Additional Publications

Pilot Phase Publications

Drake, J.M., Paull, E.O., Graham, N.A., Lee, J.K., Smith, B.A., Titz, B., Stoyanova, T., Faltermeier, C.M., Uzunangelov, V., Carlin, D.E., Fleming, D.T., Wong, C.K., Newton, Y., Sudha, S., Vashisht, A.A., Huang, J., Wohlschlegel, J.A., Graeber, T.G., Witte, O.N., and Stuart, J.M. (2016) Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. 166(4):1041-54. doi:10.1016/j.cell.2016.07.007 PMID:27499020 PMCID:PMC4985183
Lee, S., Shang, Y., Redmond, S.A., Urisman, A., Tang, A.A., Li, K.H., Burlingame, A.L., Pak, R.A., Jovičić, A., Gitler, A.D., Wang, J., Gray, N.S., Seeley, W.W., Siddique, T., Bigio, E.H., Lee, V.M., Trojanowski, J.Q., Chan, J.R., and Huang, E.J. (2016) Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Neuron. 91(1):41-55. doi:10.1016/j.neuron.2016.05.021 PMID:27321923 PMCID:PMC4938715
Adler, M., Ramm, S., Hafner, M., Muhlich, J.L., Gottwald, E.M., Weber, E., Jaklic, A., Ajay, A.K., Svoboda, D., Auerbach, S., Kelly, E.J., Himmelfarb, J., and Vaidya, V.S. (2016) A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. J Am Soc Nephrol. 27(4):1015-28. doi:10.1681/ASN.2015010060 PMID:26260164 PMCID:PMC4814182
Cancer Cell Line Encyclopedia Consortium and Genomics of Drug Sensitivity in Cancer Consortium. (2015) Pharmacogenomic agreement between two cancer cell line data sets. Nature. 528(7580):84-7. doi:10.1038/nature15736 PMID:26570998
Friedman, A.A., Amzallag, A., Pruteanu-Malinici, I., Baniya, S., Cooper, Z.A., Piris, A., Hargreaves, L., Igras, V., Frederick, D.T., Lawrence, D.P., Haber, D.A., Flaherty, K.T., Wargo, J.A., Ramaswamy, S., Benes, C.H., and Fisher, D.E. (2015) Landscape of Targeted Anti-Cancer Drug Synergies in Melanoma Identifies a Novel BRAF-VEGFR/PDGFR Combination Treatment. PLoS One. 10(10):e0140310. doi:10.1371/journal.pone.0140310 PMID:26461489 PMCID:PMC4604168
Faber, A.C., Farago, A.F., Costa, C., Dastur, A., Gomez-Caraballo, M., Robbins, R., Wagner, B.L., Rideout III, W.M., Jakubik, C.T., Ham, J., Edelman, E.J., Ebi, H., Yeo, A.T., Hata, A.N., Song, Y., Patel, N.U., March, R.J., Tam, A.T., Milano, R.J., Boisvert, J.L., Hicks, M.A., Elmiligy, S., Malstrom, S.E., Rivera, M.N., Harada, H., Windle, B.E., Ramaswamy, S., Benes, C.H., Jacks, T., and Engelman, J.A. (2015) Assessment of ABT-263 activity across a cancer cell line collection leads to a potent combination therapy for small-cell lung cancer. Proc Natl Acad Sci USA. 112(11):E1288-96. doi:10.1073/pnas.1411848112 PMID:25737542 PMCID:PMC4371986
Van Rechem, C., Black, J.C., Greninger, P., Zhao, Y., Donado, C., Burrowes, P.D., Ladd, B., Christiani, D.C., Benes, C.H., and Whetstine, J.R. (2015) A coding single-nucleotide polymorphism in lysine demethylase KDM4A associates with increased sensitivity to mTOR inhibitors. Cancer Discov. 5(3):245-54. doi:10.1158/2159-8290.CD-14-1159 PMID:25564517 PMCID:
Van Rechem, C., Black, J.C., Boukhali, M., Aryee, M.J., Gräslund, S., Haas, W., Benes, C.H., and Whetstine, J.R. (2015) Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Cancer Discov. 5(3):255-63. doi:10.1158/2159-8290.CD-14-1326 PMID:25564516 PMCID:PMC4355328
Tan, L., Nomanbhoy, T., Gurbani, D., Patricelli, M., Hunter, J., Geng, J., Herhaus, L., Zhang, J., Pauls, E., Ham, Y., Choi, H.G., Xie, T., Deng, X., Buhrlage, S.J., Sim, T., Cohen, P., Sapkota, G., Westover, K.D., and Gray, N.S. (2015) Discovery of type II inhibitors of TGFβ-activated kinase 1 (TAK1) and mitogen-activated protein kinase kinase kinase kinase 2 (MAP4K2). J Med Chem. 58(1):183-96. doi:10.1021/jm500480k PMID:25075558 PMCID:PMC4292808
Weisberg, E., Nonami, A., Chen, Z., Liu, F., Zhang, J., Sattler, M., Nelson, E., Cowens, K., Christie, A.L., Mitsiades, C., Wong, K.K., Liu, Q., Gray, N., and Griffin, J.D. (2015) Identification of Wee1 as a novel therapeutic target for mutant RAS-driven acute leukemia and other malignancies. Leukemia. 29(1):27-37. doi:10.1038/leu.2014.149 PMID:24791855 PMCID:PMC4667710
Crystal, A.S., Shaw, A.T., Sequist, L.V., Friboulet, L., Niederst, M.J., Lockerman, E.L., Frias, R.L., Gainor, J.F., Amzallag, A., Greninger, P., Lee, D., Kalsy, A., Gomez-Caraballo, M., Elamine, L., Howe, E., Hur, W., Lifshits, E., Robinson, H.E., Katayama, R., Faber, A.C., Awad, M.M., Ramaswamy, S., Mino-Kenudson, M., Iafrate, A.J., Benes, C.H., and Engelman, J.A. (2014) Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science. 346(6216):1480-6. doi:10.1126/science.1254721 PMID:25394791 PMCID:PMC4388482
Duan, Q., Flynn, C., Niepel, M., Hafner, M., Muhlich, J.L., Fernandez, N.F., Rouillard, A.D., Tan, C.M., Chen, E.Y., Golub, T.R., Sorger, P.K., Subramanian, A., and Ma’ayan, A. (2014) LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 42:W449-60. doi:10.1093/nar/gku476 PMID:24906883 PMCID:PMC4086130
Gujral, T.S., Chan, M., Peshkin, L., Sorger, P.K., Kirschner, M.W., and MacBeath, G. (2014) A noncanonical frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell. 159(4):844-56. doi:10.1016/j.cell.2014.10.032 PMID:25417160 PMCID:PMC4243058
Weisberg, E., Nonami, A., Chen, Z., Nelson, E., Chen, Y., Liu, F., Cho, H., Zhang, J., Sattler, M., Mitsiades, C., Wong, K.K., Liu, Q., Gray, N.S., and Griffin, J.D. (2014) Upregulation of IGF1R by mutant RAS in leukemia and potentiation of RAS signaling inhibitors by small-molecule inhibition of IGF1R. Clin Cancer Res. 20(21):5483-95. doi:10.1158/1078-0432.CCR-14-0902 PMID:25186968 PMCID:PMC4216757
Duan, Z., Zhang, J., Ye, S., Shen, J., Choy, E., Cote, G., Harmon, D., Mankin, H., Hua, Y., Zhang, Y., Gray, N.S., and Hornicek, F.J. (2014) A-770041 reverses paclitaxel and doxorubicin resistance in osteosarcoma cells. BMC Cancer. 14:681. doi:10.1186/1471-2407-14-681 PMID:25236161 PMCID:PMC4177239
Gustafson, W.C., Meyerowitz, J.G., Nekritz, E.A., Chen, J., Benes, C., Charron, E., Simonds, E.F., Seeger, R., Matthay, K.K., Hertz, N.T., Eilers, M., Shokat, K.M., and Weiss, W.A. (2014) Drugging MYCN through an allosteric transition in Aurora kinase A. Cancer Cell. 26(3):414-27. doi:10.1016/j.ccr.2014.07.015 PMID:25175806 PMCID:PMC4160413
Ma’ayan, A., Rouillard, A.D., Clark, N.R., Wang, Z., Duan, Q., and Kou, Y. (2014) Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol Sci. 35(9):450-60. doi:10.1016/ PMID:25109570 PMCID:PMC4153537
Kwiatkowski, N., Zhang, T., Rahl, P.B., Abraham, B.J., Reddy, J., Ficarro, S.B., Dastur, A., Amzallag, A., Ramaswamy, S., Tesar, B., Jenkins, C.E., Hannett, N.M., McMillin, D., Sanda, T., Sim, T., Kim, N.D., Look, T., Mitsiades, C.S., Weng, A.P., Brown, J.R., Benes, C.H., Marto, J.A., Young, R.A., and Gray, N.S. (2014) Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature. 511(7511):616-20. doi:10.1038/nature13393 PMID:25043025 PMCID:PMC4244910
Hays, T., Ma’ayan, A., Clark, N.R., Tan, C.M., Teixeira, A., Teixeira, A., Choi, J.W., Burdis, N., Jung, S.Y., Bajaj, A.O., O’Malley, B.W., He, J.C., Hyink, D.P., and Klotman, P.E. (2014) Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PLoS One. 9(6):e100660. doi:10.1371/journal.pone.0100660 PMID:24949636 PMCID:PMC4065073
Vempati, U.D., Chung, C., Mader, C., Koleti, A., Datar, N., Vidović, D., Wrobel, D., Erickson, S., Muhlich, J.L., Berriz, G., Benes, C.H., Subramanian, A., Pillai, A., Shamu, C.E., and Schürer, S.C. (2014) Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). J Biomol Screen. 19:803-816. doi:10.1177/1087057114522514 PMID:24518066
Wu, H., Wang, W., Liu, F., Weisberg, E.L., Tian, B., Chen, Y., Li, B., Wang, A., Wang, B., Zhao, Z., McMillin, D.W., Hu, C., Li, H., Wang, J., Liang, Y., Buhrlage, S.J., Liang, J., Liu, J., Yang, G., Brown, J.R., Treon, S.P., Mitsiades, C.S., Griffin, J.D., Liu, Q., and Gray, N.S. (2014) Discovery of a potent, covalent BTK inhibitor for B-cell lymphoma. ACS Chem Biol. 9(5):1086-91. doi:10.1021/cb4008524 PMID:24556163 PMCID:PMC4027949
Ficarro, S.B., Biagi, J.M., Wang, J., Scotcher, J., Koleva, R.I., Card, J.D., Adelmant, G., He, H., Askenazi, M., Marshall, A.G., Young, N.L., Gray, N.S., and Marto, J.A. (2014) Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. J Am Soc Mass Spectrom. 25(4):636-50. doi:10.1007/s13361-013-0811-x PMID:24496597 PMCID:PMC3971929
Clark, N.R., Hu, K.S., Feldmann, A.S., Kou, Y., Chen, E.Y., Duan, Q., and Ma’ayan, A. (2014) The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinformatics. 15:79. doi:10.1186/1471-2105-15-79 PMID:24650281 PMCID:PMC4000056
Niepel, M., Hafner, M., Pace, E.A., Chung, M., Chai, D.H., Zhou, L., Muhlich, J.L., Schoeberl, B., and Sorger, P.K. (2014) Analysis of growth factor signaling in genetically diverse breast cancer lines. BMC Biol. 12:20. doi:10.1186/1741-7007-12-20 PMID:24655548 PMCID:PMC4234128 Explore
Tang, Y. (2014) A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. Curr Protoc Chem Biol. 6(1):1-5. doi:10.1002/9780470559277.ch130140 PMID:24652619 PMCID:PMC4016950 Explore
Niederst, M.J., and Benes, C.H. (2014) EMT twists the road to PI3K. Cancer Discov. 4(2):149-51. doi:10.1158/2159-8290.CD-13-1030 PMID:24501304 PMCID:PMC3918580
Faber, A.C., Coffee, E.M., Costa, C., Dastur, A., Ebi, H., Hata, A.N., Yeo, A.T., Edelman, E.J., Song, Y., Tam, A.T., Boisvert, J.L., Milano, R.J., Roper, J., Kodack, D.P., Jain, R.K., Corcoran, R.B., Rivera, M.N., Ramaswamy, S., Hung, K.E., Benes, C.H., and Engelman, J.A. (2014) mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to
BCL-2/BCL-XL inhibition by suppressing MCL-1. Cancer Discov. 4(1):42-52. doi:10.1158/2159-8290.CD-13-0315 PMID:24163374 PMCID:PMC3973435
Paull, E.O., Carlin, D.E., Niepel, M., Sorger, P.K., Haussler, D., and Stuart, J.M. (2013) Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics. 29:2757–2764. doi:10.1093/bioinformatics/btt471 PMID:23986566 PMCID:PMC3799471 Explore
Fallahi-Sichani, M., Honarnejad, S., Heiser, L.M., Gray, J.W., and Sorger, P.K. (2013) Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol. 9:708–714. doi:10.1038/nchembio.1337 PMID:24013279 PMCID:PMC3947796 Explore
Kim, H.G., Tan, L., Weisberg, E.L., Liu, F., Canning, P., Choi, H.G., Ezell, S.A., Wu, H., Zhao, Z., Wang, J., Mandinova, A., Griffin, J.D., Bullock, A.N., Liu, Q., Lee, S.W., and Gray, N.S. (2013) Discovery of a potent and selective DDR1 receptor tyrosine kinase inhibitor. ACS Chem Biol. 8(10):2145-50. Erratum in: 9(3):840. doi:10.1021/cb400430t PMID:23899692 PMCID:PMC3800496
Tang, Y., Xie, T., Florian, S., Moerke, N., Shamu, C., Benes, C., and Mitchison, T.J. (2013) Differential Determinants of Cancer Cell Insensitivity to Antimitotic Drugs Discriminated by a One-Step Cell Imaging Assay. J Biomol Screen. 18:1062-71. doi:10.1177/1087057113493804 PMID:23788527 PMCID:PMC3783590 Explore
Niepel, M., Hafner, M., Pace, E.A., Chung, M., Chai, D.H., Zhou, L., Schoeberl, B., and Sorger, P.K. (2013) Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines. Sci Signal. 6:ra84. doi:10.1126/scisignal.2004379 PMID:24065145 PMCID:PMC3845839 Explore
Tannous, B.A., Kerami, M., Van der Stoop, P.M., Kwiatkowski, N., Wang, J., Zhou, W., Kessler, A.F., Lewandrowski, G., Hiddingh, L., Sol, N., Lagerweij, T., Wedekind, L., Niers, J.M., Barazas, M., Nilsson, R.J., Geerts, D., De Witt Hamer, P.C., Hagemann, C., Vandertop, W.P., Van Tellingen, O., Noske, D.P., Gray, N.S., and Würdinger, T. (2013) Effects of the selective MPS1 inhibitor MPS1-IN-3 on glioblastoma sensitivity to antimitotic drugs. J Natl Cancer Inst. 105(17):1322-31. doi:10.1093/jnci/djt168 PMID:23940287 PMCID:PMC3760778
Tan, C. M., Chen, E. Y., Dannenfelser, R., Clark, N. R., and Ma’ayan, A. (2013) Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics. 29:1872–1878. doi:10.1093/bioinformatics/btt319 PMID:23749960 PMCID:PMC3712222
Wong, C.K., Vaske, C.J., Ng, S., Sanborn, J.Z., Benz, S.C., Haussler, D., and Stuart, J.M. (2013) The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 41:W218–W224. doi:10.1093/nar/gkt473 PMID:23748957 PMCID:PMC3692096
McAllister, F.E., Niepel, M., Haas, W., Huttlin, E., Sorger, P.K., and Gygi, S.P. (2013) Mass Spectrometry Based Method to Increase Throughput for Kinome Analyses Using ATP Probes. Anal Chem. 85:4666–4674. doi:10.1021/ac303478g PMID:23607489 PMCID:PMC3771683 Explore
Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., and Ma’ayan, A. (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 14:128. doi:10.1186/1471-2105-14-128 PMID:23586463 PMCID:PMC3637064
Liu, Q., Xu, C., Kirubakaran, S., Zhang, X., Hur, W., Liu, Y., Kwiatkowski, N.P., Wang, J., Westover, K.D., Gao, P., Ercan, D., Niepel, M., Thoreen, C.C., Kang, S.A., Patricelli, M.P., Wang, Y., Tupper, T., Altabef, A., Kawamura, H., Held, K.D., Chou, D.M., Elledge, S.J., Janne, P.A., Wong, K.K., Sabatini, D.M., and Gray N.S. (2013) Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM and ATR. Cancer Res. 73:2574-86. doi:10.1158/0008-5472.CAN-12-1702 PMID:23436801 PMCID:PMC3760004
Benes, C.H. (2012) Functionalizing Genomic Data for Personalization of Medicine. Clinical Pharmacol Ther. 93:309–311. doi:10.1038/clpt.2012.219 PMID:23321554 PMCID:PMC3609407
Zhong, Y., Chen, E.Y., Liu, R., Chuang, P.Y., Mallipattu, S.K., Tan, C.M., Clark, N.R., Deng, Y., Klotman, P.E., Ma’ayan, A., and He, J.C. (2013) Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase. J Am Soc Nephrol. 24(5):801-11. doi:10.1681/ASN.2012060590 PMID:23559582 PMCID:PMC3636790
Duan, Q., Kou, Y., Clark, N.R., Gordonov, S., and Ma’ayan, A. (2013) Metasignatures identify two major subtypes of breast cancer. CPT Pharmacometrics Syst Pharmacol. 2:e35. doi:10.1038/psp.2013.11 PMID:23836026 PMCID:PMC3615534
Corcoran, R.B., Cheng, K.A., Hata, A.N., Faber, A.C., Ebi, H., Coffee, E.M., Greninger, P., Brown, R.D., Godfrey, J.T., Cohoon, T.J., Song, Y., Lifshits, E., Hung, K.E., Shioda, T., Dias-Santagata, D., Singh, A., Settleman, J., Benes, C.H., Mino-Kenudson, M., Wong, K.K., and Engelman, J.A. (2013) Synthetic Lethal Interaction of Combined BCL-XL and MEK Inhibition Promotes Tumor Regressions in KRAS Mutant Cancer Models. Cancer Cell. 23:121–128. doi:10.1016/j.ccr.2012.11.007 PMID:23245996 PMCID:PMC3667614
Deng, X., Elkins, J.M., Zhang, J., Yang, Q., Erazo, T., Gomez, N., Choi, H.G., Wang, J., Dzamko, N., Lee, J.D., Sim, T., Kim, N., Alessi, D.R., Lizcano, J.M., Knapp, S., and Gray, N.S. (2013) Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones. Eur J Med Chem. 70:758-67. doi:10.1016/j.ejmech.2013.10.052 PMID:24239623 PMCID:PMC3914206
Jenkins, S.L. and Ma’ayan, A. (2013) Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics. 14:119–122. doi:10.2217/pgs.12.186 PMID:23327571 PMCID:PMC3605723
Weisberg, E., Liu, Q., Zhang, X., Nelson, E., Sattler, M., Liu, F., Nicolais, M., Zhang, J., Mitsiades, C., Smith, R.W., Stone, R., Galinsky, I., Nonami, A., Griffin, J.D., and Gray, N. (2013) Selective Akt inhibitors synergize with tyrosine kinase inhibitors and effectively override stroma-associated cytoprotection of mutant FLT3-positive AML cells. PLoS One. 8(2):e56473. doi:10.1371/journal.pone.0056473 PMID:23437141 PMCID:PMC3578845
Weisberg, E., Liu, Q., Nelson, E., Kung, A.L., Christie, A.L., Bronson, R., Sattler, M., Sanda, T., Zhao, Z., Hur, W., Mitsiades, C., Smith, R., Daley, J.F., Stone, R., Galinsky, I., Griffin, J.D., and Gray, N. (2012) Using combination therapy to override stromal-mediated chemoresistance in mutant FLT3-positive AML: synergism between FLT3 inhibitors, dasatinib/multi-targeted inhibitors and JAK inhibitors. Leukemia. 26(10):2233-44. doi:10.1038/leu.2012.96 PMID:22469781 PMCID:PMC4054699
Ng, S., Collisson, E.A., Sokolov, A., Goldstein, T., Gonzalez-Perez, A., Lopez-Bigas, N., Benz, C., Haussler, D., and Stuart, J.M. (2012) PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics. 28(18):i640-i646. doi:10.1093/bioinformatics/bts402 PMID:22962493 PMCID:PMC3436829
Choi, H.G., Zhang, J., Deng, X., Hatcher, J.M., Patricelli, M.P., Zhao, Z., Alessi, D.R., and Gray, NS. (2012) Brain Penetrant LRRK2 Inhibitor. ACS Med Chem Lett. 3(8):658-662 PMID:23066449 PMCID:PMC3467149
Clark, N.R., Dannenfelser, R., Tan, C.M., Komosinski, M.E., and Ma’ayan, A. (2012) Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol. 6:89. doi:10.1186/1752-0509-6-89 PMID:22824380 PMCID:PMC3443648
Liu, Q., Ren, T., Fresques, T., Oppliger, W., Niles, B.J., Hur, W., Sabatini, D.M., Hall, M.N., Powers, T., and Gray, N.S. (2012) Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae. ACS Chem Biol. 7:982–987. doi:10.1021/cb300058v PMID:22496512 PMCID:PMC3376217
Kirouac, D.C., Saez-Rodriguez, J., Swantek, J., Burke, J.M., Lauffenburger, D.A., and Sorger, P.K. (2012) Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol. 6:29. doi:10.1186/1752-0509-6-29 PMID:22548703 PMCID:PMC3436686
Ni, J., Liu, Q., Xie, S., Carlson, C., Von, T., Vogel, K., Riddle, S., Benes, C., Eck, M., Roberts, T., Gray, N., and Zhao, J. (2012) Functional Characterization of an Isoform-Selective Inhibitor of PI3K-p110β as a Potential Anticancer Agent. Cancer Discov. 2:425–433. doi:10.1158/2159-8290.CD-12-0003 PMID:22588880 PMCID:PMC3384541
Garnett, M.J., Edelman, E.J., Heidorn, S.J., Greenman, C.D., Dastur, A., Lau, K.W., Greninger, P., Thompson, I.R., Luo, X., Soares, J., Liu, Q., Iorio, F., Surdez, D., Chen, L., Milano, R.J., Bignell, G.R., Tam, A.T., Davies, H., Stevenson, J.A., Barthorpe, S., Lutz, S.R., Kogera, F., Lawrence, K., McLaren-Douglas, A., Mitropoulos, X., Mironenko, T., Thi, H., Richardson, L., Zhou, W., Jewitt, F., Zhang, T., O’Brien, P., Boisvert, J.L., Price, S., Hur, W., Yang, W., Deng, X., Butler, A., Choi, H.G., Chang, J.W., Baselga, J., Stamenkovic, I., Engelman, J.A., Sharma, S.V., Delattre, O., Saez-Rodriguez, J., Gray, N.S., Settleman, J., Futreal, P.A., Haber, D.A., Stratton, M.R., Ramaswamy, S., McDermott, U., and Benes, C.H. (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 483:570–575. doi:10.1038/nature11005 PMID:22460902 PMCID:PMC3349233
Liu, Q., Kirubakaran, S., Hur, W., Niepel, M., Westover, K., Thoreen, C.C., Wang, J., Ni, J., Patricelli, M.P., Vogel, K., Riddle, S., Waller, D.L., Traynor, R., Sanda, T., Zhao, Z., Kang, S.A., Zhao, J., Look, A.T., Sorger, P.K., Sabatini, D.M., and Gray, N.S. (2012) Kinome-wide Selectivity Profiling of ATP-competitive Mammalian Target of Rapamycin (mTOR) Inhibitors and Characterization of Their Binding Kinetics. J Biol Chem. 287:9742–9752. doi:10.1074/jbc.M111.304485 PMID:22223645 PMCID:PMC3322972
Zhang, T., Inesta-Vaquera, F., Niepel, M., Zhang, J., Ficarro, S.B., Machleidt, T., Xie, T., Marto, J.A., Kim, N., Sim, T., Laughlin, J.D., Park, H., LoGrasso, P.V., Patricelli, M., Nomanbhoy, T.K., Sorger, P.K., Alessi, D.R., and Gray, N.S. (2012) Discovery of potent and selective covalent inhibitors of JNK. Chem Biol. 19:140–154. doi:10.1016/j.chembiol.2011.11.010 PMID:22284361 PMCID:PMC3270411
Sansone, S.A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L.A., Copeland, J., Das, S., de Daruvar, A., de Matos, P., Dix, I., Edmunds, S., Evelo, C.T., Forster, M.J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J.L., Jacob, D., Kleinjans, J. Harland, L., Haug, K., Hermjakob, H., Ho Sui, S.J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C.E., Shang, C.A., Steinbeck, C., Trefethen, A., Williams-Jones, B., Wolstencroft, K., Xenarios, I., and Hide, W. (2012) Toward interoperable bioscience data. Nat Genet. 44:121–126. doi:10.1038/ng.1054 PMID:22281772 PMCID:PMC3428019
Kwiatkowski, N., Deng, X., Wang, J., Tan, L., Villa, F., Santaguida, S., Huang, H.C., Mitchison, T., Musacchio, A., and Gray, N. (2012) Selective aurora kinase inhibitors identified using a taxol-induced checkpoint sensitivity screen. ACS Chem Biol. 7(1):185-96. doi:10.1021/cb200305u PMID:21992004 PMCID:PMC3262907
Luckert, K., Gujral, T.S., Chan, M., Sevecka, M., Joos, T.O., Sorger, P.K., Macbeath, G., and Pötz, O. (2012) A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins. Sci Signal. 5:pl1. doi:10.1126/scisignal.2002372 PMID:22234610 PMCID:PMC3465074
Prill, R.J., Saez-Rodriguez, J., Alexopoulos, L.G., Sorger, P.K., and Stolovitzky, G. (2011) Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal. 4:mr7. doi:10.1126/scisignal.2002212 PMID:21900204 PMCID:PMC3465072
Miduturu, C.V., Deng, X., Kwiatkowski, N., Yang, W., Brault, L., Filippakopoulos, P., Chung, E., Yang, Q., Schwaller, J., Knapp, S., King, R.W., Lee, J.D., Herrgard, S., Zarrinkar, P., and Gray, N.S. (2011) High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors. Chem Biol. 18(7):868-79. doi:10.1016/j.chembiol.2011.05.010 PMID:21802008 PMCID:PMC3171802
Millard, B.L., Niepel, M., Menden, M.P., Muhlich, J.L., and Sorger, P.K. (2011) Adaptive informatics for multifactorial and high-content biological data. Nat Methods. 8:487–493. doi:10.1038/nmeth.1600 PMID:21516115 PMCID:PMC3105758

See a list of HMS LINCS Phase II publications and featured Pilot Phase publications here.

Other relevant publications

Yang, R., Niepel, M., Mitchison, T.K., and Sorger, P.K. (2010) Dissecting variability in responses to cancer chemotherapy through systems pharmacology. Clin Pharmacol Ther. 88:34–38. doi:10.1038/clpt.2010.96 PMID:20520606 PMCID:PMC2941986
Alexopoulos, L.G., Saez-Rodriguez, J., Cosgrove, B.D., Lauffenburger, D.A., and Sorger, P.K. (2010) Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes. Mol Cell Proteomics. 9(9):1849-65. doi:10.1074/mcp.M110.000406 PMID:20460255 PMCID:PMC2938121
Chen, W.W., Niepel, M., and Sorger, P.K. (2010) Classic and Contemporary Approaches to Modeling Biochemical Reactions. Genes Dev. 24(17):1861-75. doi:10.1101/gad.1945410 PMID:20810646 PMCID:PMC2932968
Niepel, M., Spencer, S.L., and Sorger, P.K. (2009) Non-Genetic Cell-to-Cell Variability and the Consequences for Pharmacology. Curr Opin Chem Biol. 13:556-561. doi:10.1016/j.cbpa.2009.09.015 PMID:19833543 PMCID:PMC2975492
Saez-Rodriguez, J., Alexopoulos, L.G., Epperlein, J., Samaga, R., Lauffenburger, D.A., Klamt, S., and Sorger, P.K. (2009) Discrete Logic Modelling as a Means to Link Protein Signalling Networks with Functional Analysis of Mammalian Signal Transduction. Mol Syst Biol. 5:331. doi:10.1038/msb.2009.87 PMID:19953085 PMCID:PMC2824489
Gaudet, S., Janes, K.A., Albeck, J.G., Pace, E.A., Lauffenburger, D.A., and Sorger, P.K. (2005) A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines. Mol Cell Proteomics. 4:1569-1590. doi:10.1074/mcp.M500158-MCP200 PMID:16030008

See a list of HMS LINCS Phase II publications and featured Pilot Phase publications here.