University of Pittsburgh Department of Cell Biology

Shi Lab

The extraordinarily emergent properties of living cells have evolved largely as a consequence of the intricately ordered interactions of their biomolecular components. These cellular building blocks interact with each other to form a hierarchy of dynamic macromolecular assemblies that drive a plethora of intriguing biological processes. Unfortunately, despite their central role in cell biology, many of the macromolecular complexes identified to date remain refractory to structure-functional characterization.

Our lab is interested in the development of cutting-edge mass spectrometry-based proteomic technologies. We are also interested in elucidating the structure- functions of native macromolecular assemblies and dissecting intriguing biological pathways that regulate DNA damage response and autophagy by using multidisciplinary approaches including proteomics, cell biology, and biophysics.

  1. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.. Cell. 2016 Nov 17;167(5):1215-1228.e25. doi: 10.1016/j.cell.2016.10.028. PubMed PMID: 27839866;
  2. Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry.. J Am Soc Mass Spectrom. 2016 Jun;27(6):952-65. doi: 10.1007/s13361-016-1385-1. PubMed PMID: 27080007;
  3. Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O\'Donnell ME. The architecture of a eukaryotic replisome.. Nat Struct Mol Biol. 2015 Dec;22(12):976-82. doi: 10.1038/nsmb.3113. PubMed PMID: 26524492;
  4. Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. A strategy for dissecting the architectures of native macromolecular assemblies.. Nat Methods. 2015 Dec;12(12):1135-8. doi: 10.1038/nmeth.3617. PubMed PMID: 26436480;
  5. Cevher MA, Shi Y, Li D, Chait BT, Malik S, Roeder RG. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit.. Nat Struct Mol Biol. 2014 Dec;21(12):1028-34. doi: 10.1038/nsmb.2914. PubMed PMID: 25383669;
  6. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.. Mol Cell Proteomics. 2014 Nov;13(11):2927-43. doi: 10.1074/mcp.M114.041673. PubMed PMID: 25161197;
  7. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.. Mol Cell Proteomics. 2014 Nov;13(11):2855-70. doi: 10.1074/mcp.M114.039388. PubMed PMID: 25073740;
Postal Address:
University of Pittsburgh
Department of Cell Biology
Biomedial Science Tower 3, 9049
Telephone:  412-383-3242  
Fax:   
Email:  yi.shi@pitt.edu