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 deep learning image-based intrinsic molecular subtype classifier of breast tumors reveals tumor heterogeneity that may affect survival von Jaber, Mustafa I., Song, Bing, Taylor, Clive, Vaske, Charles J., Benz, Stephen C., Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Szeto, Christopher W.

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Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution von Cheng, Jeffrey B., Sedgewick, Andrew J., Finnegan, Alex I., Harirchian, Paymann, Lee, Jerry, Kwon, Sunjong, Fassett, Marlys S., Golovato, Justin, Gray, Matthew, Ghadially, Ruby, Liao, Wilson, Perez White, Bethany E., Mauro, Theodora M., Mully, Thaddeus, Kim, Esther A., Sbitany, Hani, Neuhaus, Isaac M., Grekin, Roy C., Yu, Siegrid S., Gray, Joe W., Purdom, Elizabeth, Paus, Ralf, Vaske, Charles J., Benz, Stephen C., Song, Jun S., Cho, Raymond J.

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Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma von North, Jeffrey P., Golovato, Justin, Vaske, Charles J., Sanborn, J. Zachary, Nguyen, Andrew, Wu, Wei, Goode, Benjamin, Stevers, Meredith, McMullen, Kevin, Perez White, Bethany E., Collisson, Eric A., Bloomer, Michele, Solomon, David A., Benz, Stephen C., Cho, Raymond J.

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The UCSC Genome Browser database: 2025 update von Perez, Gerardo, Barber, Galt P, Benet-Pages, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Christopher M, Nassar, Luis R, Raney, Brian J, Speir, Matthew L, van Baren, Marijke J, Vaske, Charles J, Haussler, David, Kent, W James, Haeussler, Maximilian

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Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling von Kristensen, Vessela N, Vaske, Charles J, Ursini-Siegel, Josie, Van Loo, Peter, Nordgard, Silje H, Sachidanandam, Ravi, Sørlie, Therese, Wärnberg, Fredrik, Haakensen, Vilde D, Helland, Åslaug, Naume, Bjørn, Perou, Charles M, Haussler, David, Troyanskaya, Olga G, Børresen-Dale, Anne-Lise

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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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Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy von Reimann, Hannah, Nguyen, Andrew, Sanborn, J Zachary, Vaske, Charles J, Benz, Stephen C, Niazi, Kayvan, Rabizadeh, Shahrooz, Spilman, Patricia, Mackensen, Andreas, Ruebner, Matthias, Hein, Alexander, Beckmann, Matthias W, van der Meijden, Edith D, Bausenwein, Judith, Kretschmann, Sascha, Griffioen, Marieke, Schlom, Jeffrey, Gulley, James L, Lee, Karin L, Hamilton, Duane H, Soon-Shiong, Patrick, Fasching, Peter A, Kremer, Anita N.

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Voltage-Gated Na+ Channel SCN5A Is a Key Regulator of a Gene Transcriptional Network That Controls Colon Cancer Invasion von HOUSE, Carrie D, VASKE, Charles J, STUART, Joshua M, LEE, Norman H, SCHWARTZ, Arnold M, OBIAS, Vincent, FRANK, Bryan, LUU, Truong, SARVAZYAN, Narine, IRBY, Rosalyn, STRAUSBERG, Robert L, HALES, Tim G

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A factor graph nested effects model to identify networks from genetic perturbations von Vaske, Charles J, House, Carrie, Luu, Truong, Frank, Bryan, Yeang, Chen-Hsiang, Lee, Norman H, Stuart, Joshua M

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Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome von Aure, Miriam Ragle, Vitelli, Valeria, Jernström, Sandra, Kumar, Surendra, Krohn, Marit, Due, Eldri U, Haukaas, Tonje Husby, Leivonen, Suvi-Katri, Vollan, Hans Kristian Moen, Lüders, Torben, Rødland, Einar, Vaske, Charles J, Zhao, Wei, Møller, Elen K, Nord, Silje, Giskeødegård, Guro F, Bathen, Tone Frost, Caldas, Carlos, Tramm, Trine, Alsner, Jan, Overgaard, Jens, Geisler, Jürgen, Bukholm, Ida R K, Naume, Bjørn, Schlichting, Ellen, Sauer, Torill, Mills, Gordon B, Kåresen, Rolf, Mælandsmo, Gunhild M, Lingjærde, Ole Christian, Frigessi, Arnoldo, Kristensen, Vessela N, Børresen-Dale, Anne-Lise, Sahlberg, Kristine K

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A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes von Harirchian, Paymann, Lee, Jerry, Hilz, Stephanie, Sedgewick, Andrew J., Perez White, Bethany E., Kesling, Michael J., Mully, Thaddeus, Golovato, Justin, Gray, Matthew, Mauro, Theodora M., Purdom, Elizabeth, Kim, Esther A., Sbitany, Hani, Bhutani, Tina, Vaske, Charles J., Benz, Stephen C., Cho, Raymond J., Cheng, Jeffrey B.

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Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM von Sedgewick, Andrew J, Benz, Stephen C, Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Vaske, Charles J

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Abstract 4512: High-throughput identification of neoepitopes for the development of patient-specific cancer immunotherapies von Nguyen, Andrew, Sanborn, J Zachary, Vaske, Charles J., Rabizadeh, Shahrooz, Niazi, Kayvan, Soon-Shiong, Patrick, Benz, Steven C.

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Transcriptomic silencing as a potential mechanism of treatment resistance von Adashek, Jacob J., Kato, Shumei, Parulkar, Rahul, Szeto, Christopher W., Sanborn, J. Zachary, Vaske, Charles J., Benz, Stephen C., Reddy, Sandeep K., Kurzrock, Razelle

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The UCSC Interaction Browser: multidimensional data views in pathway context von Wong, Christopher K, Vaske, Charles J, Ng, Sam, Sanborn, J Zachary, Benz, Stephen C, Haussler, David, Stuart, Joshua M

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Abstract 4980: T-cell receptor clonotyping and immune infiltrate quantification with whole transcriptome RNA-seq from FFPE von Sedgewick, Andrew J., Adashek, Jacob J., Szeto, Christopher W., Vaske, Charles J., Spiess, Philippe E., Benz, Stephen C.

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Abstract 556: Highly complex DNA sequencing library preparation for cfDNA enrichment panels using a single-stranded approach von Vaske, Charles J., Troll, Chris, Schwartz, Camille, Naughton, Colin, Ali, Abdullah Mahmood, Raza, Azra, Rao, Varsha, Harkins-Kincaid, Kelly, Green, Richard Edward

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Abstract 3398: Analysis of whole transcriptome RNA-seq of large numbers of clinical FFPE samples von Newton, Yulia, Golovato, Justin, Johnson, Mark, Rabizadeh, Shahrooz, Sanborn, Zack, Benz, Steve, Vaske, Charles J.

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Abstract 1188: Detecting intratumor heterogeneity of PAM50 subtypes in H&E-stained slides using deep learning von Jaber, Mustafa, Song, Bing, Taylor, Clive R., Vaske, Charles J., Szeto, Christopher W.

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