Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM

por Sedgewick, Andrew J., Benz, Stephen C., Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Vaske, Charles J.
Publicado 2013

Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer

por Rabizadeh, Shahrooz, Garner, Chad, Sanborn, John Zachary, Benz, Stephen C., Reddy, Sandeep, Soon-Shiong, Patrick
Publicado 2018

Identification of an immune gene expression signature associated with favorable clinical features in Treg-enriched patient tumor samples

por Givechian, Kevin B., Wnuk, Kamil, Garner, Chad, Benz, Stephen, Garban, Hermes, Rabizadeh, Shahrooz, Niazi, Kayvan, Soon-Shiong, Patrick
Publicado 2018

The UCSC Interaction Browser: multidimensional data views in pathway context

por Wong, Christopher K., Vaske, Charles J., Ng, Sam, Sanborn, J. Zachary, Benz, Stephen C., Haussler, David, Stuart, Joshua M.
Publicado 2013

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

por Vaske, Charles J., Benz, Stephen C., Sanborn, J. Zachary, Earl, Dent, Szeto, Christopher, Zhu, Jingchun, Haussler, David, Stuart, Joshua M.
Publicado 2010

A deep learning image-based intrinsic molecular subtype classifier of breast tumors reveals tumor heterogeneity that may affect survival

por Jaber, Mustafa I., Song, Bing, Taylor, Clive, Vaske, Charles J., Benz, Stephen C., Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Szeto, Christopher W.
Publicado 2020

Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?

por Sadanandam, Anguraj, Lal, Aseem, Benz, Stephen C., Eppenberger-Castori, Serenella, Scott, Gary, Gray, Joe W., Spellman, Paul, Waldman, Fred, Benz, Christopher C.
Publicado 2012

Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

por Newton, Yulia, Sedgewick, Andrew J., Cisneros, Luis, Golovato, Justin, Johnson, Mark, Szeto, Christopher W., Rabizadeh, Shahrooz, Sanborn, J. Zachary, Benz, Stephen Charles, Vaske, Charles
Publicado 2020

Overcoming hypoxia-induced functional suppression of NK cells

por Solocinski, Kristen, Padget, Michelle R, Fabian, Kellsye P, Wolfson, Benjamin, Cecchi, Fabiola, Hembrough, Todd, Benz, Stephen C, Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Schlom, Jeffrey, Hodge, James W
Publicado 2020

Multi-region exome sequencing of ovarian immature teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, im...

por Heskett, Michael B., Sanborn, John Z., Boniface, Christopher, Goode, Benjamin, Chapman, Jocelyn, Garg, Karuna, Rabban, Joseph T., Zaloudek, Charles, Benz, Stephen C., Spellman, Paul T., Solomon, David A., Cho, Raymond J.
Publicado 2020

A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population

por Kang, Taekyu, Yau, Christina, Wong, Christopher K., Sanborn, John Z., Newton, Yulia, Vaske, Charlie, Benz, Stephen C., Krings, Gregor, Camarda, Roman, Henry, Jill E., Stuart, Josh, Powell, Mark, Benz, Christopher C.
Publicado 2020

The UCSC cancer genomics browser: update 2011

por 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
Publicado 2011

Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma

por 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.
Publicado 2018

Case report: Complete pathologic response with first-line immunotherapy combination in a young adult with massive liver dissemination of mismatch repair–deficient metastatic colore...

por Bergamo, Francesca, Dalla Santa, Silvia, Loupakis, Fotios, Cerma, Krisida, Tosi, Anna, De Grandis, Caterina, Dalla Pietà, Anna, Gringeri, Enrico, Angerilli, Valentina, Ramondo, Gaetano, Rago, Alessandro, Cecchi, Fabiola, Benz, Stephen, Cillo, Umberto, Dei Tos, Angelo Paolo, Zagonel, Vittorina, Fassan, Matteo, Rosato, Antonio, Lonardi, Sara
Publicado 2022

A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity

por Cook, Christopher P., Taylor, Mark, Liu, Yale, Schmidt, Ralf, Sedgewick, Andrew, Kim, Esther, Hailer, Ashley, North, Jeffrey P., Harirchian, Paymann, Wang, Hao, Kashem, Sakeen W., Shou, Yanhong, McCalmont, Timothy C., Benz, Stephen C., Choi, Jaehyuk, Purdom, Elizabeth, Marson, Alexander, Ramos, Silvia B.V., Cheng, Jeffrey B., Cho, Raymond J.
Publicado 2022

Inferred Immune-Cell Activity Is an Independent Predictor of HER2-Negative Breast Cancer Prognosis and Response to Paclitaxel-Based Therapy in the GeparSepto Trial

por Fasching, Peter A., Szeto, Christopher, Denkert, Carsten, Benz, Stephen, Weber, Karsten, Spilman, Patricia, Budczies, Jan, Schneeweiss, Andreas, Stickeler, Elmar, Schmatloch, Sabine, Jackisch, Christian, Karn, Thomas, Sinn, Hans Peter, Warm, Mathias, van Mackelenbergh, Marion, Rabizadeh, Shahrooz, Schem, Christian, Heinmöller, Ernst, Mueller, Volkmar, Marmé, Frederik, Soon-Shiong, Patrick, Nekljudova, Valentina, Untch, Michael, Loibl, Sibylle
Publicado 2023

Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy

por 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.
Publicado 2021

Safety, Feasibility, and Merits of Longitudinal Molecular Testing of Multiple Metastatic Sites to Inform mTNBC Patient Treatment in the Intensive Trial of Omics in Cancer

por Burton, Kimberly A., Mahen, Elisabeth, Konnick, Eric Quentin, Blau, Sibel, Dorschner, Michael O., Ramirez, Arturo B., Schmechel, Stephen C., Song, Chaozhong, Parulkar, Rahul, Parker, Stephanie, Senecal, Francis Mark, Pritchard, Colin C., Mecham, Brigham H., Szeto, Christopher, Spilman, Patricia, Zhu, Jingchun, Gadi, Vijayakrishna K., Ronen, Roy, Stilwell, Jackie, Kaldjian, Eric, Dutkowski, Janusz, Benz, Stephen Charles, Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Blau, C. Anthony
Publicado 2022

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

por 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, White, Bethany E. Perez, 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.
Publicado 2018

Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation

por Liu, Yale, Cook, Christopher, Sedgewick, Andrew J., Zhang, Shuyi, Fassett, Marlys S., Ricardo-Gonzalez, Roberto R., Harirchian, Paymann, Kashem, Sakeen W., Hanakawa, Sho, Leistico, Jacob R., North, Jeffrey P., Taylor, Mark A., Zhang, Wei, Man, Mao-Qiang, Charruyer, Alexandra, Beliakova-Bethell, Nadejda, Benz, Stephen C., Ghadially, Ruby, Mauro, Theodora M., Kaplan, Daniel H., Kabashima, Kenji, Choi, Jaehyuk, Song, Jun S., Cho, Raymond J., Cheng, Jeffrey B.
Publicado 2020