Visualizing and interpreting cancer genomics data via the Xena platform
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
Published in Nature biotechnology (01.06.2020)
Published in Nature biotechnology (01.06.2020)
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Journal Article
The UCSC Cancer Genomics Browser: update 2015
Goldman, Mary, Craft, Brian, Swatloski, Teresa, Cline, Melissa, Morozova, Olena, Diekhans, Mark, Haussler, David, Zhu, Jingchun
Published in Nucleic acids research (28.01.2015)
Published in Nucleic acids research (28.01.2015)
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Journal Article
Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser
Cline, Melissa S, Craft, Brian, Swatloski, Teresa, Goldman, Mary, Ma, Singer, Haussler, David, Zhu, Jingchun
Published in Scientific reports (02.10.2013)
Published in Scientific reports (02.10.2013)
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Journal Article
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Vaske, Charles J., Benz, Stephen C., Sanborn, J. Zachary, Earl, Dent, Szeto, Christopher, Zhu, Jingchun, Haussler, David, Stuart, Joshua M.
Published in Bioinformatics (15.06.2010)
Published in Bioinformatics (15.06.2010)
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Journal Article
A user guide for the online exploration and visualization of PCAWG data
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
Published in Nature communications (07.07.2020)
Published in Nature communications (07.07.2020)
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A DNA hypermethylation module for the stem/progenitor cell signature of cancer
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
Published in Genome research (01.05.2012)
Published in Genome research (01.05.2012)
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Journal Article
The UCSC Cancer Genomics Browser: update 2013
Goldman, Mary, Craft, Brian, Swatloski, Teresa, Ellrott, Kyle, Cline, Melissa, Diekhans, Mark, Ma, Singer, Wilks, Chris, Stuart, Josh, Haussler, David, Zhu, Jingchun
Published in Nucleic acids research (01.01.2013)
Published in Nucleic acids research (01.01.2013)
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Journal Article
Realizing the Promise of Reverse Phase Protein Arrays for Clinical, Translational, and Basic Research: A Workshop Report
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
Published in Molecular & cellular proteomics (01.07.2014)
Published in Molecular & cellular proteomics (01.07.2014)
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Journal Article
The Human Epigenome Browser at Washington University
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
Published in Nature methods (01.12.2011)
Published in Nature methods (01.12.2011)
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Journal Article
RADIA: RNA and DNA integrated analysis for somatic mutation detection
Radenbaugh, Amie J, Ma, Singer, Ewing, Adam, Stuart, Joshua M, Collisson, Eric A, Zhu, Jingchun, Haussler, David
Published in PloS one (18.11.2014)
Published in PloS one (18.11.2014)
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Journal Article
The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
Bozdech, Zbynek, Llinás, Manuel, Pulliam, Brian Lee, Wong, Edith D, Zhu, Jingchun, DeRisi, Joseph L
Published in PLoS biology (01.10.2003)
Published in PLoS biology (01.10.2003)
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Journal Article
Comparative genomics search for losses of long-established genes on the human lineage
Zhu, Jingchun, Sanborn, J Zachary, Diekhans, Mark, Lowe, Craig B, Pringle, Tom H, Haussler, David
Published in PLoS computational biology (01.12.2007)
Published in PLoS computational biology (01.12.2007)
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Journal Article
UCSC cancer genomics browser: update 2011
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
Published in Nucleic acids research (01.01.2011)
Published in Nucleic acids research (01.01.2011)
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Journal Article
Human tRNA genes function as chromatin insulators
Raab, Jesse R, Chiu, Jonathan, Zhu, Jingchun, Katzman, Sol, Kurukuti, Sreenivasulu, Wade, Paul A, Haussler, David, Kamakaka, Rohinton T
Published in The EMBO journal (18.01.2012)
Published in The EMBO journal (18.01.2012)
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Journal Article
Toil enables reproducible, open source, big biomedical data analyses
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
Published in Nature biotechnology (01.04.2017)
Published in Nature biotechnology (01.04.2017)
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Journal Article
The chromatin accessibility landscape of primary human cancers
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
Published in Science (American Association for the Advancement of Science) (26.10.2018)
Published in Science (American Association for the Advancement of Science) (26.10.2018)
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Journal Article
Abstract 911: UCSC Xena for cancer genomics visualization and interpretation
Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David
Published in Cancer research (Chicago, Ill.) (01.07.2019)
Published in Cancer research (Chicago, Ill.) (01.07.2019)
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Journal Article
Abstract 2274: Cancer genomics visualization and interpretation using UCSC Xena
Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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