Mitochondrial respiratory gene expression is suppressed in many cancers by Ed Reznik, Qingguo Wang, Konnor La, Nikolaus Schultz, Chris Sander

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Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. by Rozita Akrami, Anders Jacobsen, Jessica Hoell, Nikolaus Schultz, Chris Sander, Erik Larsson

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Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. by Parminder K Mankoo, Ronglai Shen, Nikolaus Schultz, Douglas A Levine, Chris Sander

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A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. by Yasin Şenbabaoğlu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander

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BridgeDb app: unifying identifier mapping services for Cytoscape [v1; ref status: indexed, http://f1000r.es/3qb] by Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico

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Integrative subtype discovery in glioblastoma using iCluster. by Ronglai Shen, Qianxing Mo, Nikolaus Schultz, Venkatraman E Seshan, Adam B Olshen, Jason Huse, Marc Ladanyi, Chris Sander

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Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer by Ying Z. Mazzu, Joshua Armenia, Subhiksha Nandakumar, Goutam Chakraborty, Yuki Yoshikawa, Lina E. Jehane, Gwo‐Shu Mary Lee, Mohammad Atiq, Nabeela Khan, Nikolaus Schultz, Philip W. Kantoff

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The genomic landscape of carcinomas with mucinous differentiation by Bastien Nguyen, Francisco Sanchez-Vega, Christopher J. Fong, Walid K. Chatila, Amir Momeni Boroujeni, Fresia Pareja, Britta Weigelt, Christos Sotiriou, Denis Larsimont, Jorge S. Reis-Filho, Christine Desmedt, Nikolaus Schultz

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Expression of the Carboxy-Terminal Portion of MUC16/CA125 Induces Transformation and Tumor Invasion. by Thapi D Rao, Huasong Tian, Xun Ma, Xiujun Yan, Sahityasri Thapi, Nikolaus Schultz, Nestor Rosales, Sebastien Monette, Amy Wang, David M Hyman, Douglas A Levine, David Solit, David R Spriggs

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Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death by Haley Hieronymus, Rajmohan Murali, Amy Tin, Kamlesh Yadav, Wassim Abida, Henrik Moller, Daniel Berney, Howard Scher, Brett Carver, Peter Scardino, Nikolaus Schultz, Barry Taylor, Andrew Vickers, Jack Cuzick, Charles L Sawyers

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Molecular Subtypes of Uterine Leiomyosarcoma and Correlation with Clinical Outcome by Joyce N. Barlin, Qin C. Zhou, Mario M. Leitao, Maria Bisogna, Narciso Olvera, Karin K. Shih, Anders Jacobsen, Nikolaus Schultz, William D. Tap, Martee L. Hensley, Gary K. Schwartz, Jeff Boyd, Li-Xuan Qin, Douglas A. Levine

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Genomic analysis and clinical correlations of non-small cell lung cancer brain metastasis by Anna Skakodub, Henry Walch, Kathryn R. Tringale, Jordan Eichholz, Brandon S. Imber, Harish N. Vasudevan, Bob T. Li, Nelson S. Moss, Kenny Kwok Hei Yu, Boris A. Mueller, Simon Powell, Pedram Razavi, Helena A. Yu, Jorge S. Reis-Filho, Daniel Gomez, Nikolaus Schultz, Luke R. G. Pike

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Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. by Chad J Creighton, Anadulce Hernandez-Herrera, Anders Jacobsen, Douglas A Levine, Parminder Mankoo, Nikolaus Schultz, Ying Du, Yiqun Zhang, Erik Larsson, Robert Sheridan, Weimin Xiao, Paul T Spellman, Gad Getz, David A Wheeler, Charles M Perou, Richard A Gibbs, Chris Sander, D Neil Hayes, Preethi H Gunaratne, Cancer Genome Atlas Research Network

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Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures by Nicholas A Graham, Aspram Minasyan, Anastasia Lomova, Ashley Cass, Nikolas G Balanis, Michael Friedman, Shawna Chan, Sophie Zhao, Adrian Delgado, James Go, Lillie Beck, Christian Hurtz, Carina Ng, Rong Qiao, Johanna ten Hoeve, Nicolaos Palaskas, Hong Wu, Markus Müschen, Asha S Multani, Elisa Port, Steven M Larson, Nikolaus Schultz, Daniel Braas, Heather R Christofk, Ingo K Mellinghoff, Thomas G Graeber

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Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets by Ying-Bei Chen, Jianing Xu, Anders Jacobsen Skanderup, Yiyu Dong, A. Rose Brannon, Lu Wang, Helen H. Won, Patricia I. Wang, Gouri J. Nanjangud, Achim A. Jungbluth, Wei Li, Virginia Ojeda, A. Ari Hakimi, Martin H. Voss, Nikolaus Schultz, Robert J. Motzer, Paul Russo, Emily H. Cheng, Filippo G. Giancotti, William Lee, Michael F. Berger, Satish K. Tickoo, Victor E. Reuter, James J. Hsieh

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Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers by Walid K. Chatila, Henry Walch, Jaclyn F. Hechtman, Sydney M. Moyer, Valeria Sgambati, David M. Faleck, Amitabh Srivastava, Laura Tang, Jamal Benhamida, Dorina Ismailgeci, Carl Campos, Fan Wu, Qing Chang, Efsevia Vakiani, Elisa de Stanchina, Martin R. Weiser, Maria Widmar, Rhonda K. Yantiss, Manish A. Shah, Adam J. Bass, Zsofia K. Stadler, Lior H. Katz, Ingo K. Mellinghoff, Nilay S. Sethi, Nikolaus Schultz, Karuna Ganesh, David Kelsen, Rona Yaeger

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BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking clusterin expression in cancer associated fibroblasts with HSF1 signaling by Lee Shaashua, Aviad Ben-Shmuel, Meirav Pevsner-Fischer, Gil Friedman, Oshrat Levi-Galibov, Subhiksha Nandakumar, Debra Barki, Reinat Nevo, Lauren E. Brown, Wenhan Zhang, Yaniv Stein, Chen Lior, Han Sang Kim, Linda Bojmar, William R. Jarnagin, Nicolas Lecomte, Shimrit Mayer, Roni Stok, Hend Bishara, Rawand Hamodi, Ephrat Levy-Lahad, Talia Golan, John A. Porco, Christine A. Iacobuzio-Donahue, Nikolaus Schultz, David A. Tuveson, David Lyden, David Kelsen, Ruth Scherz-Shouval

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Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma by Jianing Xu, Ed Reznik, Ho-Joon Lee, Gunes Gundem, Philip Jonsson, Judy Sarungbam, Anna Bialik, Francisco Sanchez-Vega, Chad J Creighton, Jake Hoekstra, Li Zhang, Peter Sajjakulnukit, Daniel Kremer, Zachary Tolstyka, Jozefina Casuscelli, Steve Stirdivant, Jie Tang, Nikolaus Schultz, Paul Jeng, Yiyu Dong, Wenjing Su, Emily H Cheng, Paul Russo, Jonathan A Coleman, Elli Papaemmanuil, Ying-Bei Chen, Victor E Reuter, Chris Sander, Scott R Kennedy, James J Hsieh, Costas A Lyssiotis, Satish K Tickoo, A Ari Hakimi

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Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets by Benjamin A. Nacev, Francisco Sanchez-Vega, Shaleigh A. Smith, Cristina R. Antonescu, Evan Rosenbaum, Hongyu Shi, Cerise Tang, Nicholas D. Socci, Satshil Rana, Rodrigo Gularte-Mérida, Ahmet Zehir, Mrinal M. Gounder, Timothy G. Bowler, Anisha Luthra, Bhumika Jadeja, Azusa Okada, Jonathan A. Strong, Jake Stoller, Jason E. Chan, Ping Chi, Sandra P. D’Angelo, Mark A. Dickson, Ciara M. Kelly, Mary Louise Keohan, Sujana Movva, Katherine Thornton, Paul A. Meyers, Leonard H. Wexler, Emily K. Slotkin, Julia L. Glade Bender, Neerav N. Shukla, Martee L. Hensley, John H. Healey, Michael P. La Quaglia, Kaled M. Alektiar, Aimee M. Crago, Sam S. Yoon, Brian R. Untch, Sarah Chiang, Narasimhan P. Agaram, Meera R. Hameed, Michael F. Berger, David B. Solit, Nikolaus Schultz, Marc Ladanyi, Samuel Singer, William D. Tap

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Integrated Molecular Characterization of Testicular Germ Cell Tumors by Hui Shen, Juliann Shih, Daniel P. Hollern, Linghua Wang, Reanne Bowlby, Satish K. Tickoo, Vésteinn Thorsson, Andrew J. Mungall, Yulia Newton, Apurva M. Hegde, Joshua Armenia, Francisco Sánchez-Vega, John Pluta, Louise C. Pyle, Rohit Mehra, Victor E. Reuter, Guilherme Godoy, Jeffrey Jones, Carl S. Shelley, Darren R. Feldman, Daniel O. Vidal, Davor Lessel, Tomislav Kulis, Flavio M. Cárcano, Kristen M. Leraas, Tara M. Lichtenberg, Denise Brooks, Andrew D. Cherniack, Juok Cho, David I. Heiman, Katayoon Kasaian, Minwei Liu, Michael S. Noble, Liu Xi, Hailei Zhang, Wanding Zhou, Jean C. ZenKlusen, Carolyn M. Hutter, Ina Felau, Jiashan Zhang, Nikolaus Schultz, Gad Getz, Matthew Meyerson, Joshua M. Stuart, Rehan Akbani, David A. Wheeler, Peter W. Laird, Katherine L. Nathanson, Victoria K. Cortessis, Katherine A. Hoadley, Linghua Wang, Liu Xi, David Wheeler, Daniel Hughes, Kyle Covington, Joy C. Jayaseelan, Viktoriya Korchina, Lora Lewis, Jianhong Hu, HarshaVardhan Doddapaneni, Donna Muzny, Richard Gibbs, Katherine A. Hoadley, Daniel Hollern, Benjamin G. Vincent, Shengjie Chai, Christof C. Smith, J. Todd Auman, Yan Shi, Shaowu Meng, Tara Skelly, Donghui Tan, Umadevi Veluvolu, Piotr A. Mieczkowski, Corbin D. Jones, Matthew D. Wilkerson, Saianand Balu, Tom Bodenheimer, Alan P. Hoyle, Stuart R. Jefferys, Lisle E. Mose, Janae V. Simons, Matthew G. Soloway, Jeffrey Roach, Joel S. Parker, D. Neil Hayes, Charles M. Perou, Juliann Shih, Andrew D. Cherniack, Matthew Meyerson, Gordon Saksena, Carrie Cibulskis, Steven E. Schumacher, Rameen Beroukhim, Stacey B. Gabriel, Reanne Bowlby, Andrew J. Mungall, Denise Brooks, Katayoon Kasaian, Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Dorothy Cheung, Eric Chuah, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Yussanne Ma, Michael Mayo, Richard A. Moore, A. Gordon Robertson, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Tina Wong, Marco A. Marra, Hui Shen, Wanding Zhou, Peter W. Laird, Daniel J. Weisenberger, David J. Van Den Berg, Phillip H. Lai, Mario Berrios, Andrea Holbrook, Moiz S. Bootwalla, Dennis T. Maglinte, Joshua Armenia, Francisco Sánchez-Vega, Nikolaus Schultz, Debyani Chakravarty, Jianjiong Gao, Zachary Heins, Ritika Kundra, Angelica Ochoa, Minwei Liu, Chris Sander, Marc Ladanyi, Vesteinn Thorsson, Amie J. Radenbaugh, Yulia Newton, Joshua M. Stuart, Juok Cho, David I. Heiman, Michael S. Noble, Hailei Zhang, Gad Getz, Nils Gehlenborg, Gordon Saksena, Doug Voet, Pei Lin, Scott Frazer, Jaegil Kim, Michael S. Lawrence, Sam Meier, Timothy Defreitas, Lynda Chin, Apurva M. Hegde, Rehan Akbani, John N. Weinstein, Wenbin Liu, Gordon B. Mills, Yiling Lu, Louise C. Pyle, John Pluta, Katherine L. Nathanson, Satish K. Tickoo, Victor E. Reuter, Rohit Mehra, Leendert Looijenga, Alan H. Bryce, Flavio M. Cárcano, André L. Carvalho, Victoria K. Cortessis, Darren Feldman, Guilherme Godoy, Michael Ittmann, Jeffrey Jones, Tomislav Kulis, Seth Lerner, Davor Lessel, Katherine L. Nathanson, Carl S. Shelley, Daniel O. Vidal, Kristen M. Leraas, Tara M. Lichtenberg, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Carmen Helsel, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Sandra Cottingham, David Chesla, Charles Saller, Katherine Tarvin, Luiz Fernando Lopes, Cristovam Scapulatempo-Neto, Natália D.A. Aredes, Wolter Oosterhuis, Ad Gillis, Hans Stoop, Wil Eijkenboom, George Sandusky, Sue Ellen Martin, Manju Aron, Siamak Daneshmand, Hooman Djaladat, David Quinn, Tanya Dorff, Jochen K. Lennerz, Leigh B. Thorne, Marija Gamulin, Zeljko Kastelan, Tvrtko Hudolin, Christian Kubisch, Lori Boice, Mei Huang, Amy H. Perou, W. Kimryn Rathmell, Todd Pihl, Yunhu Wan, Qiang Sun, Rashi Naresh, Sudha Chudamani, Jia Liu, Laxmi Lolla, Ye Wu, Martin L. Ferguson, Jean C. Zenklusen, Ina Felau, Jiashan (Julia) Zhang, Margi Sheth, John A. Demchok, Liming Yang, Zhining Wang, Roy Tarnuzzer, Carolyn M. Hutter, Heidi J. Sofia, Tanja M. Davidsen

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