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

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Comprehensive molecular characterization of gastric adenocarcinoma von Bass, Adam J

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

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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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Comprehensivemolecular characterization of clear cell renal cell carcinoma

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

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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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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation von Malta, Tathiane M., Gentles, Andrew J., Weinstein, John N., Czerwińska, Patrycja, Heyn, Holger, Godwin, Andrew K., Zhang, Jiashan (Julia), Wu, Ye, Liu, Yuexin, Reynolds, Sheila, Akbani, Rehan, Kanchi, Rupa S., Ladanyi, Marc, Peto, Myron, Bowlby, Reanne, Schein, Jacqueline E., Sipahimalani, Payal, Thiessen, Nina, Cope, Leslie, Weisenberger, Daniel J., Hoyle, Alan P., Mieczkowski, Piotr A., Shi, Yan, Veluvolu, Umadevi, Zhou, Wanding, Bellair, Michelle, Creighton, Chad J., Gibbs, Richard A., Li, Wei, Xi, Liu, Zhao, Fengmei, Mardis, Elaine R., Paulauskis, Joseph, Eschbacher, Jennifer, Ittmann, Michael, Le, Xuan, Thorp, Richard, Lyadov, Vladimir, Setdikova, Galiya, Raut, Chandrajit P., Barrett, Wendi, Karlan, Beth Y., Hu, Hai, Bennett, Joseph, Chabot, John, Hibshoosh, Hanina, Potapova, Olga, Voronina, Olga, Berchuck, Andrew, McCall, Shannon, Olson, Jeffrey J., Ramalingam, Suresh, Stoop, Hans, Guillermo, Armando López, Castle, Erik, Kopp, Karla, Roberts, Lewis, Stanton, Melissa, Yang, Ju Dong, Broaddus, Russell, Guo, Charles, Moran, Cesar, Tamboli, Pheroze, Thompson, Timothy, Tsao, Anne, Wistuba, Ignacio, Haydu, Lauren, Saw, Robyn, Scolyer, Richard, Thompson, John, Reuter, Victor, Drwiega, Paul, Hung, Nguyen Phi, Pass, Harvey, Gorincioi, Ghenadie, Gilbert, Sebastien, Tamakawa, Raina, Chevalier, Simone, Morrison, Carl, Borgia, Jeffrey A., Junker, Kerstin, Bragazzi, Maria Consiglia, Moiseenko, Fedor, Duell, Rebecca, Pilarski, Robert, Senecal, Kelly, Henderson, Joel, Schadendorf, Dirk, Olabode, Oluwole, Nelson, Mark, Roggin, Kevin, Carey, Francis, Carney, Michael, Hernandez, Brenda, Walker, Joan, Valdivieso, Federico, Luketich, James, Tirapelli, Daniela, Catto, James, Kovatich, Albert J.

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The Immune Landscape of Cancer von Bortone, Dante S., Eddy, James A., Liu, Yuexin, Weinstein, John N., Holt, Robert A., Zenklusen, Jean C., Cho, Juok, Reynolds, Sheila, Liu, Wenbin, Ryan, Michael, Chakravarty, Debyani, Schultz, Nikolaus, Stuart, Joshua M., Wilkerson, Matthew D., Balasundaram, Miruna, Carlsen, Rebecca, Chuah, Eric, Holt, Robert, Lee, Darlene, Ha, Gavin, Schumacher, Steven E., Cope, Leslie, Balu, Saianand, Shi, Yan, Hinoue, Toshinori, Glenn, Robert, Miller, Christopher A., Curley, Erin, Mallery, David, Morris, Scott, Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Singh, Rosy, Le, Xuan, Thorp, Richard, Setdikova, Galiya, Shabunin, Alexey, Barrett, Wendi, Ostrom, Quinn T., Karlan, Beth Y., Hu, Hai, Latour, Mathieu, Lacombe, Louis, Su, Tao, Signoretti, Sabina, Marks, Jeffrey, Olson, Jeffrey J., Sica, Gabriel, Stoop, Hans, Pollo, Bianca, Aymerich, Marta, Stepa, Serghei, Moser, Catherine, Roberts, Lewis, Czerniak, Bogdan, Lazar, Alexander J., Jakrot, Valerie, Scolyer, Richard, Thompson, John, Wilmott, James, Reuter, Victor, Tien, Nguyen Viet, Park, Joong-Won, Pinto, Peter A., Moncrieff, Marc, Botnariuc, Natalia, Pirtac, Maria, Parfitt, Jeremy, Bifulco, Carlo, Antenucci, Anna, Grazi, Gianluca, Marino, Mirella, Chevalier, Simone, McKercher, Ginette, Naska, Theresa, Borgia, Jeffrey A., Pool, Mark, Junker, Kerstin, Moiseenko, Fedor, Hilty, Joe, Pilarski, Robert, Porten, Sima, Asa, Sylvia L., Schadendorf, Dirk, Disaia, Philip, Kelley, Robin K., Sifri, Suzanne, Mannelli, Massimo, Knutson, Tina, Sigmund, Rita, Postier, Russel, Walker, Joan, Feldman, Michael, Luketich, James, Rozek, Laura, Fong, Kwun M., Hooke, Jeffrey A., Govindan, Ramaswamy, Aredes, Natália D.

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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics von Omberg, Larsson, Wolf, Denise M., Sofia, Heidi J., Chudamani, Sudha, Lolla, Laxmi, Pihl, Todd, Lin, Pei, Chambwe, Nyasha, Kramer, Roger, Thorsson, Vesteinn, Wang, Jing, Armenia, Joshua, Chatila, Walid K., de Bruijn, Ino, Gross, Benjamin E., Brooks, Denise, Tam, Angela, Tse, Kane, Meng, Shaowu, Korchina, Viktoriya, Cordes, Matthew G., McLellan, Michael D., Miller, Christopher A., Shelton, Candace, Yena, Peggy, Wise, Lisa, Costello, Tony, Hovens, Christopher, Silveira, Henrique C.S., Singh, Rosy, Anderson, Matthew L., Duffy, Elizabeth R., Tavobilov, Mikhail, Cramer, Daniel, Horowitz, Neil, Fulop, Jordonna, Wolinsky, Yingli, Sloan, Andrew E., Mural, Richard J., Latour, Mathieu, Lacombe, Louis, Wang, Timothy, Magliocca, Kelly, Pickens, Alan, Shin, Dong M., Van Meir, Erwin G., Zhang, Hongzheng, Cuzzubbo, Stefania, Hartmann, Arndt, Stoehr, Christine, Wach, Sven, Kycler, Witold, Chung, Ki, Martin, Julie, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Gabra, Hani, Ahn, Keunsoo, Farnell, Michael, Patel, Tushar, Smallridge, Robert, Rice, David, Troncoso, Patricia, Mann, Graham, Levine, Douglas A., Singer, Samuel, Linehan, W. Marston, Melamed, Jonathan, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Bifulco, Carlo, Hayward, Nicholas, Grazi, Gianluca, de Krijger, Ronald, Birsoy, Kivanc, Brewer, Cathy, Williams, Felicia, Pool, Mark, Dinkin, Mikhail, Schoenfield, Lynn, Hansen, Paul, Asa, Sylvia L., Glenn, Pat, Jungk, Christin, Ma, Deqin, Milhem, Mohammed, Madan, Rashna, Mannel, Robert, Dos Santos, Jose Sebastião, Moyer, Jeffey, Rozek, Laura, Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Drake, Bettina, Westervelt, Peter, Lee, Jung Il, Hu, Hai

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Oncogenic Signaling Pathways in The Cancer Genome Atlas von Chatila, Walid K., Luna, Augustin, Kantheti, Havish S., Daian, Foysal, Shmulevich, Ilya, Greene, Casey S., Iavarone, Antonio, Tward, Aaron D., Meyerson, Matthew, Sofia, Heidi J., Zenklusen, Jean C., Pihl, Todd, Meier, Sam, Noble, Michael S., Kramer, Roger, Hegde, Apurva M., Li, Jun, Rao, Arvind, Abeshouse, Adam, Schultz, Nikolaus, Taylor, Barry S., Stuart, Joshua M., Wong, Christopher K., Parker, Joel S., Carlsen, Rebecca, Tam, Angela, Gabriel, Stacey B., Ha, Gavin, Schumacher, Steven E., Maglinte, Dennis T., Balu, Saianand, Skelly, Tara, Laird, Peter W., Lewis, Lora, Muzny, Donna, Santibanez, Jireh, Wang, Min, Morris, Scott, Shelton, Candace, Gerken, Mark, Costello, Tony, Reis, Rui M., Scapulatempo-Neto, Cristovam, Singh, Rosy, Duffy, Elizabeth R., Setdikova, Galiya, Devine, Karen, Ostrom, Quinn T., Deyarmin, Brenda, Kvecher, Leonid, Mural, Richard J., Latour, Mathieu, Lacombe, Louis, Lipp, Eric, Marks, Jeffrey, Pickens, Alan, Shin, Dong M., Zhang, Hongzheng, Calatozzolo, Chiara, Cuzzubbo, Stefania, Kycler, Witold, Giné, Eva, Beuschlein, Felix, Borad, Mitesh, Chandan, Vishal, Farnell, Michael, Torbenson, Michael, Logothetis, Christopher, Rice, David, Jakrot, Valerie, Mann, Graham, Moncrieff, Marc, Doruc, Serghei, Bartlett, John, Parfitt, Jeremy, Bifulco, Carlo, Hayward, Nicholas, Grazi, Gianluca, Marino, Mirella, Naska, Theresa, Borgia, Jeffrey A., Pool, Mark, Gaudio, Eugenio, Bell, Sue, Hilty, Joe, Sexton, Katherine C., Asa, Sylvia L., Schlomm, Thorsten, Prados, Michael, Smith-McCune, Karen, Bossler, Aaron, Moxley, Katherine, Carlotti, Carlos Gilberto, Swisher, Elizabeth, Korst, Robert, Rathmell, W. Kimryn, Heath, Sharon, Aredes, Natália D., Mariamidze, Armaz, Van Allen, Eliezer M.

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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer von Wolf, Denise M., Cherniack, Andrew D., Sanchez-Vega, Francisco, Sun, Qiang, Wu, Ye, Gehlenborg, Nils, Zhang, Hailei, Akbani, Rehan, Ling, Shiyun, Rao, Arvind, Phillips, Sarah M., Sun, Yichao, Benz, Christopher, Dhalla, Noreen, Robertson, A. Gordon, Sipahimalani, Payal, Wong, Tina, Weisenberger, Daniel J., Bodenheimer, Tom, Roach, Jeffrey, Simons, Janae V., Fan, Huihui, Zhou, Wanding, Dinh, Huyen, Doddapaneni, HarshaVardhan, Han, Yi, Lee, Sandra, Liu, Xiuping, Hess, Julian, Ding, Li, Fulton, Lucinda A., Shelton, Troy, Zmuda, Erik, de Carvalho, Ana C., Vidal, Daniel O., Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Shabunin, Alexey, Eckman, John, Bennett, Joseph, Rabeno, Brenda, Swanson, Patricia, Bergeron, Alain, Staugaitis, Susan M., Chabot, John, McCall, Shannon, Behera, Madhusmita, Brat, Daniel J., Force, Seth, Eijckenboom, Wil, Zwarthoff, Ellen C., Cuppini, Lucia, Murawa, Dawid, Mikkelsen, Tom, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Birrer, Michael, Ho, Thai, Nagorney, David, Meric-Bernstam, Funda, Moran, Cesar, Hersey, Peter, Synott, Maria, Mirsaidi, Cyrus, Metwalli, Adam R., Vocke, Cathy D., Goparaju, Chandra, Cernat, Mircea, Gilbert, Sebastien, Timmers, Henri, Schilero, Cathy, Manikhas, George, Chesla, David, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Davis, Amy, Elder, J. Bradley, Lehman, Norman L., Mandt, Randy, Wakely, Paul, Powers, James, Carroll, Peter R., Chan, June M., Roggin, Kevin, Fehrenbach, Ashley, Galbraith, Joseph, Knudson, Michael, Saad, Fred, Bocklage, Therese, Zuna, Rosemary, Feldman, Michael, Quintero-Aguilo, Mario, Tirapelli, Daniela, Creaney, Jenette, Shelley, Carl Simon, Bradford, Carol, Prince, Mark

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Comprehensive Characterization of Cancer Driver Genes and Mutations von Colaprico, Antonio, Cao, Song, Liang, Wen-Wei, Hess, Julian M., Ferguson, Martin L., Hutter, Carolyn M., Tarnuzzer, Roy, Wang, Zhining, Noble, Michael S., Dhankani, Varsha, Knijnenburg, Theo, Miller, Michael, Abeshouse, Adam, Ladanyi, Marc, Luna, Augustin, Wong, Christopher K., Yau, Christina, Kasaian, Katayoon, Kucherlapati, Melanie H., Danilova, Ludmila, Bootwalla, Moiz S., Fan, Cheng, Mose, Lisle E., Roach, Jeffrey, Tan, Donghui, Covington, Kyle, Donehower, Lawrence A., Drummond, Jennifer, Liu, Xiuping, Morgan, Margaret, Wheeler, David A., Appelbaum, Elizabeth L., Bailey, Matthew, Kandoth, Cyriac, Wilson, Richard K., Penny, Robert, Thompson, Eric, Zmuda, Erik, de Carvalho, Ana C., Fregnani, José H., Huntsman, David, Kohl, Bernard, Paklina, Oxana, McPherson, Christopher, Barnholtz-Sloan, Jill S., Tucker, Kelinda, Larson, Caroline, Iacocca, Mary, Bergeron, Alain, Sepulveda, Antonia, Desjardins, Laurence, Sastre, Xavier, Cheng, Feixiong, Force, Seth, Khuri, Fadlo, Owonikoko, Taofeek, Korpershoek, Esther, Looijenga, Leendert, DiMeco, Francesco, Kycler, Witold, Chung, Ki, Noushmehr, Houtan, Scarpace, Lisa, Campo, Elias, Van Bang, Nguyen, Colman, Howard, Breggia, Anne, Bryce, Alan H., Copland, John A., Petersen, Gloria, Zhang, Lizhi, Mann, Graham, Mirsaidi, Cyrus, Zaren, Howard, Stancul, Irina, Tcaciuc, Diana, Arnaout, Angel, Rassl, Doris M., Urba, Walter, Farver, Carol, Raymond, Daniel, Dinkin, Mikhail, Carpino, Guido, Dubina, Michael, Abdel-Rahman, Mohamed H., Mandt, Randy, Nguyen, Phuong, Rai, Karan, Waldmann, Jens, Fassnacht, Martin, Simon, Ronald, Fehrenbach, Ashley, von Deimling, Andreas, Jacobus, Laura, Carlotti, Carlos Gilberto, Godwin, Eryn M., Carey, Thomas, Getz, Gad, Lazar, Alexander J., Ding, Li

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