Supervisor

Si-Min He: Professor, Institute of Computing Technology, Chinese Academy of Sciences

Address

Bioinformatics Group

Institute of Computing Technology, Chinese Academy of Sciences

No.6 Zhongguancun South Road, Beijing, China, 100190

Phone: + 86 010-62600820

Email: liuchao1016@ict.ac.cn

北京海淀区中关村科学院南路6号 中科院计算所 前瞻生物信息组 刘超

邮编：100190

Research

Quantitative proteomics. Wiki:

The aim of quantitative proteomics is to obtain quantitative information about all proteins in a sample.

Rather than just providing lists of proteins identified in a certain sample, quantitative proteomics yields information about differences between samples.

For example, this approach can be used to compare samples from healthy and diseased patients.

The methods for protein identification are identical to those used in general (i.e. qualitative) proteomics, but include quantification as an additional dimension.

Education

2007-2014 Ph. D., Institute of Computing Technology, Chinese Academy of Sciences.

2003-2007 Bachelor of Science, Computer Science and Technology, Shandong University.

Honors

2012 Excellent Student Award by the institute director, ICT, CAS 中科院计算所所长优秀奖

2006 IBM Excellent Student Scholarship (only 80 students honored nationwide) IBM中国优秀学生奖学金

2006 Shandong University President Scholarship (the highest honor to students in the university) 山东大学校长奖学金

2006 Shandong University Software College Dean Scholarship (awarded every 3 years ) 山东大学计算机与软件学院院长奖学金（3年一评，并作为获奖代表发言）

2007 Shandong Province Excellent Graduate 山东省省级优秀毕业生

2005 NEC.soft Scholarship “NEC.soft”奖学金

2006 Meritorious Winner of the Interdisciplinary Contest in Modeling Certificate of Achievement (First Author) 美国大学生数学建模一等奖（第一作者）

2005 2nd Prize Winner of National Undergraduate Mathematical Modeling Contest (First Author) 全国大学生数学建模国家二等奖（第一作者）

2006 Excellent Award Winner of Freescale Cup National Undergraduate Intelligent Vehicle Invitational Tournament “飞思卡尔杯”全国大学生智能车邀请赛优胜奖（第一作者）

2005 Excellent Award Winner of the Preliminary Contest of ACM International Undergraduate Program Designing Contest ACM全球大学生程序设计大赛（北京赛区）预赛优胜奖

2005 Shandong University Excellent Chinese Communist Youth League Cadre 山东大学校级优秀团干部

Awarded with Shandong University Excellent Student Scholarship in successive years 连年荣获 山东大学优秀学生奖学金

Awarded with Shandong University Excellent Student Cadre in successive years 连年荣获 山东大学校级优秀学生干部

Publications

Major

Chao Liu, Chun-Qing Song, Zuo-Fei Yuan, Yan Fu, Hao Chi, Le-Heng Wang, Sheng-Bo Fan, Kun Zhang, Wen-Feng Zeng, Si-Min He, Meng-Qiu Dong, and Rui-Xiang Sun. pQuant improves quantitation by keeping out interfering signals and evaluating the accuracy of calculated ratios. Analytical Chemistry, 2014, 86(11): 5286–5294.

Shuo-Lei Bu, Chao Liu, Ning Liu, Ji-Long Zhao, Lian-Feng Ai, Hao Chi, Kathy L Li, Chih-Wei Chien, Alma L Burlingame, Sheng-Wei Zhang, Zhi-Yong Wang. Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis. Molecular Plant, 2017, 10(2):345-348.

Dan Tan, Qiang Li, Mei-Jun Zhang, Chao Liu, Chengying Ma, Pan Zhang, Yue-He Ding, Sheng-Bo Fan, Li Tao, Bing Yang, Xiangke Li, Shoucai Ma, Junjie Liu, Boya Feng, Xiaohui Liu, Hong-Wei Wang, Si-Min He, Ning Gao, Keqiong Ye, Meng-Qiu Dong, Xiaoguang Li. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. eLife, 2016, 5: e12509.

Yue-He Ding, Zhou Gong, Xu Dong, Kan Liu, Zhu Liu, Chao Liu, Si-Min He, Meng-Qiu Dong, Chun Tang. Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links. The Journal of Biological Chemistry, 2017, 292(4): 1187-1196.

Daniel B. McClatchy, Yuanhui Ma, Chao Liu, Benjamin D. Stein, Salvador Martínez-Bartolomé, Debbie Vasquez, Kristina Hellberg, Reuben J. Shaw, and John R. YatesIII. Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice. Journal of Proteome Research, 2015, 14(11): 4815–4822.

刘超，王海鹏，付岩，袁作飞，迟浩，王乐珩，孙瑞祥，贺思敏. 肽段反相色谱保留时间预测算法及其在蛋白质鉴定中的应用. 色谱, 2010, 28(6): 529-534.

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, 2012, 12(2): 226–235.

袁作飞, 邬龙, 刘超, 迟浩, 樊盛博, 张昆, 曾文锋, 孙瑞祥, 贺思敏. 规模化蛋白质鉴定中母离子的准确检测技术研究. 生物化学与生物物理进展, 2013, 40(1): 80-92.

Minor

Rui-Xiang Sun, Lan Luo, Long Wu, Rui-Min Wang, Wen-Feng Zeng, Hao Chi, Chao Liu, Si-Min He. pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification. Analytical Chemistry. February 4, 2016.

Hao Chi, Kun He, Bing Yang, Zhen Chen, Rui-Xiang Sun, Sheng-Bo Fan, Kun Zhang, Chao Liu, Zuo-Fei Yuan, Quan-Hui Wang, Si-Qi Liu, Meng-Qiu Dong, Si-Min He. pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data. Journal of Proteomics. July 1, 2015.

张昆, 王乐珩, 迟浩, 卜德超, 袁作飞, 刘超, 樊盛博, 陈海丰, 曾文锋, 罗海涛, 孙瑞祥, 贺思敏, 谢鹭, 赵屹. 蛋白质基因组学：运用蛋白质组技术注释基因组. 生物化学与生物物理进展, 2013, 40(4): 297-308.

代冬梅, 贺玖明, 刘超, 孙瑞祥, 张瑞萍, 阿吉艾克拜尔·艾萨, 再帕尔·阿不力孜. 采用核磁共振/液相色谱-质谱异相关谱方法开展药用植物草棉活性提取物中多组分的同步结构分析研究. 分析化学, 2011, 39(6): 781-787.

刘影, 贺玖明, 孙瑞祥, 刘超, 张瑞萍, 石建功, 再帕尔·阿不力孜. 核磁共振和液相色谱-质谱平行动态谱学方法对连翘活性提取物的同步结构分析. 分析化学, 2011, 39(3): 323-329.

Rui-Xiang Sun, Meng-Qiu Dong, Chun-Qing Song, Hao Chi, Bing Yang, Li-Yun Xiu, Li Tao, Zhi-Yi Jing, Chao Liu, Le-Heng Wang, Yan Fu, and Si-Min He. Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra. Journal of Proteome Research, 2010, 9(12): 6354–6367.

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, 2010, 9(5): 2713–2724.

Liu Chao, et al. A High Exchange Rate Algorithm Based on Improved Decision Tree. ICBBE, 2008, 869-872.

Last update: Feb. 21, 2017