Visualizing and interpreting cancer genomics data via the Xena platform von Goldman, Mary J., Craft, Brian, Hastie, Mim, Repečka, Kristupas, McDade, Fran, Kamath, Akhil, Banerjee, Ayan, Luo, Yunhai, Rogers, Dave, Brooks, Angela N., Zhu, Jingchun, Haussler, David

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The UCSC Cancer Genomics Browser: update 2015 von Goldman, Mary, Craft, Brian, Swatloski, Teresa, Cline, Melissa, Morozova, Olena, Diekhans, Mark, Haussler, David, Zhu, Jingchun

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Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser von Cline, Melissa S., Craft, Brian, Swatloski, Teresa, Goldman, Mary, Ma, Singer, Haussler, David, Zhu, Jingchun

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Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM von Vaske, Charles J., Benz, Stephen C., Sanborn, J. Zachary, Earl, Dent, Szeto, Christopher, Zhu, Jingchun, Haussler, David, Stuart, Joshua M.

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A user guide for the online exploration and visualization of PCAWG data von Goldman, Mary J., Zhang, Junjun, Fonseca, Nuno A., Cortés-Ciriano, Isidro, Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, O’Connor, Brian D., Bazant, Wojciech, Barrera, Elisabet, Muñoz-Pomer, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John N., Huber, Wolfgang, Valencia, Alfonso, Park, Peter J., Papatheodorou, Irene, Zhu, Jingchun, Ferretti, Vincent, Vazquez, Miguel

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A DNA hypermethylation module for the stem/progenitor cell signature of cancer von Easwaran, Hariharan, Johnstone, Sarah E, Van Neste, Leander, Ohm, Joyce, Mosbruger, Tim, Wang, Qiuju, Aryee, Martin J, Joyce, Patrick, Ahuja, Nita, Weisenberger, Dan, Collisson, Eric, Zhu, Jingchun, Yegnasubramanian, Srinivasan, Matsui, William, Baylin, Stephen B

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The UCSC Cancer Genomics Browser: update 2013 von Goldman, Mary, Craft, Brian, Swatloski, Teresa, Ellrott, Kyle, Cline, Melissa, Diekhans, Mark, Ma, Singer, Wilks, Chris, Stuart, Josh, Haussler, David, Zhu, Jingchun

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Realizing the Promise of Reverse Phase Protein Arrays for Clinical, Translational, and Basic Research: A Workshop Report von Akbani, Rehan, Becker, Karl-Friedrich, Carragher, Neil, Goldstein, Ted, de Koning, Leanne, Korf, Ulrike, Liotta, Lance, Mills, Gordon B., Nishizuka, Satoshi S., Pawlak, Michael, Petricoin, Emanuel F., Pollard, Harvey B., Serrels, Bryan, Zhu, Jingchun

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The Human Epigenome Browser at Washington University von Zhou, Xin, Maricque, Brett, Xie, Mingchao, Li, Daofeng, Sundaram, Vasavi, Martin, Eric A, Koebbe, Brian C, Nielsen, Cydney, Hirst, Martin, Farnham, Peggy, Kuhn, Robert M, Zhu, Jingchun, Smirnov, Ivan, Kent, W James, Haussler, David, Madden, Pamela A F, Costello, Joseph F, Wang, Ting

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RADIA: RNA and DNA integrated analysis for somatic mutation detection von Radenbaugh, Amie J, Ma, Singer, Ewing, Adam, Stuart, Joshua M, Collisson, Eric A, Zhu, Jingchun, Haussler, David

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The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum von Bozdech, Zbynek, Llinás, Manuel, Pulliam, Brian Lee, Wong, Edith D, Zhu, Jingchun, DeRisi, Joseph L

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Expression profiling of the schizont and trophozoite stages of Plasmodium falciparumwith a long-oligonucleotide microarray von Bozdech, Zbynek, Zhu, Jingchun, Joachimiak, Marcin P, Cohen, Fred E, Pulliam, Brian, DeRisi, Joseph L

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Comparative genomics search for losses of long-established genes on the human lineage von Zhu, Jingchun, Sanborn, J Zachary, Diekhans, Mark, Lowe, Craig B, Pringle, Tom H, Haussler, David

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UCSC cancer genomics browser: update 2011 von Sanborn, J. Zachary, Benz, Stephen C, Craft, Brian, Szeto, Christopher, Kober, Kord M, Meyer, Laurence, Vaske, Charles J, Goldman, Mary, Smith, Kayla E, Kuhn, Robert M, Karolchik, Donna, Kent, W. James, Stuart, Joshua M, Haussler, David, Zhu, Jingchun

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Human tRNA genes function as chromatin insulators von Raab, Jesse R, Chiu, Jonathan, Zhu, Jingchun, Katzman, Sol, Kurukuti, Sreenivasulu, Wade, Paul A, Haussler, David, Kamakaka, Rohinton T

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Toil enables reproducible, open source, big biomedical data analyses von Vivian, John, Rao, Arjun Arkal, Nothaft, Frank Austin, Ketchum, Christopher, Armstrong, Joel, Novak, Adam, Pfeil, Jacob, Narkizian, Jake, Deran, Alden D, Musselman-Brown, Audrey, Schmidt, Hannes, Amstutz, Peter, Craft, Brian, Goldman, Mary, Rosenbloom, Kate, Cline, Melissa, O'Connor, Brian, Hanna, Megan, Birger, Chet, Kent, W James, Patterson, David A, Joseph, Anthony D, Zhu, Jingchun, Zaranek, Sasha, Getz, Gad, Haussler, David, Paten, Benedict

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The chromatin accessibility landscape of primary human cancers von Corces, M Ryan, Granja, Jeffrey M, Shams, Shadi, Louie, Bryan H, Seoane, Jose A, Zhou, Wanding, Silva, Tiago C, Groeneveld, Clarice, Wong, Christopher K, Cho, Seung Woo, Satpathy, Ansuman T, Mumbach, Maxwell R, Hoadley, Katherine A, Robertson, A Gordon, Sheffield, Nathan C, Felau, Ina, Castro, Mauro A A, Berman, Benjamin P, Staudt, Louis M, Zenklusen, Jean C, Laird, Peter W, Curtis, Christina, Greenleaf, William J, Chang, Howard Y

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Genomic basis for RNA alterations in cancer von Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin

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Abstract 911: UCSC Xena for cancer genomics visualization and interpretation von Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

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A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae von Zhu, Jingchun, Jambhekar, Ashwini, Sarver, Aaron, DeRisi, Joseph

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