Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt von Durinck, Steffen, Spellman, Paul T, Birney, Ewan, Huber, Wolfgang

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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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Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets von Cassetta, Luca, Fragkogianni, Stamatina, Sims, Andrew H., Swierczak, Agnieszka, Forrester, Lesley M., Zhang, Hui, Soong, Daniel Y.H., Cotechini, Tiziana, Anur, Pavana, Lin, Elaine Y., Fidanza, Antonella, Lopez-Yrigoyen, Martha, Millar, Michael R., Urman, Alexandra, Ai, Zhichao, Spellman, Paul T., Hwang, E. Shelley, Dixon, J. Michael, Wiechmann, Lisa, Coussens, Lisa M., Smith, Harriet O., Pollard, Jeffrey W.

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Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease von Butler, Timothy M, Johnson-Camacho, Katherine, Peto, Myron, Wang, Nicholas J, Macey, Tara A, Korkola, James E, Koppie, Theresa M, Corless, Christopher L, Gray, Joe W, Spellman, Paul T

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Circulating-tumor DNA as an early detection and diagnostic tool von Butler, Timothy M, Spellman, Paul T, Gray, Joe

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Alternative Splicing in Tumors — A Path to Immunogenicity? von Slansky, Jill E, Spellman, Paul T

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Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data von Sun, Duanchen, Guan, Xiangnan, Moran, Amy E., Wu, Ling-Yun, Qian, David Z., Schedin, Pepper, Dai, Mu-Shui, Danilov, Alexey V., Alumkal, Joshi J., Adey, Andrew C., Spellman, Paul T., Xia, Zheng

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Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability von Heskett, Michael B., Vouzas, Athanasios E., Smith, Leslie G., Yates, Phillip A., Boniface, Christopher, Bouhassira, Eric E., Spellman, Paul T., Gilbert, David M., Thayer, Mathew J.

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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer von Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine, Dobrolecki, Lacey E., Chin, Koei, Aswani, Anil J., Wang, Nicholas J., Califano, Andrea, Lewis, Michael T., Tomlin, Claire J., Spellman, Paul T., Adey, Andrew, Gray, Joe W., Sears, Rosalie C.

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Detecting cancer by monitoring circulating tumor DNA von Spellman, Paul T, Gray, Joe W

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Proliferative polyploid cells give rise to tumors via ploidy reduction von Matsumoto, Tomonori, Wakefield, Leslie, Peters, Alexander, Peto, Myron, Spellman, Paul, Grompe, Markus

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 von Verhaak, Roel G.W., Hoadley, Katherine A., Purdom, Elizabeth, Wang, Victoria, Qi, Yuan, Wilkerson, Matthew D., Miller, C. Ryan, Ding, Li, Golub, Todd, Mesirov, Jill P., Alexe, Gabriele, Lawrence, Michael, O'Kelly, Michael, Tamayo, Pablo, Weir, Barbara A., Gabriel, Stacey, Winckler, Wendy, Gupta, Supriya, Jakkula, Lakshmi, Feiler, Heidi S., Hodgson, J. Graeme, James, C. David, Sarkaria, Jann N., Brennan, Cameron, Kahn, Ari, Spellman, Paul T., Wilson, Richard K., Speed, Terence P., Gray, Joe W., Meyerson, Matthew, Getz, Gad, Perou, Charles M., Hayes, D. Neil

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FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer von Fu, Xiaoyong, Jeselsohn, Rinath, Pereira, Resel, Hollingsworth, Emporia F., Creighton, Chad J., Li, Fugen, Shea, Martin, Nardone, Agostina, De Angelis, Carmine, Heiser, Laura M., Anur, Pavana, Wang, Nicholas, Grasso, Catherine S., Spellman, Paul T., Griffith, Obi L., Tsimelzon, Anna, Gutierrez, Carolina, Huang, Shixia, Edwards, Dean P., Trivedi, Meghana V., Rimawi, Mothaffar F., Lopez-Terrada, Dolores, Hilsenbeck, Susan G., Gray, Joe W., Brown, Myles, Osborne, C. Kent, Schiff, Rachel

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Mutation of SIVA, a candidate metastasis gene identified from clonally related bilateral breast cancers, promotes breast cancer cell spread in vitro and in vivo von Vermehren-Schmaedick, Anke, Peto, Myron, Wagoner, Wendy, Chiotti, Kami E, Ramsey, Elizabeth, Wang, Xiaoyan, Rakshe, Shauna, Minnier, Jessica, Sears, Rosalie, Spellman, Paul, Luoh, Shiuh-Wen

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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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Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy von Collisson, Eric A, Sadanandam, Anguraj, Olson, Peter, Gibb, William J, Truitt, Morgan, Gu, Shenda, Cooc, Janine, Weinkle, Jennifer, Kim, Grace E, Jakkula, Lakshmi, Feiler, Heidi S, Ko, Andrew H, Olshen, Adam B, Danenberg, Kathleen L, Tempero, Margaret A, Spellman, Paul T, Hanahan, Douglas, Gray, Joe W

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Epigenetic loss of heterogeneity from low to high grade localized prostate tumours von Eksi, Sebnem Ece, Chitsazan, Alex, Sayar, Zeynep, Thomas, George V., Fields, Andrew J., Kopp, Ryan P., Spellman, Paul T., Adey, Andrew C.

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Functionally defined therapeutic targets in diffuse intrinsic pontine glioma von Grasso, Catherine S, Tang, Yujie, Truffaux, Nathalene, Berlow, Noah E, Liu, Lining, Debily, Marie-Anne, Quist, Michael J, Davis, Lara E, Huang, Elaine C, Woo, Pamelyn J, Ponnuswami, Anitha, Chen, Spenser, Johung, Tessa B, Sun, Wenchao, Kogiso, Mari, Du, Yuchen, Qi, Lin, Huang, Yulun, Hütt-Cabezas, Marianne, Warren, Katherine E, Le Dret, Ludivine, Meltzer, Paul S, Mao, Hua, Quezado, Martha, van Vuurden, Dannis G, Abraham, Jinu, Fouladi, Maryam, Svalina, Matthew N, Wang, Nicholas, Hawkins, Cynthia, Nazarian, Javad, Alonso, Marta M, Raabe, Eric H, Hulleman, Esther, Spellman, Paul T, Li, Xiao-Nan, Keller, Charles, Pal, Ranadip, Grill, Jacques, Monje, Michelle

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Subtype and pathway specific responses to anticancer compounds in breast cancer von Heiser, Laura M, Sadanandam, Anguraj, Kuo, Wen-Lin, Benz, Stephen C, Goldstein, Theodore C, Ng, Sam, Gibb, William J, Wang, Nicholas J, Ziyad, Safiyyah, Tong, Frances, Bayani, Nora, Hu, Zhi, Billig, Jessica I, Dueregger, Andrea, Lewis, Sophia, Jakkula, Lakshmi, Korkola, James E, Durinck, Steffen, Pepin, François, Guan, Yinghui, Purdom, Elizabeth, Neuvial, Pierre, Bengtsson, Henrik, Wood, Kenneth W, Smith, Peter G, Vassilev, Lyubomir T, Hennessy, Bryan T, Greshock, Joel, Bachman, Kurtis E, Hardwicke, Mary Ann, Park, John W, Marton, Laurence J, Wolf, Denise M, Collisson, Eric A, Neve, Richard M, Mills, Gordon B, Speed, Terence P, Feiler, Heidi S, Wooster, Richard F, Haussler, David, Stuart, Joshua M, Gray, Joe W, Spellman, Paul T

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Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response von Boniface, Christopher T, Spellman, Paul T

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