Search Results - "Vaske, Charles"

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

“…Breast cancer intrinsic molecular subtype (IMS) as classified by the expression-based PAM50 assay is considered a strong prognostic feature, even when…”
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Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM by Vaske, Charles J., Benz, Stephen C., Sanborn, J. Zachary, Earl, Dent, Szeto, Christopher, Zhu, Jingchun, Haussler, David, Stuart, Joshua M.

“…Motivation: High-throughput data is providing a comprehensive view of the molecular changes in cancer tissues. New technologies allow for the simultaneous…”
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Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution by 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.

“…Perturbations in the transcriptional programs specifying epidermal differentiation cause diverse skin pathologies ranging from impaired barrier function to…”
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Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma by 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.

“…Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole-exome sequencing on 32 SeC,…”
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The UCSC Genome Browser database: 2025 update by 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

“…The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000…”
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Voltage-Gated Na+ Channel SCN5A Is a Key Regulator of a Gene Transcriptional Network That Controls Colon Cancer Invasion by 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

“…Voltage-gated Na(+) channels (VGSC) have been implicated in the metastatic potential of human breast, prostate, and lung cancer cells. Specifically, the SCN5A…”
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JARID1B Is a Luminal Lineage-Driving Oncogene in Breast Cancer by Yamamoto, Shoji, Wu, Zhenhua, Russnes, Hege G., Takagi, Shinji, Peluffo, Guillermo, Vaske, Charles, Zhao, Xi, Moen Vollan, Hans Kristian, Maruyama, Reo, Ekram, Muhammad B., Sun, Hanfei, Kim, Jee Hyun, Carver, Kristopher, Zucca, Mattia, Feng, Jianxing, Almendro, Vanessa, Bessarabova, Marina, Rueda, Oscar M., Nikolsky, Yuri, Caldas, Carlos, Liu, X. Shirley, Polyak, Kornelia

“…Recurrent mutations in histone-modifying enzymes imply key roles in tumorigenesis, yet their functional relevance is largely unknown. Here, we show that…”
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Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling by 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

“…We use an integrated approach to understand breast cancer heterogeneity by modeling mRNA, copy number alterations, microRNAs, and methylation in a pathway…”
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Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer by Cisneros, Luis H, Vaske, Charles, Bussey, Kimberly J

“…The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. Bacteria deploy SIM when…”
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A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes by 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.

“…Genetic variation in the NF-κB inhibitors, ABIN1 and A20, increase risk for psoriasis. While critical for hematopoietic immune cell function, these genes are…”
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Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM by Sedgewick, Andrew J, Benz, Stephen C, Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Vaske, Charles J

“…High-dimensional '-omics' profiling provides a detailed molecular view of individual cancers; however, understanding the mechanisms by which tumors evade…”
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Abstract 4512: High-throughput identification of neoepitopes for the development of patient-specific cancer immunotherapies by Nguyen, Andrew, Sanborn, J Zachary, Vaske, Charles J., Rabizadeh, Shahrooz, Niazi, Kayvan, Soon-Shiong, Patrick, Benz, Steven C.

“…Abstract Introduction: Immunotherapies such as checkpoint inhibitors, CAR T cells, NK cells, and therapeutic vaccines are revolutionizing cancer medicine…”
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Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing by Lee, Mei-Chong Wendy, Lopez-Diaz, Fernando J, Khan, Shahid Yar, Tariq, Muhammad Akram, Dayn, Yelena, Vaske, Charles Joseph, Radenbaugh, Amie J, Kim, Hyunsung John, Emerson, Beverly M, Pourmand, Nader

“…The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the…”
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Transcriptomic silencing as a potential mechanism of treatment resistance by Adashek, Jacob J, Kato, Shumei, Parulkar, Rahul, Szeto, Christopher W, Sanborn, J Zachary, Vaske, Charles J, Benz, Stephen C, Reddy, Sandeep K, Kurzrock, Razelle

“…Next-generation sequencing (NGS) has not revealed all the mechanisms underlying resistance to genomically matched drugs. Here, we performed in 1417 tumors…”
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UCSC cancer genomics browser: update 2011 by 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

“…The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and…”
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The UCSC Interaction Browser: multidimensional data views in pathway context by Wong, Christopher K, Vaske, Charles J, Ng, Sam, Sanborn, J Zachary, Benz, Stephen C, Haussler, David, Stuart, Joshua M

“…High-throughput data sets such as genome-wide protein-protein interactions, protein-DNA interactions and gene expression data have been published for several…”
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Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy by 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.

“…BackgroundTherapeutic regimens designed to augment the immunological response of a patient with breast cancer (BC) to tumor tissue are critically informed by…”
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A factor graph nested effects model to identify networks from genetic perturbations by Vaske, Charles J, House, Carrie, Luu, Truong, Frank, Bryan, Yeang, Chen-Hsiang, Lee, Norman H, Stuart, Joshua M

“…Complex phenotypes such as the transformation of a normal population of cells into cancerous tissue result from a series of molecular triggers gone awry. We…”
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Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome by 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

“…Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different…”
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Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity by Wnuk, Kamil, Sudol, Jeremi, Givechian, Kevin B., Soon-Shiong, Patrick, Rabizadeh, Shahrooz, Szeto, Christopher, Vaske, Charles

“…DNA accessibility is a key dynamic feature of chromatin regulation that can potentiate transcriptional events and tumor progression. To gain insight into…”
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