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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Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis von Udler, Miriam S, Kim, Jaegil, von Grotthuss, Marcin, Bonàs-Guarch, Sílvia, Cole, Joanne B, Chiou, Joshua, Boehnke, Michael, Laakso, Markku, Atzmon, Gil, Glaser, Benjamin, Mercader, Josep M, Gaulton, Kyle, Flannick, Jason, Getz, Gad, Florez, Jose C

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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas von Campbell, Joshua D, Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H, Pedamallu, Chandra Sekhar, Shukla, Sachet A, Guo, Guangwu, Brooks, Angela N, Murray, Bradley A, Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A, Kwiatkowski, David J, Lawrence, Michael S, Weinstein, John N, Verhaak, Roel G W, Wu, Catherine J, Hammerman, Peter S, Cherniack, Andrew D, Getz, Gad, Artyomov, Maxim N, Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew

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Scaling computational genomics to millions of individuals with GPUs von Taylor-Weiner, Amaro, Aguet, François, Haradhvala, Nicholas J, Gosai, Sager, Anand, Shankara, Kim, Jaegil, Ardlie, Kristin, Van Allen, Eliezer M, Getz, Gad

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A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma von Nassar, Amin H., Mouw, Kent W., Jegede, Opeyemi, Shinagare, Atul B., Kim, Jaegil, Liu, Chia-Jen, Pomerantz, Mark, Harshman, Lauren C., Van Allen, Eliezer M., Wei, Xiao X., McGregor, Bradley, Choudhury, Atish D., Preston, Mark A., Dong, Fei, Signoretti, Sabina, Lindeman, Neal I., Bellmunt, Joaquim, Choueiri, Toni K., Sonpavde, Guru, Kwiatkowski, David J.

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Mutational processes shape the landscape of TP53 mutations in human cancer von Giacomelli, Andrew O., Yang, Xiaoping, Lintner, Robert E., McFarland, James M., Duby, Marc, Kim, Jaegil, Howard, Thomas P., Takeda, David Y., Ly, Seav Huong, Kim, Eejung, Gannon, Hugh S., Hurhula, Brian, Sharpe, Ted, Goodale, Amy, Fritchman, Briana, Steelman, Scott, Vazquez, Francisca, Tsherniak, Aviad, Aguirre, Andrew J., Doench, John G., Piccioni, Federica, Roberts, Charles W. M., Meyerson, Matthew, Getz, Gad, Johannessen, Cory M., Root, David E., Hahn, William C.

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Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations von Wardell, Christopher P., Fujita, Masashi, Yamada, Toru, Simbolo, Michele, Fassan, Matteo, Karlic, Rosa, Polak, Paz, Kim, Jaegil, Hatanaka, Yutaka, Maejima, Kazuhiro, Lawlor, Rita T., Nakanishi, Yoshitsugu, Mitsuhashi, Tomoko, Fujimoto, Akihiro, Furuta, Mayuko, Ruzzenente, Andrea, Conci, Simone, Oosawa, Ayako, Sasaki-Oku, Aya, Nakano, Kaoru, Tanaka, Hiroko, Yamamoto, Yujiro, Michiaki, Kubo, Kawakami, Yoshiiku, Aikata, Hiroshi, Ueno, Masaki, Hayami, Shinya, Gotoh, Kunihito, Ariizumi, Shun-ichi, Yamamoto, Masakazu, Yamaue, Hiroki, Chayama, Kazuaki, Miyano, Satoru, Getz, Gad, Scarpa, Aldo, Hirano, Satoshi, Nakamura, Toru, Nakagawa, Hidewaki

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An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers von Chan, Kin, Roberts, Steven A, Klimczak, Leszek J, Sterling, Joan F, Saini, Natalie, Malc, Ewa P, Kim, Jaegil, Kwiatkowski, David J, Fargo, David C, Mieczkowski, Piotr A, Getz, Gad, Gordenin, Dmitry A

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

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Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites von Nassar, Amin H, Umeton, Renato, Kim, Jaegil, Lundgren, Kevin, Harshman, Lauren, Van Allen, Eliezer M, Preston, Mark, Dong, Fei, Bellmunt, Joaquim, Mouw, Kent W, Choueiri, Toni K, Sonpavde, Guru, Kwiatkowski, David J

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Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair von Haradhvala, Nicholas J., Polak, Paz, Stojanov, Petar, Covington, Kyle R., Shinbrot, Eve, Hess, Julian M., Rheinbay, Esther, Kim, Jaegil, Maruvka, Yosef E., Braunstein, Lior Z., Kamburov, Atanas, Hanawalt, Philip C., Wheeler, David A., Koren, Amnon, Lawrence, Michael S., Getz, Gad

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Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types von Kaiser, Vera B, Taylor, Martin S, Semple, Colin A

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Invasive Bladder Cancer: Genomic Insights and Therapeutic Promise von Kim, Jaegil, Akbani, Rehan, Creighton, Chad J, Lerner, Seth P, Weinstein, John N, Getz, Gad, Kwiatkowski, David J

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Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients von YOUNGWOOK KIM, HAMMERMAN, Peter S, LAWRENCE, Michael S, STOJANOV, Petar, CARTER, Scott L, McKENNA, Aaron, STEWART, Chip, SIVACHENKO, Andrey Y, OH, In-Jae, HONG KWAN KIM, YONG SOO CHOI, KWHANMIEN KIM, JAEGIL KIM, YOUNG MOG SHIM, KIM, Kyu-Sik, SONG, Sang-Yun, NA, Kook-Joo, CHOI, Yoon-La, HAYES, D. Neil, JHINGOOK KIM, SUKKI CHO, KIM, Young-Chul, JIN SEOK AHN, YOON, Ji-Ae, AHN, Myung-Ju, GETZ, Gad, MEYERSON, Matthew, KEUNCHIL PARK, YOOMI LEE, SUN, Jong-Mu, WILKERSON, Matthew D, CHANDRA SEKHAR PEDAMALLU, CIBULSKIS, Kristian, YEONG KYUNG YOO

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Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma von Mouw, Kent W, Cleary, James M, Reardon, Brendan, Pike, Jonathan, Braunstein, Lior Z, Kim, Jaegil, Amin-Mansour, Ali, Miao, Diana, Damish, Alexis, Chin, Joanna, Ott, Patrick A, Fuchs, Charles S, Martin, Neil E, Getz, Gad, Carter, Scott, Mamon, Harvey J, Hornick, Jason L, Van Allen, Eliezer M, D'Andrea, Alan D

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Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer von Liu, David, Abbosh, Philip, Keliher, Daniel, Reardon, Brendan, Miao, Diana, Mouw, Kent, Weiner-Taylor, Amaro, Wankowicz, Stephanie, Han, Garam, Teo, Min Yuen, Cipolla, Catharine, Kim, Jaegil, Iyer, Gopa, Al-Ahmadie, Hikmat, Dulaimi, Essel, Chen, David Y. T., Alpaugh, R. Katherine, Hoffman-Censits, Jean, Garraway, Levi A., Getz, Gad, Carter, Scott L., Bellmunt, Joaquim, Plimack, Elizabeth R., Rosenberg, Jonathan E., Van Allen, Eliezer M.

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Generalized Replica Exchange Method von Kim, Jaegil, Keyes, Thomas, Straub, John E.

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SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma von Sakthikumar, Sharadha, Elvers, Ingegerd, Kim, Jaegil, Arendt, Maja L, Thomas, Rachael, Turner-Maier, Jason, Swofford, Ross, Johnson, Jeremy, Schumacher, Steven E, Alföldi, Jessica, Axelsson, Erik, Couto, C Guillermo, Kisseberth, William C, Pettersson, Mats E, Getz, Gad, Meadows, Jennifer R S, Modiano, Jaime F, Breen, Matthew, Kierczak, Marcin, Forsberg-Nilsson, Karin, Marinescu, Voichita D, Lindblad-Toh, Kerstin

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KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors von Black, Joshua C., Manning, Amity L., Van Rechem, Capucine, Kim, Jaegil, Ladd, Brendon, Cho, Juok, Pineda, Cristiana M., Murphy, Nancy, Daniels, Danette L., Montagna, Cristina, Lewis, Peter W., Glass, Kimberly, Allis, C. David, Dyson, Nicholas J., Getz, Gad, Whetstine, Johnathan R.

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