A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors von Slyper, Michal, Porter, Caroline B. M., Ashenberg, Orr, Waldman, Julia, Drokhlyansky, Eugene, Wakiro, Isaac, Smillie, Christopher, Smith-Rosario, Gabriela, Wu, Jingyi, Dionne, Danielle, Vigneau, Sébastien, Jané-Valbuena, Judit, Tickle, Timothy L., Napolitano, Sara, Su, Mei-Ju, Patel, Anand G., Karlstrom, Asa, Gritsch, Simon, Nomura, Masashi, Waghray, Avinash, Gohil, Satyen H., Tsankov, Alexander M., Jerby-Arnon, Livnat, Cohen, Ofir, Klughammer, Johanna, Rosen, Yanay, Gould, Joshua, Nguyen, Lan, Hofree, Matan, Tramontozzi, Peter J., Li, Bo, Wu, Catherine J., Izar, Benjamin, Haq, Rizwan, Hodi, F. Stephen, Yoon, Charles H., Hata, Aaron N., Baker, Suzanne J., Suvà, Mario L., Bueno, Raphael, Stover, Elizabeth H., Clay, Michael R., Dyer, Michael A., Collins, Natalie B., Matulonis, Ursula A., Wagle, Nikhil, Johnson, Bruce E., Rotem, Asaf, Rozenblatt-Rosen, Orit, Regev, Aviv

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The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research von Painter, Corrie A., Jain, Esha, Tomson, Brett N., Dunphy, Michael, Stoddard, Rachel E., Thomas, Beena S., Damon, Alyssa L., Shah, Shahrayz, Kim, Dewey, Gómez Tejeda Zañudo, Jorge, Hornick, Jason L., Chen, Yen-Lin, Merriam, Priscilla, Raut, Chandrajit P., Demetri, George D., Van Tine, Brian A., Lander, Eric S., Golub, Todd R., Wagle, Nikhil

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Response and Acquired Resistance to Everolimus in Anaplastic Thyroid Cancer von Wagle, Nikhil, Grabiner, Brian C, Van Allen, Eliezer M, Amin-Mansour, Ali, Taylor-Weiner, Amaro, Rosenberg, Mara, Gray, Nathanael, Barletta, Justine A, Guo, Yanan, Swanson, Scott J, Ruan, Daniel T, Hanna, Glenn J, Haddad, Robert I, Getz, Gad, Kwiatkowski, David J, Carter, Scott L, Sabatini, David M, Jänne, Pasi A, Garraway, Levi A, Lorch, Jochen H

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Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma von Jerby-Arnon, Livnat, Neftel, Cyril, Shore, Marni E., Weisman, Hannah R., Mathewson, Nathan D., McBride, Matthew J., Haas, Brian, Izar, Benjamin, Volorio, Angela, Boulay, Gaylor, Cironi, Luisa, Richman, Alyssa R., Broye, Liliane C., Gurski, Joseph M., Luo, Christina C., Mylvaganam, Ravindra, Nguyen, Lan, Mei, Shaolin, Melms, Johannes C., Georgescu, Christophe, Cohen, Ofir, Buendia-Buendia, Jorge E., Segerstolpe, Asa, Sud, Malika, Cuoco, Michael S., Labes, Danny, Gritsch, Simon, Zollinger, Daniel R., Ortogero, Nicole, Beechem, Joseph M., Petur Nielsen, G., Chebib, Ivan, Nguyen-Ngoc, Tu, Montemurro, Michael, Cote, Gregory M., Choy, Edwin, Letovanec, Igor, Cherix, Stéphane, Wagle, Nikhil, Sorger, Peter K., Haynes, Alex B., Mullen, John T., Stamenkovic, Ivan, Rivera, Miguel N., Kadoch, Cigall, Wucherpfennig, Kai W., Rozenblatt-Rosen, Orit, Suvà, Mario L., Riggi, Nicolò, Regev, Aviv

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MicroRNA-Mediated Suppression of the TGF-β Pathway Confers Transmissible and Reversible CDK4/6 Inhibitor Resistance von Cornell, Liam, Wander, Seth A., Visal, Tanvi, Wagle, Nikhil, Shapiro, Geoffrey I.

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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution von Rood, Jennifer E., Coffey, Robert J., Demir, Emek, Ghosh, Sharmistha, Iacobuzio-Donahue, Christine A., Jané-Valbuena, Judit, Mazzilli, Sarah A., Pe’er, Dana, Tan, Kai, Aguilar, Ruben A., Babur, Ozgun, Boland, Genevieve, Bosse, Kristopher, Bott, Matthew, Boyden, Ed, Brooks, James, Cerami, Ethan, Chang, Young Hwan, Chaudhary, Ojasvi, Chen, Alyce A., Chen, Feng, Chun, Jaeyoung, Cisneros, Luis, Contrepois, Kevin, Creason, Allison L., Demir, Emek, Diskin, Sharon, Drewes, Julia, Eng, Jennifer, Erwin, Graham, Flaherty, Keith, Gao, Jianjiong, Gao, Vianne R., Giannakis, Marios, Gowers, Kate, Gray, Joe W., Greenleaf, William, Gresham, Jeremy, Hacohen, Nir, Harris, Kathleen A., Hayashi, Akimasa, Herndon, John M., Huh, Won Jae, Ijaz, Heba, Izar, Benjamin, Johnson, Brett E., Kaestner, Klaus, Kim, Albert H., Kopytra, Mateusz, Kundaje, Anshul, Lau, Ken S., Lee, Hayan, Lenburg, Marc, Lim, Kian-Huat, Lin, Yiyun, Lively, Tracy, Longabaugh, William J.R., Ma, Cynthia X., Marks, Jeffrey, Masilionais, Ignas, McKinley, Eliot T., McMichael, Joshua F., Mosse, Yael, Ness, Reid, Nikolov, Milen, Oberdoerffer, Philipp, Offin, Michael, Olson, Anastasiya, Ossandon, Miguel, Polyak, Kornelia, Reid, Mary, Roy, Sudipta, Ryser, Marc D., Schrag, Deborah, Sears, Rosalie C., Shalek, Alex, Sheng, Jeff, Shoghi, Kooresh I., Sibley, Alexander B., Sorger, Peter K., Southard-Smith, Austin, Srivastava, Sudhir, Storm, Phillip, Sullivan, Ryan, Suvà, Mario, Thorsson, Vésteinn, Tran, Linh, Veis, Deborah J., Vossough, Arastoo, Wagle, Nikhil, Wang, Liang-Bo, West, Robert, Wu, Chi-yun, Wyczalkowski, Matthew A., Xie, Yubin, Yang, Xiaolu, Zhang, Mianlei, Zhang, Yantian, Zhou, Daniel Cui, Zhuang, Xiaowei

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Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies von Nayar, Utthara, Cohen, Ofir, Kapstad, Christian, Cuoco, Michael S., Waks, Adrienne G., Wander, Seth A., Painter, Corrie, Freeman, Samuel, Persky, Nicole S., Marini, Lori, Helvie, Karla, Oliver, Nelly, Rozenblatt-Rosen, Orit, Ma, Cynthia X., Regev, Aviv, Winer, Eric P., Lin, Nancy U., Wagle, Nikhil

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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors von Adalsteinsson, Viktor A., Ha, Gavin, Freeman, Samuel S., Choudhury, Atish D., Stover, Daniel G., Parsons, Heather A., Gydush, Gregory, Reed, Sarah C., Rotem, Denisse, Rhoades, Justin, Loginov, Denis, Livitz, Dimitri, Rosebrock, Daniel, Leshchiner, Ignaty, Kim, Jaegil, Stewart, Chip, Rosenberg, Mara, Francis, Joshua M., Zhang, Cheng-Zhong, Cohen, Ofir, Oh, Coyin, Ding, Huiming, Polak, Paz, Lloyd, Max, Mahmud, Sairah, Helvie, Karla, Merrill, Margaret S., Santiago, Rebecca A., O’Connor, Edward P., Jeong, Seong H., Leeson, Rachel, Barry, Rachel M., Kramkowski, Joseph F., Zhang, Zhenwei, Polacek, Laura, Lohr, Jens G., Schleicher, Molly, Lipscomb, Emily, Saltzman, Andrea, Oliver, Nelly M., Marini, Lori, Waks, Adrienne G., Harshman, Lauren C., Tolaney, Sara M., Van Allen, Eliezer M., Winer, Eric P., Lin, Nancy U., Nakabayashi, Mari, Taplin, Mary-Ellen, Johannessen, Cory M., Garraway, Levi A., Golub, Todd R., Boehm, Jesse S., Wagle, Nikhil, Getz, Gad, Love, J. Christopher, Meyerson, Matthew

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ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation von Li, Zheqi, McGinn, Olivia, Wu, Yang, Bahreini, Amir, Priedigkeit, Nolan M., Ding, Kai, Onkar, Sayali, Lampenfeld, Caleb, Sartorius, Carol A., Miller, Lori, Rosenzweig, Margaret, Cohen, Ofir, Wagle, Nikhil, Richer, Jennifer K., Muller, William J., Buluwela, Laki, Ali, Simak, Bruno, Tullia C., Vignali, Dario A. A., Fang, Yusi, Zhu, Li, Tseng, George C., Gertz, Jason, Atkinson, Jennifer M., Lee, Adrian V., Oesterreich, Steffi

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Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling von WAGLE, Nikhil, EMERY, Caroline, MEYERSON, Matthew, GARRAWAY, Levi A, BERGER, Michael F, DAVIS, Matthew J, SAWYER, Allison, POCHANARD, Panisa, KEHOE, Sarah M, JOHANNESSEN, Cory M, MACCONAILL, Laura E, HAHN, William C

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Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer von Barroso-Sousa, Romualdo, Keenan, Tanya E, Pernas, Sonia, Exman, Pedro, Jain, Esha, Garrido-Castro, Ana C, Hughes, Melissa, Bychkovsky, Brittany, Umeton, Renato, Files, Janet L, Lindeman, Neal I, MacConaill, Laura E, Hodi, F Stephen, Krop, Ian E, Dillon, Deborah, Winer, Eric P, Wagle, Nikhil, Lin, Nancy U, Mittendorf, Elizabeth A, Van Allen, Eliezer M, Tolaney, Sara M

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Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations von Jeselsohn, Rinath, Bergholz, Johann S., Pun, Matthew, Cornwell, MacIntosh, Liu, Weihan, Nardone, Agostina, Xiao, Tengfei, Li, Wei, Qiu, Xintao, Buchwalter, Gilles, Feiglin, Ariel, Abell-Hart, Kayley, Fei, Teng, Rao, Prakash, Long, Henry, Kwiatkowski, Nicholas, Zhang, Tinghu, Gray, Nathanael, Melchers, Diane, Houtman, Rene, Liu, X. Shirley, Cohen, Ofir, Wagle, Nikhil, Winer, Eric P., Zhao, Jean, Brown, Myles

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Clinical Analysis and Interpretation of Cancer Genome Data von Van Allen, Eliezer M, Wagle, Nikhil, Levy, Mia A

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Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma von Perry, Jennifer A, Kiezun, Adam, Tonzi, Peter, Van Allen, Eliezer M, Carter, Scott L, Baca, Sylvan C, Cowley, Glenn S, Bhatt, Ami S, Rheinbay, Esther, Pedamallu, Chandra Sekhar, Helman, Elena, Taylor-Weiner, Amaro, McKenna, Aaron, DeLuca, David S, Lawrence, Michael S, Ambrogio, Lauren, Sougnez, Carrie, Sivachenko, Andrey, Walensky, Loren D, Wagle, Nikhil, Mora, Jaume, de Torres, Carmen, Lavarino, Cinzia, Dos Santos Aguiar, Simone, Yunes, Jose Andres, Brandalise, Silvia Regina, Mercado-Celis, Gabriela Elisa, Melendez-Zajgla, Jorge, Cárdenas-Cardós, Rocío, Velasco-Hidalgo, Liliana, Roberts, Charles W M, Garraway, Levi A, Rodriguez-Galindo, Carlos, Gabriel, Stacey B, Lander, Eric S, Golub, Todd R, Orkin, Stuart H, Getz, Gad, Janeway, Katherine A

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A Landscape of Driver Mutations in Melanoma von Hodis, Eran, Watson, Ian R., Kryukov, Gregory V., Arold, Stefan T., Imielinski, Marcin, Theurillat, Jean-Philippe, Nickerson, Elizabeth, Auclair, Daniel, Li, Liren, Place, Chelsea, DiCara, Daniel, Ramos, Alex H., Lawrence, Michael S., Cibulskis, Kristian, Sivachenko, Andrey, Voet, Douglas, Saksena, Gordon, Stransky, Nicolas, Onofrio, Robert C., Winckler, Wendy, Ardlie, Kristin, Wagle, Nikhil, Wargo, Jennifer, Chong, Kelly, Morton, Donald L., Stemke-Hale, Katherine, Chen, Guo, Noble, Michael, Meyerson, Matthew, Ladbury, John E., Davies, Michael A., Gershenwald, Jeffrey E., Wagner, Stephan N., Hoon, Dave S.B., Schadendorf, Dirk, Lander, Eric S., Gabriel, Stacey B., Getz, Gad, Garraway, Levi A., Chin, Lynda

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FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer von Fu, Xiaoyong, Pereira, Resel, De Angelis, Carmine, Veeraraghavan, Jamunarani, Nanda, Sarmistha, Qin, Lanfang, Cataldo, Maria L., Sethunath, Vidyalakshmi, Mehravaran, Sepideh, Gutierrez, Carolina, Chamness, Gary C., Feng, Qin, O’Malley, Bert W., Selenica, Pier, Weigelt, Britta, Reis-Filho, Jorge S., Cohen, Ofir, Wagle, Nikhil, Nardone, Agostina, Jeselsohn, Rinath, Brown, Myles, Rimawi, Mothaffar F., Osborne, C. Kent, Schiff, Rachel

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The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma von Van Allen, Eliezer M, Wagle, Nikhil, Sucker, Antje, Treacy, Daniel J, Johannessen, Cory M, Goetz, Eva M, Place, Chelsea S, Taylor-Weiner, Amaro, Whittaker, Steven, Kryukov, Gregory V, Hodis, Eran, Rosenberg, Mara, McKenna, Aaron, Cibulskis, Kristian, Farlow, Deborah, Zimmer, Lisa, Hillen, Uwe, Gutzmer, Ralf, Goldinger, Simone M, Ugurel, Selma, Gogas, Helen J, Egberts, Friederike, Berking, Carola, Trefzer, Uwe, Loquai, Carmen, Weide, Benjamin, Hassel, Jessica C, Gabriel, Stacey B, Carter, Scott L, Getz, Gad, Garraway, Levi A, Schadendorf, Dirk

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A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition von Whittaker, Steven R, Theurillat, Jean-Philippe, Van Allen, Eliezer, Wagle, Nikhil, Hsiao, Jessica, Cowley, Glenn S, Schadendorf, Dirk, Root, David E, Garraway, Levi A

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Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine von Van Allen, Eliezer M, Wagle, Nikhil, Stojanov, Petar, Perrin, Danielle L, Cibulskis, Kristian, Marlow, Sara, Jane-Valbuena, Judit, Friedrich, Dennis C, Kryukov, Gregory, Carter, Scott L, McKenna, Aaron, Sivachenko, Andrey, Rosenberg, Mara, Kiezun, Adam, Voet, Douglas, Lawrence, Michael, Lichtenstein, Lee T, Gentry, Jeff G, Huang, Franklin W, Fostel, Jennifer, Farlow, Deborah, Barbie, David, Gandhi, Leena, Lander, Eric S, Gray, Stacy W, Joffe, Steven, Janne, Pasi, Garber, Judy, MacConaill, Laura, Lindeman, Neal, Rollins, Barrett, Kantoff, Philip, Fisher, Sheila A, Gabriel, Stacey, Getz, Gad, Garraway, Levi A

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ERK mutations confer resistance to mitogen-activated protein kinase pathway inhibitors von Goetz, Eva M, Ghandi, Mahmoud, Treacy, Daniel J, Wagle, Nikhil, Garraway, Levi A

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