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Yan Fu, Ph.D., Associate Professor |
Research area
- Bioinformatics: Application and development of statistical and machine learning methods for important biological problems;
- computational proteomics and mass spectrometry: I am currently interested in developing algorithms and tools for protein identification from LC-MS/MS data, especially those for detection of post-translational modifications, which are known to play important roles in biological activities and present information not elucidated in genomes.
- I am also a member of JDL
Software tools
- pFind: a database-searching engine for peptide & protein identification via tandem mass spectrometry
- pCluster: a clustering tool for modification detection using LC, MS or MS/MS information
- pMatch: an open MS/MS library search tool for identification of peptides and their modifications
Recent publications (All publications)
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Yan Fu, Liyun
Xiu, Wei Jia, Ding Ye, et al. DeltAMT: a statistical algorithm for fast
detection of protein modifications from LC-MS/MS data. Molecular & Cellular Proteomics,
10(5):M110.000455, 2011. (pdf)
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Yan Fu, Rong Pan, Qiang Yang, Wen Gao. Query-Adaptive Ranking with Support Vector
Machines for Protein Homology Prediction. In Proceedings of the 7th International Symposium on
Bioinformatics Research and Applications (ISBRA2011). Lecture
Notes in Bioinformatics, 6674:320–331, 2011. (pdf)
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Ding Ye, Yan Fu, Ruixiang Sun, et al. Open
MS/MS Spectral Library Search to Identify Unanticipated Post-Translational
Modifications and Increase Spectral Identification Rate. In Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular
Biology (ISMB 2010). Bioinformatics, 26(12):i399-i406, 2010. (pdf)
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Yan Fu, Wei Jia, Zhuang Lu, et al. Efficient
discovery of abundant post-translational modifications and spectral pairs using
peptide mass and retention time differences. The Seventh Asia-Pacific
Bioinformatics Conference (APBC 2009). BMC Bioinformatics. 10(Suppl 1):S50, 2009. (pdf)
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Wei Jia, Zhuang Lu, Yan Fu, et al. A
strategy for precise and large-scale identification of core fucosylated
glycoproteins. Molecular &
Cellular Proteomics. 8:913-923, 2009. (pdf)
Talks
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On the false
discovery rate control in proteomic analysis of post-translational
modifications. The 9th International
Bioinformatics Workshop (IBW2011), Xi'an, China, July 12, 2011.
- Query-Adaptive Ranking with Support Vector Machines for Protein Homology Prediction. The 7th International Symposium on Bioinformatics Research and Applications (ISBRA2011), Changsha, China, May 29, 2011.
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Unrestrictive
Modification Detection Based on Related Spectral Pairs. The First China Workshop on Computational
Proteomics (CNCP2010), Beijing, China, Nov 11, 2010.
- In-depth detection of protein modifications using pFind software. Mass Spectrometry Conference of China (MSC2010). Changchun, China, Aug 1, 2010.
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pFind: a
software platform for protein identification from LC-MS/MS data. The 9th China-Japan-Korea Bioinformatics Training
Course and Bioinformatics Symposium, Shanghai, China, Apr 22, 2010.
- Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences. The Seventh Asia-Pacific Bioinformatics Conference (APBC 2009), Beijing, China, Jan 16, 2009.
- Mining Tandem Mass Spectral Data to Develop a More Accurate Mass Error Model for Peptide Identification. Pacific Symposium on Biocomputing (PSB2007), Maui, Hawaii, Jan 30, 2007.
Activities
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Referee for Proteomics, BMC Bioinformatics,
Journal of Computer Science and Technology, Statistics and Its Interface,
International Journal of Machine Learning and Cybernetics, Data Mining and
Knowledge Discovery, IEEE Transactions on Computational Biology and
Bioinformatics, OMICS Publishing Group, etc.
Honors & awards
- Outstanding Researcher 2009, ICT, Chinese Academy of Sciences
- Academic One-Hundred Stars 2008, ICT, Chinese Academy of Sciences
- President Scholarship 2007, Chinese Academy of Sciences
- Microsoft Fellowship 2004, Microsoft Research Asia
- Winner of ACM KDD Cup 2004's Bioinformatics Task (paper and technical report)
Photos
