RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues von Yizhak, Keren, Aguet, François, Kim, Jaegil, Hess, Julian M., Kübler, Kirsten, Grimsby, Jonna, Frazer, Ruslana, Zhang, Hailei, Haradhvala, Nicholas J., Rosebrock, Daniel, Livitz, Dimitri, Li, Xiao, Arich-Landkof, Eila, Shoresh, Noam, Stewart, Chip, Segrè, Ayellet V., Branton, Philip A., Polak, Paz, Ardlie, Kristin G., Getz, Gad

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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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Resistance to checkpoint blockade therapy through inactivation of antigen presentation von Sade-Feldman, Moshe, Jiao, Yunxin J., Chen, Jonathan H., Rooney, Michael S., Barzily-Rokni, Michal, Eliane, Jean-Pierre, Bjorgaard, Stacey L., Hammond, Marc R., Vitzthum, Hans, Blackmon, Shauna M., Frederick, Dennie T., Hazar-Rethinam, Mehlika, Nadres, Brandon A., Van Seventer, Emily E., Shukla, Sachet A., Yizhak, Keren, Ray, John P., Rosebrock, Daniel, Livitz, Dimitri, Adalsteinsson, Viktor, Getz, Gad, Duncan, Lyn M., Li, Bo, Corcoran, Ryan B., Lawrence, Donald P., Stemmer-Rachamimov, Anat, Boland, Genevieve M., Landau, Dan A., Flaherty, Keith T., Sullivan, Ryan J., Hacohen, Nir

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A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer von Polak, Paz, Kim, Jaegil, Braunstein, Lior Z, Karlic, Rosa, Haradhavala, Nicholas J, Tiao, Grace, Rosebrock, Daniel, Livitz, Dimitri, Kübler, Kirsten, Mouw, Kent W, Kamburov, Atanas, Maruvka, Yosef E, Leshchiner, Ignaty, Lander, Eric S, Golub, Todd R, Zick, Aviad, Orthwein, Alexandre, Lawrence, Michael S, Batra, Rajbir N, Caldas, Carlos, Haber, Daniel A, Laird, Peter W, Shen, Hui, Ellisen, Leif W, D'Andrea, Alan D, Chanock, Stephen J, Foulkes, William D, Getz, Gad

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Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma von Gopal, Raj K., Kübler, Kirsten, Calvo, Sarah E., Polak, Paz, Livitz, Dimitri, Rosebrock, Daniel, Sadow, Peter M., Campbell, Braidie, Donovan, Samuel E., Amin, Salma, Gigliotti, Benjamin J., Grabarek, Zenon, Hess, Julian M., Stewart, Chip, Braunstein, Lior Z., Arndt, Peter F., Mordecai, Scott, Shih, Angela R., Chaves, Frances, Zhan, Tiannan, Lubitz, Carrie C., Kim, Jiwoong, Iafrate, A. John, Wirth, Lori, Parangi, Sareh, Leshchiner, Ignaty, Daniels, Gilbert H., Mootha, Vamsi K., Dias-Santagata, Dora, Getz, Gad, McFadden, David G.

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The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy von Landau, Dan A., Sun, Clare, Rosebrock, Daniel, Herman, Sarah E. M., Fein, Joshua, Sivina, Mariela, Underbayev, Chingiz, Liu, Delong, Hoellenriegel, Julia, Ravichandran, Sarangan, Farooqui, Mohammed Z. H., Zhang, Wandi, Cibulskis, Carrie, Zviran, Asaf, Neuberg, Donna S., Livitz, Dimitri, Bozic, Ivana, Leshchiner, Ignaty, Getz, Gad, Burger, Jan A., Wiestner, Adrian, Wu, Catherine J.

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A community effort to create standards for evaluating tumor subclonal reconstruction von Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P’ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter, Boutros, Paul C.

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Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer von Tewari, Alok K., Cheung, Alexander T.M., Crowdis, Jett, Conway, Jake R., Camp, Sabrina Y., Wankowicz, Stephanie A., Livitz, Dimitri G., Park, Jihye, Lis, Rosina T., Bosma-Moody, Alice, He, Meng Xiao, AlDubayan, Saud H., Zhang, Zhenwei, McKay, Rana R., Leshchiner, Ignaty, Brown, Myles, Balk, Steven P., Getz, Gad, Taplin, Mary-Ellen, Van Allen, Eliezer M.

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Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction von Salcedo, Adriana, Tarabichi, Maxime, Buchanan, Alex, Espiritu, Shadrielle M G, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Leshchiner, Ignaty, Anastassiou, Dimitris, Guan, Yuanfang, Jang, Gun Ho, Mootor, Mohammed F E, Haase, Kerstin, Deshwar, Amit G, Zou, William, Umar, Imaad, Dentro, Stefan, Wintersinger, Jeff A, Chiotti, Kami, Demeulemeester, Jonas, Jolly, Clemency, Sycza, Lesia, Ko, Minjeong, Wedge, David C, Morris, Quaid D, Ellrott, Kyle, Van Loo, Peter, Boutros, Paul C

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Author Correction: The evolutionary history of 2,658 cancers von Gerstung, Moritz, Jolly, Clemency, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Rosebrock, Daniel, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vázquez-García, Ignacio, Haase, Kerstin, Jerman, Lara, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Marek, Demeulemeester, Jonas, Schumacher, Steven, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter

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Two-dimensional gas chromatography/mass spectrometry, physical property modeling and automated production of component maps to assess the weathering of pollutants von Antle, Patrick M., Zeigler, Christian D., Livitz, Dimitri G., Robbat, Albert

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Mechanisms of acquired resistance to rapalogs in metastatic renal cell carcinoma von Hamieh, Lana, Choueiri, Toni K, Ogórek, Barbara, Khabibullin, Damir, Rosebrock, Daniel, Livitz, Dimitri, Fay, Andre, Pignon, Jean-Christophe, McDermott, David F, Agarwal, Neeraj, Gao, Wenhua, Signoretti, Sabina, Kwiatkowski, David J

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Framework for quality assessment of whole genome cancer sequences von Whalley, Justin P., Buchhalter, Ivo, Rheinbay, Esther, Raine, Keiran M., Stobbe, Miranda D., Kleinheinz, Kortine, Werner, Johannes, Beltran, Sergi, Gut, Marta, Hübschmann, Daniel, Hutter, Barbara, Livitz, Dimitri, Perry, Marc D., Rosenberg, Mara, Saksena, Gordon, Trotta, Jean-Rémi, Eils, Roland, Gerhard, Daniela S., Campbell, Peter J., Schlesner, Matthias, Gut, Ivo G.

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Insights into Chemically Fueled Supramolecular Polymers von Sharko, Anastasiia, Livitz, Dimitri, De Piccoli, Serena, Bishop, Kyle J. M., Hermans, Thomas M.

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Resolving the phylogenetic origin of glioblastoma via multifocal genomic analysis of pre-treatment and treatment-resistant autopsy specimens von Brastianos, Priscilla K., Nayyar, Naema, Rosebrock, Daniel, Leshchiner, Ignaty, Gill, Corey M., Livitz, Dimitri, Bertalan, Mia S., D’Andrea, Megan, Hoang, Kaitlin, Aquilanti, Elisa, Chukwueke, Ugonma N., Kaneb, Andrew, Chi, Andrew, Plotkin, Scott, Gerstner, Elizabeth R., Frosch, Mathew P., Suva, Mario L., Cahill, Daniel P., Getz, Gad, Batchelor, Tracy T.

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The evolutionary history of 2,658 cancers von Gerstung, Moritz, Jolly, Clemency, Leshchiner, Ignaty, Dentro, Stefan C., Gonzalez, Santiago, Rosebrock, Daniel, Mitchell, Thomas J., Rubanova, Yulia, Anur, Pavana, Yu, Kaixian, Tarabichi, Maxime, Deshwar, Amit, Wintersinger, Jeff, Kleinheinz, Kortine, Vázquez-García, Ignacio, Haase, Kerstin, Jerman, Lara, Sengupta, Subhajit, Macintyre, Geoff, Malikic, Salem, Donmez, Nilgun, Livitz, Dimitri G., Cmero, Marek, Demeulemeester, Jonas, Schumacher, Steven, Fan, Yu, Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Boutros, Paul C., Bowtell, David D., Zhu, Hongtu, Getz, Gad, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter

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Automating Bayesian inference and design to quantify acoustic particle levitation von Dhatt-Gauthier, Kiran, Livitz, Dimitri, Bishop, Kyle J. M.

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Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma von Hruban, Ralph H., Moffitt, Richard A., Gupta, Manaswi, Getz, Gad, Gabriel, Stacey B., Meyerson, Matthew, Laird, Peter W., Loher, Phillipe, Rigoutsos, Isidore, Telonis, Aristeidis G., Mezlini, Aziz M., Hoadley, Katherine A., Murray, Bradley A., Hess, Julian, Zhang, Hailei, Tiao, Grace, Schumacher, Steven E., Noble, Michael S., Gehlenborg, Nils, Lawrence, Michael S., Bowlby, Reanne, Birol, Inanc, Weinstein, John N., Spellman, Paul T., Liu, Yuexin, Paul, Drwiega, Smyrk, Thomas, Gerken, Mark, Lau, Kevin, Renkel, Jeremy, Wise, Lisa, Yena, Peggy, Zmuda, Erik, Shih, Juliann, Balasundaram, Miruna, Chu, Andy, Chuah, Eric, Dhalla, Noreen, Mungall, Andrew J., Thiessen, Nina, Brooks, Denise, Balu, Saianand, Jefferys, Stuart R., Jones, Corbin D., Mose, Lisle E., Shi, Yan, Simons, Janae V., Soloway, Matthew G., Tan, Donghui, Chaffee, Kari, Oberg, Ann, Wheeler, David A., Bartlett, John, Stephen, Yeager, Howard, Zaren, Breggia, Anne, Shroff, Rachna T., Liu, Jia, Lolla, Laxmi, Pihl, Todd, Roggin, Kevin, Becker, Karl-Friedrich, Boice, Lori, Pretti da Cunha Tirapelli, Daniela, Huelsenbeck-Dill, Lori, Jenkins, Roger, Kemp, Rafael, Lyadov, Vladimir, Maithel, Shishir, Manikhas, Georgy, Montgomery, Eric, Noushmehr, Houtan, Owonikoko, Taofeek, Rieger-Christ, Kimberly, Sica, Gabriel, Su, Tao, Sullivan, Travis, Tarvin, Katherine, Urbanski, Stefan, Curley, Erin, Gardner, Johanna, Shelton, Candace, Bathe, Oliver, Hibshoosh, Hanina, Radenbaugh, Amie, Berrios, Mario, Bootwalla, Moiz S., Maglinte, Dennis T., Triche, Timothy J., Weisenberger, Daniel J., Kucherlapati, Melanie, Meier, Sam, Tempero, Margaret, Bailey, Peter, Gill, Anthony, Kench, James, Demchok, John A., Ferguson, Martin L., Tarnuzzer, Roy, Wang, Zhining

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Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes von Chapuy, Bjoern, Stewart, Chip, Dunford, Andrew J., Kim, Jaegil, Kamburov, Atanas, Redd, Robert A., Lawrence, Mike S., Roemer, Margaretha G. M., Li, Amy J., Ziepert, Marita, Staiger, Annette M., Wala, Jeremiah A., Ducar, Matthew D., Leshchiner, Ignaty, Rheinbay, Ester, Taylor-Weiner, Amaro, Coughlin, Caroline A., Hess, Julian M., Pedamallu, Chandra S., Livitz, Dimitri, Rosebrock, Daniel, Rosenberg, Mara, Tracy, Adam A., Horn, Heike, van Hummelen, Paul, Feldman, Andrew L., Link, Brian K., Novak, Anne J., Cerhan, James R., Habermann, Thomas M., Siebert, Reiner, Rosenwald, Andreas, Thorner, Aaron R., Meyerson, Matthew L., Golub, Todd R., Beroukhim, Rameen, Wulf, Gerald G., Ott, German, Rodig, Scott J., Monti, Stefano, Neuberg, Donna S., Loeffler, Markus, Pfreundschuh, Michael, Trümper, Lorenz, Getz, Gad, Shipp, Margaret A.

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Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies von Guièze, Romain, Liu, Vivian M., Rosebrock, Daniel, Jourdain, Alexis A., Hernández-Sánchez, María, Martinez Zurita, Aina, Sun, Jing, Ten Hacken, Elisa, Baranowski, Kaitlyn, Thompson, Philip A., Heo, Jin-Mi, Cartun, Zachary, Aygün, Ozan, Iorgulescu, J. Bryan, Zhang, Wandi, Notarangelo, Giulia, Livitz, Dimitri, Li, Shuqiang, Davids, Matthew S., Biran, Anat, Fernandes, Stacey M., Brown, Jennifer R., Lako, Ana, Ciantra, Zoe B., Lawlor, Matthew A., Keskin, Derin B., Udeshi, Namrata D., Wierda, William G., Livak, Kenneth J., Letai, Anthony G., Neuberg, Donna, Harper, J. Wade, Carr, Steven A., Piccioni, Federica, Ott, Christopher J., Leshchiner, Ignaty, Johannessen, Cory M., Doench, John, Mootha, Vamsi K., Getz, Gad, Wu, Catherine J.

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