: 用于翻译后修饰检测的质谱数据聚类软件
4. pMatchGlyco: 基于谱库搜索的Ｎ糖鉴定软件
5. PTMiner: 蛋白质修饰位点定位和质控软件
6. SAVControl: 氨基酸突变质量控制软件
7. LFAQ: 肽段定量效率预测和无偏非标蛋白质定量软件
8. AP3: 肽段可检测性预测软件
9. DeepDigest: 肽段酶切概率预测软件
10. TransferFDR/PEP: 肽鉴定的迁移FDR/fdr估计软件
11. TDFDR: 基于target-decoy竞争的多重假设检验FDR控制方法