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2.  Deshaies, R.J., Fish, L.E., and Jagendorf, A.T. (1984). Permeability of chloroplast envelopes to Mg2+. Effects on protein synthesis. Plant Physiol. 74, 956-961.

3.  Deshaies, R.J., and Schekman, R. (1987). A yeast mutant defective at an early stage in import of secretory protein precursors into the endoplasmic reticulum. J. Cell Biol. 105, 633-645.

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5.  Bohni, P.C., Deshaies, R.J., and Schekman, R. (1988). SEC11 is required for signal peptide processing and yeast cell growth. J. Cell Biol. 106, 1035-1042.

6.  Deshaies, R.J., Koch, B.D., and Schekman, R. (1988). The role of stress proteins in membrane biogenesis. Trends Biochem. Sci. 13, 384-388.

7.  Deshaies, R.J., Kepes, F., and Bohni, P.C. (1989). Genetic dissection of the early stages of protein secretion in yeast. Trends Genet. 5, 87-93.

8.  Deshaies, R.J., and Schekman, R. (1989). SEC62 encodes a putative membrane protein required for protein translocation into the yeast endoplasmic reticulum. J. Cell Biol. 109, 2653-2664.

9.  Rothblatt, J.A., Deshaies, R.J., Sanders, S.L., Daum, G., and Schekman, R. (1989). Multiple genes are required for proper insertion of secretory proteins into the endoplasmic reticulum in yeast. J. Cell Biol. 109, 2641-2652.

10.  Deshaies, R.J. and Schekman, R. (1990). Structural and functional dissection of Sec62p, a membrane-bound component of the yeast endoplasmic reticulum protein import machinery. Mol. Cell. Biol. 10, 6024-6035.

11.  Deshaies, R.J., Sanders, S., Feldheim, D., and Schekman, R. (1991). Assembly of yeast Sec proteins involved in translocation into the endoplasmic reticulum into a membrane-bound multisubunit complex. Nature 349, 806-808.

12.  Stirling, C.J., Rothblatt, J., Hosobuchi, M., Deshaies, R., and Schekman, R. (1992). Protein translocation mutants defective in the insertion of integral membrane proteins into the endoplasmic reticulum. Mol. Biol. Cell 3, 129-142.

13.  Esnault, Y., Blondel, M.O., Deshaies, R.J., Schekman, R. and Kepes, F. (1993). The yeast SSS1 gene is essential for secretory protein translocation and encodes a conserved protein of the endoplasmic reticulum. EMBO J. 12, 4083-4093.

14.  Booher, R.N., Deshaies, R.J. and Kirschner, M.W. (1993). Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins. EMBO J. 12, 3417-3426.

15.  Li, J.J. and Deshaies, R. J. (1993). Exercising self-restraint: discouraging illicit acts of S and M in eukaryotes. Cell 74, 223-226.

16.  Deshaies, R.J., Chau, V., and Kirschner, M.W. (1995). Ubiquitination of the G1 cyclin Cln2p by a Cdc34p-dependent pathway. EMBO J. 14, 303-312.

17.  Deshaies, R.J. and Kirschner, M.W. (1995). G1 cyclin-dependent activation of p34CDC28 in vitro. Proc. Natl. Acad. Sci. USA 92, 1182-1186.

18.  Gerber, M.R., Farrell, A., Deshaies, R.J., Herskowitz, I. and Morgan, D.O. (1995). CDC37 is required for association of the protein kinase CDC28 with G1 and mitotic cyclins. Proc. Natl. Acad. Sci. USA 92, 4651-4655.

19.  Banerjee, A., Deshaies, R.J., and Chau, V. (1995). Characterization of a dominant negative mutant of the cell cycle ubiquitin-conjugating enzyme Cdc34. J. Biol. Chem. 270, 26209-26215.

20.  Deshaies, R.J. (1995). Make it or break it: the role of ubiquitin-dependent proteolysis in cellular regulation. Trends Cell Bio. 5, 428-434.

21.  Deshaies, R.J. (1995). The self-destructive personality of a cell cycle in transition. Curr. Opin. Cell Biol. 7, 781-789.

22.  King, R.W., Deshaies, R.J., Peters, J.M., and Kirschner, M.W. (1996). How proteolysis drives the cell cycle. Science 274, 1652-1659.

23.  Deshaies, R.J. (1997). Phosphorylation and proteolysis: partners in the regulation of cell division in budding yeast. Curr. Opin. Genet. Dev. Biol. 7, 7-16.

24.  Verma, R., Chi, Y., and Deshaies, R.J. (1997). Cell-free ubiquitination of cell cycle regulators in budding yeast extracts. Methods Enzymol. 283, 366-376.

25.  Verma, R., Feldman, R.M.R., and Deshaies, R. J. (1997). SIC1 is ubiquitinated in vitro by a pathway that requires CDC4, CDC34, and cyclin/CDK activities. Mol. Biol. Cell 8, 1427-1437.

26.  Verma, R., Annan, R., Huddleston, M., Carr, S., Reynard, G., and Deshaies, R.J. (1997). Phosphorylation of Sic1p by G1 cyclin/Cdk is required for its degradation and entry into S phase. Science 278, 455-460.

27.  Feldman, R.M.R., Correll, C.C., Kaplan, K.B., and Deshaies, R.J. (1997). A Complex of Cdc4, Skp1, and Cdc53/Cullin Catalyzes Ubiquitination of the Phosphorylated CDK Inhibitor Sic1. Cell 91, 221-230.

28.  Henchoz, S., Chi, Y., Catarin, B., Herskowitz, I., Deshaies, R.J., and Peter, M. (1997). Phosphorylation and ubiquitin-dependent degradation of the cyclin-dependent kinase inhibitor Far1p in budding yeast. Genes Dev. 11, 3046-3060.

29.  Lyapina, S.L., Correll, C.C., Kipreos, E.T., and Deshaies, R.J. (1998). Human CUL1 forms an evolutionarily conserved ubiquitin ligase complex (SCF) with SKP1 and an F-box protein. Proc. Natl. Acad. Sci. USA 95, 7451-7456.

30.  Peters, J.-M., King, R.W., and Deshaies, R.J. (1998). Cell cycle control by ubiquitin-dependent proteolysis. In Ubiquitin and the Biology of the Cell (Ed. J.-M. Peters et al.) Plenum Press, NY.     

31.  Shou, W., Seol, J.H., Shevchenko, A., Baskerville, C., Moazed, D., Chen, Z.W.S., Jang, J., Shevchenko, A., Charbonneau, H., and Deshaies, R.J. (1999). Exit from mitosis triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97, 233-244.

32.  Deshaies R.J., and Jacks T. (1999). Cell multiplication peering in and peering out: regulation of and by the cell cycle. Curr. Opin. Cell Biol. 11, 705-707.

33.  Straight, A.F., Shou, W., Dowd, G.J., Turck, C.W., Deshaies, R.J., Johnson, A.D., and Moazed, D. (1999). Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97, 245-256.

34.  Seol, J.H., Feldman, R.M.R., Zachariae, W., Shevchenko, A., Correll, C.C., Lyapina, S., Chi, Y., Galova, M., Claypool, J., Sandmeyer, S., Nasmyth, K., Shevchenko, A., and Deshaies, R.J. (1999). Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34. Genes Dev. 13, 1614-1626.

35.  Freed, E., Lacey, K.R., Huie, P., Lyapina, S.A., Deshaies, R.J., Stearns, T., and Jackson, P.K. (1999). Components of an SCF ubiquitin ligase localize to the centrosome and regulate the centrosome duplication cycle. Genes Dev. 13, 2242-2257.

36.  Deshaies, R.J. (1999). SCF and cullin/RING H2-based ubiquitin ligases. Annu. Rev. Cell Dev. Biol. 15, 435-467.

37.  Verma, R., and Deshaies, R.J. (2000). A proteasome howdunit: the case of the missing signal. Cell 101, 341-344.

38.  Deshaies, R.J., and Meyerowitz, E.M. (2000). COP1 patrols the night beat. Nat. Cell Biol. 2, E102-E104.

39.  Reynard, G.J., Reynolds, W., Verma, R., and Deshaies, R.J. (2000). CKS1 is required for G1 cyclin/CDK activity in budding yeast. Mol. Cell Biol. 20, 5858-5864.

40.  Verma, R., Chen, S., Feldman, R., Schieltz, D., Yates, J., and Deshaies, R.J. (2000). Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11, 3425-39.

41.  Blondel, M., Galan, J.M., Chi, Y., Lafourcade, C., Longaretti, C., Deshaies, R.J., and Peter, M. (2000). Nuclear-specific degradation of Far1 is controlled by the localization of the F-box protein Cdc4. EMBO J. 19, 6085-6097.

42.  Annan, R.S, Huddleston, M.J., Verma, R., Deshaies, R.J., and Carr, S.A. (2001). A multidimensional electrospray MS-based approach to phosphopeptide mapping. Anal. Chem. 73, 393-404.

43.  Lippincott J., Shannon K.B., Shou W., Deshaies R.J., Li R. (2001). The Tem1 small GTPase controls actomyosin and septin dynamics during cytokinesis. J. Cell Sci. 7, 1379-86.

44.  Traverso, E.E., Baskerville, C., Liu, Y., Shou, W., James, P., Deshaies, R.J., Charbonneau, H. (2001). Characterization of the net1 cell cycle-dependent regulator of the Cdc14 phosphatase from budding yeast. J. Biol. Chem. 276, 21924-31.

45.  Seol, J.H., Shevchenko, A., Shevchenko, A., and Deshaies, R.J. (2001). Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly. Nat. Cell Biol. 4, 384-91.

46.  Galan, J.-M., Wiederkehr, A., Seol, J.H., Deshaies, R.J., Riezman, H., and Peter, M. (2001). Skp1p and the F-box protein Rcy1p form a non-SCF complex involved in recycling of the SNARE Snc1p in yeast. Mol. Cell Biol. 9, 3105-17.

47.  Chi, Y., Huddleston, M.J., Zhang, X., Young, R.A., Annan, R.S., Carr, S.A., and Deshaies, R.J. (2001). Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 9, 1078-92.

48.  Schwechheimer, C., Serino, G., Callis, J., Crosby, W.L., Lyapina, S., Deshaies, R.J., Gray W.M. Estelle M., Deng, X.W. (2001). Interactions of the COP9 signalosome with the E3 ubiquitin ligase SCFTIRI in mediating auxin response. Science 18, 1379-82.

49.  Lyapina, S., Cope, G., Shevchenko, A., Serino, G., Tsuge, T., Zhou,C., Wolf, D.A., Wei, N., Shevchenko, A., and Deshaies, R.J. (2001). Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalsome. Science 18, 1382-5.

50.  Mah, A.S., Jang, J., and Deshaies, R.J. (2001). Protein kinase Cdc15 activates the Dbf2-Mob1 kinase complex. Proc. Natl. Acad. Sci. USA 13, 7325-30.

51.  Sakamoto, K.M., Kim, K.B., Kumagai, A., Mercurio, F., Crews, C.C., and Deshaies, R.J. (2001). Protacs: Chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl. Acad. Sci. USA 98, 8554-9.

52.  Zhou, C., Seibert, V., Geyer, R., Rhee, E., Lyapina, S., Cope, Greg., Deshaies R.J., Wolf, D.A. (2001). The fission yeast COP9/ signalosome is involved in cullin modification by ubiquitin-related Ned8p. BMC Biochem. 2, 7.

53.  Shou, W., Sakamoto, K.M., Keener, J., Morimoto, K.W., Traverso, E., Azzam, R., Hoppe, G.J., Feldman, R.M., DeModena, J., Moazed, D., Charbonneau, H., Nomura, M., and Deshaies, R.J. (2001). Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit. Mol. Cell 8, 45-55.

54.  Verma, R., McDonald, W.H., Yates, J.R. III, and Deshaies, R.J. (2001). Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields fully active S phase cyclin-Cdk. Mol. Cell 8, 439-48.

55.  Wu, G., Lyapina, S., Das, I., Li, J., Guerney, M., Chui, I., Deshaies R.J., and Kitajewski, J. (2001). SEL-10, a negative regulator of notch signaling, targets notch for ubiquitin-mediated protein degradation. Mol. Cell Biol. 21, 7403-15.

56.  Deshaies, R.J., and Eilers, M. (2001). Editorial Review: Cell Multiplication. Curr. Opin. Cell Biol. 13, 729-730.

57.  Deshaies, R.J. and Ferrell, J.E. (2001). Multisite phosphorylation and the countdown to S phase. Cell 107, 819-822.

58.  Deshaies, R.J., Seol, J.H., McDonald, W.H., Cope, G., Lyapina, S.,Shevchenko, A., Shevchenko A., Verma, R., and Yates, J.R. (2002). Charting the protein complexome in yeast by mass spectrometry. Mol. Cell. Prot. 1, 3-10.

59.  Shou, W., and Deshaies, R.J. (2002). Multiple telophase arrest bypassed (tab) mutants alleviate the essential requirement for Cdc15 in exit from mitosis in S. cerevisiae. BMC Genet. 3, 4.

60.  Shou, W., Azzam, R., Chen, S.L., Huddleston, M.J., Baskerville, C., Charbonneau, H., Annan, R.S., Carr, S.A., and Deshaies, R.J. (2002). Cdc5 influences phosphorylation of Net1 and disassembly of the RENT complex. BMC Mol. Biol. 3, 3.

61.  Shou, W., Verma, R., Annan, R.S., Huddleston, M.J., Chen, S.L., and Deshaies R.J. (2002). Mapping phosphorylation sites in proteins by mass spectrometry. Method. Enzymol. 351, 279-296.

62.  Loughrey Chen S., Huddleston, M.J., Shou, W., Deshaies, R.J., Annan, R.S., and Carr, S.A. (2002). Mass spectrometry-based methods for phosphorylation site mapping of hyperphosphorylated proteins applied to Net1, a regulator of exit from mitosis in yeast. Mol. Cell. Prot. 1, 186-96.

63.  Verma, R., Aravind L., Oania, R., McDonald, W.H., Yates, J. R. III, Koonin, E.V. and Deshaies, R.J. (2002). Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611-615.

64.  Cope, G.A., Suh, G.S., Aravind, L., Schwarz, S.E., Zipursky, S.L., Koonin, E.V. and Deshaies, R.J. (2002). Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of NEDD8 from CUL1. Science 298, 608-611.

65.  Park C.J., Song, S., Lee P.R., Shou W., Deshaies R.J. and Lee K.S (2003). Loss of CDC5 function in saccharomyces cerevisiae leads to defects in Swe1p regulation and Bfa1p/Bub2p-independent cytokinesis. Genetics 163, 21-33.

66.  Petroski, M.D, and Deshaies, R.J. (2003). Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. Mol. Cell 11, 1435-44.

67.  Petroski, M.D, and Deshaies, R.J. (2003). Redundant degrons ensure the rapid destruction of sic1 at the g1 /s transition of the budding yeast cell cycle. Cell Cycle 2, 410-1.

68.  Cope, G.A., and Deshaies, R.J. (2003). COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases. Cell 114, 663-71.

69.  Lipford, J.R., and Deshaies, R.J. (2003). Diverse roles for ubiquitin-dependent proteolysis in transcriptional activation. Nat. Cell Biol. 5, 845-50.

70.  Sakamoto, K.M., Kim, K.B., Verma, R., Ransick, A., Stein, B., Crews, C.M., and Deshaies, R.J. (2003). Development of protacs to target cancer-promoting proteins for ubiquitination and degradation. Mol. Cell. Proteomics 2, 1350-1358.

71.  Ambroggio, X.I., Rees, D.C., and Deshaies, R.J. (2004). JAMM: A metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biol. 2, 0113-0119.

72.  Baumeister, W., Bachmair, A., Chau, B., Cohen, R., Coffino, P., DeMartino, G., Deshaies, R., et al. (2004). Varshavsky's Contributions (in Letters). Science 19, 1290-1292.

73.  Graumann, J., Dunipace, L.A., Seol, J.H., McDonald, W.H., Yates, J.R. III, Wold, B.J., and Deshaies, R.J. (2004). Applicability of TAP-MudPIT to pathway proteomics in yeast. Mol. Cell. Proteomics 3, 266-237.

74.  Schneekloth, J.S. Jr., Fonseca, F.N., Koldobskiy, M., Mandal, A., Deshaies, R., Sakamoto, K., and Crews, C.M. (2004). Chemical genetic control of protein levels: selective in vivo targeted degradation. J. Am. Chem. Soc. 126, 3748-3754.

75.  Wertz, I.E., O'Rourke, K.M., Zhang, Z., Dornan, D., Arnott, D., Deshaies, R.J., and Dixit, V.M. (2004). Human De-etiolated-1 regulates cJun by assembling a CUL 4A ubiquitin ligase. Science 303, 1371-1374.

76.  Verma, R., Oania, R., Graumann, J., and Deshaies, R.J. (2004). Multiubiquitin chain receptors define a layer of substrate selectivity in the ubiquitin-proteasome system. Cell 118, 99-110.

77.  Azzam, R., Chen, S.L., Shou, W., Mah, A.S., Alexandru, G., Nasmyth, K., Annan, R.S., Carr, S.A., and Deshaies, R.J. (2004). Phosphorylation by cyclin B-Cdk underlies release of mitotic exit. Science 305, 516-519.

78.  Verma, R., Peters, N.R., Tochtrop, G.P., Sakamoto, K.M., D'Onofrio, M., Varadan, R., Fushman, D., Deshaies, R.J., and King, R.W. (2004). Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain. Science 306, 117-120.

79.  Petroski, M.D. and Deshaies, R. J. (2005). Function and regulation of cullin-RING ubiquitin ligases. Nat. Rev. Mol. Cell. Biol. 6, 9-20.

80.  Mayor, T., Lipford, J.R., Graumann, J., Smith G.T., and Deshaies, R.J. (2005). Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets. Mol. Cell. Proteomics 4, 741-751.

81.  Lipford, J.R., Smith, G.T., Chi, Y., and Deshaies, R.J. (2005). A putative stimulatory role for activator turnover in gene expression. Nature 438, 113-116.

82.  Mah, A.S., Elia, A.E.H., Devgan, G, Ptacek, J., Schutkowski, M., Snyder, M., Yaffe, M.B., and Deshaies, R.J. (2005). Substrate specificity analysis of protein kinase complex Dbf20Mob1 by peptide library and proteome array screening. BMC Biochem. 6, 22.

83.  Mayor, T. and Deshaies, R.J. (2005). Two-step affinity purification of multiubiquitylated proteins from Saccharomyces cerevisiae. Method. Enzymol. 399, 385-392.

84.  Verma, R. and Deshaies, R.J. (2005). Assaying degradation and deubiquitination of a ubiquitinated substrate by purified 26S proteasomes. Method. Enzymol. 398, 391-399.

85.  Petroski, M.D. and Deshaies, R.J. (2005). In vitro reconstitution of SCF substrate ubiquitination with purified proteins. Method. Enzymol. 398, 143-158.

86.  Petroski, M.D. and Deshaies, R.J. (2005). Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34. Cell 123, 1107-1120.

87.  Cope, G.A. and Deshaies, R.J. (2006). Targeted silencing of JabI /Csn5 in human cells downregulates SCF activity through reduction of F-box protein levels. BMC Biochem. 7, 1.

88.  Sharon, M., Taverner, T., Ambroggio, X.I., Deshaies, R.J., and Robinson, C.V. (2006). Structural organization of the 19% proteasome lid: Insights from MS of intact complexes. PloS Biol. 4, 1314-1323 (e267).

89.  Petroski, M.D., Kleiger, G., and Deshaies, R.J. (2006). Evaluation of a diffusion-driven mechanism for substrate ubiquitination by the SCF-Cdc34 ubiquitin ligase complex. Mol Cell 24, 523-534.

90.  Ghaboosi, N. and Deshaies, R.J. (2007). A conditional yeast E1 mutant blocks the ubiquitin-proteasome pathway and reveals a role for ubiquitin conjugates in targeting Rad23 to the proteasome. Mol. Biol. Cell 18, 1953-63.

91.  Mayor, T., Graumann, J., Bryan, J., Maccoss, M.J., and Deshaies, R.J. (2007). Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol. Cell. Proteomics 6, 1885-1895.

92.  Haririnia, A., Verma, R., Purohit, N., Twarog, M.Z., Deshaies, R.J., Bolon, D., and Fushman, D. (2008). Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins. J. Mol. Biol. 375, 9 79-996.

93.  Goh, A.M., Walters, J.K., Elsasser, S., Verma, R., Deshaies, R.J., Finley, D., and Howley, P.M. (2008). Components of the ubiquitin-proteasome pathway compete for surfaces on Rad32 family proteins. BMC Biochem. 9, 4.

94.  Alexandru, G., Graumann, J., Smith, G.T., Kolawa, N.J., Fang, R., and Deshaies, R.J. (2008). UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1a turnover. Cell 134, 804-816.

95.  Saha, A. and Deshaies, R. J. (2008). Multimodal activation of the ubiquitin ligase SCF by Nedd8 conjugation. Mol. Cell 32, 21-31.

96.  Rodriguez-Gonzalez, A., Cyrus, K., Salcius, M., Kim, K., Crews, C.M., Deshaies, R.J., and Sakamoto, K.M. (2008). Targeting steroid hormone receptors for ubiquitination and degradation in breast and prostate cancer. Oncogene 27, 7201-7211.

97.  Collins, G.A., Lipford, J.R., Deshaies, R.J., Tansey, W.P.  (2009).  Gal4 turnover and transcription activation (Brief Communication Arising).  Nature 461, (8 October) E7.

98.  Mohl, D.A., Huddleston, M.J., Collingwood, T.S., Annan, R.S., and Deshaies, R.J. (2009). Dbf2-Mob1 drives relocalization of protein phosphatase Cdc14 to the cytoplasm during exit from mitosis. J. Cell Biol. 184, 527-539.

99.  Machida, K., Tsukamoto, H., Mkrtchyan, H., Duan, L., Dynnyk, A., Liu, H.M., Asahina, K., Govindarajan, S., Ray, R., Ou, J.H., Seki, E., Deshaies, R., Miyake, K., and Lai, M.M. (2009). Toll-like receptor 4 mediates synergism between alcohol and HCV in hepatic oncogenesis involving stem cell marker Nanog. Proc. Nat. Acad. Sci. USA 106, 1548-1553.

100.  Oh, Y.M., Kwon, Y.E., Kim, J.M., Bae, S.J., Lee, B.K., Yoo, S.J., Chung, C.H., Deshaies R.J., Seol, J.H. (2009) Chfr is linked to tumour metastasis through the downregulation of HDAC1. Nat. Cell Biol. 11, 295-302.

101.  Deshaies, R.J. (2009). Drug discovery: Fresh target for cancer therapy (News & Views). Nature 458, 709-710.

102.  Deshaies, R.J. and Joazeiro, C.A.P. (2009). RING domain E3 ubiquitin ligases. Annu. Rev. Biochem. 78, 399-434.

103.  Kleiger, G., Hao, B., Mohl, D.A., and Deshaies, R.J. (2009). The acidic tail of the Cdc34 ubiquitin-conjugating enzyme functions in both binding to and catalysis with ubiquitin ligase SCFCDC4. J. Biol. Chem. 284, 36012-36023.

104.  Kleiger, G., Saha, A., Lewis, S., Kuhlman, B., and Deshaies, R.J. (2009). Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell 139, 957-968.

105.  Pierce, N., Kleiger, G., Shan, S., and Deshaies, R.J. (2009). Detection of sequential ubiquitination on a millisecond time-scale. Nature 462, 615-619.

106.  Radhakrishnan, S.K., Lee, C.S., Young, P., Beskow, A, Chan, J.Y., and Deshaies, R.J. (2010). Transcription factor Nrf1 mediates the proteasome recovery pathway after proteasome inhibition in mammalian cells. Mol. Cell 38, 17-28.

107.  Aghajan, M., Jonai, N., Flick, K., Fu, F., Luo, M., Cai, X., Ouni, I., Pierce, N., Tang, X., Lomenick, B., Damoiseaux, R., Hao, R., Del Moral, P.M., Verma, R., Li, Y., Li, C., Houk, K.N., Jung, M.E., Zheng, N., Huang, L., Deshaies, R.J., Kaiser, P., and Huang, J. (2010). Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase. Nat. Biotechnol. 28, 738-742.

108.  Collins, G.A., Gomez, T.A., Deshaies, R.J., and Tansey, W.P. (2010). Combined chemical and genetic approach to inhibit proteolysis by the proteasome. Yeast 27, 965-974.

109.  Tyrell, A., Flick, K., Kleiger, G., Zhang, H., Deshaies, R.J., and Kaiser, P.  (2010).  Physiologically relevant and portable tandem ubiquitin-binding domain stabilizes polyubiquitylated proteins.  Proc. Natl. Acad. Sci. USA 107, 19796-19801.

110.  Deshaies, R.J., Emberley, E.D., and Saha, A. (2010). Control of cullin-ring ubiquitin ligase activity by Nedd8.  Subcell. Biochem. 54, 41-56.

111.  Verma, R., Oania, R., Fang, R., Smith, G.T., and Deshaies, R.J. (2011). Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol. Cell 41, 82-92.

112.  Chou, T.F., Brown, S.J., Minond, D., Nordin, B.E., Li, K., Jones, A.C., Chase, P., Porubsky, P.R., Stoltz, B.M., Schoenen, F.J., Patricelli, M.P., Hodder, P., Rosen, H., and Deshaies, R.J. (2011) Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways. Proc. Natl. Acad. Sci. USA 108, 4834-4839.

113.  Saha, A., Lewis, S., Kleiger, G., Kuhlman, B., and Deshaies, R.J. (2011). Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate.  Mol. Cell 42, 75-83.

114.  Lee, J.E., Sweredoski, M.J., Graham, R.L., Kolawa, N.J., Smith, G.T., Hess, S., and Deshaies, R.J. (2011). The steady-state repertoire of human SCF Ubiquitin ligase complexes does not require ongoing Nedd8 conjugation. Mol. Cell. Proteomics 10, 6460 1-9.

115.  Chou, T.F. and Deshaies, R.J. (2011).  Quantitative cell-based protein degradation assays to identify and classify drugs that target the ubiquitin-proteasome system.  J. Biol. Chem. 286, 16546-16554.

116.  Chou, T.F. and Deshaies, R.J. (2011).  Development of p97 AAA ATPase inhibitors.  Autophagy 7, 1091-1092.

117.  Gomez, T.A., Kolawa, N., Gee, M., Sweredoski, M.J., and Deshaies, R.J. (2011) Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1. BMC Biol. 9, 33.

118.  Rabut, G., Le Dez, G., Verma, R., Makhnevych, T., Knebel, A., Kurz, T., Boone, C., Deshaies, R.J. and Peter, M. (2011). The TFIIH subunit Tfb3 regulates cullin neddylation. Mol. Cell. 43, 488-495.

119.  Sohn, C.H., Lee, J.E., Sweredoski, M.J., Graham, R.L., Smith, G.T., Hess, S., Czerwieniec, G., Loo, J.A., Deshaies, R.J., Beauchamp, J.L. (2012). Click chemistry facilitates formation of reporter ions and simplified synthesis of amine-reactive multiplexed isobaric tags for protein quantification. J. Am. Chem. Soc. 134, 2672-2680.

120.  Haines, D.S., Lee, J.E., Beauparlant, S.L., Kyle, D.B., den Besten, W., Sweredoski, M.J., Graham, R.L., Hess, S., and Deshaies, R.J.  (2012). Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking.  Mol. Cell. Proteomics 11, M111.016444.

121.  Sohn, C.H., Agnew, H.D., Lee, J.E., Sweredoski, M.J., Graham, R.L., Smith, G.T., Hess, S., Czerwieniec, G., Loo, J.A., Heath, J.R., Deshaies, R.J., and Beauchamp, J.L.  (2012). Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions. Anal. Chem. 84, 2662-2669.

122.  Besten, W.D., Verma, R., Kleiger, G., Oania, R.S., and Deshaies, R.J. (2012). NEDD8 links cullin-RING ubiquitin ligase function to the p97 pathway.  Nat. Struct. Mol. Biol. 19, 511-516.

123.  Emberley, E.D., Mosadeghi, R., and Deshaies, R.J. (2012). Deconjugation of Nedd8 from Cul1 is directly regulated by Skp1-Fbox and substrate, and CSN inhibits deneddylated SCF by a non-catalytic mechanism. J. Biol. Chem. 287, 29679-29689.

124.  Oh, Y., Chang, K.J., Orlean, P., Wloka, C., Deshaies, R., and Bi, E. (2012). Mitotic exit kinase Dbf2 directly phosphorylates chitin synthase Chs2 to regulate cytokinesis in budding yeast. Mol. Biol. Cell. 23, 2445-2456.

125.  Chou, T.F., Li, K., Frankowski, K.J., Schoenen, F.J.,  and Deshaies, R.J. (2013). Structure-activity relationship study reveals ML240 and ML241 as potent and selective inhibitors of p97 ATPase. Chem. Med. Chem. 8, 297-312.

126.  Verma, R., Oania, R.S., Kolawa, N.J., and Deshaies, R.J. (2013). Cdc48/p97 promotes degradation of aberrant nascent polypeptides bound to the ribosome. Elife 2, e00308.

127.  Pierce, N.W., Lee, J.E., Liu, X., Sweredoski, M.J., Graham, R.L., Larimore, E.A., Rome, M., Zheng, N., Clurman, B.E., Hess, S., Shan, S.O., and Deshaies, R.J. (2013). Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins. Cell 153, 206-215.

128.  Chou, T.F., Li, K., Nordin, B.E., Porubsky, P., Frankowski, K., Patricelli, M.P., Aubé, J., Schoenen, F.J., and Deshaies, R. (2013). Selective, reversible inhibitors of the AAA ATPase p97.  Probe Reports from the NIH Molecular Libraries Program [Internet], National Center for Biotechnology Information, 2010-April 14, 2011 (updated May 1, 2013).

129.  Kurimchak, A., Haines, D.S., Garriga, J., Wu, S., De Luca, F., Sweredoski, M.J., Deshaies, R.J., Hess, S., and Graña, A. (2013). Activation of p107 by FGF, which is essential for chondrocyte cell cycle exit, is mediated by the PP2A/B55a holoenzyme.  Mol. Cell. Biol. 33, 3330-3342.

130.  Kolawa, N.J., Sweredoski, M.J., Graham, R.L.J., Oania, R., Hess, S., and Deshaies, R.J.  (2013). Perturbations to the ubiquitin conjugate proteome in yeast Dubx mutants identify Ubx2 as a regulator of membrane lipid composition.  Mol. Cell. Proteomics 12, 2791-2803.

131.  Radhakrishnan, S.K., den Besten, W. and Deshaies, R.J.  (2013).  p97-dependent retrotranslocation and proteolytic processing govern formation of active Nrf1 upon proteasome inhibition. eLife 3, e01856.

132.  Honarpour, N., Rose, C.M., Brumbaugh, J., Anderson, J., Graham, R.L., Sweredoski, M.J., Hess, S., Coom, J.J. and Deshaies, R.J. (2014). FBXL16 binds PP2A and regulates differentiation of embryonic stem cells along the FLK1+ lineage.  Mol. Cell. Proteomics 13, 780-791.

133.  Chou, T.F., Bulfer, S.L., Weihl, C.C., Li, K., Lis, L.G., Walters, M.A., Schoenen, F.J., Lin, H.J., Deshaies, R.J., and Arkin, M.R.  (2014).  Specific inhibition of p97/VCP ATPase and kinetic analysis demonstrate interaction between D1 and D2 ATPase domains. J. Mol. Biol. 426, 2886-2899.

134.  Chan, N.C., den Besten, W., Sweredoski, M.J., Hess, S., Deshaies, R.J., and Chan, D.C.  (2014).  Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2. J. Biol. Chem.  289, 19789-19799.

135.  Deshaies, RJ.  (2014).  Structural biology: Corralling a protein-degradation regulator.  Nature 512, 145-146.

136.  Fang, N.N., Chan, G.T., Zhu, M., Comyn, S.A., Persaud, A., Deshaies, R.J., Rotin, D., Gsponer, J., Mayor, T.  (2014).  Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress.  Nat. Cell Biol. [Epublished ahead of print 10/26/14]

137.  Deshaies, R.J.  (2014).  Proteotoxic crisis, the ubiquitin-proteasone system, and cancer therapy.  BMC Biol. 12:94.

138.  Pulvino, M., Chen, L., Oleksyn, D., Li, J., Compitello, G., Rossi, R., Spence, S., Balakrishnan, V., Jordan, C., Poligone, B., Casulo, C., Burack, R., Shapiro, J.L., Bernstein, S., Friedberg, J.W., Deshaies, R.J., Land, H., and Zhao, J.  (2015).  Inhibition of COP9-signalosome (CSN) deneddylating activity and tumor growth of diffuse large B-cell lymphomas by doxycycline.  Oncotarget 6, 14796-14813.

139.  Deshaies, R.J. (2015).  Protein degradation: Prime time for PROTACs.  Nat. Chem. Biol. 11, 634-635.

140.  Alverez, C., Bulfer, S.L., Chakrasali, R., Chimenti, M.S., Deshaies R.J., Green, N., Kelly, M., LaPorte, M.G., Lewis, T.S., Liang, M., Moore, W.J., Neitz, R.J., Peshkov, V.A., Walters, M.A., Zhang, F., Arkin, M.R., Wipf, P., Huryn, D.M.  (2016). Allosteric indoleamide inhibitors of p97: Identification of a novel probe of the ubiquitin pathway. ACS Med. Chem. Lett. 2, 182-187. 

141.  Banerjee, S., Bartesaghi, A., Merk, A., Prashant, R., Bulfer, S. L., Yan, Y., Green, N., Mroczkowski, B., Neitz, R.J., Wipf, P., Falconieri, V., Deshaies, R.J., Milne, J.L.S., Huryn, D., Arkin, M., Subramaniam, S.  ( 2016).  2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.  Science 351, 871-875.

142.  Nguyen, T.V., Lee, J.E., Sweredoski, M.J., Yang, S.J., Jeon, S.J., Harrison, J.S., Yim, J.H., Lee, S.G., Handa, H., Kuhlman, B., Jeong, J.S., Reitsma, J.M., Park, C.S., Hess, S., Deshaies, R.J.  (2016).  Glutamine triggers acetylation-dependent degradation of glutamine synthetase via the thalidomide receptor cereblon.  Mol. Cell 6, 809-820.

143.  Mosadeghi, R., Reichermeier, K.M., Winkler, M., Schreiber, A., Reitsma, J.M., Zhang, Y., Stengel, F., Cao, J., Kim, M., Sweredoski, M.J., Hess, S., Leitner, A., Aebersold, R., Peter, M., Deshaies, R.J., Enchev, R.I.  (2016).  Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle.  eLife 5, e12102.

144.  Sung, M.K., Reitsma, J.M., Sweredoski, M.J., Hess, S., Deshaies, R.J.  (2016).  Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system.  Mol. Biol. Cell 27, 2642-2652.

145.  Xue, L., Blythe, E.E., Freiberger, E.C., Mamrosh, J., Hebert, A.S., Reitsma, J.M., Hess, S., Coon, J.J., Deshaies, R.J.  VCP-adaptor interactions are exceptionally dynamic and subject to differential modulation by a VCP inhibitor.  Mol. Cell. Proteomics 15, 2970-2986.

146.  Sung, M.K., Porras-Yakushi, T.R., Reitsma, J.M., Huber, F.M., Sweredoski, M.J., Hoelz, A., Hess, S., Deshaies, R.J.  (2016).  A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins.  eLife, epublished ahead of print August 23, 2016. doi:10.7554/eLife.19105.

147.  Kleiger, G. and Deshaies, R.  (2016).  Tag Team Ubiquitin Ligases.  Cell 166, 1080-1081.

148.  Vangala, J.R, Sotzny, F., Kruger, E., Deshaies, R.J., Radhakrishnan, S.K.  (2016).  Nrf1 can be processed and activated in a proteasome-independent manner.  Curr. Biol. 26, R834-835.

149.  Reiterer, V, Figueras-Puig C., Le Guerroue F., Confalonieri, S., Vecchi, M., Jalapothu, D., Kanse, S.M., Deshaies, R.J., Di Fiore, P.P., Behrends, C., Farhan, H.  (2016).  The pseudophosphatase STYX targets the F-box of FBXW7 and inhibits SCFFBXW7 function.  EMBO J., epublished ahead of print December 22, 2016. doi: 10.15252/embj.201694795.