From human genome to cancer genome: the first decade von Wheeler, David A, Wang, Linghua

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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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Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas von Donehower, Lawrence A., Soussi, Thierry, Korkut, Anil, Liu, Yuexin, Schultz, Andre, Cardenas, Maria, Li, Xubin, Babur, Ozgun, Hsu, Teng-Kuei, Lichtarge, Olivier, Weinstein, John N., Akbani, Rehan, Wheeler, David A.

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MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data von Fan, Yu, Xi, Liu, Hughes, Daniel S T, Zhang, Jianjun, Zhang, Jianhua, Futreal, P Andrew, Wheeler, David A, Wang, Wenyi

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Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon von Jaksik, Roman, Wheeler, David A, Kimmel, Marek

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Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed von Hicks, Stephanie, Wheeler, David A., Plon, Sharon E., Kimmel, Marek

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Genetic Mechanisms of Immune Evasion in Colorectal Cancer von Grasso, Catherine S, Giannakis, Marios, Wells, Daniel K, Hamada, Tsuyoshi, Mu, Xinmeng Jasmine, Quist, Michael, Nowak, Jonathan A, Nishihara, Reiko, Qian, Zhi Rong, Inamura, Kentaro, Morikawa, Teppei, Nosho, Katsuhiko, Abril-Rodriguez, Gabriel, Connolly, Charles, Escuin-Ordinas, Helena, Geybels, Milan S, Grady, William M, Hsu, Li, Hu-Lieskovan, Siwen, Huyghe, Jeroen R, Kim, Yeon Joo, Krystofinski, Paige, Leiserson, Mark D M, Montoya, Dennis J, Nadel, Brian B, Pellegrini, Matteo, Pritchard, Colin C, Puig-Saus, Cristina, Quist, Elleanor H, Raphael, Ben J, Salipante, Stephen J, Shin, Daniel Sanghoon, Shinbrot, Eve, Shirts, Brian, Shukla, Sachet, Stanford, Janet L, Sun, Wei, Tsoi, Jennifer, Upfill-Brown, Alexander, Wheeler, David A, Wu, Catherine J, Yu, Ming, Zaidi, Syed H, Zaretsky, Jesse M, Gabriel, Stacey B, Lander, Eric S, Garraway, Levi A, Hudson, Thomas J, Fuchs, Charles S, Ribas, Antoni, Ogino, Shuji, Peters, Ulrike

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Landscape of Somatic Retrotransposition in Human Cancers von Lee, Eunjung, Iskow, Rebecca, Yang, Lixing, Gokcumen, Omer, Haseley, Psalm, Luquette, Lovelace J., Lohr, Jens G., Harris, Christopher C., Ding, Li, Wilson, Richard K., Wheeler, David A., Gibbs, Richard A., Kucherlapati, Raju, Lee, Charles, Kharchenko, Peter V., Park, Peter J.

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Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma von Moss, Tyler J, Qi, Yuan, Xi, Liu, Peng, Bo, Kim, Tae-Beom, Ezzedine, Nader E, Mosqueda, Maribel E, Guo, Charles C, Czerniak, Bogdan A, Ittmann, Michael, Wheeler, David A, Lerner, Seth P, Matin, Surena F

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Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors von Patel, Akash J., Wan, Ying-Wooi, Al-Ouran, Rami, Revelli, Jean-Pierre, Cardenas, Maria F., Oneissi, Mazen, Xi, Liu, Jalali, Ali, Magnotti, John F., Muzny, Donna M., Doddapaneni, HarshaVardhan, Sebastian, Sherly, Heck, Kent A., Goodman, J. Clay, Gopinath, Shankar P., Liu, Zhandong, Rao, Ganesh, Plon, Sharon E., Yoshor, Daniel, Wheeler, David A., Zoghbi, Huda Y., Klisch, Tiemo J.

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Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing von Newman, Scott, Nakitandwe, Joy, Kesserwan, Chimene A., Azzato, Elizabeth M., Wheeler, David A., Rusch, Michael, Shurtleff, Sheila, Hedges, Dale J., Hamilton, Kayla, Foy, Scott G., Edmonson, Michael N., Thrasher, Andrew, Bahrami, Armita, Orr, Brent A., Klco, Jeffery M., Gu, Jiali, Harrison, Lynn W., Wang, Lu, Clay, Michael R., Ouma, Annastasia, Silkov, Antonina, Liu, Yanling, Zhang, Zhaojie, Liu, Yu, Brady, Samuel W., Zhou, Xin, Chang, Ti-Cheng, Pande, Manjusha, Davis, Eric, Becksfort, Jared, Patel, Aman, Wilkinson, Mark R., Rahbarinia, Delaram, Kubal, Manish, Maciaszek, Jamie L., Pastor, Victor, Knight, Jay, Gout, Alexander M., Wang, Jian, Gu, Zhaohui, Mullighan, Charles G., McGee, Rose B., Quinn, Emily A., Nuccio, Regina, Mostafavi, Roya, Gerhardt, Elsie L., Taylor, Leslie M., Valdez, Jessica M., Hines-Dowell, Stacy J., Pappo, Alberto S., Robinson, Giles, Johnson, Liza-Marie, Pui, Ching-Hon, Ellison, David W., Downing, James R., Zhang, Jinghui, Nichols, Kim E.

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Mutational landscape of aggressive cutaneous squamous cell carcinoma von Pickering, Curtis R, Zhou, Jane H, Lee, J Jack, Drummond, Jennifer A, Peng, S Andrew, Saade, Rami E, Tsai, Kenneth Y, Curry, Jonathan L, Tetzlaff, Michael T, Lai, Stephen Y, Yu, Jun, Muzny, Donna M, Doddapaneni, Harshavardhan, Shinbrot, Eve, Covington, Kyle R, Zhang, Jianhua, Seth, Sahil, Caulin, Carlos, Clayman, Gary L, El-Naggar, Adel K, Gibbs, Richard A, Weber, Randal S, Myers, Jeffrey N, Wheeler, David A, Frederick, Mitchell J

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Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication von Shinbrot, Eve, Henninger, Erin E, Weinhold, Nils, Covington, Kyle R, Göksenin, A Yasemin, Schultz, Nikolaus, Chao, Hsu, Doddapaneni, HarshaVardhan, Muzny, Donna M, Gibbs, Richard A, Sander, Chris, Pursell, Zachary F, Wheeler, David A

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Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups von Sumazin, Pavel, Chen, Yidong, Treviño, Lisa R., Sarabia, Stephen F., Hampton, Oliver A., Patel, Kayuri, Mistretta, Toni‐Ann, Zorman, Barry, Thompson, Patrick, Heczey, Andras, Comerford, Sarah, Wheeler, David A., Chintagumpala, Murali, Meyers, Rebecka, Rakheja, Dinesh, Finegold, Milton J., Tomlinson, Gail, Parsons, D. Williams, López‐Terrada, Dolores

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Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis von Chakraborty, Rikhia, Hampton, Oliver A., Shen, Xiaoyun, Simko, Stephen J., Shih, Albert, Abhyankar, Harshal, Lim, Karen Phaik Har, Covington, Kyle R., Trevino, Lisa, Dewal, Ninad, Muzny, Donna M., Doddapaneni, Harshavardhan, Hu, Jianhong, Wang, Linghua, Lupo, Philip J., Hicks, M. John, Bonilla, Diana L., Dwyer, Karen C., Berres, Marie-Luise, Poulikakos, Poulikos I., Merad, Miriam, McClain, Kenneth L., Wheeler, David A., Allen, Carl E., Parsons, D. Williams

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Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design von Rokita, Jo Lynne, Rathi, Komal S., Cardenas, Maria F., Upton, Kristen A., Jayaseelan, Joy, Cross, Katherine L., Pfeil, Jacob, Egolf, Laura E., Way, Gregory P., Farrel, Alvin, Kendsersky, Nathan M., Patel, Khushbu, Gaonkar, Krutika S., Modi, Apexa, Berko, Esther R., Lopez, Gonzalo, Vaksman, Zalman, Mayoh, Chelsea, Nance, Jonas, McCoy, Kristyn, Haber, Michelle, Evans, Kathryn, McCalmont, Hannah, Bendak, Katerina, Böhm, Julia W., Marshall, Glenn M., Tyrrell, Vanessa, Kalletla, Karthik, Braun, Frank K., Qi, Lin, Du, Yunchen, Zhang, Huiyuan, Lindsay, Holly B., Zhao, Sibo, Shu, Jack, Baxter, Patricia, Morton, Christopher, Kurmashev, Dias, Zheng, Siyuan, Chen, Yidong, Bowen, Jay, Bryan, Anthony C., Leraas, Kristen M., Coppens, Sara E., Doddapaneni, HarshaVardhan, Momin, Zeineen, Zhang, Wendong, Sacks, Gregory I., Hart, Lori S., Krytska, Kateryna, Mosse, Yael P., Gatto, Gregory J., Sanchez, Yolanda, Greene, Casey S., Diskin, Sharon J., Vaske, Olena Morozova, Haussler, David, Gastier-Foster, Julie M., Kolb, E. Anders, Gorlick, Richard, Li, Xiao-Nan, Reynolds, C. Patrick, Kurmasheva, Raushan T., Houghton, Peter J., Smith, Malcolm A., Lock, Richard B., Raman, Pichai, Wheeler, David A., Maris, John M.

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Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis von Chakraborty, Rikhia, Burke, Thomas M., Hampton, Oliver A., Zinn, Daniel J., Lim, Karen Phaik Har, Abhyankar, Harshal, Scull, Brooks, Kumar, Vijetha, Kakkar, Nipun, Wheeler, David A., Roy, Angshumoy, Poulikakos, Poulikos I., Merad, Miriam, McClain, Kenneth L., Parsons, D. Williams, Allen, Carl E.

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RNAseqCNV: analysis of large-scale copy number variations from RNA-seq data von Bařinka, Jan, Hu, Zunsong, Wang, Lu, Wheeler, David A., Rahbarinia, Delaram, McLeod, Clay, Gu, Zhaohui, Mullighan, Charles G.

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Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma von Chen, Fengju, Zhang, Yiqun, Şenbabaoğlu, Yasin, Ciriello, Giovanni, Yang, Lixing, Reznik, Ed, Shuch, Brian, Micevic, Goran, De Velasco, Guillermo, Shinbrot, Eve, Noble, Michael S., Lu, Yiling, Covington, Kyle R., Xi, Liu, Drummond, Jennifer A., Muzny, Donna, Kang, Hyojin, Lee, Junehawk, Tamboli, Pheroze, Reuter, Victor, Shelley, Carl Simon, Kaipparettu, Benny A., Bottaro, Donald P., Godwin, Andrew K., Gibbs, Richard A., Getz, Gad, Kucherlapati, Raju, Park, Peter J., Sander, Chris, Henske, Elizabeth P., Zhou, Jane H., Kwiatkowski, David J., Ho, Thai H., Choueiri, Toni K., Hsieh, James J., Akbani, Rehan, Mills, Gordon B., Hakimi, A. Ari, Wheeler, David A., Creighton, Chad J.

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Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas von Donehower, Lawrence A., Soussi, Thierry, Korkut, Anil, Liu, Yuexin, Schultz, Andre, Cardenas, Maria, Li, Xubin, Babur, Ozgun, Hsu, Teng-Kuei, Lichtarge, Olivier, Weinstein, John N., Akbani, Rehan, Wheeler, David A.

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