Publications

Institute of Computing Technology,

Chinese Academy of Sciences,

Beijing, China

Leheng Wang, Wenping Wang, Hao Chi, Yanjie Wu, You Li, Yan Fu, Chen Zhou, Ruixiang Sun, Haipeng Wang, Chao Liu, Zuofei Yuan, Liyun Xiu, Si-Min He. An efficient parallelization of phosphorylated peptide and protein identification. Rapid Communications in Mass Spectrometry, 24(12):1791 - 1798, 2010.[pdf][abstract]

Ding Ye, Yan Fu, Rui-Xiang Sun, Hai-Peng Wang, Zuo-Fei Yuan, Hao Chi and Si-Min He. Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate. Proceedings of the 18th Annual International Conference on Intelligent System for Molecular Biology (ISMB 2010).
(Also appears in Bioinformatics, 26(12), i399-i406, 2010.).[pdf][abstract]

Hao Chi , Rui-Xiang Sun , Bing Yang , Chun-Qing Song , Leheng Wang , Chao Liu , Yan Fu , Zuo-Fei Yuan , Hai-Peng Wang , Si-Min He and Meng-Qiu Dong. pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra. Journal of Proteome Research, 9 (5), 2713–2724, 2010.[pdf][abstract]

You Li, Hao Chi, Le-Heng Wang, Hai-Peng Wang, Yan Fu, Zuo-Fei Yuan, Su-Jun Li, Yan-Sheng Liu, Rui-Xiang Sun, Rong Zeng, Si-Min He. Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing. Rapid Communications in Mass Spectrometry, 24:807 - 814, 2010.[pdf][abstract]

Jingfen Zhang, Dong Xu, Wen Gao, Guohui Lin and Simin He. Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification. Rapid Commun. Mass Spectrom. 2009; 23: 3448–3456.[pdf][abstract]

Wei Jia, Zhuang Lu, Yan Fu, 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][abstract]

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. Accepted by APBC 2009, BMC Bioinformatics, 10(Suppl 1): S50, 2009.[pdf][abstract]

Jing-Fen Zhang, Si-Min He, Charles X.Ling, Xing-Jun Cao, Rong Zeng and Wen Gao. PeakSelect:preprocessing tandem mass spectra for better peptide identification. Rapid Communications in Mass Spectrometry,22,1203-1212,2008 [pdf][abstract]

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][abstract]

Yan Fu, Wen Gao, Si-Min He, Rui-Xiang Sun, Hu Zhou, Rong Zeng. Mining tandem mass spectral data for more accurate mass error model for peptide identification. Proceedings of the 12th Pacific Symposium on Biocomputing, 421-432, 2007 [pdf][abstract]

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] [abstract]

Hai-Peng Wang, Yan Fu, Rui-Xiang Sun, Si-Min He, Rong Zeng, Wen Gao. An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry. Proceedings of the Pacific Symposium on Biocomputing, 303-314, 2006 [pdf] [abstract]

De-Quan Li, Wen Gao, Charles X. Ling, Xiaobiao Wang, Rui-Xiang Sun, and Si-Min He. IndexToolkit: An Open Source Toolbox to Index Protein Data-bases for High-throughput Proteomics. Bioinformatics, 22(20), 2572-2573, 2006 [pdf][abstract]

Jing-Fen Zhang, Wen Gao, Jingjing Cai, Si-Min He, Rong Zeng, and Run-Sheng Chen, Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra, IEEE/ACM Transactions on Computational Biology and Bioinformatics,2(3), 217-230, 2005 [pdf][abstract]

Jing-Fen Zhang, Si-Min He, Jingjing Cai, Xing-Jun Cao, Rui-Xiang Sun, Yan Fu, Rong Zeng and Wen Gao, Preprocessing of tandem mass spectrometric data based on decision tree classification, Genomics, Proteomics & Bioinformatics, 3(4), 231-237, 2005 [pdf][abstract]

De-Quan Li, Yan Fu, Rui-Xiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Si-Min He and Wen Gao. pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics, 21(13), 3049-3050, 2005 [pdf][abstract]

Yan Fu, Qiang Yang, Rui-Xiang Sun, De-Quan Li, Rong Zeng, Charles X. Ling, Wen Gao. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 20, 1948-1954, 2004 [pdf][abstract]

Yan Fu, Qiang Yang, Charles X. Ling, Hai-Peng Wang, De-Quan Li, Rui-Xiang Sun, Hu Zhou, Rong Zeng, Yiqiang Chen, Si-Min 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, 544–553 [pdf][abstract]