Yi Shi, Ph.D.

  • Assistant Professor
  • Department of Cell Biology

Education & Training

  • B.E, Dalian University of Technology, 1999-2003
  • Ph.D., Baylor College of Medicine, 2006-2011
  • Postdoc, The Rockefeller University, 2011-2016
  • Assistant Professor, University of Pittsburgh 2017-present

Research Interest Summary

We are interested in the development of cutting-edge proteomic technologies and their applications in basic biological discoveries & human diseases such as aging and neurodegenerative disorders.

Research Categories

Research Interests

My lab is interested in the development of cutting-edge mass spectrometry-based proteomic technologies. We are particularly interested in elucidating the structure- function of large native macromolecular assemblies and dissecting biological pathways that regulate autophagy and aging by using multidisciplinary approaches including proteomics, cell biology, and biophysics. We are also interested in developing cutting-edge nanobody based technologies to investigate the spatial & temporal regulation of the mammalian mitochondrial proteomes, and their roles in aging and neurogenerative disorders.

Representative Publications

Seung Joong Kim*, Javier Fernandez-Martinez*, Ilona Nudelman*, Yi Shi*, Wenzhu Zhang*, Barak Raveh, Thurston Herricks, Brian D. Slaughter, Joanna Hogan, Paula Upla, Ilan E. Chemmama, Riccardo Pellarin, Ignacia Echeverria, Manjunatha Shivaraju, Azraa S. Chaudhury, Junjie Wang, Rosemary Williams, Jay R. Unruh, Charles H. Greenberg, Erica Y. Jacobs, Zhiheng Yu, M. Jason de la Cruz, Roxana Mironska, David L. Stokes, John D. Aitchison, Martin F. Jarrold, Jennifer L. Gerton, Steven J. Ludtke, Christopher W. Akey, Brian T. Chait, Andrej Sali, and Michael P. Rout. Molecular Architecture of the Nuclear Pore Complex. Nature (under revision, *equal contribution)

Fernandez-Martinez, J.*, Kim, S.J.*, Shi, Y.,* Paula, U.*, Pallerin, R.*, Zenklusen, D., Chemmama, I, Nudelman, I., Wang, J.J., Timney, B., Williams, R., Strokes, D.L., Chait, B.T., Sali, A., and Rout, M.P . (2016). Structure and function of the cytoplasmic mRNA export platform. Cell 167 (5), 1215-1228. (* equal contribution)

Chait, B.T., Cadene, M., Olinares, P.D., Rout, M.P. & Shi, Y. (2016). Revealing Higher Order Protein Structure Using Mass Spectrometry. JASMS 27, 952-965.

Shi, Y., Pellarin, R., Fridy, P.C., Fernandez-Martinez, J., Thompson, M.K., Li, Y., Wang, Q.J., Sali, A., Rout, M.P., and Chait, B.T. (2015). A strategy for dissecting the architectures of native macromolecular assemblies. Nature Methods 12, 1135-1138.

Sun, J., Shi, Y., Georgescu, R.E., Yuan, Z., Chait, B.T., Li, H., and O'Donnell, M.E. (2015). The architecture of a eukaryotic replisome. Nat Struct Mol Biol 22, 976-982.

Cevher, M.A., Shi, Y., Li, D., Chait, B.T., Malik, S., and Roeder, R.G. (2014). Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 21, 1028-1034.

Shi, Y.*, Fernandez-Martinez, J.*, Tjioe, E.*, Pellarin, R.*, Kim, S.J.*, Williams, R., Schneidman-Duhovny, D., Sali, A., Rout, M.P., and Chait, B.T. (2014). Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex. Molecular & Cellular Proteomics 13, 2927-2943.

Malovannaya, A., Lanz, R.B., Jung, S.Y., Bulynko, Y., Le, N.T., Chan, D.W., Ding, C., Shi, Y., Yucer, N., Krenciute, G., et al. (2011). Analysis of the human endogenous coregulator complexome. Cell 145, 787-799.

Shi, Y., Xu, P., and Qin, J. (2011b). Ubiquitinated proteome: ready for global? Molecular & Cellular Proteomics 10, R110 006882.

Shi, Y., Chan, D.W., Jung, S.Y., Malovannaya, A., Wang, Y., and Qin, J. (2011a). A data set of human endogenous protein ubiquitination sites. Molecular & Cellular Proteomics 10, M110 002089.

Full List of Publications