Kunming, Yunnan, 2012/08/16.

Zuo-Fei YUAN

Gender: Male
Birth Date: 1982/09/08
Hometown: Xiantao,Hubei
Email: yuanzuofei@ict.ac.cn / feifei82@gmail.com
Phone: +86-10-62601016 (office) / +86 13811825909 (mobile)
Address: No.6 Kexueyuan South Road Zhongguancun, Haidian District, Beijing 100190

RESEARCH INTERESTS

Computational proteomics, protein identification and quantification,
preprocessing for MS and MS/MS, peptide scoring and validation,
data analysis and pipeline designing, modification discovery,
spectral library search, de novo, proteogenomics search.

EDUCATION

Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China, July 2012
Ph.D. in Computer Science
Advisor: Dr. Si-Min He
Thesis Topic: Peptide Identification Based on Large-scale Mass Spectra

Central South University, Changsha, China, July 2004
B.S. in Computer Science
Advisor: Dr. Dong-Jun Huang
Thesis Topic: The Design and Implementation of the JPEG Static Image Codecs Software

RESEARCH EXPERIENCE

Institute of Computing Technology, Chinese Academy of Sciences
Advisor: Dr. Si-Min He

Accurate Determination of Monoisotopic Peaks in High-resolution Mass Spectra
September 2008 - July 2012

• Developed an effective approach to judge overlapping isotopic clusters, designed a new scoring function to identify
  co-eluted peptides, and proposed a universal approach to validate methods for monoisotopic peak determination.
• Implemented our method with Python in three weeks, published a paper on Proteomics, wrote a review, and filed a patent.
• Contributed to the study of iPRG 2010 for phosphopeptides and the identification of core fucosylated glycoproteins.

In-depth Analysis of Massive Spectral Data
November 2007 - July 2012

• Initiated an analysis pipeline that includes preprocessing, modification discovery, parameter determination by pre-search,
  the second database search and filtering, spectral library search, proteogenomics search, sample comparison, and cloud computing.
• Validated search results based on the target-decoy approach and SVM for multiple search engines, e.g., pFind, Mascot and SEQUEST.
• Contributed to the study of iPRG 2008 for iTRAQ spectra, the study of iPRG 2011 for ETD spectra,
  and the 18O labeling quantification of core fucosylated glycoproteins.

Initiating the Application of pFind at the Institute of Zoology, Chinese Academy of Sciences
September 2009 - July 2012

• Provided technique support and software training for a biological engineer.
• Distributed the feedback to the tool authors, and obtained some new findings.
• Made pFind as a fast, convenient, and functional identification studio outside our group for the first time.

ADDITIONAL PROFESSIONAL EXPERIENCE

The Third MaxQuant Summer School in Max Planck Institute of Biochemistry
Munich, Germany, May 2011

• Learned the forefront techniques in computational proteomics, consulted with tutors about peptide identification,
  and communicated with participants about their research work.

The First China Workshop on Computational Proteomics
Beijing, China, November 2010

• Designed the workshop program, trained 61 participants from China and USA on database search,
  and organized participants for registration, meals, and the workshop.
• Communicated with participants about computational proteomics, and collaborated with experts.

Preprocessing Tandem Mass Spectra for Better Peptide Identification
April - October 2006

• Implemented the Gaussian Mixture Model in C/C++ to find the baseline in a spectrum.
• Integrated the preprocessing algorithm into a pipeline toolbox, and designed an automatic testing strategy to test the preprocessing algorithm.
• Supported the publication on RCM by providing materials, such as webpage and test cases.

AWARDS

Excellent Student Award by the institute director, ICT, CAS, 2011
Excellent Student Award of Joint Research & Development Laboratory, ICT, CAS, 2010
Excellent Student Award of Advanced Computing Research Laboratory, ICT, CAS, 2009
Excellent Student Award of Advanced Computing Research Laboratory, ICT, CAS, 2007
Second Prize of Outstanding Undergraduate Thesis, Central South University, 2004
National Scholarship Award, Central South University, 2002

PUBLICATIONS

1. Zuo-Fei Yuan, Long Wu, Chao Liu, Hao Chi, Sheng-Bo Fan, Kun Zhang, Wen-Feng Zeng, Rui-Xiang Sun, Si-Min He.
Accurate determination of precursor ions for peptides in large-scale protein identification.
Accepted by Prog. Biochem. Biophys., 2012.
2. 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, 12:226-235.
3. 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.
Accepted by ISMB 2010, Bioinformatics, 2010, 26(12), i399-i406.
4. 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, 2010, 24:807-814.
5. 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.
6. 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, 2010, 24(12):1791-1798.
7. 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, 2009, 10(Suppl 1):S50.
8. 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, 2009, 8:913-923.
9. 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, 2007, 21, 2985-2991.

Last Modified: 2012/09/05