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Seminars & Events
From?Scientific Administration Office of IBP
October 08, 2008
IBP Seminar: Driving Biological Discovery Using Quantitative Mass Spectrometry
| what: |
Driving Biological Discovery Using Quantitative Mass Spectrometry |
| who: |
Prof. John R. Yates III
Dept. of Chem. Physiology, The Scripps Research Institute, CA, USA |
| when: |
Wednesday, October 14, 2008
10?00 a.m. |
| where: |
Lecture Hall , Institute of Biophysics |
| Host: |
Prof. Fuquan Yang |
| More Information: |
Curriculum Vitae (CV)
NAMEYates III, John R. POSITION TITLEProfessor, Chemical Physiology
EDUCATION/TRAINING
INSTITUTION AND LOCATION DEGREE(if applicable) YEAR(s) FIELD OF STUDY
University of Maine, Orono ME B.A. 1980 Zoology
University of Maine, Orono ME M.S. 1983 Chemistry
University of Virginia, Charlottesville, VA Ph.D. 1987 Chemistry
University of Virginia, Charlottesville, VA Postdoctoral 1987-1988 Chemistry
California Inst. of Technology, Pasadena, CA Postdoctoral 1988-1989 Biology
A. Positions
6/89-7/91 Prize Fellow-Biotechnology, Dept Biology, CIT, Pasadena, CA
7/91-8/92 Member of the Beckmann Institute, CIT, Pasadena, CA
9/92 ?7/98 Assistant Professor, Molecular Biotechnology, U Washington, Seattle, WA
7/98-1/00 Associate Professor, Molecular Biotechnology, U Washington, Seattle, WA
8/93-1/00 Adjunct Assistant Professor, Ctr for Bioengineering, U Washington, Seattle, WA
2/1/00-12/01 Associate Professor, Dept Cell Biology, Scripps Research Institute,La Jolla, CA
12/01-Present Professor, Dept Chem Physiology, The Scripps Research Institute, La Jolla, CA
3/1/03-4/1/04 Sr. Research Fellow, Protein and Metabolite Dynamics, Diversa, La Jolla, CA
10/1/03 Editorial Review Board, Science
Honors and Awards
1985-87 Dupont Chemistry Fellowship, University of Virginia; 1989-91 Prize Fellowship in Biotechnology, California Institute of Technology; 1996 American Society for Mass Spectrometry Research Award; 1998 Pehr Edman Award in Protein Chemistry; 2000 Dieter and Inge Hoehn Lecture in Bioanalytical Chemistry, Northeastern University; 2001 Robert Kroc Lecture in Endocrinology, Mayo Clinic Rochester MN; 2001 Genome Technologies All Star in Proteomics; 2004 Biemann Award, 2005 HUPO Distinguished Achievement Award in Proteomics, 2006 Hebert Sober Award ASBMB, 2006 Christian Anfinsen Award - Protein Society
B. Selected peer-reviewed publications (from 415 publications)
1. An approach to correlate MS/MS data to amino acid sequences in a protein database, J. K. Eng, A. L. McCormack, and J. R. Yates III, J. American Soc. Mass Spectrom 1994;5:976-989.
2. A method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database, J. Yates III, J. Eng, A. McCormack, D. Schieltz, Ana.l Chem. 1995; 67:1426-36.
3. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low femtomole level, A. L. McCormack, D. Schieltz, J. K. Eng, B. Goode, S. Yang, G. Barnes, D. Drubin, and J. R. Yates, III, Analytical. Chemistry 1997; 69:767-776.
4. Identifying SNPS expressed in Proteins: Rapid identification of amino acid sequence variations by LC/MS/MS with SEQUEST data analysis, C. L. Gatlin, J. K. Eng, S. T. Terashita, J. C. Detter, J. R. Yates III, Analytical Chemistry 2000;72:757-763.
5. Large Scale analysis of the yeast proteome via multidimensional protein identification technology, M.P. Washburn, D. Wolters, and J. R. Yates III, Nature Biotechnology 2001;19:242-247.
6. Phospho-regulation of Kinetochore-Microtubule attachments by the Aurora kinase Ip11p, I. Cheeseman, S. Anderson, M. Jwa, E. Green, J-S. Kang, J. R. Yates III, C. Chan, D. Drubin, and G. Barnes, Cell 2002;111:163-172.
7. Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome, R. Verma, L. Aravind, R. Oania, W. H. McDonald, J. R. Yates III, E.V. Koonin, and R. J. Deshaies, Science 2002; 298: 611-5.
8. A Proteomic View of the Plasmodium falciparum Life Cycle, L. Florens, M. P. Washburn, J. D. Raine, R.M. Anthony, M. Grainger||, J. D. Haynes, J. K. Moch, N. Muster, J.B. Sacci, D. L. Tabb*, A. A. Witney, D. Wolters, Y. Wu, M. J. Gardner, A. A. Holder|, R. E. Sinden, J. R. Yates III, and D. J. Carucci, Nature 2002; 419: 520-6.
9. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii, J. M. Carlton, S. V. Angiuoli, B. B. Suh, T. W. Kooij, M. Pertea, J. C. Silva, M. D. Ermolaeva, J. E. Allen, J. D. Selengut, H. L. Koo, J. D. Peterson, M. Pop, D. S. Kosack, M. F. Shumway, S. L. Bidwell, S. J. Shallom, S. E. van Aken, S. B. Riedmuller, T. V. Feldblyum, J. K. Cho, J. Quackenbush, M. Sedegah, A. Shoaibi, L. M. Cummings, K, Florens, J. R. Yates III, J. D. Raine, R. E. Sinden, M. A. Harris, D. A. Cunningham, P. R. Preiser, L. W. Bergman, A. B. Vaidya, L. H. van Lin, C. J. Janse, A. P. Waters, H. O. Smith, O. R. White, S. L. Salzberg, J. C. Venter, C. M. Fraser, S. L. Hoffman, M. J. Gardner, and D. J. Carucci. Nature 2002; 419: 512-19.
10. A Method for the Comprehensive Proteomic Analysis of Membrane Proteins, C. C. Wu, M. J. MacCoss, K. E. Howell, and J. R. Yates III, Nature Biotechnology 2003;21:532-538.
11. Wnt Proteins are Lipid-Modified and Can Act as Stem Cell Growth Factors, K. Willert, J. Brown, E. Danenberg, A. Duncan, I. L. Weissman, T. Reya, J. R. Yates III, R. Nusse, Nature 2003;423: 448-52.
12. Novel Membrane Proteins With Potential Disease Links Found By Subtractive Proteomics, E. C. Schrimer, L. Florens, T. Guan, J. R. Yates III, and L. Gerace, Science 2003; 301:1380-1382.
13. Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5, R. A. de Bruin, W. H. McDonald, T. I. Kalashnikova, J. R. Yates III, C. Wittenberg, Cell 2004;117:887-898.
14. Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms, A.R. Skop, H. Liu, J. R. Yates III, B. J. Meyer, R. Heald, Science 2004; 305:61-66.
15. A novel approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. J. D. Venable, M. Dong, J. Wohlschlegel, A. Dillin J. R. Yates III, Nature Methods 1, 39-45, 2004.
16. .Phermone dependent destruction of the Tec1 Transcription factor is required for MAP kinase Signaling Specificity in Yeast, M. Z. Bao, M.A. Schwartz, G. T. Cantin, J. R. Yates, H. Madhani, Cell, 119, 1-20, (2004)
17. Acetylation by Tip60 Is Required for Selective Histone Variant Exchange at DNA Lesions, Thomas Kusch, Laurence Florens, W. Hayes MacDonald, Selene K. Swanson, Robert L. Glaser, John R. Yates III, Susan M. Abmayr, Michael P. Washburn, & Jerry L. Workman, Science 2004 306, 2084-7.
18. Chd1 mediates SAGA and SLIK dependent acetylation via chromodomain recognition of methylated histone H3., Marilyn G. Pray-Grant, Jeremy A. Daniel, David Schieltz, Grant A. Hartzog, C. David Allis, John R. Yates III, and Patrick A. Grant, Nature 2005 433, 434-8.
19. RNA-dependent cysteine biosynthesis in archaea, A. Sauerwald, W. Zhu, T. A. Major, H. Roy, S. Palioura, D. Jahn, W. Whitman, J. R. Yates, 3rd, M. Ibba and D. S?ll, Science 2005 307, 1969-1972.
20. J. Huang, G. Phillips, A. Roth, L. Pedraza, W. Shan, W. Belkaid, S. Mi, A. Fex-Svenningsen, L. Florens, J. Yates III, & D. Colman, Glial membranes at the CNS node of Ranvier prevent neurite outgrowth, Science 2005, 310, 1813-7.
21. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell, 123, 581-92 (2005)
22. M. Karakozova, M. Kozak, C. Wong, A. Bailey, J. Yates, III, & A. Kashina, Arginylation of beta actin regulates actin cytoskeleton and cell motility, Science 2006, 313, 192-6.
23.`P. Sun, L. New, B. Moser, Y. Li, R. Liao, N. Yoshizuka, Q. Deng, M. Yamout, M-Q. Dong, J. Yates III, P. Wright, & J. Han, PRAK Mediates Oncogenic Ras-induced Senescence and Tumor Suppression by Regulating p53 Activity Cell 2007, 128, 295-308
24. M-Q. Dong, J. Venable, N. Au, T. Xu, S. Park, D. Cociorva, J. Johnson, A. Dillin, J. Yates, III, Quantitative Mass Spectrometry Identifies New Insulin/IGF-1 Signaling Targets, Science 2007, 317, 660-663.
25. Dentin, R., Hedrick, S., Xie, J., Yates, J., 3rd, and Montminy, M. (2008). Hepatic glucose sensing via the CREB coactivator CRTC2. Science 319, 1402-1405.
26. Park, S.K., Venable, J.D., Xu, T., and Yates, J.R., 3rd (2008). A quantitative analysis software tool for mass spectrometry-based proteomics. Nature Methods 5, 319-322.
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