Emerging landscape of oncogenic signatures across human cancers von Ciriello, Giovanni, Miller, Martin L, Aksoy, Bülent Arman, Senbabaoglu, Yasin, Schultz, Nikolaus, Sander, Chris

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Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations von Babur, Özgün, Gönen, Mithat, Aksoy, Bülent Arman, Schultz, Nikolaus, Ciriello, Giovanni, Sander, Chris, Demir, Emek

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Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal von Gao, Jianjiong, Aksoy, Bülent Arman, Dogrusoz, Ugur, Dresdner, Gideon, Gross, Benjamin, Sumer, S Onur, Sun, Yichao, Jacobsen, Anders, Sinha, Rileen, Larsson, Erik, Cerami, Ethan, Sander, Chris, Schultz, Nikolaus

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The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data von Cerami, Ethan, Gao, Jianjiong, Dogrusoz, Ugur, Gross, Benjamin E, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Jacobsen, Anders, Byrne, Caitlin J, Heuer, Michael L, Larsson, Erik, Antipin, Yevgeniy, Reva, Boris, Goldberg, Arthur P, Sander, Chris, Schultz, Nikolaus

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Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis von Vedanayagam, Jeffrey, Chatila, Walid K., Aksoy, Bülent Arman, Majumdar, Sonali, Skanderup, Anders Jacobsen, Demir, Emek, Schultz, Nikolaus, Sander, Chris, Lai, Eric C.

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Pan-Cancer Analysis of Mutation Hotspots in Protein Domains von Miller, Martin L., Reznik, Ed, Gauthier, Nicholas P., Aksoy, Bülent Arman, Korkut, Anil, Gao, Jianjiong, Ciriello, Giovanni, Schultz, Nikolaus, Sander, Chris

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Chemotherapy resistance in diffuse type gastric adenocarcinoma is mediated by RhoA activation in cancer stem-like cells von Yoon, Changhwan, Cho, Soo-Jeong, Aksoy, Bülent Arman, Park, Do Joong, Schultz, Nikolaus, Ryeom, Sandra W., Yoon, Sam S.

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A Landscape of Metabolic Variation across Tumor Types von Reznik, Ed, Luna, Augustin, Aksoy, Bülent Arman, Liu, Eric Minwei, La, Konnor, Ostrovnaya, Irina, Creighton, Chad J., Hakimi, A. Ari, Sander, Chris

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PaxtoolsR: pathway analysis in R using Pathway Commons von Luna, Augustin, Babur, Özgün, Aksoy, Bülent Arman, Demir, Emek, Sander, Chris

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SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps von Sari, Mecit, Bahceci, Istemi, Dogrusoz, Ugur, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Babur, Özgün, Demir, Emek

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KMT2C mutations in diffuse type gastric adenocarcinoma promote epithelial-to-mesenchymal transition von Cho, Soo-Jeong, Yoon, Changhwan, Lee, Jun Ho, Chang, Kevin K., Lin, Jian-xian, Kim, Young-Ho, Kook, Myeong-Cherl, Aksoy, Bülent Arman, Park, Do Joong, Ashktorab, Hassan, Smoot, Duane T., Schultz, Nikolaus, Yoon, Sam S.

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Pattern search in BioPAX models von Babur, Özgün, Aksoy, Bülent Arman, Rodchenkov, Igor, Sümer, Selçuk Onur, Sander, Chris, Demir, Emek

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Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging von Czech, Eric, Aksoy, Bulent Arman, Aksoy, Pinar, Hammerbacher, Jeff

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Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells von Korkut, Anil, Wang, Weiqing, Demir, Emek, Aksoy, Bülent Arman, Jing, Xiaohong, Molinelli, Evan J, Babur, Özgün, Bemis, Debra L, Onur Sumer, Selcuk, Solit, David B, Pratilas, Christine A, Sander, Chris

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Pathway Commons 2019 Update: integration, analysis and exploration of pathway data von Rodchenkov, Igor, Babur, Ozgun, Luna, Augustin, Aksoy, Bulent Arman, Wong, Jeffrey V, Fong, Dylan, Franz, Max, Siper, Metin Can, Cheung, Manfred, Wrana, Michael, Mistry, Harsh, Mosier, Logan, Dlin, Jonah, Wen, Qizhi, O’Callaghan, Caitlin, Li, Wanxin, Elder, Geoffrey, Smith, Peter T, Dallago, Christian, Cerami, Ethan, Gross, Benjamin, Dogrusoz, Ugur, Demir, Emek, Bader, Gary D, Sander, Chris

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Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis von Snyder, Alexandra, Nathanson, Tavi, Funt, Samuel A, Ahuja, Arun, Buros Novik, Jacqueline, Hellmann, Matthew D, Chang, Eliza, Aksoy, Bulent Arman, Al-Ahmadie, Hikmat, Yusko, Erik, Vignali, Marissa, Benzeno, Sharon, Boyd, Mariel, Moran, Meredith, Iyer, Gopa, Robins, Harlan S, Mardis, Elaine R, Merghoub, Taha, Hammerbacher, Jeff, Rosenberg, Jonathan E, Bajorin, Dean F

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Using biological pathway data with paxtools von Demir, Emek, Babur, Ozgün, Rodchenkov, Igor, Aksoy, Bülent Arman, Fukuda, Ken I, Gross, Benjamin, Sümer, Onur Selçuk, Bader, Gary D, Sander, Chris

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Coral: Clear and Customizable Visualization of Human Kinome Data von Metz, Kathleen S., Deoudes, Erika M., Berginski, Matthew E., Jimenez-Ruiz, Ivan, Aksoy, Bulent Arman, Hammerbacher, Jeff, Gomez, Shawn M., Phanstiel, Douglas H.

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Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial von Rubinsteyn, Alex, Kodysh, Julia, Hodes, Isaac, Mondet, Sebastien, Aksoy, Bulent Arman, Finnigan, John P, Bhardwaj, Nina, Hammerbacher, Jeffrey

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PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8 + T Cells von Bowers, Jacob S, Majchrzak, Kinga, Nelson, Michelle H, Aksoy, Bulent Arman, Wyatt, Megan M, Smith, Aubrey S, Bailey, Stefanie R, Neal, Lillian R, Hammerbacher, Jeffrey E, Paulos, Chrystal M

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