Publications

Artz, J.D., Wernimont, A.K., Allali-Hassani, A., Zhao, Y., Amani, M., Lin, Y.H., Senisterra, G., Wasney, G.A., Fedorov, O., King, O., Roos, A., Lunin, V.V., Qiu, W., Finerty, P. Jr., Hutchinson, A., Chau, I., von Delft, F., Mackenzie F., Lew, J., Kozieradzki, I., Vedadi, M., Schapira, M., Zhang, C., Shokat, K., Heightman, T. and Hui, R. (2011) The Cryptosporidium parvum Kinome. BMC Genomics, 12(1):478.

Statsuk, A.V. and Shokat, K.M. (2011) Covalent cross-linking of kinases with their corresponding Peptide substrates. Methods Mol. Biol. 795:179-90.

Schoenborn, J.R., Tan, Y.X., Zhang, C., Shokat, K.M. and Weiss, A. (2011) Feedback circuits monitor and adjust Basal lck-dependent events in T cell receptor signaling. Sci. Signal., 4(190):ra59.

Wang, B.T., Ducker, G.S., Barczak, A.J., Barbeau, R., Erle, D.J. and Shokat, K.M. (2011) The mammalian target of rapamycin regulates cholesterol biosynthetic gene expression and exhibits a rapamycin-resistant transcriptional profile. Proc. Natl. Acad. Sci. U S A., 108(37):15201-6.

Garske, A.L., Peters, U., Cortesi, A.T., Perez, J.L. and Shokat, K.M. (2011) Chemical genetic strategy for targeting protein kinases based on covalent complementarity. Proc. Natl. Acad. Sci. USA., 108(37):15046-52.

Yoshii, A., Murata, Y., Kim, J., Zhang, C., Shokat, K.M. and Constantine-Paton, M. (2011) TrkB and Protein Kinase M {zeta} Regulate Synaptic Localization of PSD-95 in Developing Cortex. J. Neurosci., 31(33):11894-904.

Salomon, D., Zhang, C., Shokat, K.M. and Sessa, G. (2011) Sensitizing Plant Protein Kinases to Specific Inhibition by ATP-Competitive Molecules. Methods Mol. Biol. 2011;779:185-97.

Korennykh, A.V., Egea, P.F., Korostelev, A.A., Finer-Moore, J., Stroud, R.M., Zhang, C., Shokat, K.M., and Walter, P. (2011) Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1. BMC Biol., 9(1):48.

Korennykh, A.V., Korostelev, A.A., Egea, P.F., Finer-Moore, J., Stroud, R.M., Zhang, C., Shokat, K.M. and Walter, P. Structural and functional basis for RNA cleavage by Ire1. (2011) BMC Biol. 9:47.

Mirzoeva, O.K., Hann, B., Hom, Y.K., Debnath, J., Aftab, D., Shokat, K. and Korn, W.M. (2011) Autophagy suppression promotes apoptotic cell death in response to inhibition of the PI3K-mTOR pathway in pancreatic adenocarcinoma. J. Mol. Med. (Berl), 89(9):877-89.

Merrick, K.A., Wohlbold, L., Zhang, C., Allen, J.J., Horiuchi, D., Huskey, N.E., Goga, A., Shokat, K.M. and Fisher, R.P. (2011) Switching Cdk2 on or off with small molecules to reveal requirements in human cell proliferation. Mol. Cell., 42(5):624-36.

Dar, A.C. and Shokat, K.M. (2011) The evolution of protein kinase inhibitors from antagonists to agonists of cellular signaling. Annu. Rev. Biochem., 80:769-95.

Brennan, D.F., Dar, A.C., Hertz, N.T., Chao, W.C., Burlingame, A.L., Shokat, K.M., and Barford, D. (2011) A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK. Nature, 472(7343):366-9.

Nakamura, J.L., Phong, C., Pinarbasi, E., Kogan, S.C., Vandenberg, S., Horvai, A.E., Faddegon, B.A., Fiedler, D., Shokat, K., Houseman, B.T., Chao, R., Pieper, R.O. and Shannon, K. (2011) Dose-dependent effects of focal fractionated irradiation on secondary malignant neoplasms in Nf1 mutant mice. Cancer Res., 71(1):106-15.

Bodenmiller, B., Wanka, S., Kraft, C., Urban, J., Campbell, D., Pedrioli, P.G., Gerrits, B., Picotti, P., Lam, H., Vitek, O., Brusniak, M.Y., Roschitzki, B., Zhang, C., Shokat, K.M., Schlapbach, R., Colman-Lerner, A., Nolan, G.P., Nesvizhskii, A.I., Peter, M., Loewith, R., von Mering, C. and Aebersold, R. (2011) Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.  Sci. Signal., 3(153):rs4.

Bandyopadhyay, S., Mehta, M., Kuo, D., Sung, M.K., Chuang, R., Jaehnig, E.J., Bodenmiller, B., Licon, K., Copeland, W., Shales, M., Fiedler, D., Dutkowski, J., Guénolé, A., van Attikum, H., Shokat, K.M., Kolodner, R.D., Huh, W.K., Aebersold, R., Keogh, M.C., Krogan, N.J. and Ideker, T. (2011) Rewiring of genetic networks in response to DNA damage. Science, 330(6009):1385-9. Erratum in: Science, 331(6015):284.

Chuluunbaatar, U., Roller, R., Feldman, M.E., Brown, S., Shokat, K.M. and Mohr, I. (2011) Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication. Genes Dev., 24(23):2627-39.

Su. T., Bryant, D.M., Luton F., Vergés, M., Ulrich, S.M., Hansen, K.C., Datta, A., Eastburn, D.J., Burlingame, A.L., Shokat, K.M. and Mostov, K.E. (2010) A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor.  Nat. Cell Biol., 12(12):1143-53.

Au-Yeung, B.B., Levin, S.E., Zhang, C., Hsu, L.Y., Cheng, D.A., Killeen, N., Shokat, K.M. and Weiss, A. (2010) A genetically selective inhibitor demonstrates a function for the kinase Zap70 in regulatory T cells independent of its catalytic activity. Nat. Immunol., 11(12):1085-92.

Gomez-Sjoberg, R. Leyrat, A.A., Houseman, B.T., Shokat, K. and Quake, S.R. (2010) Biocompatibility and Reduced Drug Absorption of Sol-Gel-Treated Poly(dimethyl siloxane) for Microfluidic Cell Culture Applications. Anal. Chem. 2010 Oct 11.

Tak, E., Lee, S., Lee, J., Rashid, M.A., Kim, Y.W., Park, J.H., Park, W.S., Shokat, K.M., Ha, J. and Kim, S.S. (2010) Human carbonyl reductase 1 upregulated by hypoxia renders resistance to apoptosis in hepatocellular carcinoma cells.  J. Hepatol., 54(2):328-39.

Tietjen, J.R., Zhang, D.W., Rodríguez-Molina, J.B., White, B.E., Akhtar, M.S., Heidemann, M., Li, X., Chapman, R.D., Shokat, K., Keles, S., Eick, D. and Ansari, A.Z. (2010) Chemical-genomic dissection of the CTD code.  Nat. Struct. Mol. Biol. 17(9):1154-61.

Chou, W.H., Wang, D., McMahon, T., Qi, Z.H., Song, M., Zhang, C., Shokat, K.M. and Messing, R.O. (2010) GABAA receptor trafficking is regulated by protein kinase C{varepsilon} and the N-ethylmaleimide-sensitive factor.
J. Neurosci. 30(42):13955-65.

Fan, Q.W., Cheng, C., Hackett, C., Feldman, M., Houseman, B.T., Nicolaides, T., Haas-Kogan, D., James, C.D., Oakes, S.A., Debnath, J., Shokat, K.M. and Weiss, W.A. (2010) Akt and autophagy cooperate to promote survival of drug-resistant glioma.  Sci. Signal.  3(147):ra81.

Maciejowski, J., George, K.A., Terret, M.E., Zhang, C., Shokat, K.M., Jallepalli, P.V. (2010) Mps1 directs the assembly of Cdc20 inhibitory complexes during interphase and mitosis to control M phase timing and spindle checkpoint signaling.  J. Cell. Biol. 190(1):89-100.  

Okuzumi, T., Ducker, G.S., Zhang, C., Aizenstein, B., Hoffman, R. and Shokat, K.M. (2010) Synthesis and evaluation of indazole based analog sensitive Akt inhibitors.  Mol. Biosyst. 6(8):1389-402.

Feldman, M.E. and Shokat, K.M. (2010) New Inhibitors of the PI3K-Akt-mTOR Pathway: Insights into mTOR Signaling from a New Generation of Tor Kinase Domain Inhibitors (TORKinibs).  Curr. Top Microbiol. Immunol. 2010 Jun 12. [Epub ahead of print]

Lourido, S., Shuman, J., Zhang, C., Shokat, K.M., Hui, R. and Sibley, L.D. (2010)  Calcium-dependent protein kinase 1 is an essential regulator of exocytosis in Toxoplasma.  Nature. 465(7296):359-62.

Sliedrecht, T., Zhang, C., Shokat, K.M. and Kops, G.J. (2010) Chemical genetic inhibition of Mps1 in stable human cell lines reveals novel aspects of Mps1 function in mitosis. PLoS One, 5(4):e10251.

Lu, M., Wang, J., Jones, K.T., Ives, H.E., Feldman, M.E., Yao, L.J., Shokat, K.M., Ashrafi, K. and Pearce, D. (2010) mTOR Complex-2 Activates ENaC by Phosphorylating SGK1.  J. Am. Soc. Nephrol., 21(5):811-8.

Shokat, K.M. (2010) A Drug-Drug Interaction Crystallizes a New Entry Point into the UPR.  Mol Cell. 38(2):161-163.

Amin, D.N., Sergina, N., Ahuja, D., McMahon, M., Blair, J.A., Wang, D., Hann, B., Koch, K.M., Shokat, K.M. and Moasser, M.M. (2010) Resiliency and vulnerability in the HER2-HER3 tumorigenic driver.  Sci. Transl. Med. 2(16):16ra7.  

Dail, M., Li, Q., McDaniel, A., Wong, J., Akagi, K., Huang, B., Kang, H.C., Kogan, S.C., Shokat, K., Wolff, L., Braun, B.S. and Shannon, K. (2010) Mutant Ikzf1, KrasG12D, and Notch1 cooperate in T lineage leukemogenesis and modulate responses to targeted agents.  Proc. Natl. Acad. Sci. U S A. 2010 Mar 16;107(11):5106-11.

Miller, S., Tavshanjian, B., Oleksy, A,, Perisic, O., Houseman, B.T., Shokat, K.M. and Williams, R.L. (2010) Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34. Science, 327(5973):1638-42.

Poulikakos, P.I., Zhang, C., Bollag, G., Shokat, K.M. and Rosen, N. (2010) RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature, 464(7287):427-30.

An, S., Kyoung, M., Allen, J.J, Shokat, K.M., Benkovic, S.J, (2010) Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2.  J. Biol. Chem., 285(15):11093-9.

Hsieh, A.C., Costa, M., Zollo, O., Davis, C., Feldman, M., Testa, J., Meyuhas, O., Shokat, K.M. and Ruggero, D. (2010) Genetic dissection of the oncogenic mTOR pathway reveals druggable addiction to translational control via 4EBP-eIF4E Cancer Cell, 17(3):249-61.

Williams, O., Houseman, B.T., Kunkel, E.J., Aizenstein, B., Hoffman, R., Knight, Z.A. and Shokat, K.M. (2010) Discovery of dual inhibitors of the immune cell PI3Ks p110d and p110g:  a prototype for new anti-inflammatory drugs.  Chemistry & Biology, 17(2):123-34.

Carlson, H.K., Plate, L., Price, M.S., Allen, J.J., Shokat, K.M. and Marletta, M.A. (2009) Use of a Semisynthetic Epitope to Probe Histidine Kinase Activity and Regulation.  Anal. Biochem., 397(2):139-43.

Roux, J., Carles, M., Koh, H., Goolaerts, A., Ganter, M.T., Chesebro, B.B., Howard, M., Houseman, B.T., Finkbeiner, W., Shokat, K.M., Paquet, A.C., Matthay, M.A. and Pittet, J.F. (2009) TGF-{beta}1 inhibits CFTR-dependent cAMP-stimulated alveolar epithelial fluid transport via a PI3K-dependent mechanism.  J. Biol. Chem. 285(7):4278-90.

Knight, Z.A., Lin, H. and Shokat, K.M. (2010) Targeting the cancer kinome through polypharmacology.  Nat. Rev. Cancer., 10(2):130-7.

Berndt, A., Miller, S., Williams, O., Le, D.D., Houseman, B.T., Pacold, J.I., Gorrec, F., Hon, W.C., Liu, Y., Rommel, C., Gaillard, P., Rückle, T., Schwarz, M.K., Shokat, K.M., Shaw, J.P. and Williams, R.L. (2010) The p110 delta structure: mechanisms for selectivity and potency of new PI(3)K inhibitors. Nat. Chem. Biol. 6(2):117-24.

Niu, H., Wan, L., Busygina, V., Kwon, Y., Allen, J.A., Li, X., Kunz, R.C., Kubota, K., Wang, B., Sung, P., Shokat, K.M., Gygi, S.P. and Hollingsworth, N.M. (2009) Regulation of meiotic recombination via Mek1-mediated Rad54 phosphorylation.  Mol. Cell., 36(3):393-404.

Sos, M.L., Fischer, S., Ullrich, R., Peifer, M., Heuckmann, J.M., Koker, M., Heynck, S., Stückrath, I., Weiss, J., Fischer, F., Michel, K., Goel, A., Regales, L., Politi, K.A., Perera, S., Getlik, M., Heukamp, L.C., Ansén, S., Zander, T., Beroukhim, R., Kashkar, H., Shokat ,K.M., Sellers, W.R., Rauh, D., Orr, C., Hoeflich, K.P., Friedman, L., Wong, K.K., Pao, W. and Thomas, R.K. (2009) Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer. Proc. Natl. Acad. Sci. U S A., 106(43):18351-6.

Herbert, S.P., Huisken, J., Kim, T.N., Feldman, M.E., Houseman, B.T., Wang, R.A., Shokat, K.M. and Stainier, D.Y. (2009) Arterial-venous segregation by selective cell sprouting: an alternative mode of blood vessel formation. Science, 326(5950):294-8.

Glover-Cutter, K., Larochelle, S., Erickson, B., Zhang, C., Shokat, K., Fisher, R.P. and Bentley, D.L. (2009) TFIIH-associated Cdk7 kinase functions in phosphorylation of CTD Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II.Mol. Cell Biol.,(20):5455-64.

de Lartigue, J., Polson, H., Feldman, M., Shokat, K., Tooze, S.A., Urbé, S. and Clague, M.J. (2009) PIKfyve regulation of endosome-linked pathways. Traffic, 10(7):883-93.

Liu, Y., Warfield, L., Zhang, C., Luo, J., Allen, J., Lang, W.H., Ranish, J., Shokat, K.M. and Hahn, S. (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol. Cell Bio. 29(17):4852-63.

Burkard, M.E., Maciejowski, J., Rodriguez-Bravo, V., Repka, M., Lowery, D.M., Clauser, K.R., Zhang, C., Shokat, K.M., Carr, S.A., Yaffe, M.B.and Jallepalli, P.V. (2009) Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells.  PLoS Biol. 7(5):e1000111.

Okuzumi, T., Fiedler, D., Zhang, C., Gray, D.C., Aizenstein, B., Hoffman, R. and Shokat, K.M. (2009) Inhibitor hijacking of Akt activation.  Nat. Chem. Biol. 5(7):484-493.

Justman, Q., Ferrell, J., El-Samad, H. and Shokat, K. M. (2009) Threshold Tuning by a Single Kinase Through Specific Feedback Architecture.  Science, 324(5926):509-12.

Salomon, D., Bonshtien, A., Mayrose, M., Zhang, C., Shokat, K.M. and Sessa, G. (2009) Bypassing kinase activity of the tomato Pto resistance protein with small-molecule ligands. J. Biol. Chem., 284(22):15289-98.

Niedermeier, M., Hennessy, B.T., Knight, Z.A., Henneberg, M., Hu, J., Kurtova, A.V., Wierda, W.G., Keating, M.J., Shokat, K.M. and Burger, J.A. (2009) Isoform-selective phosphoinositide 3'-kinase inhibitors inhibit CXCR4 signaling and overcome stromal cell-mediated drug resistance in chronic lymphocytic leukemia: a novel therapeutic approach. Blood., 113(22):5549-57.

Wong, C.H., Baehner, F.L., Spassov, D.S., Ahuja, D., Wang, D., Hann, B., Blair, J., Shokat, K., Welm, A.L. and Moasser, M.M. (2009) Phosphorylation of the SRC epithelial substrate trask is tightly regulated in normal epithelia but widespread in many human epithelial cancers.  Clin. Cancer Res., 15(7):2311-22.

Viladevall, L., St Amour, C.V., Rosebrock, A., Schneider, S., Zhang, C., Allen, J.J., Shokat, K.M., Schwer, B., Leatherwood, J.K. and Fisher, R.P. (2009) TFIIH and P-TEFb coordinate transcription with capping enzyme recruitment at specific genes in fission yeast.  Mol. Cell., 33(6):738-51.

Feldman, M., Apsel, B., Uotila, A., Loewith, R., Knight, Z.A., Ruggero, D. and Shokat, K.M. (2009) Active-Site Inhibitors of mTOR Target Rapamycin-Resistant Outputs of mTORC1 and mTORC2. PLoSBiology, 7(2):e38.

Fiedler, D., Braberg, H., Chechik, G., Cagney, G., Mehta, M., Mukherjee, P., Andrea, C., Silva, A.C., Shales, M., Collins, S.R., van Wageningen, S., Kemmeren, P., Holstege, F. C.P., Weissman, J.S., Christopher-Keogh, M., Koller, D., Shokat, K.M. and Krogan, N.J. (2008) A Genetic Map of the S. cerevisiae Phosphorylation Network.  Cell, 36(5):952-63.

Korennykh, A.V., Egea, P.F., Korostelev, A.A., Finer-Moore, J., Zhang, C., Shokat, K.M., Stroud, R.M. and Walter P. (2008) The unfolded protein response signals through high-order assembly of Ire1.  Nature, 457(7230):687-93.

Wang, H., Kakaradov, B., Collins, S.R., Karotki, L., Fiedler, D., Shales, M., Shokat, K.M., Walther, T., Krogan, N.J., Koller, D. (2009) A complex-based reconstruction of the S. cerevisiae interactome. Mol. Cell Proteomics., 8(6):1361-81.

Sly, L.M., Hamilton, M.J., Kuroda, E., Ho, V.W., Antignano, .FL., Omeis, S.L., van Netten-Thomas, C.J., Wong, D., Brugger, H.K., Williams, O., Feldman, M.E., Houseman, B.T., Fiedler, D., Shokat, K.M. and Krystal, G. (2009) SHIP prevents lipopolysaccharide from triggering an anti-viral response in mice. Blood, 113(13):2945-54.

Korennykh, A.V., Egea, P.F., Korostelev, A.A., Finer-Moore, J., Zhang, C., Shokat, K.M., Stroud, R.M. and Walter P. (2009) The unfolded protein response signals through high-order assembly of Ire1. Nature, 457(7230):687-93.

Fan, Q.W., Cheng, C., Knight, Z.A., Haas-Kogan, D., Stokoe, D., James, C.D., McCormick, F., Shokat, K.M., Weiss, W.A. (2009) EGFR Signals to mTOR Through PKC and Independently of Akt in Glioma. Sci. Signal., 2(55):ra4.

Mirzoeva, O.K., Das, D., Heiser, L.M., Bhattacharya, S., Siwak, D., Gendelman, R., Bayani, N., Wang, N.J., Neve, R.M., Guan, Y., Hu, Z., Knight, Z., Feiler, H.S., Gascard, P., Parvin, B., Spellman, P.T., Shokat, K.M., Wyrobek, A.J., Bissell, M.J., McCormick, F., Kuo, W.L., Mills, G.B., Gray, J.W, and Korn, W.M. (2009) Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition.  Cancer Res.,69(2):565-72.

Li, S., Makovets, S., Matsuguchi, T., Blethrow, J.D., Shokat, K.M. and Blackburn, E.H. (2009) Cdk1-dependent phosphorylation of Cdc13 coordinates telomere elongation during cell-cycle progression. Cell, 136(1):50-61.

Miller, A.L., Zhang, C., Shokat, K.M. and Lowell, C.A. (2009) Generation of a novel system for studying spleen tyrosine kinase function in macrophages and B cells.  J. Immunol., 182(2):988-98.

Morgan, D.J., Weisenhaus, M., Shum, S., Su, T., Zheng, R., Zhang, C., Shokat, K.M., Hille, B., Babcock, D.F. and McKnight GS. (2008) Tissue-specific PKA inhibition using a chemical genetic approach and its application to studies on sperm capacitation.  Proc. Natl. Acad. Sci. U S A., 105(52):20740-5.

Shirra, M.K., McCartney, R.R., Zhang, C., Shokat, K.M., Schmidt, M.C. and Arndt, K.M. (2008) A chemical-genomics study identifies Snf1 as a repressor of Gcn4 translation. J. Biol. Chem., 283(51):35889-98.

Choi, D.S., Wei, W., Deitchman, J.K., Kharazia, V.N., Lesscher, H.M., McMahon, T., Wang, D., Qi, Z.H., Sieghart, W., Zhang, C., Shokat, K.M., Mody, I. and Messing, R.O. (2008) Protein kinase Cdelta regulates ethanol intoxication and enhancement of GABA-stimulated tonic current. J. Neurosci., 28(46):11890-9.

Kang, J., Yang, M., Li, B., Qi, W., Zhang, C., Shokat, K.M., Tomchick, D.R., Machius, M. and Yu, H. (2008) Structure and substrate recruitment of the human spindle checkpoint kinase Bub1.  Mol. Cell., 32(3):394-405.

Dar, A.C., Lopez, M.S. and Shokat, K.M. (2008) Small Molecule Recognition of c-Src via the Imatinib-Binding Conformation. Chem. Biol., 15(10):1015-22.

Chaisuparat, R., Hu, J., Jham, B.C., Knight, Z.A., Shokat, K.M. and Montaner, S. (2008) Dual inhibition of PI3Kalpha and mTOR as an alternative treatment for Kaposi's sarcoma.  Cancer Res., 68(20):8361-8.

Apsel, B., Blair, J.A., Gonzalez, B., Nazif, T.M., Feldman, M.E., Aizenstein, B., Hoffman, R., Williams, R.L., Shokat, K.M. and Knight, Z.A. (2008) Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases. Nat. Chem. Biol., 4(11):691-9.

Kurischko, C., Kuravi, V.K., Wannissorn, N., Nazarov, P.A., Husain, M., Zhang, C., Shokat, K.M., McCaffery, J.M. and Luca, F,C. (2008) The Yeast LATS/Ndr Kinase Cbk1 Regulates Growth via Golgi-dependent Glycosylation and Secretion.Mol. Biol. Cell., 19(12):5559-78.

Oda, K., Okada, J., Timmerman, L., Rodriguez-Viciana, P., Stokoe, D., Shoji, K., Taketani, Y., Kuramoto, H., Knight, Z.A., Shokat, K.M. and McCormick, F. (2008) PIK3CA cooperates with other phosphatidylinositol 3'-kinase pathway mutations to effect oncogenic transformation. Cancer Res., 68(19):8127-36.

Bateman, R.L., Rauh, D., Tavshanjian, B. and Shokat, K.M.(2008) Human carbonyl reductase 1 is an S-nitrosoglutathione reductase.J. Biol. Chem., 283(51):35756-62.

Kim, J.S., Lilley, B.N., Zhang, C., Shokat, K.M., Sanes, J.R. and Zhen, M. (2008) A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation.  Neural Develop., 3:23.

Lu, X., Simon, M.D., Chodaparambil, J.V., Hansen, J.C., Shokat, K.M. and Luger, K. (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat. Struct. Mol. Biol., 15(10):1122-4.

Johnson, A.W., Chen, X., Crombag, H.S., Zhang, C., Smith, D.R., Shokat, K.M., Gallagher, M., Holland, P.C. and Ginty, D.D. (2008) The brain-derived neurotrophic factor receptor TrkB is critical for the acquisition but not expression of conditioned incentive value. Eur. J. Neurosci., 2008 Jul 30. [Epub ahead of print]

Kharas, M.G., Janes, M.R., Scarfone, V.M., Lilly, M.B., Knight, Z.A., Shokat, K.M. and Fruman, D.A. (2008) Ablation of PI3K blocks BCR-ABL leukemogenesis in mice, and a dual PI3K/mTOR inhibitor prevents expansion of human BCR-ABL leukemia cells. J. Clin. Invest., 118(9):3038-3050.

Zunder, E.R., Knight, Z.A., Houseman, B.T., Apsel, B. and Shokat, K.M. (2008) Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110 alpha. Cancer Cell, 14(2):180-92.

Wang, J., Knight, Z.A., Fiedler, D., Williams, O., Shokat, K.M. and Pearce, D. (2008) Activity of the p110-{alpha} subunit of phosphatidylinositol-3-kinase is required for activation of epithelial sodium transport. Am. J. Physiol. Renal Physiol., 295(3):F843-50.

Hoon, S., Smith, A.M., Wallace, I.M., Suresh, S., Miranda, M., Fung, E., Proctor, M., Shokat, K.M., Zhang, C., Davis, R.W., Giaever, G., StOnge, R.P. and Nislow, C. (2008) An integrated platform of genomic assays reveals small-molecule bioactivities. Nat. Chem. Biol., 4(8):498-506.

Kim, H.H., Abdelmohsen, K., Lal, A., Pullmann, R., Jr., Yang, X., Galban, S., Srikantan, S., Martindale, J.L., Blethrow, J., Shokat, K.M. and Gorospe, M. (2008) Nuclear HuR accumulation through phosphorylation by Cdk1. Genes Dev., 22(13):1804-15.

Sordet, O., Larochelle, S., Nicolas, E., Stevens, E.V., Zhang, C., Shokat, K.M., Fisher, R.P. and Pommier, Y. (2008) Hyperphosphorylation of RNA polymerase II in response to topoisomerase I cleavage complexes and its association with transcription- and BRCA1-dependent degradation of topoisomerase I. J. Mol. Biol., 381(3):540-9.

Park, S., Chapuis, N., Bardet, V., Tamburini, J., Gallay, N., Willems, L., Knight, Z.A., Shokat, K.M., Azar, N., Viguié, F., Ifrah, N., Dreyfus, F., Mayeux, P., Lacombe, C. and Bouscary D. (2008) PI-103, a dual inhibitor of Class IA phosphatidylinositide 3-kinase and mTOR, has antileukemic activity in AML. Leukemia. 2008 Jun 12. [Epub ahead of print]

Tamgüney, T., Zhang, C., Fiedler, D., Shokat, K., Stokoe, D. (2008) Analysis of 3-phosphoinositide-dependent kinase-1 signaling and function in ES cells.  Exp. Cell Res., 314(11-12):2299-312.

Sauer, S., Bruno, L., Hertweck, A., Finlay, D., Leleu, M., Spivakov, M., Knight, Z.A., Cobb, B.S., Cantrell, D., O'Connor, E., Shokat, K.M., Fisher, A.G., Merkenschlager, M. (2008) T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR. Proc. Natl. Acad. Sci. U. S. A., 105(22):7797-802.

Torbett, N.E., Luna, A., Knight, Z.A., Houk, A., Moasser, M., Weiss, W., Shokat, K.M. and Stokoe, D. (2008) A chemical screen in diverse breast cancer cell lines reveals genetic enhancers and suppressors of sensitivity to PI3K isotype-selective inhibition. Biochem J. 2008 May 22. [Epub ahead of print]

Chen, J.S., Zhou, L.J., Entin-Meer, M., Yang, X., Donker, M., Knight, Z.A., Weiss, W., Shokat, K.M., Haas-Kogan, D., Stokoe, D. (2008) Characterization of structurally distinct, isoform-selective phosphoinositide 3'-kinase inhibitors in combination with radiation in the treatment of glioblastoma. Mol. Cancer Ther., 7(4):841-50.

Levin, S.E., Zhang, C., Kadlecek, T.A., Shokat, K.M. and Weiss, A. (2008) Inhibition of ZAP-70 kinase activity via an analog-sensitive allele blocks T cell receptor and CD28 superagonist signaling. J. Biol. Chem., 283(22):15419-30.

Wan, L., Niu, H., Futcher, B., Zhang, C., Shokat, K.M., Boulton, S.J. and Hollingsworth, N.M.  (2008)  Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast.
Genes Dev., 22(3):386-97.

Blethrow, J.D., Glavy, J.S., Morgan, D.O. and Shokat K.M. (2008)
Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates.  Proc. Natl. Acad. Sci. U S A. 5;105(5):1442-7.

Balla, A., Tuymetova, G., Toth, B., Szentpetery, Z., Zhao, X., Knight, Z.A., Shokat, K.M., Steinbach, P.J. and Balla, T. (2008) Design of Drug-Resistant Alleles of Type-III Phosphatidylinositol 4-Kinases Using Mutagenesis and Molecular Modeling.  Biochemistry, 47(6):1599-607.

Balla, A., Ju Kim, Y., Varnai, P., Szentpetery, Z., Knight, Z., Shokat, K.M. and Balla, T. (2007) Maintenance of Hormone-sensitive Phosphoinositide Pools in the Plasma Membrane Requires Phosphatidylinositol 4-Kinase III{alpha}.  Mol. Biol. Cell, 19(2):711-721

Snead, J.L., Sullivan, M., Lowery, D.M., Cohen, M.S., Zhang, C., Randle, D.H., Taunton, J., Yaffe, M.B., Morgan, D.O. and Shokat, K.M. (2007) A Coupled Chemical-Genetic and Bioinformatic Approach to Polo-like Kinase Pathway Exploration.  Chem. Biol,14(11):1261-72.

Weiss, W.A., Taylor, S.S. and Shokat, K.M. (2007) Recognizing and exploiting differences between RNAi and small-molecule inhibitors.  Nat. Chem. Biol., 3(12):739-44.

Gregan, J., Zhang, C., Rumpf, C., Cipak, L., Li, Z., Uluocak, P., Nasmyth, K., Shokat, K.M. (2007) Construction of conditional analog-sensitive kinase alleles in the fission yeast Schizosaccharomyces pombe.  Nat. Protoc., 2(11):2996-3000.

Hung, C.H., Thomas, L., Ruby, C.E., Atkins, K.M., Morris, N.P., Knight, Z.A., Scholz, I., Barklis, E., Weinberg, A.D., Shokat, K.M. and Thomas, G. (2007)  HIV-1 Nef assembles a Src family kinase-ZAP-70/Syk-PI3K cascade to downregulate cell-surface MHC-I.  Cell Host Microbe, 1(2):121-33.

Rubenstein, E.M., McCartney, R.R., Zhang, C., Shokat, K.M., Shirra, M.K., Arndt, K.M. and Schmidt, M.C. (2008) Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase.  J. Biol. Chem., 283(1):222-30.

Knight, Z.A., Feldman, M.E., Balla, A., Balla, T., and Shokat, K.M. (2007) A membrane capture assay for lipid kinase activity.  Nat. Protoc., 2(10):2459-66.

Lin, J.H., Li, H., Yasumura, D., Cohen, H.R., Zhang, C., Panning, B., Shokat, K.M., Lavail, M.M. and Walter, P. (2007) IRE1 signaling affects cell fate during the unfolded protein response.  Science, 318(5852):944-9.

Bateman, R., Rauh, D. and Shokat, K.M. (2007) Glutathione traps formaldehyde by formation of a bicyclo[4.4.1]undecane adduct. Org. Biomol. Chem., 5(20):3363-7.

Estebanez-Perpina, E., Arnold, A.A., Nguyen, P., Rodrigues, E.D., Mar, E., Bateman, R., Pallai, P., Shokat, K.M., Baxter, J.D., Guy, R.K., Webb, P. and Fletterick, R.J. (2007) A surface on the androgen receptor that allosterically regulates coactivator binding. Proc. Natl. Acad. Sci. USA, 104(41):16074-79.

Das, M., Jiang, F., Sluss, H.K., Zhang, C., Shokat, K.M., Flavell, R.A., Davis, R.J. (2007) Suppression of p53-dependent senescence by the JNK signal transduction pathway.  Proc. Natl. Acad. Sci. USA, 104(40):15759-64.

Qi, Z.H., Song, M., Wallace, M.J., Wang, D., Newton, P.M., McMahon, T., Chou, W.H., Zhang, C., Shokat, K.M. and Messing, R.M. (2007) Protein kinase C epsilon regulates GABAA receptor sensitivity to ethanol and benzodiazepines through phosphorylation of gamma 2 subunits. J. Biol. Chem. Epub ahead of print

Knight, Z.A., Garrison, J.L., Chan, K., King, D. and Shokat, K.M. (2007) A Remodelled Protease That Cleaves Phosphotyrosine Substrates. J. Amer. Chem. Soc., 129:11672-11673.

Fan, Q.W., Cheng, C.K., Nicolaides, T.P., Hackett, C.S., Knight, Z.A., Shokat, K.M. and Weiss, W.A. (2007) A Dual Phosphoinositide-3-kinase (alpha)/mTOR Inhibitor Cooperates with Blockate of Epdiermal Growth Factor Receptor in PTEN-Mutant Glioma. Cancer Res., 67, 7960-7965.

Allen, J.J., Li, M., Brinkworth, C.S., Paulson, J.L., Wang, D., Hubner, A., Chou, W.H., Davis, R.J., Burlingame, A.L., Messing, R.O., Katayama, C.D., Hedrick, S.M. and Shokat, K.M. (2007) A semisynthetic epitope for kinase substrates. Nat. Methods, 4(6):511-6.

Kanin, E.I., Kipp, R.T., Kung, C., Slattery, M., Viale, A., Hahn, S., Shokat, K.M. and Ansari, A.Z. (2007) Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proc Natl Acad Sci U S A., 104(14):5812-7.

Larochelle, S., Merrick, K.A., Terret, M.E., Wohlbold, L., Barboza, N.M., Zhang, C., Shokat, K.M, Jallepalli, P.V. and Fisher, R.P. (2007) Requirements for Cdk7 in the assembly of Cdk1/cyclin B and activation of Cdk2 revealed by chemical genetics in human cells. Mol. Cell, 25(6):839-50.

Knight, Z.A. and Shokat, K.M. (2007) Chemically targeting the PI3K family.  Biochem. Soc. Trans., 35(Pt 2):245-9.

Burkard, M.E., Randall, C.L., Larochelle, S., Zhang, C., Shokat, K.M., Fisher, R.P. and Jallepalli, P.V. (2007) Chemical genetics reveals the requirement for Polo-like kinase 1 activity in positioning RhoA and triggering cytokinesis in human cells. Proc Natl Acad Sci U S A., 104(11):4383-8.

Simon, M.D., Chu, F., Racki, L.R., de la Cruz, C.C., Burlingame, A.L., Panning, B., Narlikar, G.J. and Shokat, K.M. (2007) The site-specific installation of methyl lysine analogs into recombinant histones. Cell, 128(5):1003-1012.

Blair, J.A., Rauh, D., Kung, C., Yun, C.-H., Fan, Q.-W., Zhang, C., Eck, M.J., Weiss, W.A. and Shokat, K.M. (2007)  Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nat. Chem. Biol., 3(4):229-238.

Knight, Z.A. and Shokat, K.M. (2007) Chemical genetics: where genetics and pharmacology meet.  Cell, 128(3):425-30.

Simon, M.D. Feldman, M.E., Rauh, D., Maris, A.E., Wemmer, D.E. and Shokat, K.M. (2007) The structure and properties of a re-engineered homeodomain protein-DNA interface. ACS Chemical Biology, 1(12):755-60.

Sergina, N., Rausch, M., Wang, D., Blair, J., Hann, B., Shokat, K.M. and Moasser, M.M. (2007) Resistance to HER family tyrosine kinase inhibitors by the kinase inactive HER3.  Nature, 445(7126):437-41.

Allen, J.J. and  Shokat, K.M. (2006)Chemical genomics: dialed in transcriptional network control with non-steroidal glucocorticoid receptor modulators. ACS Chem Biol., 1(3):139-40.

Wan, L., Zhang, C., Shokat, K.M., Hollingsworth, N.M. (2006) Chemical inactivation of Cdc7 kinase in budding yeast results in a reversible arrest that allows efficient cell synchronization prior to meiotic recombination. Genetics, 174(4):1767-74.

Toth, B., Balla, A., Ma, H., Knight, Z.A., Shokat, K.M. and Balla, T. (2006) Phosphatidylinositol 4-kinase IIIbeta regulates the transport of ceramide between the endoplasmic reticulum and Golgi.  J Biol Chem., 281(47):36369-77.

Jaeschke, A., Karasarides, M., Ventura, J.J., Ehrhardt, A., Zhang, C., Flavell, R.A., Shokat, K.M. and Davis, R.J. (2006) JNK2 is a positive regulator of the cJun transcription factor. Mol. Cell. 23(6):899-911

Van Keymeulen, A., Wong, K., Knight, Z.A., Govaerts, C., Hahn, K.M., Shokat, K.M. and Bourne, H.R. (2006) To stabilize neutrophil polarity, PIP3 and Cdc42 augment RhoA activity at the back as well as signals at the front.  J Cell Biol., 174(3):437-45.

Brodersen, P., Petersen, M., Bjorn Nielsen, H., Zhu, S., Newman, M.A., Shokat, K.M., Rietz, S., Parker, J. and Mundy, J. (2006) Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4. Plant J., 47(4):532-46.

Wei, F., Wang, G.D., Zhang, C., Shokat, K.M., Wang, H., Tisen, J.Z., Liauw, J. and Zhuo, M. (2006) Forebrain overexpression of CaMKII abolishes cingulate long term depression and reduces mechanical allodynia and thermal hyperalgesia.  Mol. Pain., 15;2(1):21.

Fan, Q-W., Knight, Z.A., Goldenberg, D.D., Yu, W., Mostov, K.E., Stokoe, D., Shokat, K.M. and Weiss, W.A.  (2006) A dual PI3 kinase/mTOR inhibitor reveals emergent efficacy in glioma.  Cancer Cell, 9:341-349.

Sturgeon, C.M., Knight, Z.A., Shokat, K.M. and Roberge, M.  (2006) Effect of combined DNA repair inhibition and G2 checkpoint inhibition on cell cycle progression after DNA damage.  Mol. Cancer Ther., 5(4):885-892.

Wohlbold, L., Larochelle, S., Liao, J.C., Livshits, G., Singer, J., Shokat, K.M. and Fisher, R.P. (2006) The cyclin-dependent kinase (CDK) Family member PNQALRE/CCRK supports cell proliferation but has no intrinsic CDK-activating kinase (CAK) activity. Cell Cycle, 5(5):546-54.

Kung, C., Kenski, D.M., Krukenberg, K., Madhani, H.D. and Shokat, K.M. (2006) Selective kinase inhibition by exploiting differential pathway sensitivity. Chem Biol., Apr;13(4):399-407.

Knight, Z.A., Gonzalez-Perez, B., Feldman, M.E., Zunder, E., Goldenberg, D., Balla, A., Balla, T., Loewith, R., Weiss W.A., Williams, R.L. and Shokat, K.M. (2006) A pharmacological map of the PI3-K family defines a role for p110a in insulin signaling. Cell, in press.

Fan, Q.W., Knight, Z.A., Goldenberg, D.A., Stokoe, D., Weiss, W.A. and Shokat, K.M. (2006) A family-based chemical screen identifies cooperative inhibition of mTOR and p110a in glioma, Cancer Cell, submitted

Ventura, J.J., Hubner, A., Zhang, C., Flavell, R.A., Shokat, K.M. and Davis, R.J. (2006) Chemical Genetic Analysis of the Time Course of Signal Transduction by JNK. Mol Cell. 21(5):701-10.

Pinsky, B.A., Kung, C., Shokat, K.M. and Biggins, S. (2006) The Ipl1-Aurora protein kinase activates the spindle checkpoint by creating unattached kinetochores. Nat Cell Biol., 8(1):78-83.

Larochelle, S., Batliner, J., Gamble, M.J., Barboza, N.M., Kraybill, B.C., Blethrow, J.D., Shokat, K.M. and Fisher, R.P. (2006) Dichotomous but stringent substrate selection by the dual-function Cdk7 complex revealed by chemical genetics. Nat Struct Mol Biol., 13(1):55-62.

Dephoure, N., Howson, R.W., Blethrow, J.D., Shokat, K.M. and O'Shea, E.K. (2005) Combining chemical genetics and proteomics to identify protein kinase substrates. Proc Natl Acad Sci U S A., 102(50):17940-5.

Juris, S.J., Shah, K., Shokat, K., Dixon, J.E. and Vacratsis, P.O.(2006) Identification of otubain 1 as a novel substrate for the Yersinia protein kinase using chemical genetics and mass spectrometry. FEBS Lett., 580(1):179-83.

Kenski, D.M., Zhang, C., von Zastrow, M. and Shokat, K.M. (2005) Chemical genetic engineering of G protein-coupled receptor kinase 2. J Biol Chem., 280(41):35051-61.

D'Aquino, K.E., Monje-Casas, F., Paulson, J., Reiser, V., Charles, G.M., Lai, L., Shokat, K.M. and Amon, A. (2005) The protein kinase Kin4 inhibits exit from mitosis in response to spindle position defects. Mol Cell., 19(2):223-34.

Zhang, C., Kenski, D.M., Paulson, J.L., Bonshtien, A., Sessa, G. Cross, J.V., Templeton, D.J. and Shokat, K.M. (2005) A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases. Nature Methods, 2(6):435-441.

Cohen, M.C., Zhang, C., Shokat, K.M., Taunton, J. (2005) Structural Bioinformatics-Based Design of Selective, Irreversible Kinase Inhibitors. Science, 308:1318-1321.

Knight, Z.A. and Shokat, K.M. (2005) Features of selective kinase inhibitors. Chemistry & Biology, 12(6):621-637.

Masahiro Tanaka, Raynard Bateman, Daniel Rauh, Eugeni Vaisberg, Shyam Ramachandani, Chao Zhang, Kirk C. Hansen, Alma L. Burlingame, Jay K. Trautman, Kevan M. Shokat, and Cynthia L. Adams. (2005) An Unbiased Cell Morphology Based Screen for New Biologically Active Small Molecules. PLOS Biology, 3(5):e128.

Shokat, K.M. (2005) Chemicals Call Bacteria, and A New Membrane Protein Machine Answers. Cell, 121:163-166.

Murattani, M., Kung, C, Shokat, K.M. and Tansey, W.P. (2005) The F box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell, 120(6):887-899.

Allen, J., Lazerwith, S.E. and Shokat, K.M. (2005) Bio-orthogonal Affinity Purification of Direct Kinase Substrates. J. Amer. Chem. Soc., 127(15):5288-5289.

Chen, X., Ye, H., Kuruvilla, R., Ramanan, N., Scangos, K.W., Zhang, C., Johnson, N.M., England, P.M., Shokat, K.M. and Ginty, D.D. (2005) A chemical-genetic approach to studying neurotrophin signaling. Neuron, 46(1):13-21.

Alaimo, P.J., Knight, Z.A. and Shokat, K.M. (2005) Targeting the gatekeeper residue in phosphoinositide 3-kinases. Bioorg & Med Chem, 12:2825-2836.

Kung C, Kenski DM, Dickerson SH, Howson RW, Kuyper LF, Madhani HD, Shokat KM. (2005) Chemical genomic profiling to identify intracellular targets of a multiplex kinase inhibitor. Proc Natl Acad Sci. 102(10):3587-3592.

Kung, C. and Shokat, K.M. (2005) Small-Molecule Kinase-Inhibitor Target Assessment. Chembiochem 6(3):523-526.

Jones, M.H., Huneycutt, B.J., Pearson, C.G., Zhang, C., Morgan, G., Shokat, K., Bloom, K., Winey, M. (2005) Chemical genetics reveals a role for Mps1 kinase in kinetochore attachment during mitosis. Curr Biol. 15(2):160-5.

Kunkel, E.J., Plavec, I., Nguyen, D., Melrose, J., Rosler, E.S., Kao, L.T., Wang, Y., Hytopoulos, E., Bishop, A.C., Bateman, R., Shokat, K.M., Butcher, E.C. and Berg, E.L. (2004) Rapid structure-activity and selectivity analysis of kinase inhibitors by BioMAP analysis in complex human primary cell-based models. Assay Drug Dev Technol. 2(4):431-41.

Wong, S., McLaughlin, J., Cheng, D., Zhang, C., Shokat, K.M. and Witte, O.N. (2004) Sole BCR-ABL inhibition is insufficient to eliminate all myeloproliferative disorder cell populations. Proc Natl Acad Sci U S A., 101(50):17456-61.

Simon, M.D., Sato, K., Weiss, G.A. and Shokat, K.M. (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res, 32(12):3623-31.

Maly, D.J., Allen, J.A. and Shokat, K.M. (2004) A Mechanism-Based Crosslinker for the Identification of Kinase-Substrate Pairs. J. Am. Chem. Soc. 126(30):9160-61.

Knight, Z.A., Chiang, G., Alaimo, P.J., Kenski, D.M., Ho, C.B., Coan, K., Abraham, R., and Shokat, K.M.* (2004) Isoform-specific phosphoinositide 3-kinase inhibitors from an arylmorpholine scaffold. Bioorg Med Chem. 12(17):4749-59.

Sato, K., Simon, M.D., Levin, A.M., Gothard, C.M., Shokat, K.M. and Weiss, G.A. (2004) Dissecting the Engrailed-DNA Interaction by Phage-Displayed Alanine Shotgun Scanning. Chem. Biol. 11(7):1017-23.

Simon, M.D. and Shokat, K.M.* (2004) Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide. J. Am. Chem. Soc. 126(26):8078-79.

Provance, D.W., Jr., Gourley, C.R., Silan, C.M., Cameron, L.C., Shokat, K.M., Goldenring, J.R., Shah, K., Gillespie, P.G. and Mercer, J.A. (2004) From the Cover: Chemical-genetic inhibition of a sensitized mutant myosin Vb demonstrates a role in peripheral-pericentriolar membrane traffic. Proc. Natl. Acad. Sci. USA. 17:101(7):1868-73.

Liu, Y., Kung, C., Fishburn, J., Ansari, A.Z., Shokat, K.M. and Hahn, S. (2004) Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol. Cell. Biol. 24(4):1721-35.

Hindley, A.D., Park, S., Wang, L., Shah, K., Wang, Y., Hu, X., Shokat, K.M., Kolch, W., Sedivy, J.M., Yeung, K.C. (2004) Engineering the serine/threonine protein kinase Raf-1 to utilize an orthogonal analogue of ATP substituted at the N(6) position. FEBS Lett. 556(1-3):26-34.

Zhang, C. and Shokat, K.M. (2003) Engineering Protein Kinases with Specificity for Unnatural Nucleotides and Inhibitors. Handbook of Cell Signaling Vol. 1 Chapter 98:583-587.

Fan, Q., Specht, K.M., Zhang, C., Goldenberg , D.D., Shokat, K.M. and Weiss, W.A. (2003) Combinatorial Efficacy Achieved Through Two Point Blockade Within a Signaling Pathway—A Chemical Genetic Approach. Cancer Res. 63(24):8930-8.

Papa, F.R., Zhang, C., Shokat, K., and Walter, P. (2003) Bypassing a Kinase Activity with an ATP-Competitive Drug. Science 302(5650):1533-7.

Wan, L., De Los Santos, T., Zhang, C., Shokat, K., Hollingsworth, N.M. (2003) Mek1 kinase activity functions downstream of RED1 in the regulation of meiotic DSB repair in budding yeast. Mol. Biol. Cell 15(1):11-23.

Ubersax, J.A., Woodbury, E.L., Quang, P.N., Paraz, M., Blethrow, J.D., Shah, K., Shokat, K.M. and Morgan, D.O. (2003) Targets of the Cyclin-Dependent Kinase Cdk1. Nature 425(6960):859-64.

Wang, H., Shimizu, E., Tang, Y.P., Cho, M., Kyin, M., Zuo, W., Robinson, D.A., Alaimo, P.J., Zhang, C., Morimoto, H., Zhuo, M., Feng, R., Shokat, K.M. and Tsien, J.Z. (2003) Inducible Protein Knockout Reveals Temporal Requirement of CaMKII Reactivation For Memory Consolidation in the Brain. Proc. Natl. Acad. Sci. USA, 100(7):4287-92.

Knight, Z.A., Schilling, B., Row, R.H., Gibson, B.W. and Shokat, K.M. (2003) Phosphospecific Proteolysis: A Chemoenzymatic Approach for Mapping the Phosphoproteome, Nature Biotechnology 21(9):1047-54.

Sreenivasan, A., Bishop, A.C., Shokat, K.M., Kellogg, D. (2003) “Specific Inhibition of Elm1 kinase activity in vivo reveals a G1 function. Mol. Cell. Bio. 23(17)6327-37.

Denzel, A., Hare, K.J., Zhang, C., Shokat, K., Jenkinson, E.J., Anderson, G. and Hayday, A. (2003) Cutting edge: a chemical genetic system for the analysis of kinases regulating T cell development. J. Immunol. 171(2):519-23.

Shah, K. and Shokat, K.M. (2003) A chemical genetic approach for the identification of direct substrates of protein kinases. Methods Mol. Biol. 233:253-71.

Ulrich S.M., Kenski D., and Shokat, K.M. (2003) Engineering a "methionine clamp" into Src family kinases specificity towards unnatural ATP analogs. Biochemistry 42(26):7915-21.

Eblen S.T., Kumar N.C., Shah K., Henderson M.J., Watts, C.K., Shokat K.M. and Weber M.J. (2003) Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs. J. Biol. Chem. 278(17):14926-35.

Sekiya-Kawasaki M., Groen A.C., Cope M.J., Kaksonen M., Watson H.A., Zhang C., Shokat K.M., Wendland B., McDonald K.L., McCaffery J.M. and Drubin, D.G. (2002) Dynamic Phosphoregulation of Actin and Endocytosis Revealed by Real-Time Chemical-Genetic Analysis. J. Cell Biol. 162(5):765-72.

Alaimo P.J., Shogren-Knaak, M.A., Shokat, K.M. (2002) Chemical genetic analysis of protein kinase cascades. Scientific World Journal 2(1 Suppl 2):108-10.

Benjamin, K.R., Zhang, C., Shokat, K.M., and Herskowitz, I. (2002) Control of Landmark Events in Meiosis by the CDK Cdc28 and the Meiosis-Specific Kinase Ime2. Genes and Dev. 17(12)1524-39.

Abeliovich, H., Zhang, C., Dun, Jr., W.A., Shokat, K.M. and Klionsky, D.J. (2002) Chemical Genetic Analysis of Apg1 Reveals a Non-Kinase Role in the Induction of Autophagy. Mol. Biol. Cell 14(2):477-90.

Ulrich, S.M., Sallee, N.A., and Shokat, K.M. (2002) Conformational Restraint is a Critical Determinant of Unnatural Nucleotide Recognition by Protein Kinases. Bioorg. & Med. Chem. Ltrs. 12:3223-3227.

Buzko, O. and Shokat, K.M. (2002) A kinase sequence database: sequence alignments and family assignment. Bioinformatics 18(9):1274-75.

Kraybill, B., Blethrow, J., Morgan, D. & Shokat, K.M. (2002) Inhibitor scaffolds as new allele specific kinase substrates. J. Am. Chem. Soc., 124:12118-12128.

Weiss, E.L., Kurischko, C., Zhang, C., Shokat, K., Drubin, D and Luca, F.C. (2002) The Saccharomyces cerevisiae Mob2p-Cbk1p kinase complex promotes polarized growth and acts with the mitotic Exit Network to facilitate daughter cell-specific localization of Ace2p transcription factor. J.Cell Biol. 158(5):885-900.

Fan, Q., Zhang, C., Shokat, K.M. and Weiss, W.A. (2002) Chemical Genetic Blockade of Transformation Reveals Dependence on Aberrant Oncogenic Signaling. Current Biology 12:1386-94.

Buzko, OV, Bishop, AC and Shokat, KM (2002) Modified Auto Dock for accurate docking of protein kinase inhibitors. J. Comput. Aided Mol. Des., 16(2):113-27.

Shokat, K.M. and Velleca, M. (2002) Novel chemical genetic approaches to the discovery of signal transduction inhibitors. Drug Discovery Today 7:872-879.

Ulrich, S. and Shokat, K. (2002) Green fluorescent protein-based protein kinase biosensor substrates. Methods Mol. Biol. 183:275-85.

Specht, K. and Shokat, K.M. (2002) The Emerging Power of Chemical Genetics. Current Opinion in Cell Biology 14:155-159.

Nieswender, C.M., Ishihara, R.W., Judge, L.M., Zhang, C., Shokat, K.M. and McKnight, G.S. (2002) Protein Engineering of Protein Kinase: A Catalytic Subunits Results in the Acquisition of Novel Inhibitor Sensitivity. J. Biol. Chem. 10:107.

Shah, K. & Shokat, K.M. (2002) A Chemical Genetic Screen for Direct v-Src Substrates Reveals Ordered Assembly of a Retrograde Signaling Pathway. Chem. and Biology 9:35-47.

Holt, J.R., Gillespie, S.K., Provance, Jr., D.W., Shah, K., Shokat, K.M., Corey, D.P., Mercer, J.A., and Gillespie, P.G., (2002) A Chemical-Genetic Strategy Demonstrates Myosin 1c Mediates Adaptation by Hair Cells. Cell 108:371-81.

Witucki, L.A., Huang, X., Shah, K., Liu, Y., Kyin, S., Eck, M.J., Shokat, K.M. (2002) “Mutant Tyrosine Kinases with Unnatural Nucleotide Specificity Retain the Structure and Phospho-acceptor Specificity of the Wild-Type Enzyme. Chemistry & Biology 9(1):25-33.

Ting, A.Y., Witte, K., Shah, K., Kraybill, B., Shokat, K.M., Schultz, P.G. (2001) Phage-display evolution of tyrosine kinases with altered nucleotide specificity. Biopolymers 60(3):220-8.

Schauder, S., Shokat, K,, Surette, M.G., Bassler, B.L. (2001) The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol. Microbiol. 41(2):463-76.

Carroll, A.S., Bishop, A.C., DeRisi, J.L., Shokat, K.M. and O'Shea, E.K. (2001) Chemical Inhibition of the Pho85 Cyclin-Dependent Kinase Reveals a Role in the Environmental Stress Response. Proc. Natl. Acad. Sci. 98(22):12578-83.

Shogren-Knaak , M. , Alaimo, P. J. and Shokat, K. M. (2001) Recent Advances in Chemical Approaches to the Study of Biological Systems. Ann. Rev. Cell Develop. Biol. 17:405-33.

Alaimo, P. J., Shogren-Knaak, M. and Shokat, K. M. (2001) Chemical Genetic Approaches for the Elucidation of Signaling Pathways. Curr Opin Chem Biol 5:360-367.

Habelhah, H., Shah, K., Huang, L., Burlingame, A.L, Shokat, K.M. and Ronai, Z. (2001) Identification of a New JNK Substrate Using ATP Pocket Mutant ADK and a Corresponding ATP Analogue. J. Biol. Chem. 276(21):18090-5.

Habelhah, H., Shah, K., Huang, L., Ostareck-Lederer, A., Burlingame, A.L., Shokat, K.M., Hentze, M.W., and Ronai, Z. (2001) ERK Phosphorylation Drives Cytoplasmic Accumulation of hnRNP-K and Inhibition of mRNA Translation. Nature Cell Bio. 3:325-330.

Bishop, A.C., Buzko, O. & Shokat, K.M. (2001) Magic Bullets for Protein Kinases. Trends in Cell Biology 11:167-72.

Weiss, E.L., Bishop, A.C., Shokat, K.M., and Drubin, D.G. (2000) Chemical genetic analysis of the budding yeast p21-activated kinase Cla4p. Nature Cell Bio. 5:677-685.

Liu, Y., Witucki, L., Shah, K., Bishop, A.C., and Shokat, K.M. (2000) Src-Abl Tyrosine Kinase Chimeras: Replacement of the Adenine Binding Pocket of c-Abl with v-Src to Swap Nucleotide and Inhibitor Specificities. Biochemistry 39(47):14400-14408.

Ulrich, S., Buzko, O., Shah, K, and Shokat, K.M. (2000) Towards Engineering of an Orthogonal Protein Kinase/Nucleotide Triphosphate Pair. Tetrahedron Seminars-in-Print 56:9495-9502.

Armstrong, J.I., Portley, A.R., Chang, Y.T., Nierengarten, D.M., Cook, B.N., Bowman, K.G., Bishop, A., Gray, N.S., Shokat, K.M., Schultz, P.G., Bertozzi, C.R. (2000) Discovery of Carbohydrate Sulfotransferase Inhibitors from a Kinase-Directed Library. Agnew. Chem. Int. Ed. Engl. 39:1303-1306

Bishop, A,C., Ubersax, J.A, Petsch, D.C., Matheos, D., Blethrow, J.A., Gray, N.S, Schultz, P.G, Shimizu, E., Tsien, J.Z., Rose, M.D., Wood, J.L., Morgan, D.O., & Kevan M. Shokat. (2000) A Chemical Switch for Inhibitor Sensitive Alleles of any Protein Kinase. Nature 407:395-401.

Bishop, A.,Buzko, O., Heyeck-Dumas, S., Jung, I., Kraybill, B., Liu, Y., Shah, K., Ulrich, S., Witucki, L., Yang, F., Zhang, C., and Shokat, K.M. (2000) Unnatural Ligands for Engineered Proteins: New Tools for Chemical Genetics. Ann. Rev. Biophys. Biomolec. Struct. 29:577-606.

Weintraub, B.C., Jun, J.E., Bishop, A., Shokat, K.M., Goodnow, C.C. (2000) Entry of B Cell Receptor into Signaling Domains is Inhibited in Tolerant B Cells. J. Exp. Med. 191(8):1443-8.

Buzko, O. V. & Shokat, K.M. (1999) Blocking HIV Entry. Nature Structural Biology 6:906-908.

Liu, Y, Bishop, A., Witucki, L., Kraybill, B., Shimizu, E., Tsien, J., Ubersax, J., Blethrow, J., Morgan, D.A., Shokat, K.M. (1999) “Structural Basis for Selective Inhibition of Src Family Kinases by PP1. Chemistry & Biology 6:671-678.

Gillespie, P.G., Gillespie, S.K.H., Mercer, J.A., Shah, K., and Shokat, K.M. (1999) Engineering of the Myosin-Ib Nucleotide-Binding Pocket to Create Selective Sensitivity to N6-Modified ADP Analogs. J. Biol. Chem. 274(44):31373-81.

Bishop, A.C., Kung, C-Y., Shah, K., Witucki, L., Shokat, K.M., and Liu, Y. (1999) Generation of Monospecific Nanomolar Tyrosine Kinase Inhibitors via a Chemical Genetic Approach. J. Amer. Chem. Soc., 121 (4), 627-631.

Bishop, A.C. & Shokat, K.M. (1999) Acquisition of Inhibitor-Sensitive Protein Kinases Through Protein Design. Pharm. and Therap. 82:337-346.

Yang, F., Liu, Y., Bixby, S., Friedman, J., Shah, K., & Shokat, K.M. (1999) Highly Efficient Green Fluorescent Protein Based Kinase Substrates. Anal. Biochem. 266:167-173.

Liu, Y., Shah, K., Yang, F., Witucki, L., & Shokat, K.M. (1998) A Molecular Gate Which Controls Unnatural ATP Analog Recognition by the Tyrosine Kinase v-Src. Bioorganic & Medicinal Chemistry 6:1219-1226.

Liu, Y., Shah, K., Yang, F., Witucki, L., Shokat, K.M. (1998) Engineering Src Family Protein Kinases With Unnatural Nucleotide Specificity. Chemistry & Biology 5(2):91-102.

Bishop, A.C., Shah, K., Liu, Y., Witucki, L., Kung, C.-Y., Shokat, K.M. (1998) Design of allele specific inhibitors to probe protein kinase signaling. Current Biology 8:257-266.

Surrey, T., Elowitz, M., Wolf, P.E., Yang, F., Nedelec, F., Shokat, K.M., and Leibler, S. (1998) Chromophore-assisted light inactivation and self-organization of microtubules and motors. Proc. Natl. Acad. Sci., USA 95(8):4293-4298.

Bishop, A.C., Moore, D., Scanlan, T.S., & Shokat, K.M. (1997) Screening a Hydroxystilbene Library for Selective Inhibition of the B Cell Antigen Receptor Kinase Cascade. Tetrahedron Symposia-in-Print 53(35):11995-12004.

Shah, K., Liu, Y., Diermengian, C. & Shokat, K.M. (1997) Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc. Natl. Acad. Sci. USA, 94, 3565-3570.

Liblau, R.S., Tisch, R., Shokat, K., Yang, X.-D., Dumont, N., Goodnow, C.C. & McDevitt, H.O. (1996) Inravenous Injection of High Dose Soluble Antigen Induces Thymic and Peripheral Cell Apoptosis. Proc. Natl. Acad. Sci. USA 93:3031-3036.

Shokat, K.M. (1995) Tyrosine Kinases: Modular Signaling Enzymes With Tunable Specificities. Chemistry & Biology 2:509-513.

Shokat, K.M. & Goodnow, C.C. (1995) Antigen-Induced B Cell Death and Elimination During Germinal Center Immune Responses. Nature (London) 375:334-338.

Goodnow, C.C., Cyster, J.G., Hartley, S.B., Bell, S.E., Cooke, M.P., Healy, J.L., Akkaraju, S., Rathmell, J.C., Pogue, S.L. and Shokat, K.M. (1995) Self-Tolerance Checkpoints in B Lymphocyte Development. Adv. in Immunol. 59:279-345.

Liblau, R., Pearson, C., Shokat, K.M., & McDevitt, H.O. (1995) Apoptosis in T cell
Development. Imm. Rev. 15:75-90.

Shokat, K.M., Uno, T., & Schultz, P.G. (1994) Mechanistic Studies of An Antibody-Catalyzed Elimination Reaction. J. Am. Chem. Soc. 116:2261-2270.

Cooke, M. P., Heath, A. W., Shokat, K. M., Yongjun, Z., Finkelman, F. D., Linsley, P. S., Howard, M. & Goodnow, C. C. (1994) Immunoglobulin Signal Transduction Guides The Specificity of B Cell-T Cell Interactions and is Blocked in Tolerant Self-Reactive B Cells. J. Exp. Med. 179:425-438.

Shokat, K. M. & Schultz, P. G. (1994) “Catalytic Antibodies” in Cell and Molecular Biology ed. Stephen J. Wolfe Wadworth Publishing, Belmont, CA.

Shokat, K. M. & Schultz, P. G. (1991) Catalytic Antibodies: An Overview of Design Strategies and Their Applications. Welsch Foundation Symposium XXXV “Chemistry at the Frontiers of Medicine" 19-42.

Shokat, K. M. & Schultz, P. G. (1991) Redirecting the Immune Response: Ligand-Mediated Immunogenicity. J. Am. Chem. Soc. 113:1861-1862.

Shokat, K. M. & Schultz, P. G. (1991) Catalytic Antibodies. Meth. in Enzymology 203:327-351.

Shokat, K. M. & Schultz, P. G. (1990) The Generation of Catalytic Antibodies Containing Catalytic Residues. Ciba Foundation Symposium No. 159:118-135.

Shokat, K. M., Ko, M. K., Scanlan, T. S., Kochersperger, L., Yonkovich, S., Thaisrivongs, S. & Schultz, P. G. (1990) Catalytic Antibodies: A New Class of Transition State Analogues Used to Elicit Hydrolytic Antibodies. Angew. Chem. Int. Ed. Engl. 29:1296-1310.

Shokat, K. M. & Schultz, P. G. (1990) Catalytic Antibodies. Ann. Rev. Immun. 8:335-355.

Shokat, K. M., Leumann, C. L., Sugasawara, R. & Schultz, P. G. (1989) A New Strategy for the Generation of Catalytic Antibodies. Nature (London) 338:269-272.

Shokat, K. M., Leumann, C. H., Sugasawara, R. & Schultz, P. G. (1988) An Antibody-Mediated Redox Reaction. Angew. Chem. Int. Ed. Engl. 27:1172-1174.

McClard, R. W. & Shokat, K. M, (1987) Does the Bifunctional Uridylate Synthase Channel Orotidine 5'-Phosphate? Biochemistry 26:3378-3385.

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