29. Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2. Yihu Xie, Bradley P. Clarkea, Yong Joon Kimb, Austin L. Iveya, Pate S. Hilla, Yi Shi, and Yi Ren. bioRxiv 2021.01.04.425184

28. A resource of high-quality nanobodies for drug delivery. Shen Z, Xiang Y, Vegara S, Chen A, Xiao Z, Santiago U, Jin C, Sang Z, Luo J, Chen K, Schneidman-Duhovny D, Camacho C, Calero G, Hu B, Shi Y (2020). bioRxiv: 2020.08.19.257725.

27. Xiang, Y., Sang, Z., Bitton, L., Xu, J., Liu, Y., Schneidman-Duhovny, D., and Shi, Y (2020). Integrative proteomics identifies thousands of distinct and high-affinity nanobodies. Cell Systems. (accepted)

26. Xiang, Y., Nambulli, S., Xiao, Z., Liu, H., Sang, Z., Duprex, W.P., Schneidman-Duhovny, D., Zhang, C., and Shi, Y. (2020). Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science. (2020)

This work has been highlighted by numerous media and journalists worldwide

25. Yufei Xiang, Zhuolun Shen, and Yi Shi. Chemical cross-linking and mass spectrometric (CX-MS) analysis of the endogenous yeast exosome complexes. (2020). Methods in Molecular Biology.

24. Sai J Ganesan, Michael J Feyder, Ilan E Chemmama, Fei Fang, Michael P Rout, Brian T Chait, Yi Shi, Mary Munson, Andrej Sali. Integrative Structure and Function of the Yeast Exocyst Complex. (2020). Protein Science.


23. Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, B.C., Andrews, P., Bernfur, K., Borchers, C., Brodie, N.I., Bruce, J.E., Cao, Y., Shi, Y., et al. (2019). First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Analytical Chemistry 91, 6953-6961.

22. Yaqun Teng, Tribhuwan Yadav, Meihan Duan, Jun Tan, Yufei Xiang, Boya Gao, Jianquan Xu, Zhuobin Liang, Yang Liu, Satoshi Nakajima, Yi Shi, Arthur S Levine, Lee Zou, Li Lan (2018). ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB. Nature communications 9, 4115.


21. Jishage, M., Yu, X., Shi, Y., Ganesan, S.J., Chen, W.Y., Sali, A., Chait, B.T., Asturias, F.J., and Roeder, R.G. (2018). Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol 25, 859-867.

20. Kim, S.J.*, Fernandez-Martinez, J.*, Nudelman, I.*, Shi, Y.*, Zhang, W.*, Raveh, B., Herricks, T., Slaughter, B.D., Hogan, J., Paula, U., Chemmama, I., Pallerin, R., Echeverria, I., Shivaraju, M., Chaudhury, A.S., Wang, J.J., Williams, R., Unruh, J.R., Greenberg, C.H., Jacobs, E.Y.,

Yu, Z., De la Cruz, M.J., Mironska, R., Strokes, D.L., Aitchison, J.D., Jarrold, M.F., Gerton, J.L., Ludtke, S.J., Akey, C.W., Chait, B.T., Sali, A., and Rout, M.P. Structure and Functional Anatomy of the Nuclear Pore Complex (2018). Nature 555, 475-482. PMID: 29539637

“An Architectural Guide to the Nuclear Pore Complex”- Comments from the NIH director Francis Collins

Publications prior to 2017:

19. Fernandez-Martinez J*, Kim SJ*, Shi Y*, Paula U*, Pellerin R*, Zenklusen D, Chemmama I, Nudelman I, Wang JJ, Timney, B, Williams R, Strokes DL, Chait BT, Sali A, and Rout MP . (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 167, 1–14

Preview by: Gozalo, A. & Capelson, M. A New Path through the Nuclear Pore. Cell 167, 1159-1160 2016.

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

17. Hunziker, M., Barandun, J., Petfalski, E., Tan, D., Delan-Forino, C., Molloy, K.R., Kim, K.H., Dunn-Davies, H., Shi, Y., Chaker-Margot, M., et al. (2016). UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. Nature Communications 7, 12090.

16. 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.

15. 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.

14. LoPiccolo, J., Kim, S.J., Shi, Y., Wu, B., Wu, H., Chait, B.T., Singer, R.H., Sali, A., Brenowitz, M., Bresnick, A.R., et al. (2015). Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85alpha Homodimer. Journal of Biological Chemistry  290, 30390-30405.

13. Morris, D.H., Yip, C.K., Shi, Y., Chait, B.T., and Wang, Q.J. (2015). Beclin 1-Vps34 Complex Architecture: Understanding the Nuts and Bolts of Therapeutic Targets. Frontiers in biology 10, 398-426.

12. 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.

11. 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.

10. Algret, R., Fernandez-Martinez, J., Shi, Y., Kim, S.J., Pellarin, R., Cimermancic, P., Cochet, E., Sali, A., Chait, B.T., Rout, M.P., et al. (2014). Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway. Molecular & Cellular Proteomics 13, 2855-2870.

9. Kim, S.J., Fernandez-Martinez, J., Sampathkumar, P., Martel, A., Matsui, T., Tsuruta, H., Weiss, T.M., Shi, Y., Markina-Inarrairaegui, A., Bonanno, J.B., et al. (2014). Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Molecular & Cellular Proteomics 13, 2911-2926.

8. Yucer, N., Shi, Y., Wang, Y. (2013) Protein Ubiquitination in IR-Induced DNA Damage Response. Intech.

Krenciute, G., Liu, S.F., Yucer, N., Shi, Y., Ortiz, P., Liu, Q.M., Kim, B.J., Odejimi, A.O., Leng, M., Qin, J., et al. (2013). Nuclear BAG6-UBL4A-GET4 Complex Mediates DNA Damage Signaling and Cell Death. Journal of Biological Chemistry 288, 20547-20557.

7. Fan, Y.*, Shi, Y.*, Liu, S.*, Mao, R., An, L., Zhao, Y., Zhang, H., Zhang, F., Xu, G., Qin, J., et al. (2012). Lys48-linked TAK1 polyubiquitination at lysine-72 downregulates TNFalpha-induced NF-kappaB activation via mediating TAK1 degradation. Cell Signal 24, 1381-1389.

6. 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.

5. 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.

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

3. Fan, Y., Yu, Y., Shi, Y., Sun, W., Xie, M., Ge, N., Mao, R., Chang, A., Xu, G., Schneider, M.D., et al. (2010). Lysine 63-linked polyubiquitination of TAK1 at lysine 158 is required for tumor necrosis factor alpha- and interleukin-1beta-induced IKK/NF-kappaB and JNK/AP-1 activation. Journal of Biological Chemistry  285, 5347-5360.

2. Sun, W., Tan, X., Shi, Y., Xu, G., Mao, R., Gu, X., Fan, Y., Yu, Y., Burlingame, S., Zhang, H., et al. (2010). USP11 negatively regulates TNFalpha-induced NF-kappaB activation by targeting on IkappaBalpha. Cell Signal 22, 386-394.

1. Xu, G., Tan, X., Wang, H., Sun, W., Shi, Y., Burlingame, S., Gu, X., Cao, G., Zhang, T., Qin, J., et al. (2010). Ubiquitin-specific peptidase 21 inhibits tumor necrosis factor alpha-induced nuclear factor kappaB activation via binding to and deubiquitinating receptor-interacting protein 1. Journal of Biological Chemistry 285, 969-978.

© 2016-2019 by the Shi Lab University of Pittsburgh Pittsburgh PA 15213

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