University of Pittsburgh Department of Cell Biology
  • Research

    Nature is our best inventor: our lab is interested in the development of cutting-edge mass spectrometry-based proteomics technologies for the analysis of biomolecules and macromolecular assemblies. Recently, fascinated by the exciting biomedical potentials of camelid single-chain VHH antibodies (so-called nanobodies), we have begun to develop methods and informatics to revolutionize the discovery and characterizations of nanobodies.  In parallel, we are harnessing these tools that we developed and biomolecules from nature for biomedical applications, disease diagnosis, and treatment. Using integrative structural biology approaches, we are also interested in understanding the mechanisms of antigen-antibody binding.
  • Publications

    1. Xiang Y, Nambulli S, Xiao Z, Liu H, Sang Z, Duprex WP, Schneidman-Duhovny D, Zhang C, Shi Y. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.. Science. 2020 Dec 18;370(6523):1479-1484. doi: 10.1126/science.abe4747. PubMed PMID: 33154108;
    2. Xiang Y, Nambulli S, Xiao Z, Liu H, Sang Z, Duprex WP, Schneidman-Duhovny D, Zhang C, Shi Y. Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2.. bioRxiv. 2020 Aug 25;():. pii: 2020.08.24.264333. doi: 10.1101/2020.08.24.264333. PubMed PMID: 32869034;
    3. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Integrative structure and functional anatomy of a nuclear pore complex.. Nature. 2018 Mar 14;():. doi: 10.1038/nature26003. PubMed PMID: 29539637;
    4. 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;
    5. 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;
    6. 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;
    7. 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;
    8. 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;
    9. 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;
    10. 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;


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