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: PMC4355226 |
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| 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/j.tips.2014.07.001 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 |
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| 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.