Genomic evolution of cancer models: perils and opportunities von Ben-David, Uri, Beroukhim, Rameen, Golub, Todd R.

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Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate von Chakraborty, Abhishek A, Laukka, Tuomas, Myllykoski, Matti, Ringel, Alison E, Booker, Matthew A, Tolstorukov, Michael Y, Meng, Yuzhong Jeff, Meier, Samuel R, Jennings, Rebecca B, Creech, Amanda L, Herbert, Zachary T, McBrayer, Samuel K, Olenchock, Benjamin A, Jaffe, Jacob D, Haigis, Marcia C, Beroukhim, Rameen, Signoretti, Sabina, Koivunen, Peppi, Kaelin, Jr, William G

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Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities von Nichols, Caitlin A., Gibson, William J., Brown, Meredith S., Kosmicki, Jack A., Busanovich, John P., Wei, Hope, Urbanski, Laura M., Curimjee, Naomi, Berger, Ashton C., Gao, Galen F., Cherniack, Andrew D., Dhe-Paganon, Sirano, Paolella, Brenton R., Beroukhim, Rameen

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Genetic and transcriptional evolution alters cancer cell line drug response von Ben-David, Uri, Siranosian, Benjamin, Ha, Gavin, Tang, Helen, Oren, Yaara, Hinohara, Kunihiko, Strathdee, Craig A., Dempster, Joshua, Lyons, Nicholas J., Burns, Robert, Nag, Anwesha, Kugener, Guillaume, Cimini, Beth, Tsvetkov, Peter, Maruvka, Yosef E., O’Rourke, Ryan, Garrity, Anthony, Tubelli, Andrew A., Bandopadhayay, Pratiti, Tsherniak, Aviad, Vazquez, Francisca, Wong, Bang, Birger, Chet, Ghandi, Mahmoud, Thorner, Aaron R., Bittker, Joshua A., Meyerson, Matthew, Getz, Gad, Beroukhim, Rameen, Golub, Todd R.

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

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Cas9 activates the p53 pathway and selects for p53-inactivating mutations von Enache, Oana M., Rendo, Veronica, Abdusamad, Mai, Lam, Daniel, Davison, Desiree, Pal, Sangita, Currimjee, Naomi, Hess, Julian, Pantel, Sasha, Nag, Anwesha, Thorner, Aaron R., Doench, John G., Vazquez, Francisca, Beroukhim, Rameen, Golub, Todd R., Ben-David, Uri

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SvABA: genome-wide detection of structural variants and indels by local assembly von Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen

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Landscape of Genomic Alterations in Pituitary Adenomas von Bi, Wenya Linda, Horowitz, Peleg, Greenwald, Noah F, Abedalthagafi, Malak, Agarwalla, Pankaj K, Gibson, Wiliam J, Mei, Yu, Schumacher, Steven E, Ben-David, Uri, Chevalier, Aaron, Carter, Scott, Tiao, Grace, Brastianos, Priscilla K, Ligon, Azra H, Ducar, Matthew, MacConaill, Laura, Laws, Jr, Edward R, Santagata, Sandro, Beroukhim, Rameen, Dunn, Ian F

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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing von 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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Absolute quantification of somatic DNA alterations in human cancer von Carter, Scott L, Cibulskis, Kristian, Helman, Elena, McKenna, Aaron, Shen, Hui, Zack, Travis, Laird, Peter W, Onofrio, Robert C, Winckler, Wendy, Weir, Barbara A, Beroukhim, Rameen, Pellman, David, Levine, Douglas A, Lander, Eric S, Meyerson, Matthew, Getz, Gad

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Pan-cancer patterns of somatic copy number alteration von Zack, Travis I, Schumacher, Steven E, Carter, Scott L, Cherniack, Andrew D, Saksena, Gordon, Tabak, Barbara, Lawrence, Michael S, Zhang, Cheng-Zhong, Wala, Jeremiah, Mermel, Craig H, Sougnez, Carrie, Gabriel, Stacey B, Hernandez, Bryan, Shen, Hui, Laird, Peter W, Getz, Gad, Meyerson, Matthew, Beroukhim, Rameen

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Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition von Wong, Gabrielle S., Zhou, Jin, Liu, Jie Bin, Wu, Zhong, Xu, Xinsen, Li, Tianxia, Xu, David, Schumacher, Steven E., Puschhof, Jens, McFarland, James, Zou, Charles, Dulak, Austin, Henderson, Les, Xu, Peng, O’Day, Emily, Rendak, Rachel, Liao, Wei-li, Cecchi, Fabiola, Hembrough, Todd, Schwartz, Sarit, Szeto, Christopher, Rustgi, Anil K., Wong, Kwok-Kin, Diehl, J. Alan, Jensen, Karin, Graziano, Francesco, Ruzzo, Annamaria, Fereshetian, Shaunt, Mertins, Philipp, Carr, Steven A., Beroukhim, Rameen, Nakamura, Kenichi, Oki, Eiji, Watanabe, Masayuki, Baba, Hideo, Imamura, Yu, Catenacci, Daniel, Bass, Adam J.

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Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations von Brastianos, Priscilla K, Horowitz, Peleg M, Santagata, Sandro, Jones, Robert T, McKenna, Aaron, Getz, Gad, Ligon, Keith L, Palescandolo, Emanuele, Van Hummelen, Paul, Ducar, Matthew D, Raza, Alina, Sunkavalli, Ashwini, MacConaill, Laura E, Stemmer-Rachamimov, Anat O, Louis, David N, Hahn, William C, Dunn, Ian F, Beroukhim, Rameen

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A molecularly integrated grade for meningioma von Driver, Joseph, Hoffman, Samantha E, Tavakol, Sherwin, Woodward, Eleanor, Maury, Eduardo A, Bhave, Varun, Greenwald, Noah F, Nassiri, Farshad, Aldape, Kenneth, Zadeh, Gelareh, Choudhury, Abrar, Vasudevan, Harish N, Magill, Stephen T, Raleigh, David R, Abedalthagafi, Malak, Aizer, Ayal A, Alexander, Brian M, Ligon, Keith L, Reardon, David A, Wen, Patrick Y, Al-Mefty, Ossama, Ligon, Azra H, Dubuc, Adrian M, Beroukhim, Rameen, Claus, Elizabeth B, Dunn, Ian F, Santagata, Sandro, Linda Bi, Wenya

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Epigenetic targeting of Hedgehog pathway transcriptional output through BET bromodomain inhibition von Tang, Yujie, Gholamin, Sharareh, Schubert, Simone, Willardson, Minde I, Lee, Alex, Bandopadhayay, Pratiti, Bergthold, Guillame, Masoud, Sabran, Nguyen, Brian, Vue, Nujsaubnusi, Balansay, Brianna, Yu, Furong, Oh, Sekyung, Woo, Pamelyn, Chen, Spenser, Ponnuswami, Anitha, Monje, Michelle, Atwood, Scott X, Whitson, Ramon J, Mitra, Siddhartha, Cheshier, Samuel H, Qi, Jun, Beroukhim, Rameen, Tang, Jean Y, Wechsler-Reya, Rob, Oro, Anthony E, Link, Brian A, Bradner, James E, Cho, Yoon-Jae

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Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations von Poduri, Annapurna, Evrony, Gilad D., Cai, Xuyu, Elhosary, Princess Christina, Beroukhim, Rameen, Lehtinen, Maria K., Hills, L. Benjamin, Heinzen, Erin L., Hill, Anthony, Hill, R. Sean, Barry, Brenda J., Bourgeois, Blaise F.D., Riviello, James J., Barkovich, A. James, Black, Peter M., Ligon, Keith L., Walsh, Christopher A.

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The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis von Gibson, William J, Hoivik, Erling A, Halle, Mari K, Taylor-Weiner, Amaro, Cherniack, Andrew D, Berg, Anna, Holst, Frederik, Zack, Travis I, Werner, Henrica M J, Staby, Kjersti M, Rosenberg, Mara, Stefansson, Ingunn M, Kusonmano, Kanthida, Chevalier, Aaron, Mauland, Karen K, Trovik, Jone, Krakstad, Camilla, Giannakis, Marios, Hodis, Eran, Woie, Kathrine, Bjorge, Line, Vintermyr, Olav K, Wala, Jeremiah A, Lawrence, Michael S, Getz, Gad, Carter, Scott L, Beroukhim, Rameen, Salvesen, Helga B

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An in-tumor genetic screen reveals that the BET bromodomain protein, BRD4, is a potential therapeutic target in ovarian carcinoma von Baratta, Maria Giuseppina, Schinzel, Anna C., Zwang, Yaara, Bandopadhayay, Pratiti, Bowman-Colin, Christian, Kutt, Jennifer, Curtis, Jennifer, Piao, Huiying, Wong, Laura C., Kung, Andrew L., Beroukhim, Rameen, Bradner, James E., Drapkin, Ronny, Hahn, William C., Liu, Joyce F., Livingston, David M.

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Genomic landscape of intracranial meningiomas von Bi, Wenya Linda, Abedalthagafi, Malak, Horowitz, Peleg, Agarwalla, Pankaj K, Mei, Yu, Aizer, Ayal A, Brewster, Ryan, Dunn, Gavin P, Al-Mefty, Ossama, Alexander, Brian M, Santagata, Sandro, Beroukhim, Rameen, Dunn, Ian F

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The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset von Ceol, Craig J., Houvras, Yariv, Jane-Valbuena, Judit, Bilodeau, Steve, Orlando, David A., Battisti, Valentine, Fritsch, Lauriane, Lin, William M., Hollmann, Travis J., Ferré, 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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