GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers by Mermel, Craig H., Schumacher, Steven E., Hill, Barbara, Meyerson, Matthew L., Beroukhim, Rameen, Getz, Gad

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Major copy proportion analysis of tumor samples using SNP arrays by Li Cheng, Beroukhim Rameen, Weir Barbara A, Winckler Wendy, Garraway Levi A, Sellers William R, Meyerson Matthew

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Major copy proportion analysis of tumor samples using SNP arrays by Li, Cheng, Beroukhim, Rameen, Weir, Barbara A., Winckler, Wendy, Garraway, Levi A., Sellers, William R., Meyerson, Matthew L.

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Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability by Drier, Yotam, Lawrence, Michael S., Carter, Scott L., Stewart, Chip, Gabriel, Stacey B., Meyerson, Matthew L., Beroukhim, Rameen, Getz, Gad, Lander, Eric Steven

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Amplification of phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis by Locasale Jason W, Grassian Alexandra, Beroukhim Rameen, Meyerson Matthew, Wagner Gerhard, Asara John M, Brugge Joan S, Vander Heiden Matthew G, Cantley Lewis C

Targeting cancer gene dependencies with anthrax-mediated delivery of peptide nucleic acids by Lu, Zeyu, Paolella, Brenton R, Truex, Nicholas L, Loftis, Alexander R, Liao, Xiaoli, Rabideau, Amy E, Brown, Meredith S, Busanovich, John, Beroukhim, Rameen, Pentelute, Bradley L

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Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids by Lu, Zeyu, Paolella, Brenton R., Truex, Nicholas L., Loftis, Alexander R., Liao, Xiaoli, Rabideau, Amy E., Brown, Meredith S., Busanovich, John, Beroukhim, Rameen, Pentelute, Bradley L.

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CloneSifter: enrichment of rare clones from heterogeneous cell populations by Feldman, David, Tsai, FuNien, Garrity, Anthony J, O’Rourke, Ryan, Brenan, Lisa, Ho, Patricia, Gonzalez, Elizabeth, Konermann, Silvana, Johannessen, Cory M, Beroukhim, Rameen, Bandopadhayay, Pratiti, Blainey, Paul C

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Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth by Holst, Frederik, Hoivik, Erling A., Taylor-Weiner, Amaro, Schumacher, Steven E., Asmann, Yan W., Grossmann, Patrick, Trovik, Jone, Necela, Brian M., Thompson, E. Aubrey, Salvesen, Helga B., Cherniack, Andrew D., Gibson, William J, Beroukhim, Rameen, Meyerson, Matthew L.

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Cancer Vulnerabilities Unveiled by Genomic Loss by Nijhawan, Deepak, Zack, Travis I., Ren, Yin, Strickland, Matthew R., Lamothe, Rebecca, Schumacher, Steven E., Tsherniak, Aviad, Besche, Henrike C., Rosenbluh, Joseph, Shehata, Shyemaa, Cowley, Glenn S., Weir, Barbara A., Goldberg, Alfred L., Mesirov, Jill P., Root, David E., Beroukhim, Rameen, Hahn, William C., Bhatia, Sangeeta N

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Predicting clinical response to anticancer drugs using an ex vivo platform that captures tumour heterogeneity by Majumder, Biswanath, Baraneedharan, Ulaganathan, Thiyagarajan, Saravanan, Radhakrishnan, Padhma, Narasimhan, Harikrishna, Dhandapani, Muthu, Brijwani, Nilesh, Pinto, Dency D., Prasath, Arun, Shanthappa, Basavaraja U., Thayakumar, Allen, Surendran, Rajagopalan, Babu, Govind K., Shenoy, Ashok M., Kuriakose, Moni A., Bergthold, Guillaume, Horowitz, Peleg, Loda, Massimo, Beroukhim, Rameen, Agarwal, Shivani, Sengupta, Shiladitya, Sundaram, Mallikarjun, Majumder, Pradip K.

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Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation by Salvesen, H. B., Carter, Scott L., Mannelqvist, M., Dutt, Amit, Getz, Gad, Stefansson, I. M., Raeder, M. B., Sos, M. L., Engelsen, I. B., Trovik, J., Wik, E., Greulich, Heidi, Bo, T. H., Jonassen, I., Thomas, R. K., Zander, T., Garraway, Levi A., Oyan, A. M., Sellers, W. R., Kalland, K. H., Meyerson, Matthew L., Akslen, L. A., Beroukhim, Rameen

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The SETDB1 histone methyltransferase is recurrently amplified in and accelerates melanoma by Ceol, Craig J., Houvras, Yariv, Jane-Valbuena, Judit, Bilodeau, Steve, Orlando, David A., Battisti, Valentine, Fritsch, Lauriane, Lin, William M., Hollmann, Travis J., Ferre, Fabrizio, Bourque, Caitlin, Burke, Christopher J., Turner, Laura, Uong, Audrey, Johnson, Laura A., Beroukhim, Rameen, Mermel, Craig H., Loda, Massimo, Ait-Si-Ali, Slimane, Garraway, Levi A., Young, Richard A., Zon, Leonard I.

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Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability by Paolella, Brenton R, Urbanski, Laura M, Alberta, John A, Bandopadhayay, Pratiti, Nichols, Caitlin A, Agarwalla, Pankaj K, Brown, Meredith S, Lamothe, Rebecca, Yu, Yong, Choi, Peter S, Obeng, Esther A, Heckl, Dirk, Vazquez, Francisca, Buhrlage, Sara J, Stiles, Charles D, Reed, Robin, Gibson, William J, Zack, Travis Ian, Wei, Guo, Wang, Belinda, Tsherniak, Aviad, Weir, Barbara A, Root, David, Cowley, Glenn S, Ebert, Benjamin L, Hahn, William, Beroukhim, Rameen

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Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis by Locasale, Jason W., Grassian, Alexandra R., Melman, Tamar, Lyssiotis, Costas A., Mattaini, Katherine Ruth, Bass, Adam J., Heffron, Gregory J., Metallo, Christian M., Muranen, Taru, Sharfi, Hadar, Sasaki, Atsuo T., Anastasiou, Dimitrios, Mullarky, Edouard, Vokes, Natalie I., Sasaki, Mika, Beroukhim, Rameen, Stephanopoulos, Gregory, Ligon, Azra H., Meyerson, Matthew L., Richardson, Andrea L., Chin, Lynda, Wagner, Gerhard, Asara, John M., Brugge, Joan S., Cantley, Lewis C., Vander Heiden, Matthew G.

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Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells by Reitman, Zachary J., Paolella, Brenton R., Bergthold, Guillaume, Pelton, Kristine, Becker, Sarah, Jones, Robert, Sinai, Claire E., Malkin, Hayley, Huang, Ying, Grimmet, Leslie, Herbert, Zachary T., Sun, Yu, Weatherbee, Jessica L., Alberta, John A., Daley, John F., Rozenblatt-Rosen, Orit, Condurat, Alexandra L., Qian, Kenin, Khadka, Prasidda, Segal, Rosalind A., Haas-Kogan, Daphne, Filbin, Mariella G., Suva, Mario L., Regev, Aviv, Stiles, Charles D., Kieran, Mark W., Goumnerova, Liliana, Ligon, Keith L., Shalek, Alexander K, Bandopadhayay, Pratiti, Beroukhim, Rameen

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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing by Viswanathan, Srinivas R., Ha, Gavin, Hoff, Andreas M., Wala, Jeremiah A., Carrot-Zhang, Jian, Whelan, Christopher W., Haradhvala, Nicholas J., Freeman, Samuel S., Reed, Sarah C., Rhoades, Justin, Polak, Paz, Cipicchio, Michelle, Wankowicz, Stephanie A., Wong, Alicia, Kamath, Tushar, Zhang, Zhenwei, Gydush, Gregory J., Rotem, Denisse, Love, J. Christopher, Getz, Gad, Gabriel, Stacey, Zhang, Cheng-Zhong, Dehm, Scott M., Nelson, Peter S., Van Allen, Eliezer M., Choudhury, Atish D., Adalsteinsson, Viktor A., Beroukhim, Rameen, Taplin, Mary-Ellen, Meyerson, Matthew

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Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma by Bandopadhayay, Pratiti, Piccioni, Federica, O’Rourke, Ryan, Ho, Patricia, Gonzalez, Elizabeth M., Buchan, Graham, Qian, Kenin, Gionet, Gabrielle, Girard, Emily, Coxon, Margo, Rees, Matthew G., Brenan, Lisa, Dubois, Frank, Shapira, Ofer, Greenwald, Noah F., Pages, Melanie, Balboni Iniguez, Amanda, Paolella, Brenton R., Meng, Alice, Sinai, Claire, Roti, Giovanni, Dharia, Neekesh V., Creech, Amanda, Tanenbaum, Benjamin, Khadka, Prasidda, Tracy, Adam, Tiv, Hong L., Hong, Andrew L., Coy, Shannon, Rashid, Rumana, Lin, Jia-Ren, Cowley, Glenn S., Lam, Fred Chiu-Lai, Goodale, Amy, Lee, Yenarae, Schoolcraft, Kathleen, Vazquez, Francisca, Hahn, William C., Tsherniak, Aviad, Bradner, James E., Yaffe, Michael B, Milde, Till, Pfister, Stefan M., Qi, Jun, Schenone, Monica, Carr, Steven A., Ligon, Keith L., Kieran, Mark W., Santagata, Sandro, Olson, James M., Gokhale, Prafulla C., Jaffe, Jacob D., Root, David E., Stegmaier, Kimberly, Johannessen, Cory M., Beroukhim, Rameen

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The whole-genome landscape of medulloblastoma subtypes by Northcott, Paul A., Buchhalter, Ivo, Morrissy, A. Sorana, Hovestadt, Volker, Weischenfeldt, Joachim, Ehrenberger, Tobias, Gröbner, Susanne, Segura-Wang, Maia, Zichner, Thomas, Rudneva, Vasilisa A., Warnatz, Hans-Jörg, Sidiropoulos, Nikos, Phillips, Aaron H., Schumacher, Steven, Kleinheinz, Kortine, Waszak, Sebastian M., Erkek, Serap, Jones, David T. W., Worst, Barbara C., Kool, Marcel, Zapatka, Marc, Jäger, Natalie, Chavez, Lukas, Hutter, Barbara, Bieg, Matthias, Paramasivam, Nagarajan, Heinold, Michael, Gu, Zuguang, Ishaque, Naveed, Jäger-Schmidt, Christina, Imbusch, Charles D., Jugold, Alke, Hübschmann, Daniel, Risch, Thomas, Amstislavskiy, Vyacheslav, Gonzalez, Francisco German Rodriguez, Weber, Ursula D., Wolf, Stephan, Robinson, Giles W., Zhou, Xin, Wu, Gang, Finkelstein, David, Liu, Yanling, Cavalli, Florence M. G., Luu, Betty, Ramaswamy, Vijay, Wu, Xiaochong, Koster, Jan, Ryzhova, Marina, Cho, Yoon-Jae, Pomeroy, Scott L., Herold-Mende, Christel, Schuhmann, Martin, Ebinger, Martin, Liau, Linda M., Mora, Jaume, McLendon, Roger E., Jabado, Nada, Kumabe, Toshihiro, Chuah, Eric, Ma, Yussanne, Moore, Richard A., Mungall, Andrew J., Mungall, Karen L., Thiessen, Nina, Tse, Kane, Wong, Tina, Jones, Steven J. M., Witt, Olaf, Milde, Till, Von Deimling, Andreas, Capper, David, Korshunov, Andrey, Yaspo, Marie-Laure, Kriwacki, Richard, Gajjar, Amar, Zhang, Jinghui, Beroukhim, Rameen, Fraenkel, Ernest, Korbel, Jan O., Brors, Benedikt, Schlesner, Matthias, Eils, Roland, Marra, Marco A., Pfister, Stefan M., Taylor, Michael D., Lichter, Peter

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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad

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