Bingwen Lu, Ph.D.

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

     
          1-858-784-1000 ext. 3077

Research Interest:

      Computational Biology and Bioinformatics; Computational mass spectrometry and Proteomics.

Invited Review Panels:

      Referee (direct invitation from Journal Editors) for:
          Bioinformatics,
          Analytical Chemistry,
          Nucleic Acids Research,
          Proteomics,
          Molecular Systems Biology,
          Genome Research,
          Genome Biology,
          BMC Bioinformatics,
          BMC Research Notes

Other Professional Activities:

      Fellow for IPAM Proteomics 2004.

      Member of American Society of Mass Spectrometry.

      Member of HUPO.

Book (Monograph):

• Algorithmic study on mass spectrometry and proteomics. VDM Publishing.
  

Book Chapters:

• 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
• Bingwen Lu; Xu, T.; Park, S.K.; Yates, J.R. (2009) Shotgun Protein Identification and Quantification by Mass Spectrometry. (Book chapter in "Methods in Molecular Biology", In press)

Peer-reviewed Publications:

2010

• Koulov AV*, Lapointe P*, Lu B*, Razvi A, Coppinger J, Dong MQ, Matteson J, Laister R, Arrowsmith C, Yates JR 3rd, Balch WE. (2010) Biological and Structural Basis for Aha1 Regulation of Hsp90 ATPase Activity in Maintaining Proteostasis in the Human Disease Cystic Fibrosis. Mol Biol Cell. 2010 Jan 20. [Epub ahead of print] (PubMed )
  * co-first authors

2009

• Ambatipudi K, Lu B, Hagen FK, Melvin JE, Yates JR. (2009) Quantitative Analysis of Age Specific Variation in the Abundance of Human Female Parotid Salivary Proteins. Journal of Proteome Research . 8: 5093-5102. (PubMed )
  
• Chen, Y.*.; Bingwen Lu*; Yang, Q.; Fearns, C.; Yates, J.R., III; Lee, J.D. (2009) Combined Integrin Phosphoproteomic Analyses and siRNA-based Functional Screening Identified Key Regulators for Cancer Cell Adhesion and Migration Cancer Research 69(8): 3713-3720. (PubMed )
  * co-first authors
• Chen, R.*;Yang, Q.*; Bingwen Lu*; Yi, W.*; Cantin, G.*; Chen, Y.; Fearns, C.; Yates, J.; Lee, J.D. (2009) CDC25B mediates rapamycin-induced oncogenic responses in cancer cells. Cancer Research 69(6):2663-2668 (PubMed )
  * co-first authors
• Gonzalez-Begne M*; Bingwen Lu*; Han X*; Hagen F; Hand A; Melvin J; Yates JR 3rd (2009) Proteomic Analysis of Human Parotid Gland Exosomes by Multidimensional Protein Identification Technology (MudPIT). Journal of Proteome Research (PubMed )
  * co-first authors
• Ma, L.; Tsai, M.Y.; Wang, S.; Bingwen Lu; Chen, R.; Yates, J.R.; Zhu, X.; Zheng, Y. (2009) Requirement of Nudel and Dynein for assembly of the lamin B spindle matrix. Nature Cell Biology 7(11):4743-4755 (PubMed )
• Cui Z, Chen X, Bingwen Lu, Park SK, Xu T, Xie Z, Xue P, Hou J, Hang H, Yates JR III, Yang F (2009) Preliminary Quantitative Profile of Differential Expression between Rat L6 Myoblasts and Myotubes by Stable Isotope Labeling by Amino acids in Cell Culture. Proteomics 9(5): 1274-1292. (PubMed )

2008

• Liao L, McClatchy DB, Park SK, Xu T, Bingwen Lu, Yates JR 3rd.(2008) Quantitative Analysis of Brain Nuclear Phosphoproteins Identifies Developmentally Regulated Phosphorylation Events. Journal of Proteome Research 7: 4743-4755. (Abstract)
• 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. 7(8): 3628-3634. (Abstract) (PDF)
• 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)
• 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. (PubMed)
• 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) (Cited by These Articles)
• 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)

2007 and before

• 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)
• 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.(PubMed)
• 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)
• 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)
• 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)
• 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)
• 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.
• 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)
• 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)

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