Nozzle: a report generation toolkit for data analysis pipelines von Gehlenborg, Nils, Noble, Michael S, Getz, Gad, Chin, Lynda, Park, Peter J

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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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TGCat: The Chandra Transmission Grating Data Catalog and Archive von Huenemoerder, David P, Mitschang, Arik, Dewey, Daniel, Nowak, Michael A, Schulz, Norbert S, Nichols, Joy S, Davis, John E, Houck, John C, Marshall, Herman L, Noble, Michael S, Morgan, Doug, Canizares, Claude R

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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data von Gao, Galen F., Parker, Joel S., Reynolds, Sheila M., Silva, Tiago C., Wang, Liang-Bo, Zhou, Wanding, Akbani, Rehan, Bailey, Matthew, Balu, Saianand, Berman, Benjamin P., Brooks, Denise, Chen, Hu, Cherniack, Andrew D., Demchok, John A., Ding, Li, Felau, Ina, Gaheen, Sharon, Gerhard, Daniela S., Heiman, David I., Hernandez, Kyle M., Hoadley, Katherine A., Jayasinghe, Reyka, Kemal, Anab, Knijnenburg, Theo A., Laird, Peter W., Mensah, Michael K.A., Mungall, Andrew J., Robertson, A. Gordon, Shen, Hui, Tarnuzzer, Roy, Wang, Zhining, Wyczalkowski, Matthew, Yang, Liming, Zenklusen, Jean C., Zhang, Zhenyu, Liang, Han, Noble, Michael S.

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Comprehensive genomic characterization of head and neck squamous cell carcinomas von Lawrence, Michael S, Sougnez, Carrie, Lichtenstein, Lee, Cibulskis, Kristian, Lander, Eric, Gabriel, Stacey B, Getz, Gad

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Comprehensive molecular characterization of gastric adenocarcinoma von Bass, Adam J

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Comprehensive molecular characterization of urothelial bladder carcinoma von Weinstein, John N, Akbani, Rehan, Broom, Bradley M, Wang, Wenyi, Verhaak, Roeland G. W, McConkey, David

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Comprehensivemolecular characterization of clear cell renal cell carcinoma

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Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer von Wang, Yumeng, Xu, Xiaoyan, Maglic, Dejan, Dill, Michael T, Mojumdar, Kamalika, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Tsang, Yiu Huen, Moreno, Daniela, Bhavana, Venkata Hemanjani, Peng, Xinxin, Ge, Zhongqi, Chen, Hu, Li, Jun, Chen, Zhongyuan, Zhang, Huiwen, Han, Leng, Du, Di, Creighton, Chad J, Mills, Gordon B, Camargo, Fernando, Liang, Han

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Genetic effects on gene expression across human tissues von Battle, Alexis, Brown, Christopher D, Engelhardt, Barbara E, Montgomery, Stephen B

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Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma von Robertson, A. Gordon, Gibb, Ewan A., Oba, Junna, Uzunangelov, Vladislav, Walter, Vonn, Danilova, Ludmila, Kimes, Patrick K., Babur, Ozgun, Akbani, Rehan, Bristow, Christopher A., Iype, Lisa, Beroukhim, Rameen, Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Carlsen, Rebecca, Cebulla, Colleen M., Chin, Lynda, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cibulskis, Kristian, Cope, Leslie, Coupland, Sarah E., Defreitas, Timothy, Demchok, John A., Desjardins, Laurence, Esmaeli, Bita, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gibb, Ewan A., Griewank, Klaus G., Heiman, David I., Helsel, Carmen, Hu, Xin, Jefferys, Stuart R., Leraas, Kristen M., Lichtenberg, Tara M., Liu, Jia, Iype, Lisa, Ma, Yussanne, Mariani, Odette, Marra, Marco A., Meier, Sam, Meyerson, Matthew, Mungall, Andrew J., Mungall, Karen L., Murray, Bradley A., Naresh, Rashi, Oba, Junna, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Protopopov, Alexei, Radenbaugh, Amie, Rai, Karan, Ramirez, Nilsa C., Ren, Xiaojia, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Schadendorf, Dirk, Schumacher, Steven E., Seidman, Jonathan, Seth, Sahil, Sethi, Geetika, Sheth, Margi, Shi, Yan, Singh, Arun D., Sipahimalani, Payal, Soloway, Matthew G., Sun, Huandong, Tan, Donghui, Tang, Ming, Tse, Kane, Uzunangelov, Vladislav, Verhaak, Roel G.W., Walter, Vonn, Wan, Yunhu, Weinstein, John N., Williams, Michelle D., Woodman, Scott E., Yang, Liming, Yang, Lixing, Yau, Christina, Zhang, Hailei, Zmuda, Erik, Benz, Christopher, Mills, Gordon B., Verhaak, Roel G.W., Gershenwald, Jeffrey E., Schoenfield, Lynn, Abdel-Rahman, Mohamed H., Stern, Marc-Henri, Cebulla, Colleen M., Woodman, Scott E.

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Improving genetic diagnosis in Mendelian disease with transcriptome sequencing von Cummings, Beryl B, Marshall, Jame L, Tukiainen, Taru, Lek, Monkol, Donkervoort, Sandra, Foley, A. Reghan, Bolduc, Veronique, Waddell, Leigh B, Sandaradura, Sarah A, O'Grady, Gina L, Estrella, Elicia, Reddy, Hemakumar M, Zhao, Fengmei, Weisburd, Ben, Karczewski, Konrad J, O'Donnell-Luria, Anne H, Birnbaum, Daniel, Sarkozy, Anna, Hu, Ying, Gonorazky, Hernan, Claeys, Kristi, Joshi, Adam Bournazos, Oates, Emily C, Ghaoui, Roula, Davis, Mark R, Laing, Nigel G, Topf, Ana, Genotype-Tissue Expression (GTEx) Consortium, Kang, Peter B, Beggs, Alan H, North, Kathryn N, Straub, Volker, Dowling, James J, Muntoni, Francesco, Clarke, Nigel F, Cooper, Sandra T, Bönnemann, Carsten G, Guigó Serra, Roderic

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Scientific computation with JavaSpaces von NOBLE, Michael S, ZLATEVA, Stoyanka

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Co-expression networks reveal the tissue-specific regulation of transcription and splicing von Saha, Ashis, Kim, Yungil, Gewirtz, Ariel D H, Jo, Brian, Gao, Chuan, McDowell, Ian C, Engelhardt, Barbara E, Battle, Alexis

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lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer von Wang, Zehua, Yang, Bo, Zhang, Min, Guo, Weiwei, Wu, Zhiyuan, Wang, Yue, Jia, Lin, Li, Song, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, de Krijger, Ronald, The Cancer Genome Atlas Research Network

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Identifying cis -mediators for trans -eQTLs across many human tissues using genomic mediation analysis von Yang, Fan, Wang, Jiebiao, Pierce, Brandon L, Chen, Lin S

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Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients von Kahles, André, Lehmann, Kjong Van, Toussaint, Nora C, Hüser, Matthias, Stark, Stefan G, Sachsenberg, Timo, Stegle, Oliver, Kohlbacher, Oliver, Sander, Chris, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Looijenga, Leendert, Timmers, Henri, de Krijger, Ronald, The Cancer Genome Atlas Research Network

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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation von Malta, Tathiane M, Sokolov, Artem, Gentles, Andrew J, Burzykowski, Tomasz, Poisson, Laila, Weinstein, John N, Kamińska, Bożena, Huelsken, Joerg, Omberg, Larsson, Gevaert, Olivier, Colaprico, Antonio, Czerwińska, Patrycja, Mazurek, Sylwia, Mishra, Lopa, Heyn, Holger, Krasnitz, Alex, Godwin, Andrew K, Lazar, Alexander J, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, de Krijger, Ronald, The Cancer Genome Atlas Research Network

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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics von Liu, Jianfang, Lichtenberg, Tara M, Hoadley, Katherine A, Poisson, Laila M, Lazar, Alexander J, Cherniack, Andrew D, Kovatich, Albert J, Benz, Christopher, Levine, Douglas A, Lee, Adrian V, Omberg, Larsson, Wolf, Denise M, Shriver, Craig D, Thorsson, Vesteinn, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, de Krijger, Ronald, The Cancer Genome Atlas Research Network

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Genomic and Functional Approaches to Understanding Cancer Aneuploidy von Taylor, Alison M, Shih, Juliann, Ha, Gavin, Gao, Galen F, Zhang, Xiaoyang, Berger, Ashton C, Schumacher, Steven E, Wang, Chen, Hu, Hai, Liu, Jianfang, Lazar, Alexander J, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, de Krijger, Ronald, The Cancer Genome Atlas Research Network

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