Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets von Cassetta, Luca, Fragkogianni, Stamatina, Sims, Andrew H., Swierczak, Agnieszka, Forrester, Lesley M., Zhang, Hui, Soong, Daniel Y.H., Cotechini, Tiziana, Anur, Pavana, Lin, Elaine Y., Fidanza, Antonella, Lopez-Yrigoyen, Martha, Millar, Michael R., Urman, Alexandra, Ai, Zhichao, Spellman, Paul T., Hwang, E. Shelley, Dixon, J. Michael, Wiechmann, Lisa, Coussens, Lisa M., Smith, Harriet O., Pollard, Jeffrey W.

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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes von Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Rosebrock, Daniel, Schumacher, Steven E., Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Wedge, David C., Dentro, Stefan C., Leshchiner, Ignaty, Gerstung, Moritz, Jolly, Clemency, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D., Cao, Shaolong, Cmero, Marek, Cun, Yupeng, Dawson, Kevin J., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew, Getz, Gad, Ha, Gavin, Imielinski, Marcin, Ji, Yuan, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Livitz, Dimitri G., Malikic, Salem, Markowetz, Florian, Martincorena, Inigo, Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Salcedo, Adriana, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Spiro, Oliver, Vázquez-García, Ignacio, Vembu, Shankar, Wheeler, David A., Yao, Xiaotong, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter

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Circulating-tumor DNA as an early detection and diagnostic tool von Butler, Timothy M, Spellman, Paul T, Gray, Joe

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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer von Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine, Dobrolecki, Lacey E., Chin, Koei, Aswani, Anil J., Wang, Nicholas J., Califano, Andrea, Lewis, Michael T., Tomlin, Claire J., Spellman, Paul T., Adey, Andrew, Gray, Joe W., Sears, Rosalie C.

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Detecting cancer by monitoring circulating tumor DNA von Spellman, Paul T, Gray, Joe W

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Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease von Butler, Timothy M, Johnson-Camacho, Katherine, Peto, Myron, Wang, Nicholas J, Macey, Tara A, Korkola, James E, Koppie, Theresa M, Corless, Christopher L, Gray, Joe W, Spellman, Paul T

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 von Verhaak, Roel G.W., Hoadley, Katherine A., Purdom, Elizabeth, Wang, Victoria, Qi, Yuan, Wilkerson, Matthew D., Miller, C. Ryan, Ding, Li, Golub, Todd, Mesirov, Jill P., Alexe, Gabriele, Lawrence, Michael, O'Kelly, Michael, Tamayo, Pablo, Weir, Barbara A., Gabriel, Stacey, Winckler, Wendy, Gupta, Supriya, Jakkula, Lakshmi, Feiler, Heidi S., Hodgson, J. Graeme, James, C. David, Sarkaria, Jann N., Brennan, Cameron, Kahn, Ari, Spellman, Paul T., Wilson, Richard K., Speed, Terence P., Gray, Joe W., Meyerson, Matthew, Getz, Gad, Perou, Charles M., Hayes, D. Neil

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FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer von Fu, Xiaoyong, Jeselsohn, Rinath, Pereira, Resel, Hollingsworth, Emporia F., Creighton, Chad J., Li, Fugen, Shea, Martin, Nardone, Agostina, De Angelis, Carmine, Heiser, Laura M., Anur, Pavana, Wang, Nicholas, Grasso, Catherine S., Spellman, Paul T., Griffith, Obi L., Tsimelzon, Anna, Gutierrez, Carolina, Huang, Shixia, Edwards, Dean P., Trivedi, Meghana V., Rimawi, Mothaffar F., Lopez-Terrada, Dolores, Hilsenbeck, Susan G., Gray, Joe W., Brown, Myles, Osborne, C. Kent, Schiff, Rachel

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Epigenetic loss of heterogeneity from low to high grade localized prostate tumours von Eksi, Sebnem Ece, Chitsazan, Alex, Sayar, Zeynep, Thomas, George V., Fields, Andrew J., Kopp, Ryan P., Spellman, Paul T., Adey, Andrew C.

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Integrated analysis of germline and somatic variants in ovarian cancer von Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D. M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li

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Subtype and pathway specific responses to anticancer compounds in breast cancer von Heiser, Laura M, Sadanandam, Anguraj, Kuo, Wen-Lin, Benz, Stephen C, Goldstein, Theodore C, Ng, Sam, Gibb, William J, Wang, Nicholas J, Ziyad, Safiyyah, Tong, Frances, Bayani, Nora, Hu, Zhi, Billig, Jessica I, Dueregger, Andrea, Lewis, Sophia, Jakkula, Lakshmi, Korkola, James E, Durinck, Steffen, Pepin, François, Guan, Yinghui, Purdom, Elizabeth, Neuvial, Pierre, Bengtsson, Henrik, Wood, Kenneth W, Smith, Peter G, Vassilev, Lyubomir T, Hennessy, Bryan T, Greshock, Joel, Bachman, Kurtis E, Hardwicke, Mary Ann, Park, John W, Marton, Laurence J, Wolf, Denise M, Collisson, Eric A, Neve, Richard M, Mills, Gordon B, Speed, Terence P, Feiler, Heidi S, Wooster, Richard F, Haussler, David, Stuart, Joshua M, Gray, Joe W, Spellman, Paul T

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Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response von Boniface, Christopher T, Spellman, Paul T

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Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma von Wang, Nicholas J, Sanborn, Zachary, Arnett, Kelly L, Bayston, Laura J, Liao, Wilson, Proby, Charlotte M, Leigh, Irene M, Collisson, Eric A, Gordon, Patricia B, Jakkula, Lakshmi, Pennypacker, Sally, Zou, Yong, Sharma, Mimansa, North, Jeffrey P, Vemula, Swapna S, Mauro, Theodora M, Neuhaus, Isaac M, LeBoit, Philip E, Hur, Joe S, Park, Kyunghee, Huh, Nam, Kwok, Pui-Yan, Arron, Sarah T, Massion, Pierre P, Bale, Allen E, Haussler, David, Cleaver, James E, Gray, Joe W, Spellman, Paul T, South, Andrew P, Aster, Jon C, Blacklow, Stephen C, Cho, Raymond J

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Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability von Heskett, Michael B., Vouzas, Athanasios E., Smith, Leslie G., Yates, Phillip A., Boniface, Christopher, Bouhassira, Eric E., Spellman, Paul T., Gilbert, David M., Thayer, Mathew J.

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A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma von Collisson, Eric A, Trejo, Christy L, Silva, Jillian M, Gu, Shenda, Korkola, James E, Heiser, Laura M, Charles, Roch-Philippe, Rabinovich, Brian A, Hann, Byron, Dankort, David, Spellman, Paul T, Phillips, Wayne A, Gray, Joe W, McMahon, Martin

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Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination von Sanborn, J. Zachary, Chung, Jongsuk, Purdom, Elizabeth, Wang, Nicholas J., Kakavand, Hojabr, Wilmott, James S., Butler, Timothy, Thompson, John F., Mann, Graham J., Haydu, Lauren E., Saw, Robyn P. M., Busam, Klaus J., Lo, Roger S., Collisson, Eric A., Hur, Joe S., Spellman, Paul T., Cleaver, James E., Gray, Joe W., Huh, Nam, Murali, Rajmohan, Scolyer, Richard A., Bastian, Boris C., Cho, Raymond J.

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ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins von Thayer, Mathew, Heskett, Michael B, Smith, Leslie G, Spellman, Paul T, Yates, Phillip A

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Genomic and transcriptional aberrations linked to breast cancer pathophysiologies von Chin, Koei, DeVries, Sandy, Fridlyand, Jane, Spellman, Paul T., Roydasgupta, Ritu, Kuo, Wen-Lin, Lapuk, Anna, Neve, Richard M., Qian, Zuwei, Ryder, Tom, Chen, Fanqing, Feiler, Heidi, Tokuyasu, Taku, Kingsley, Chris, Dairkee, Shanaz, Meng, Zhenhang, Chew, Karen, Pinkel, Daniel, Jain, Ajay, Ljung, Britt Marie, Esserman, Laura, Albertson, Donna G., Waldman, Frederic M., Gray, Joe W.

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A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes von Neve, Richard M., Chin, Koei, Fridlyand, Jane, Yeh, Jennifer, Baehner, Frederick L., Fevr, Tea, Clark, Laura, Bayani, Nora, Coppe, Jean-Philippe, Tong, Frances, Speed, Terry, Spellman, Paul T., DeVries, Sandy, Lapuk, Anna, Wang, Nick J., Kuo, Wen-Lin, Stilwell, Jackie L., Pinkel, Daniel, Albertson, Donna G., Waldman, Frederic M., McCormick, Frank, Dickson, Robert B., Johnson, Michael D., Lippman, Marc, Ethier, Stephen, Gazdar, Adi, Gray, Joe W.

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Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response von Boniface, Christopher T, Spellman, Paul T

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