MSIsensor: microsatellite instability detection using paired tumor-normal sequence data von Niu, Beifang, Ye, Kai, Zhang, Qunyuan, Lu, Charles, Xie, Mingchao, McLellan, Michael D, Wendl, Michael C, Ding, Li

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VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing von Koboldt, Daniel C, Zhang, Qunyuan, Larson, David E, Shen, Dong, McLellan, Michael D, Lin, Ling, Miller, Christopher A, Mardis, Elaine R, Ding, Li, Wilson, Richard K

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Mutational landscape and significance across 12 major cancer types von Kandoth, Cyriac, McLellan, Michael D., Vandin, Fabio, Ye, Kai, Niu, Beifang, Lu, Charles, Xie, Mingchao, Zhang, Qunyuan, McMichael, Joshua F., Wyczalkowski, Matthew A., Leiserson, Mark D. M., Miller, Christopher A., Welch, John S., Walter, Matthew J., Wendl, Michael C., Ley, Timothy J., Wilson, Richard K., Raphael, Benjamin J., Ding, Li

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples von Koboldt, Daniel C., Chen, Ken, Wylie, Todd, Larson, David E., McLellan, Michael D., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Ding, Li

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Clonal Architecture of Secondary Acute Myeloid Leukemia von Walter, Matthew J, Shen, Dong, Ding, Li, Shao, Jin, Koboldt, Daniel C, Chen, Ken, Larson, David E, McLellan, Michael D, Dooling, David, Abbott, Rachel, Fulton, Robert, Magrini, Vincent, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Fan, Xian, Grillot, Marcus, Witowski, Sarah, Heath, Sharon, Frater, John L, Eades, William, Tomasson, Michael, Westervelt, Peter, DiPersio, John F, Link, Daniel C, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Graubert, Timothy A

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Age-related mutations associated with clonal hematopoietic expansion and malignancies von Xie, Mingchao, Lu, Charles, Wang, Jiayin, McLellan, Michael D, Johnson, Kimberly J, Wendl, Michael C, McMichael, Joshua F, Schmidt, Heather K, Yellapantula, Venkata, Miller, Christopher A, Ozenberger, Bradley A, Welch, John S, Link, Daniel C, Walter, Matthew J, Mardis, Elaine R, Dipersio, John F, Chen, Feng, Wilson, Richard K, Ley, Timothy J, Ding, Li

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Proteogenomics connects somatic mutations to signalling in breast cancer von Mertins, Philipp, Mani, D. R., Ruggles, Kelly V., Gillette, Michael A., Clauser, Karl R., Wang, Pei, Wang, Xianlong, Qiao, Jana W., Cao, Song, Petralia, Francesca, Kawaler, Emily, Mundt, Filip, Krug, Karsten, Tu, Zhidong, Lei, Jonathan T., Gatza, Michael L., Wilkerson, Matthew, Perou, Charles M., Yellapantula, Venkata, Huang, Kuan-lin, Lin, Chenwei, McLellan, Michael D., Yan, Ping, Davies, Sherri R., Townsend, R. Reid, Skates, Steven J., Wang, Jing, Zhang, Bing, Kinsinger, Christopher R., Mesri, Mehdi, Rodriguez, Henry, Ding, Li, Paulovich, Amanda G., Fenyö, David, Ellis, Matthew J., Carr, Steven A.

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Protein-structure-guided discovery of functional mutations across 19 cancer types von Niu, Beifang, Scott, Adam D, Sengupta, Sohini, Bailey, Matthew H, Batra, Prag, Ning, Jie, Wyczalkowski, Matthew A, Liang, Wen-Wei, Zhang, Qunyuan, McLellan, Michael D, Sun, Sam Q, Tripathi, Piyush, Lou, Carolyn, Ye, Kai, Mashl, R Jay, Wallis, John, Wendl, Michael C, Chen, Feng, Ding, Li

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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation von Chen, Ken, Wallis, John W, McLellan, Michael D, Larson, David E, Kalicki, Joelle M, Pohl, Craig S, McGrath, Sean D, Wendl, Michael C, Zhang, Qunyuan, Locke, Devin P, Shi, Xiaoqi, Fulton, Robert S, Ley, Timothy J, Wilson, Richard K, Ding, Li, Mardis, Elaine R

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Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes von Leiserson, Mark D M, Vandin, Fabio, Wu, Hsin-Ta, Dobson, Jason R, Eldridge, Jonathan V, Thomas, Jacob L, Papoutsaki, Alexandra, Kim, Younhun, Niu, Beifang, McLellan, Michael, Lawrence, Michael S, Gonzalez-Perez, Abel, Tamborero, David, Cheng, Yuwei, Ryslik, Gregory A, Lopez-Bigas, Nuria, Getz, Gad, Ding, Li, Raphael, Benjamin J

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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes von Graubert, Timothy A, Shen, Dong, Ding, Li, Okeyo-Owuor, Theresa, Lunn, Cara L, Shao, Jin, Krysiak, Kilannin, Harris, Christopher C, Koboldt, Daniel C, Larson, David E, McLellan, Michael D, Dooling, David J, Abbott, Rachel M, Fulton, Robert S, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Grillot, Marcus, Baty, Jack, Heath, Sharon, Frater, John L, Nasim, Talat, Link, Daniel C, Tomasson, Michael H, Westervelt, Peter, DiPersio, John F, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Walter, Matthew J

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Systematic discovery of complex insertions and deletions in human cancers von Ye, Kai, Wang, Jiayin, Jayasinghe, Reyka, Lameijer, Eric-Wubbo, McMichael, Joshua F, Ning, Jie, McLellan, Michael D, Xie, Mingchao, Cao, Song, Yellapantula, Venkata, Huang, Kuan-lin, Scott, Adam, Foltz, Steven, Niu, Beifang, Johnson, Kimberly J, Moed, Matthijs, Slagboom, P Eline, Chen, Feng, Wendl, Michael C, Ding, Li

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Integrated analysis of germline and somatic variants in ovarian cancer von Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D. M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li

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Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing von Ding, Li, Ley, Timothy J., Larson, David E., Miller, Christopher A., Koboldt, Daniel C., Welch, John S., Ritchey, Julie K., Young, Margaret A., Lamprecht, Tamara, McLellan, Michael D., McMichael, Joshua F., Wallis, John W., Lu, Charles, Shen, Dong, Harris, Christopher C., Dooling, David J., Fulton, Robert S., Fulton, Lucinda L., Chen, Ken, Schmidt, Heather, Kalicki-Veizer, Joelle, Magrini, Vincent J., Cook, Lisa, McGrath, Sean D., Vickery, Tammi L., Wendl, Michael C., Heath, Sharon, Watson, Mark A., Link, Daniel C., Tomasson, Michael H., Shannon, William D., Payton, Jacqueline E., Kulkarni, Shashikant, Westervelt, Peter, Walter, Matthew J., Graubert, Timothy A., Mardis, Elaine R., Wilson, Richard K., DiPersio, John F.

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Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif von Hamilton, Mark P., Rajapakshe, Kimal, Hartig, Sean M., Reva, Boris, McLellan, Michael D., Kandoth, Cyriac, Ding, Li, Zack, Travis I., Gunaratne, Preethi H., Wheeler, David A., Coarfa, Cristian, McGuire, Sean E.

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DNMT3A Mutations in Acute Myeloid Leukemia von Ley, Timothy J, Ding, Li, Walter, Matthew J, McLellan, Michael D, Lamprecht, Tamara, Larson, David E, Kandoth, Cyriac, Payton, Jacqueline E, Baty, Jack, Welch, John, Harris, Christopher C, Lichti, Cheryl F, Townsend, R. Reid, Fulton, Lucinda A, Fulton, Robert S, Dooling, David J, Koboldt, Daniel C, Schmidt, Heather, Zhang, Qunyuan, Osborne, John R, Lin, Ling, O'Laughlin, Michelle, McMichael, Joshua F, Delehaunty, Kim D, McGrath, Sean D, Magrini, Vincent J, Vickery, Tammi L, Hundal, Jasreet, Cook, Lisa L, Conyers, Joshua J, Swift, Gary W, Reed, Jerry P, Alldredge, Patricia A, Wylie, Todd, Walker, Jason, Kalicki, Joelle, Watson, Mark A, Heath, Sharon, Shannon, William D, Varghese, Nobish, Nagarajan, Rakesh, Westervelt, Peter, Tomasson, Michael H, Link, Daniel C, Graubert, Timothy A, DiPersio, John F, Mardis, Elaine R, Wilson, Richard K

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An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer von Ruggles, Kelly V., Tang, Zuojian, Wang, Xuya, Grover, Himanshu, Askenazi, Manor, Teubl, Jennifer, Cao, Song, McLellan, Michael D., Clauser, Karl R., Tabb, David L., Mertins, Philipp, Slebos, Robbert, Erdmann-Gilmore, Petra, Li, Shunqiang, Gunawardena, Harsha P., Xie, Ling, Liu, Tao, Zhou, Jian-Ying, Sun, Shisheng, Hoadley, Katherine A., Perou, Charles M., Chen, Xian, Davies, Sherri R., Maher, Christopher A., Kinsinger, Christopher R., Rodland, Karen D., Zhang, Hui, Zhang, Zhen, Ding, Li, Townsend, R. Reid, Rodriguez, Henry, Chan, Daniel, Smith, Richard D., Liebler, Daniel C., Carr, Steven A., Payne, Samuel, Ellis, Matthew J., Fenyő, David

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Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma von Gutmann, David H, McLellan, Michael D, Hussain, Ibrahim, Wallis, John W, Fulton, Lucinda L, Fulton, Robert S, Magrini, Vincent, Demeter, Ryan, Wylie, Todd, Kandoth, Cyriac, Leonard, Jeffrey R, Guha, Abhijit, Miller, Christopher A, Ding, Li, Mardis, Elaine R

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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome von Ley, Timothy J., Mardis, Elaine R., Ding, Li, Fulton, Bob, McLellan, Michael D., Chen, Ken, Dooling, David, Dunford-Shore, Brian H., McGrath, Sean, Hickenbotham, Matthew, Cook, Lisa, Abbott, Rachel, Larson, David E., Koboldt, Dan C., Pohl, Craig, Smith, Scott, Hawkins, Amy, Abbott, Scott, Locke, Devin, Hillier, LaDeana W., Miner, Tracie, Fulton, Lucinda, Magrini, Vincent, Wylie, Todd, Glasscock, Jarret, Conyers, Joshua, Sander, Nathan, Shi, Xiaoqi, Osborne, John R., Minx, Patrick, Gordon, David, Chinwalla, Asif, Zhao, Yu, Ries, Rhonda E., Payton, Jacqueline E., Westervelt, Peter, Tomasson, Michael H., Watson, Mark, Baty, Jack, Ivanovich, Jennifer, Heath, Sharon, Shannon, William D., Nagarajan, Rakesh, Walter, Matthew J., Link, Daniel C., Graubert, Timothy A., DiPersio, John F., Wilson, Richard K.

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Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation von Li, Lijin, Zhang, Xiuli, Wang, Xiaoli, Kim, Samuel W, Herndon, John M, Becker-Hapak, Michelle K, Carreno, Beatriz M, Myers, Nancy B, Sturmoski, Mark A, McLellan, Michael D, Miller, Christopher A, Johanns, Tanner M, Tan, Benjamin R, Dunn, Gavin P, Fleming, Timothy P, Hansen, Ted H, Goedegebuure, S Peter, Gillanders, William E

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