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       Shiwei Sun
  

 

Shiwei Sun, Ph.D.
Name:
   Shiwei Sun
Academic Title:
   associate professor
Primary Appointment:
   Bioinformatics
School:
 Institute of Computing Technology, Chinese Academy of Sciences
email:   dwsun@ict.ac.cn
Lab Website:
   www.bioinfo.org.cn
EDUCATION
2002～2007 Bioinformatics Research Group,
Institute of Computing Technology, 
Chinese Academy of Sciences
Ph.D. Computer Sciense
1998～2001 Nankai University, Tianjin, China
Master. Physical Chemistry
1994～1998 Nankai University, Tianjin, China
bachelor. Physical Chemistry
 
POSITIONS AND EXPERIENCES
 
2005~present Assistant Investigator, Institute of Computing Technology, Chinese Academy of Sciences
 
2001～2005 Practice Investigator, Institute of Computing Technology, Chinese Academy of Sciences
 
 RESEARCH OVERVIEW
 

Tandem mass spectrometry is a powerful technique for characterizing a proteome. Our group relies upon the detailed information yielded by the mass spectrometer to identify proteins from complex mixtures. We draw upon biology, chemistry, and computer science to increase the scope, sensitivity, and throughput of technologies for practical proteomics.

 
   Biologists provide the questions that drive our research. By identifying complexes that are poorly understood or organism-wide issues that require further exploration, we find a wealth of problems in biology that are tractable only through proteomic strategies.

 
   Analytical chemists and biochemists improve our tools for revealing the proteins present in biological samples. Targets for optimization include the isolations used to obtain proteins from biological materials, the subsequent steps to generate peptides from these proteins, and the separation of peptides en route to the mass spectrometer. Chemistry is vital to increasing the overall power of proteomic technology.

 
   Computer science yields tools operating at two scales. First, the sequence corresponding to each peptide's tandem mass spectrum must be identified. Once those identifications have been completed, additional tools are needed to summarize and organize these identifications. Proteomics by tandem mass spectrometry requires powerful informatics capabilities.


   By drawing these disciplines together, we are producing improved tools and techniques for proteomics. For more information, consult my publications.
 
 RESEARCH INTERESTS
 
Computational Biology and Bioinformatics; Computational mass spectrometry and Proteomics
 
AWARDS
employee of year 2006 of Institute of Computing&Technology.
Publications: Journal Articles
Shiwei Sun, Fuquan Yang, Qing Yang, Hong Zhang,Yaojun Wang, Dongbo Bu and Bin Ma. MS-Simulator: Predicting y ion intensities for peptides with two charges based on the intensity ratio of neighboring ions. Accepted by J. Proteome Res.
Zhang S, Wang Y, Bu D, Zhang H, Sun S*. ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. BMC Bioinformatics 2011, 12:346 (17 August 2011)

Qiao Y, Zhang H, Bu D, Sun S*. PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum. BMC Bioinformatics 2011, 12:234 (15 June 2011)

Shiwei Sun, Chungong Yu, Yantao Qiao, Yu Lin,Gongjin Dong,Changning Liu, Jingfen Zhang, Zhuo Zhang, Jinjin Cai, Hong Zhang  and Dongbo Bu. Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra. J. Proteome Res., 7 ( 01 ), 202 – 208 , 2008 . 10.1021

Chungong Yu, Yu Lin, Shiwei Sun, JingJing Cai, Jinfen Zhang, Zhuo Zhang, Runsheng Chen, Dongbo Bu, “An iterative algorithm to quantify the factors influencing peptide fragmentation for ms/ms spectrum” J Bioinform Comput Biol. 2007 Apr ;5 (2):297-311 17589963

 

Shiwei Sun, Yi Zhao, Yishan Jiao, Yifei Yin, Lun Cai, Yong Zhang, Hongchao Lu, Runsheng Chen and Dongbo Bu 

Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm.  FEBS  Letters Vol. 580, No7  pp.  1891-1896
Zhang Yong ; Li Shaojuan ; Skogerbø Geir ; Zhang Zhihua ; Zhu Xiaopeng ; Zhang Zefeng ; Sun Shiwei ; Lu Hongchao ; Shi Baochen ; Chen Runsheng "Phylophenetic properties of metabolic pathway topologies as revealed by global analysis” BMC Bioinformatics. 2006; 7: 252. Published online 2006 May 9. doi: 10.1186/1471-2105-7-252

Yong Zhang, Shiwei  Sun, Tao  Wu, Jie  Wang,  Changning  Liu,  Lan  Chen,  Xiaopeng  Zhu,  Yi  Zhao,  Zhihuang  Zhang, Baochen  Shi,  Hongchao  Lu and Runsheng Chen. Identifying Hfq-binding small RNA targets in Escherichia coli. Biochem Biophys Res Commun. 2006 May 12;343(3):950-5. Epub 2006 Mar 20.

 
Wei Deng, Xiaopeng Zhu, Geir Skogerbø, Yi Zhao Zhuo Fu, Yudong Wang, Housheng He, Lun Cai, Hong Sun, Changning Liu, Biao Li, Baoyan Bai, Jie Wang, Dong Jia, Shiwei Sun, Hang He, Yan Cui, Yu Wang, Dongbo Bu and Runsheng Chen “Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression” Genome Research 16:20-29, 2006
Dongbo Bu, Yi Zhao, Lun Cai, Hong Xue, Xiaopeng Zhu, Hongchao Lu Jingfen Zhang, Shiwei Sun, Lunjiang Ling, Nan Zhang, Guojie Li and Runsheng Chen. "Topological structure analysis of the protein-protein interaction network in budding yeast" Nucleic Acids Research,2003.Vol.31, No.9 2443-2450
Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu and Runsheng Chen. A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinformatics Published online 2006 April 26. doi: 10.1186/1471-2105-7-222.
 
Publications: Proceedings Articles
Shiwei Sun, Yaojun Wang, Bin Ma and Dongbo Bu. MS-Simulator: Predicting y ion intensities for peptides with two charges based on the intensity ratio of neighboring ions. Accepted by RECOMB Satellite Conference on Computational Proteomics 2012.

Gongjin Dong, Yantao Qiao, Yu Lin, Shiwei Sun, Chungong Yu, Dongbo Bu.A Training-Set-Free Stochastic Model For Peptide Identification. poster, accepted by Recomb 2008

Yantao Qiao, Shiwei Sun, Gongjin Dong, Yu Lin, Chungong Yu,Dongbo Bu. A Novel Scoring Scheme to Evaluate the Match of the Peptide and Mass Spectrum. poster, accepted by Recomb 2008

Yu Lin, Yaotao Qiao, Shiwei Sun, Chungong Yu,  Gongjin Dong and Dongbo Bu. A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. accepted by Recomb 2008

Chungong Yu, Yu Lin, Shiwei Sun, JingJing Cai, Jinfen Zhang, Zhuo Zhang, Runsheng Chen, Dongbo Bu, “An iterative algorithm to quantify the factors influencing peptide fragmentation for ms/ms spectrum” computational systems bioinformatics, CSB2006 ISBN 1-86094-700-X 353-360