ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context von Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Dalla Favera, Riccardo, Califano, Andrea

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Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning von Gönen, Mehmet, Margolin, Adam A

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Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis von Tsujikawa, Takahiro, Kumar, Sushil, Borkar, Rohan N., Azimi, Vahid, Thibault, Guillaume, Chang, Young Hwan, Balter, Ariel, Kawashima, Rie, Choe, Gina, Sauer, David, El Rassi, Edward, Clayburgh, Daniel R., Kulesz-Martin, Molly F., Lutz, Eric R., Zheng, Lei, Jaffee, Elizabeth M., Leyshock, Patrick, Margolin, Adam A., Mori, Motomi, Gray, Joe W., Flint, Paul W., Coussens, Lisa M.

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The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition von Sperber, Henrik, Mathieu, Julie, Wang, Yuliang, Ferreccio, Amy, Hesson, Jennifer, Xu, Zhuojin, Fischer, Karin A., Devi, Arikketh, Detraux, Damien, Gu, Haiwei, Battle, Stephanie L., Showalter, Megan, Valensisi, Cristina, Bielas, Jason H., Ericson, Nolan G., Margaretha, Lilyana, Robitaille, Aaron M., Margineantu, Daciana, Fiehn, Oliver, Hockenbery, David, Blau, C. Anthony, Raftery, Daniel, Margolin, Adam A., Hawkins, R. David, Moon, Randall T., Ware, Carol B., Ruohola-Baker, Hannele

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Chemical Genomics Identifies Small-Molecule MCL1 Repressors and BCL-xL as a Predictor of MCL1 Dependency von Wei, Guo, Margolin, Adam A., Haery, Leila, Brown, Emily, Cucolo, Lisa, Julian, Bina, Shehata, Shyemaa, Kung, Andrew L., Beroukhim, Rameen, Golub, Todd R.

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Systematic Assessment of Analytical Methods for Drug Sensitivity Prediction from Cancer Cell Line Data von Neto, Elias, Margolin, Adam, Friend, Stephen, Jang, In, Guinney, Justin

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Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy von Medler, Terry R., Murugan, Dhaarini, Horton, Wesley, Kumar, Sushil, Cotechini, Tiziana, Forsyth, Alexandra M., Leyshock, Patrick, Leitenberger, Justin J., Kulesz-Martin, Molly, Margolin, Adam A., Werb, Zena, Coussens, Lisa M.

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Assessing the clinical utility of cancer genomic and proteomic data across tumor types von Yuan, Yuan, Van Allen, Eliezer M, Omberg, Larsson, Wagle, Nikhil, Amin-Mansour, Ali, Sokolov, Artem, Byers, Lauren A, Xu, Yanxun, Hess, Kenneth R, Diao, Lixia, Han, Leng, Huang, Xuelin, Lawrence, Michael S, Weinstein, John N, Stuart, Josh M, Mills, Gordon B, Garraway, Levi A, Margolin, Adam A, Getz, Gad, Liang, Han

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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection von Ewing, Adam D, Houlahan, Kathleen E, Hu, Yin, Ellrott, Kyle, Caloian, Cristian, Yamaguchi, Takafumi N, Bare, J Christopher, P'ng, Christine, Waggott, Daryl, Sabelnykova, Veronica Y, Kellen, Michael R, Norman, Thea C, Haussler, David, Friend, Stephen H, Stolovitzky, Gustavo, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity von Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, Wilson, Christopher J., Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, Garraway, Levi A.

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Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells von Basso, Katia, Saito, Masumichi, Sumazin, Pavel, Margolin, Adam A., Wang, Kai, Lim, Wei-Keat, Kitagawa, Yukiko, Schneider, Christof, Alvarez, Mariano J., Califano, Andrea, Dalla-Favera, Riccardo

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svpluscnv: analysis and visualization of complex structural variation data von Lopez, Gonzalo, Egolf, Laura E, Giorgi, Federico M, Diskin, Sharon J, Margolin, Adam A

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Genome-wide identification of post-translational modulators of transcription factor activity in human B cells von Califano, Andrea, Wang, Kai, Saito, Masumichi, Bisikirska, Brygida C, Alvarez, Mariano J, Lim, Wei Keat, Rajbhandari, Presha, Shen, Qiong, Nemenman, Ilya, Basso, Katia, Margolin, Adam A, Klein, Ulf, Dalla-Favera, Riccardo

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection von Lee, Anna Y, Ewing, Adam D, Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E, Bare, J Christopher, Espiritu, Shadrielle Melijah G, Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N, Kellen, Michael R, Chen, Ken, Norman, Thea C, Friend, Stephen H, Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C

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Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas von Omberg, Larsson, Ellrott, Kyle, Yuan, Yuan, Kandoth, Cyriac, Wong, Chris, Kellen, Michael R, Friend, Stephen H, Stuart, Josh, Liang, Han, Margolin, Adam A

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An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences von Gurun, Burcu, Horton, Wesley, Murugan, Dhaarini, Zhu, Biqing, Leyshock, Patrick, Kumar, Sushil, Byrne, Katelyn T, Vonderheide, Robert H, Margolin, Adam A, Mori, Motomi, Spellman, Paul T, Coussens, Lisa M, Speed, Terence P

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ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens von Shao, Diane D, Tsherniak, Aviad, Gopal, Shuba, Weir, Barbara A, Tamayo, Pablo, Stransky, Nicolas, Schumacher, Steven E, Zack, Travis I, Beroukhim, Rameen, Garraway, Levi A, Margolin, Adam A, Root, David E, Hahn, William C, Mesirov, Jill P

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Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies von Nikolova, Olga, Moser, Russell, Kemp, Christopher, Gönen, Mehmet, Margolin, Adam A

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Identifying the Proteins to Which Small-Molecule Probes and Drugs Bind in Cells von Ong, Shao-En, Schenone, Monica, Margolin, Adam A., Li, Xiaoyu, Do, Kathy, Doud, Mary K., Mani, D. R., Kuai, Letian, Wang, Xiang, Wood, John L., Tolliday, Nicola J., Koehler, Angela N., Marcaurelle, Lisa A., Golub, Todd R., Gould, Robert J., Schreiber, Stuart L., Carr, Steven A.

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Theory and Limitations of Genetic Network Inference from Microarray Data von MARGOLIN, ADAM A., CALIFANO, ANDREA

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