UW Genome Sciences

Research:

The Villén Lab seeks to develop and apply novel technologies for proteome characterization to answer fundamental questions in cell biology and disease. We use quantitative mass spectrometry to measure dynamic changes in protein abundances, protein post-translational modification states, and to characterize interaction partners across multiple cellular states.

We are particularly interested in studying protein phosphorylation as a general regulatory mechanism in the cell involved in a myriad of functions: how phosphorylation is integrated into the multiple responses to shape the proteome, and how signaling circuits evolved to accommodate proteome functional complexity.

Selected Publications:

Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J. & Gygi, S. P. (2006). A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24, 1285-1292.

Villen, J., Beausoleil, S. A., Gerber, S. A. & Gygi, S. P. (2007). Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U. S. A. 104, 1488-1493.

Guo, A., Villen, J., Kornhauser, J., Lee, K. A., Stokes, M. P., Rikova, K., Possemato, A., Nardone, J., Innocenti, G., Wetzel, R., Wang, Y., MacNeill, J., Mitchell, J., Gygi, S. P., Rush, J., Polakiewicz, R. D. & Comb, M. J. (2008). Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U. S. A. 105, 692-697.

Villen, J. & Gygi, S. P. (2008). The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 3, 1630-1638.

Villen, J., Beausoleil, S. A. & Gygi, S. P. (2008). Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics 8, 4444-4452.

Baek, D.*, Villen, J.*, Shin, C.*, Camargo, F. D., Gygi, S. P. & Bartel, D. P. (2008). The impact of microRNAs on protein output. Nature 455, 64-71. (* equal contribution)

Holt, L. J.*, Tuch, B. B.*, Villen, J.*, Johnson, A. D., Gygi, S. P. & Morgan, D. O. (2009). Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325, 1682-1686. (* equal contribution)