Research

Key Publications

Lobingier, B. T., Hüttenhain, R., Eichel, K., Miller, K. B., Ting, A. Y., von Zastrow, M. & Krogan, N. J. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell 169, 350–360.e12 (2017).

Du, D., Roguev, A., Gordon, D. E., Chen, M., Chen, S.-H., Shales, M., Shen, J. P., Ideker, T., Mali, P., Qi, L. S. & Krogan, N. J. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat. Methods 14, 577–580 (2017).

Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A. N., Sanchez, K. S., Thomas, A., Kuo, C.-C., Du, D., Roguev, A., Lewis, N. E., Chang, A. N., Kreisberg, J. F., Krogan, N., Qi, L., Ideker, T. & Mali, P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat. Methods (2017).

Crawford, B., Adams, S. B., Sittler, T., van den Akker, J., Chan, S., Leitner, O., Ryan, L., Gil, E. & van ’t Veer, L. Multi-gene panel testing for hereditary cancer predisposition in unsolved high-risk breast and ovarian cancer patients. Breast Cancer Res. Treat. 163, 383–390 (2017).

Brand, T. M., Hartmann, S., Bhola, N. E., Peyser, N. D., Li, H., Zeng, Y., Isaacson Wechsler, E., Ranall, M. V., Bandyopadhyay, S., Duvvuri, U., LaVallee, T. M., Jordan, R. C. K., Johnson, D. E. & Grandis, J. R. Human Papillomavirus Regulates HER3 Expression in Head and Neck Cancer: Implications for Targeted HER3 Therapy in HPV(+) Patients. Clin. Cancer Res. 23, 3072–3083 (2017).

Carter, H., Marty, R., Hofree, M., Gross, A., Jensen, J., Fisch, K. M., Wu, X., DeBoever, C., Van Nostrand, E. L., Song, Y., Wheeler, E., Kreisberg, J. F., Lippman, S. M., Yeo, G., Gutkind, J. S. & Ideker, T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. (2017). 

Miller, R. E., Brough, R., Bajrami, I., Williamson, C. T., McDade, S., Campbell, J., Kigozi, A., Rafiq, R., Pemberton, H., Natrajan, R., Joel, J., Astley, H., Mahoney, C., Moore, J. D., Torrance, C., Gordan, J. D., Webber, J. T., Levin, R. S., Shokat, K. M., Bandyopadhyay, S., Lord, C. J. & Ashworth, A. Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib. Mol. Cancer Ther. 15, 1472–1484 (2016).

Rugo, H. S., Olopade, O. I., DeMichele, A., Yau, C., van ’t Veer, L. J., Buxton, M. B., Hogarth, M., Hylton, N. M., Paoloni, M., Perlmutter, J., Symmans, W. F., Yee, D., Chien, A. J., Wallace, A. M., Kaplan, H. G., Boughey, J. C., Haddad, T. C., Albain, K. S., Liu, M. C., Isaacs, C., Khan, Q. J., Lang, J. E., Viscusi, R. K., Pusztai, L., Moulder, S. L., Chui, S. Y., Kemmer, K. A., Elias, A. D., Edmiston, K. K., Euhus, D. M., Haley, B. B., Nanda, R., Northfelt, D. W., Tripathy, D., Wood, W. C., Ewing, C., Schwab, R., Lyandres, J., Davis, S. E., Hirst, G. L., Sanil, A., Berry, D. A., Esserman, L. J. & I-SPY 2 Investigators. Adaptive Randomization of Veliparib-Carboplatin Treatment in Breast Cancer. N. Engl. J. Med. 375, 23–34 (2016).

Park, J. W., Liu, M. C., Yee, D., Yau, C., van ’t Veer, L. J., Symmans, W. F., Paoloni, M., Perlmutter, J., Hylton, N. M., Hogarth, M., DeMichele, A., Buxton, M. B., Chien, A. J., Wallace, A. M., Boughey, J. C., Haddad, T. C., Chui, S. Y., Kemmer, K. A., Kaplan, H. G., Isaacs, C., Nanda, R., Tripathy, D., Albain, K. S., Edmiston, K. K., Elias, A. D., Northfelt, D. W., Pusztai, L., Moulder, S. L., Lang, J. E., Viscusi, R. K., Euhus, D. M., Haley, B. B., Khan, Q. J., Wood, W. C., Melisko, M., Schwab, R., Helsten, T., Lyandres, J., Davis, S. E., Hirst, G. L., Sanil, A., Esserman, L. J., Berry, D. A. & I-SPY 2 Investigators. Adaptive Randomization of Neratinib in Early Breast Cancer. N. Engl. J. Med. 375, 11–22 (2016).

Verba, K. A., Wang, R. Y.-R., Arakawa, A., Liu, Y., Shirouzu, M., Yokoyama, S. & Agard, D. A. Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. Science 352, 1542–1547 (2016).

Li, H., Wheeler, S., Park, Y., Ju, Z., Thomas, S. M., Fichera, M., Egloff, A. M., Lui, V. W., Duvvuri, U., Bauman, J. E., Mills, G. B. & Grandis, J. R. Proteomic Characterization of Head and Neck Cancer Patient-Derived Xenografts. Mol. Cancer Res. 14, 278–286 (2016).

Hedberg, M. L., Goh, G., Chiosea, S. I., Bauman, J. E., Freilino, M. L., Zeng, Y., Wang, L., Diergaarde, B. B., Gooding, W. E., Lui, V. W. Y., Herbst, R. S., Lifton, R. P. & Grandis, J. R. Genetic landscape of metastatic and recurrent head and neck squamous cell carcinoma. J. Clin. Invest. 126, 1606 (2016).

Yamaguchi, K., Iglesias-Bartolomé, R., Wang, Z., Callejas-Valera, J. L., Amornphimoltham, P., Molinolo, A. A., Cohen, E. E., Califano, J. A., Lippman, S. M., Luo, J. & Gutkind, J. S. A synthetic-lethality RNAi screen reveals an ERK-mTOR co-targeting pro-apoptotic switch in PIK3CA+ oral cancers. Oncotarget 7, 10696–10709 (2016).

Callejas-Valera, J. L., Iglesias-Bartolome, R., Amornphimoltham, P., Palacios-Garcia, J., Martin, D., Califano, J. A., Molinolo, A. A. & Gutkind, J. S. mTOR inhibition prevents rapid-onset of carcinogen-induced malignancies in a novel inducible HPV-16 E6/E7 mouse model. Carcinogenesis 37, 1014–1025 (2016).

Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., Borges-Rivera, D., Pochet, N., Robinson, J. T., Demchak, B., Hull, T., Ben-Artzi, G., Blankenberg, D., Barber, G. P., Lee, B. T., Kuhn, R. M., Nekrutenko, A., Segal, E., Ideker, T., Reich, M., Regev, A., Chang, H. Y. & Mesirov, J. P. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat. Methods 13, 245–247 (2016).

Magbanua, M. J. M., Wolf, D. M., Yau, C., Davis, S. E., Crothers, J., Au, A., Haqq, C. M., Livasy, C., Rugo, H. S., I-SPY 1 TRIAL Investigators, Esserman, L., Park, J. W. & van ’t Veer, L. J. Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and response. Breast Cancer Res. 17, 73 (2015).

Pratt, D., Chen, J., Welker, D., Rivas, R., Pillich, R., Rynkov, V., Ono, K., Miello, C., Hicks, L., Szalma, S., Stojmirovic, A., Dobrin, R., Braxenthaler, M., Kuentzer, J., Demchak, B. & Ideker, T. NDEx, the Network Data Exchange. Cell Syst 1, 302–305 (2015).

Krogan, N. J., Lippman, S., Agard, D. A., Ashworth, A. & Ideker, T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol. Cell 58, 690–698 (2015).

Demchak, B., Hull, T., Reich, M., Liefeld, T., Smoot, M., Ideker, T. & Mesirov, J. P. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 3, 151 (2014).

Gross, A. M., Orosco, R. K., Shen, J. P., Egloff, A. M., Carter, H., Hofree, M., Choueiri, M., Coffey, C. S., Lippman, S. M., Hayes, D. N., Cohen, E. E., Grandis, J. R., Nguyen, Q. T. & Ideker, T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat. Genet. 46, 939–943 (2014).

Hofree, M., Shen, J. P., Carter, H., Gross, A. & Ideker, T. Network-based stratification of tumor mutations. Nat. Methods 10, 1108–1115 (2013).