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Molecular Medicine


John Yates III, Ph.D.

Department of Molecular Medicine
California Campus
Laboratory Website
(858) 784-8862

Scripps Research Joint Appointments

Department of Neuroscience
Faculty, Graduate Program

Research Focus

Genomic and EST sequencing projects are providing a sequence infrastructure that is changing how protein biochemistry is practiced. These data along with mass spectrometry provide the cornerstone technologies fueling the proteomics revolution. Our group is focused on developing tools and strategies in proteomics to answer basic biological questions. By coupling the additional amino acid sequence information that can be obtained using peptide tandem mass spectrometry to "back-end" database searching and "front-end" separative techniques, we are able to directly analyze extremely complex protein mixtures. The applications for these technologies vary from analyzing purified protein complexes to studying host-pathogen interactions in diseases such as malaria or anthrax. We are further extending these applications to find post-translational modifications to the proteins within these same complex mixtures.


M.S., Chemistry, University of Maine, 1983
Ph.D., Chemistry, University of Virginia, 1987
B.A., Zoology, University of Maine, 1980

Awards & Professional Activities

Associate Editor, Analytical Chemistry Board of Reviewing Editors Science Biemann Award 2004 American Society for Mass Spectrometry Research Award 1996 Pehr Edman Award 1998

Selected References

Skop, A. R., Liu, H., Yates, J. R., Meyer, B. J., Heald, R. Functional proteomic analysis of the mammalian midbody reveals conserved cell division components, Science 305, 61-6. 2004

Eric C. Schrimer, Laurence Florens, Tinglu Guan, John R. Yates III, and Larry Gerace Novel Membrane Proteins With Potential Disease Links Found By Subtractive Proteomics, Science 301, 1380-1382. 2003

Christine C. Wu, Michael J. MacCoss, Kathryn E. Howell, John R. Yates, III A novel method for the comprehensive proteomic analysis of membrane proteins: Identification, Modifications, and Topology, Nature Biotechnology 21, 262-7. 2003

Boddy, M.N., Gaillard, P.H.L., McDonald, W.H., Shanahan, P., Yates, J.R., 3rd, Russell, P. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell 107, 537-548. 2001


Scientists Identify Thousands of Proteins Associated with the Deadliest Form of Malaria

Molecular Medicine Seminar Series
Center for Physiological Proteomics
Department Contacts

CA Faculty

Asahara, Hiroshi
Balch, William E.
Boddy, Michael
Buxbaum, Joel
Catz, Sergio
Conti, Bruno
Cravatt, Benjamin
D'Lima, Darryl
DerMardirossian, Celine
Deryugina, Elena
Elias, Darlene
Encalada, Sandra
Felding, Brunhilde
Fowler, Velia
Friedlander, Martin
Gerace, Larry
Gottesfeld, Joel
Griffin, John
Hanneken, Anne
Heeb, Mary Jo
Henderson, Scott
Hoch, James
Johnson, Eric
Kanaji, Taisuke
Koziol, James
Lamia, Katja
Lazzerini Denchi, Eros
Lipton, Stuart
Loring, Jeanne F.
Loskutoff, David
Lotz, Martin
Makarenkova, Helen P.
Mc Millan, Robert
Miles, Lindsey
Milner, Richard
Modena, Brian
Mosnier, Laurent
Paulson, James C.
Perego, Marta
Petrascheck, Michael
Pollard, Kenneth Michael
Quigley, James P.
Reed, Steven
Roberts, Edward
Rosen, Hugh
Ruggeri, Zaverio
Russell, Paul
Saez, Enrique
Smider, Vaughn
Srinivasan, Supriya
Steinhubl, Steven
Sutcliffe, J.
Tan, Eng
Topol, Eric
Vanderklish, Peter
Vogt, Peter K.
Wiseman, Luke
Wittenberg, Curt
Wolan, Dennis W.
Wu, Peng
Wu, Xiaohua
Yang, Xiang-Lei
Yates III, John

FL Faculty

Bannister, Thomas
Bohn, Laura M.
Cameron, Michael
Duckett, Derek
Gill, Matt
Griffin, Patrick
Hansen, Scott
Joazeiro, Claudio
Kamenecka, Theodore
Kissil, Joseph
Luo, Junli
McDonald, Patricia
Miller, Courtney
Niedernhofer, Laura
Phinney, Donald G.
Robbins, Paul
Scampavia, Louis
Schimmel, Paul
Smith, Roy
Spicer, Timothy

Affiliated Faculty

Cline, Hollis
Kojetin, Douglas
Lairson, Luke
Paegel, Brian
Rumbaugh, Gavin
Shen, Ben
Solt, Laura A
Su, Andrew
Wu, Chunlei
Ye, Li

Adjunct Faculty