Bingwen Lu, Ph.D.

Department of Cell Biology
The Scripps Research Institute, SR11
10550 North Torrey Pines Rd.
La Jolla, CA 92037

     
          1-858-784-1000 ext. 3077

Background:

Research Interest:

      Computational Biology and Bioinformatics; Computational mass spectrometry and Proteomics.

Professional Activities:

      Referee (direct request from Journal Editors) for:
          Analytical Chemistry ,
          Nucleic Acids Research,
          Proteomics,
          Genome Research,
          Journal of Computational Biology,
          RECOMB.

      Fellow for IPAM Proteomics 2004.

      Member of American Society of Mass Spectrometry.

      Member of HUPO.

1. Preuss Dissertation Fellowship, 2004-2005, USC College of Letters, Arts and Sciences.
2. IPAM Proteomics Fellow, March 8 - June 11, 2004.
3. Outstanding teaching award, Department of Biological Sciences, 2002, USC.
4. 4th Place, USC Associated Computer Engineers and Scientists Programming Contest, 2001, USA.
5. Beijing University Huikai Fellowship, 1994-1995.
6. Third Prize, Chaoshan Xinghe Academy Prize, Guangdong Province, 1991, China.
7. Third Prize, Chaoshan Xinghe Academy Prize, Guangdong Province, 1990, China.
8. Second Prize, Guangdong Province High School Chemistry Contest, 1990, China.

Publications:
      (Note: Some links below will take you away from this website.)

1. Bingwen Lu, Daniel McClatchy, Jin Young Kim, John R. Yates III (2008) Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry. Proteomics (In Press)
2. Bingwen Lu, Cristian I. Ruse, John R. Yates III (2008) Colander: A probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search. Journal of Proteome Research (In Press)
3. Ruse CI, McClatchy DB, Bingwen Lu, Cociorva D, Motoyama A, Park SK, Yates JR 3rd. (2008) Motif-specific sampling of phosphoproteomes. Journal of Proteome Research. 7(5):2140-2150. (Abstract)
4. Dimaggio PA Jr, Floudas CA, Bingwen Lu, Yates III JR. (2008) A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry. Journal of Proteome Research, 7: 1584-1593.
5. Bingwen Lu, Akira Motoyama, Cristian Ruse, John Venable, John R. Yates (2008) Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data. Analytical Chemistry, 80: 2018-2025 (Abstract) (PDF)
6. GT Cantin, W Yi, Bingwen Lu, SK Park, T Xu, JD Lee, JR Yates III (2008) Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. Journal of Proteome Research. 7: 1346-1351.(Abstract) (PDF)
7. Bingwen Lu, Cristian Ruse, Tao Xu, Sung Kyu Park, John Yates III (2007) Automatic Validation of Phosphopeptide Identifications from Tandem Mass Spectra. Analytical Chemistry. 79: 1301-1310. Abstract (PDF) (Cited by These Articles)
8. Thomas, SN., Bingwen Lu, Nikolskaya, T., Yuri N., and Yang AJ. MudPIT (Multidimensional Protein Identification Technology) for identification of post-translational protein modifications in complex biological mixtures. (book chapter) In Redox proteomics: from protein modifications to cellular dysfunction and diseases. (2006) Wiley InterScience. Buy from Amazon
9. Bingwen Lu (2005) Algorithmic study on mass spectrometry and proteomics. Ph.D. Dissertation. University of Southern California, Los Angeles, California, USA. (PDF)
10. BA Soreghan, Bingwen Lu, SN Thomas, K Duff, EA Rakhmatulin, T Nikolskaya, T Chen, & AJ. Yang (2005) Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1+AbetaPP mouse model of Alzheimer's disease. The Journal of Alzheimer’s Disease. 8: 227-241.
11. MJ Chen, V Vijaykumar, Bingwen Lu, B Xia, N Li (2005) Cis- and trans-cinnamic acids have different effects on the catalytic properties of Arabidopsis phenylalanine ammonia lyases PAL1, PAL2, and PAL4. Journal of Integrative Plant Biology 47: 67-75.
12. Bingwen Lu, Ting Chen (2004) Algorithms for de novo peptide sequencing via tandem mass spectrometry. Drug Discovery Today: BioSilico 2: 85-90.   (PDF) (Cited by These Articles)
13. Bingwen Lu, Ting Chen (2003) A Suffix Tree Approach to the Interpretation of Tandem Mass Spectra: Applications to Peptides of Nonspecific Digestion and Post-translational Modifications. Bioinformatics Suppl. 2 (ECCB'03): II113-II121.  (PDF) (Cited by These Articles)
14. Bingwen Lu, Ting Chen (2003) A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology 10: 1-12.   (PDF) (Cited by These Articles)
15. Bingwen Lu, Ho Yan Yu, Lai Kwan Pei, Man Yu Wong and Ning Li (2002) Prolonged exposure to ethylene stimulates the negative gravitropic responses of Arabidopsis inflorescence stems and hypocotyls. Functional Plant Biology 29(8): 989-999. (Abstract)
16. Bingwen Lu, Lai-Kwan Pei, Wai-Kin Chan, Hong Zhang, Guang Zhu, Jiayang Li and Ning Li (2001) The dual effects of ethylene on the negative gravicurvature of Arabidopsis inflorescence, an intriguing action model for the plant hormone ethylene. Chinese Science Bulletin 46(4): 279-283.
17. Bingwen Lu, Jun Wang, Ning Li, (2000) Ethylene as a gaseous reporter molecule for monitoring gene expression in cultured cells. BioTechniques 28: 646-648. (PDF)
18. Yimin Chen, Bingwen Lu, Dik Hagenbeek, Ning Li and Shang Fa Yang (1999) A Nucleotide Sequence of Musa accuminata cv Cavendish Grand Nain (AAA) Encoding an Ethylene Inducible 1-Aminocyclopropane-1-Carboxylate Synthase (Accession No. AJ223186). (PGR99-062). Plant Physiology 120: 339-340.
19. Bingwen Lu, Bing Yu, Ning LI (1999) Expression of a novel ethylene-producing bifunctional fusion enzyme in yeast. Botanical Bulletin of Academia Sinica 40: 107-114. (PDF)

1. Sub-DeNovo: A sub-optimal program for de novo peptide sequencing using tandem mass spectrometry.
2. DeBunker: A software tool for validating phosphopeptide identification from tandem mass spectrometry.
3. Colander: A software tool for selecting CID phosphopeptide spectra prior to database search.

Links: English Chinese Dictionary