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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.
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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) |
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Shiwei Sun, |
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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
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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
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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.
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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 |
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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 |
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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 |
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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 |