Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing by Helman, Elena, Lawrence, Michael S., Stewart, Chip, Sougnez, Carrie, Getz, Gad, Meyerson, Matthew L.

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Copy Number Variation detection from 1000 Genomes project exon capture sequencing data by Wu Jiantao, Grzeda Krzysztof R, Stewart Chip, Grubert Fabian, Urban Alexander E, Snyder Michael P, Marth Gabor T

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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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Expression divergence measured by transcriptome sequencing of four yeast species by Busby Michele A, Gray Jesse M, Costa Allen M, Stewart Chip, Stromberg Michael P, Barnett Derek, Chuang Jeffrey H, Springer Michael, Marth Gabor T

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Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation by Costello, Maura, Pugh, Trevor J., Fennell, Timothy, Stewart, Chip, Lichtenstein, Lee, Meldrim, James C., Fostel, Jennifer L., Friedrich, Dennis C., Perrin, Danielle, Dionne, Danielle, Kim, Sharon, Gabriel, Stacey B., Fisher, Sheila, Getz, Gad, Lander, Eric Steven

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Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing by Taylor-Weiner, Amaro, Stewart, Chip, Carter, Scott L., Cibulskis, Kristian, McKenna, Aaron, Dooley, Alison, Sougnez, Carrie, Park, Jennifer, Farago, Anna F., Dayton, Talya, Shefler, Erica, Gabriel, Stacey, Getz, Gad, McFadden, David Glenn, Papagiannakopoulos, Thales, Bhutkar, Arjun, Vernon, Amanda, Malstrom, Scott E., Heimann, Megan Kristianne, Parker, Jennifer E., Chen, Frances K., Jacks, Tyler E.

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Paired exome analysis of Barrett's esophagus and adenocarcinoma by Stachler, Matthew D, Taylor-Weiner, Amaro, Peng, Shouyong, McKenna, Aaron, Agoston, Agoston T, Odze, Robert D, Davison, Jon M, Nason, Katie S, Loda, Massimo, Leshchiner, Ignaty, Stewart, Chip, Stojanov, Petar, Seepo, Sara, Lawrence, Michael S, Ferrer-Torres, Daysha, Lin, Jules, Chang, Andrew C, Gabriel, Stacey B, Beer, David G, Getz, Gad, Carter, Scott L, Bass, Adam J, Lander, Eric Steven

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Paired exome analysis of Barrett's esophagus and adenocarcinoma by Stachler, Matthew D, Taylor-Weiner, Amaro, Peng, Shouyong, McKenna, Aaron, Agoston, Agoston T, Odze, Robert D, Davison, Jon M, Nason, Katie S, Loda, Massimo, Leshchiner, Ignaty, Stewart, Chip, Stojanov, Petar, Seepo, Sara, Lawrence, Michael S, Ferrer-Torres, Daysha, Lin, Jules, Chang, Andrew C, Gabriel, Stacey B, Beer, David G, Getz, Gad, Carter, Scott L, Bass, Adam J, Lander, Eric Steven

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Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia by Landau, Dan A., Carter, Scott L., Stojanov, Petar, McKenna, Aaron, Stevenson, Kristen, Lawrence, Michael S., Sougnez, Carrie, Stewart, Chip, Sivachenko, Andrey, Wang, Lili, Wan, Youzhong, Zhang, Wandi, Shukla, Sachet A., Vartanov, Alexander, Fernandes, Stacey M., Saksena, Gordon, Cibulskis, Kristian, Tesar, Bethany, Gabriel, Stacey B., Hacohen, Nir, Meyerson, Matthew L., Neuberg, Donna S., Brown, Jennifer R., Getz, Gad, Wu, Catherine J., Lander, Eric Steven

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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma by Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A., Lander, Eric Steven

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Recurrent and functional regulatory mutations in breast cancer by Parasuraman, Prasanna, Tiao, Grace, Kim, Jaegil, Taylor-Weiner, Amaro, Rodriguez-Cuevas, Sergio, Rosenberg, Mara, Hess, Julian, Stewart, Chip, Maruvka, Yosef E., Stojanov, Petar, Seepo, Sara, Cibulskis, Carrie, Tracy, Adam, Pugh, Trevor J., Lee, Jesse, Zheng, Zongli, Ellisen, Leif W., Iafrate, A. John, Boehm, Jesse S., Baselga, Jose, Hidalgo-Miranda, Alfredo, Shioda, Toshi, Bernards, Andre, Engreitz, Jesse Michael, Lander, Eric Steven, Rheinbay, Esther, Lawrence, Michael, Cortes, Maria, Gabriel, Stacey, Golub, Todd, Getz, Gad Asher, Meyerson, Matthew L.

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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors by Ha, Gavin, Freeman, Samuel S., Choudhury, Atish D., Stover, Daniel G., Parsons, Heather A., Gydush, Gregory, Reed, Sarah C., Rotem, Denisse, Rhoades, Justin, Livitz, Dimitri, Rosebrock, Daniel, Leshchiner, Ignaty, Kim, Jaegil, Stewart, Chip, Rosenberg, Mara, Francis, Joshua M., Zhang, Cheng-Zhong, Cohen, Ofir, Oh, Coyin, Polak, Paz, Lloyd, Max, Mahmud, Sairah, Helvie, Karla, Merrill, Margaret S., Santiago, Rebecca A., O’Connor, Edward P., Jeong, Seong H., 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, Meyerson, Matthew, Adalsteinsson, Viktor A., Loginov, Denis, Ding, Huiming, Leeson, Rachel, Barry, Rachel M, Love, John C

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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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The Molecular Taxonomy of Primary Prostate Cancer by Abeshouse, Adam, Ahn, Jaeil, Akbani, Rehan, Ally, Adrian, Amin, Samirkumar, Andry, Christopher D., Annala, Matti, Aprikian, Armen, Armenia, Joshua, Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barbieri, Christopher E., Bauer, Thomas, Benz, Christopher C., Bergeron, Alain, Beroukhim, Rameen, Berrios, Mario, Bivol, Adrian, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., dos Reis, Rodolfo Borges, Boutros, Paul C., Bowen, Jay, Bowlby, Reanne, Boyd, Jeffrey, Breggia, Anne, Brimo, Fadi, Brooks, Denise, Broom, Bradley M., Bryce, Alan H., Bubley, Glenn, Burks, Eric, Butterfield, Yaron S.N., Button, Michael, Canes, David, Carlotti, Carlos G., Carlsen, Rebecca, Carroll, Peter R., Cartun, Richard, Carver, Brett S., Chan, June M., Chang, Matthew T., Chen, Yu, Costello, Anthony J., Cherniack, Andrew D., Chevalier, Simone, Cho, Juok, Chu, Andy, Chuah, Eric, Chudamani, Sudha, Ciriello, Giovanni, Clarke, Amanda, Cooperberg, Matthew R., Corcoran, Niall M., Cowan, Janet, Crain, Daniel, Curley, Erin, David, Kerstin, Demchok, John A., Demichelis, Francesca, Dhalla, Noreen, Dhir, Rajiv, Doueik, Alexandre, Drake, Bettina, Dvinge, Heidi, Dyakova, Natalya, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Freedland, Stephen, Fu, Yao, Bristow, Christopher A., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gerstein, Mark B., Godwin, Andrew K., Gopalan, Anuradha, Graefen, Markus, Graim, Kiley, Gribbin, Thomas, Guin, Ranabir, Gupta, Manaswi, Hadjipanayis, Angela, Haider, Syed, Hamel, Lucie, Hayes, D. Neil, Hess, Julian, Hoadley, Katherine A., Holbrook, Andrea H., Holt, Robert A., Holway, Antonia, Hovens, Christopher M., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Juhl, Hartmut, Kahles, Andre, Kane, Christopher J., Kasaian, Katayoon, Kerger, Michael, Khurana, Ekta, Kim, Jaegil, Klein, Robert J., Kucherlapati, Raju, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Latour, Mathieu, Lawrence, Michael S., Lau, Kevin, LeBien, Tucker, Lee, Darlene, Lee, Semin, Lehmann, Kjong-Van, Leraas, Kristen M., Leshchiner, Ignaty, Leung, Robert, Libertino, John A., Lichtenberg, Tara M., Linehan, W. Marston, Ling, Shiyun, Lippman, Scott M., Liu, Jia, Liu, Wenbin, Lochovsky, Lucas, Logothetis, Christopher, Lolla, Laxmi, Longacre, Teri, Lu, Yiling, Luo, Jianhua, Ma, Yussanne, Mahadeshwar, Harshad S., Mallery, David, Mariamidze, Armaz, Marra, Marco A., Mayo, Michael, McCall, Shannon, McKercher, Ginette, Meng, Shaowu, Mes-Masson, Anne-Marie, Merino, Maria J., Mieczkowski, Piotr A., Mills, Gordon B., Mills Shaw, Kenna R., Minner, Sarah, Moinzadeh, Alireza, Moore, Richard A., Morris, Scott, Morrison, Carl, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Myers, Jerome B., Naresh, Rashi, Nelson, Joel, Nelson, Mark A., Nelson, Peter S., Newton, Yulia, Noble, Michael S., Noushmehr, Houtan, Nykter, Matti, Pantazi, Angeliki, Parfenov, Michael, Parker, Joel S., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Piche, Alain, Pihl, Todd, Pinto, Peter A., Prandi, Davide, Protopopov, Alexei, Ramirez, Nilsa C., Rao, Arvind, Rathmell, W. Kimryn, Ratsch, Gunnar, Ren, Xiaojia, Reuter, Victor E., Reynolds, Sheila M., Rhie, Suhn K., Rieger-Christ, Kimberly, Roach, Jeffrey, Robertson, A. Gordon, Robinson, Brian, Rubin, Mark A., Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Sandusky, George, Sauter, Guido, Sboner, Andrea, Scardino, Peter T., Scarlata, Eleonora, Schein, Jacqueline E., Schlomm, Thorsten, Schmidt, Laura S., Schultz, Nikolaus, Schumacher, Steven E., Neder, Luciano, Seth, Sahil, Sharp, Alexis, Shelton, Candace, Shelton, Troy, Shen, Hui, Shen, Ronglai, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simko, Jeffry, Simon, Ronald, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sorcini, Andrea, Stepa, Serghei, Stewart, Chip, Stewart, John, Stuart, Joshua M., Sullivan, Travis B., Sun, Charlie, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Taylor, Barry S., Teebagy, Patrick, Tenggara, Imelda, Tetu, Bernard, Tewari, Ashutosh, Thiessen, Nina, Thompson, Timothy, Thorne, Leigh B., Tirapelli, Daniela P., Tomlins, Scott A., Trevisan, Felipe Amstalden, Troncoso, Patricia, True, Lawrence D., Tsourlakis, Maria Christina, Tyekucheva, Svitlana, Van Allen, Eliezer, Van Den Berg, David J., Veluvolu, Umadevi, Vocke, Cathy D., Wan, Yunhu, Wang, Qingguo, Wang, Wenyi, Wang, Zhining, Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wise, Lisa, Witte, John, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xu, Andrew W., Yadav, Shalini S., Yang, Liming, Yang, Lixing, Yau, Christina, Ye, Huihui, Yena, Peggy, Zeng, Thomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan, Zhang, Wei, Zhong, Yi, Zhu, Kelsey, Zmuda, Erik, Cancer Genome Atlas Research Network, Carmell, Michelle, Carter, Scott, Chin, Lynda, Cibulskis, Kristian, Getz, Gad Asher, Heiman, David, Lander, Eric Steven, Lin, Pei, Loda, Massimo, Seidman, Jonathan, Sougnez, Carrie L, Verhaak, Roel, Voet, Douglas, Bradley, Robert K., Meyerson, Matthew L., Park, Peter J.

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