Enter the Matrix: Factorization Uncovers Knowledge from Omics von Stein-O’Brien, Genevieve L., Arora, Raman, Culhane, Aedin C., Favorov, Alexander V., Garmire, Lana X., Greene, Casey S., Goff, Loyal A., Li, Yifeng, Ngom, Aloune, Ochs, Michael F., Xu, Yanxun, Fertig, Elana J.

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Serum microRNA biomarkers for detection of non-small cell lung cancer von Hennessey, Patrick T, Sanford, Tiffany, Choudhary, Ashish, Mydlarz, Wojciech W, Brown, David, Adai, Alex Tamas, Ochs, Michael F, Ahrendt, Steven A, Mambo, Elizabeth, Califano, Joseph A

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Activation of the NOTCH Pathway in Head and Neck Cancer von WENYUE SUN, GAYKALOVA, Daria A, SUN AHN, FERTIG, Elana, SIDRANSKY, David, HOUGHTON, Jeffery, BUDDAVARAPU, Kalyan, SANFORD, Tiffany, CHOUDHARY, Ashish, DARDEN, Will, ADAI, Alex, LATHAM, Gary, OCHS, Michael F, BISHOP, Justin, SHARMA, Rajni, WESTRA, William H, HENNESSEY, Patrick, CHUNG, Christine H, CALIFANO, Joseph A, MAMBO, Elizabeth, ARNAOUTAKIS, Demetri, YAN LIU, LOYO, Myriam, AGRAWAL, Nishant, HOWARD, Jason, RYAN LI

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Novel insight into mutational landscape of head and neck squamous cell carcinoma von Gaykalova, Daria A, Mambo, Elizabeth, Choudhary, Ashish, Houghton, Jeffery, Buddavarapu, Kalyan, Sanford, Tiffany, Darden, Will, Adai, Alex, Hadd, Andrew, Latham, Gary, Danilova, Ludmila V, Bishop, Justin, Li, Ryan J, Westra, William H, Hennessey, Patrick, Koch, Wayne M, Ochs, Michael F, Califano, Joseph A, Sun, Wenyue

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Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts von Hennessey, Patrick T, Ochs, Michael F, Mydlarz, Wojciech W, Hsueh, Wayne, Cope, Leslie, Yu, Wayne, Califano, Joseph A

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Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma von Li, Ryan, Ochs, Michael F, Ahn, Sun Mi, Hennessey, Patrick, Tan, Marietta, Soudry, Ethan, Gaykalova, Daria A, Uemura, Mamoru, Brait, Mariana, Shao, Chunbo, Westra, William, Bishop, Justin, Fertig, Elana J, Califano, Joseph A

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CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data von Fertig, Elana J., Ding, Jie, Favorov, Alexander V., Parmigiani, Giovanni, Ochs, Michael F.

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Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer von Smith, Ian M, Glazer, Chad A, Mithani, Suhail K, Ochs, Michael F, Sun, Wenyue, Bhan, Sheetal, Vostrov, Alexander, Abdullaev, Ziedulla, Lobanenkov, Victor, Gray, Andrew, Liu, Chunyan, Chang, Steven S, Ostrow, Kimberly L, Westra, William H, Begum, Shahnaz, Dhara, Mousumi, Califano, Joseph

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Correction: Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma von Gaykalova, Daria A, Mambo, Elizabeth, Choudhary, Ashish, Houghton, Jeffery, Buddavarapu, Kalyan, Sanford, Tiffany, Darden, Will, Adai, Alex, Hadd, Andrew, Latham, Gary, Danilova, Ludmila V, Bishop, Justin, Li, Ryan J, Westra, William H, Hennessey, Patrick, Koch, Wayne M, Ochs, Michael F, Califano, Joseph A, Sun, Wenyue

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Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis von Fertig, Elana J, Markovic, Ana, Danilova, Ludmila V, Gaykalova, Daria A, Cope, Leslie, Chung, Christine H, Ochs, Michael F, Califano, Joseph A

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Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer von Afsari, Bahman, Guo, Theresa, Considine, Michael, Florea, Liliana, Kagohara, Luciane T, Stein-O'Brien, Genevieve L, Kelley, Dylan, Flam, Emily, Zambo, Kristina D, Ha, Patrick K, Geman, Donald, Ochs, Michael F, Califano, Joseph A, Gaykalova, Daria A, Favorov, Alexander V, Fertig, Elana J

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LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates von Wang, Guoli, Kossenkov, Andrew V, Ochs, Michael F

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A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells von Kent, Oliver A., Mullendore, Michael E., Wentzel, Eric A., López-Romero, Pedro, Tan, Aik Choon, Hector, Alvarez, West, Kristen, Ochs, Michael F., Hidalgo, Manuel, Arking, Dan E., Maitra, Anirban, Mendell, Joshua T.

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Integrative discovery of epigenetically derepressed cancer testis antigens in NSCLC von Glazer, Chad A, Smith, Ian M, Ochs, Michael F, Begum, Shahnaz, Westra, William, Chang, Steven S, Sun, Wenyue, Bhan, Sheetal, Khan, Zubair, Ahrendt, Steven, Califano, Joseph A

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ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor von Rink, Lori, Ochs, Michael F, Zhou, Yan, von Mehren, Margaret, Godwin, Andrew K

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Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data von OCHS, Michael F, RINK, Lori, TARN, Chi, MBURU, Sarah, TAGUCHI, Takahiro, EISENBERG, Burton, GODWIN, Andrew K

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Evaluating optimal therapy robustness by virtual expansion of a sample population, with a case study in cancer immunotherapy von Barish, Syndi, Ochs, Michael F., Sontag, Eduardo D., Gevertz, Jana L.

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MAGEB2 is activated by promoter demethylation in head and neck squamous cell carcinoma von Pattani, Kavita M, Soudry, Ethan, Glazer, Chad A, Ochs, Michael F, Wang, Hao, Schussel, Juliana, Sun, Wenyue, Hennessey, Patrick, Mydlarz, Wojciech, Loyo, Myriam, Demokan, Semra, Smith, Ian M, Califano, Joseph A

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Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma von Fertig, Elana J, Ren, Qing, Cheng, Haixia, Hatakeyama, Hiromitsu, Dicker, Adam P, Rodeck, Ulrich, Considine, Michael, Ochs, Michael F, Chung, Christine H

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Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor von Rink, Lori, Skorobogatko, Yuliya, Kossenkov, Andrew V, Belinsky, Martin G, Pajak, Thomas, Heinrich, Michael C, Blanke, Charles D, von Mehren, Margaret, Ochs, Michael F, Eisenberg, Burton, Godwin, Andrew K

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