Search Results - "Mose, Lisle E"

Genetic determinants of cellular addiction to DNA polymerase theta by Feng, Wanjuan, Simpson, Dennis A., Carvajal-Garcia, Juan, Price, Brandon A., Kumar, Rashmi J., Mose, Lisle E., Wood, Richard D., Rashid, Naim, Purvis, Jeremy E., Parker, Joel S., Ramsden, Dale A., Gupta, Gaorav P.

“…Polymerase theta (Pol θ, gene name Polq ) is a widely conserved DNA polymerase that mediates a microhomology-mediated, error-prone, double strand break (DSB)…”
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ABRA: improved coding indel detection via assembly-based realignment by Mose, Lisle E, Wilkerson, Matthew D, Hayes, D Neil, Perou, Charles M, Parker, Joel S

“…Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used…”
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Prognostic value of B cells in cutaneous melanoma by Selitsky, Sara R, Mose, Lisle E, Smith, Christof C, Chai, Shengjie, Hoadley, Katherine A, Dittmer, Dirk P, Moschos, Stergios J, Parker, Joel S, Vincent, Benjamin G

“…Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell…”
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Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings by Seifert, Bryce A, O'Daniel, Julianne M, Amin, Krunal, Marchuk, Daniel S, Patel, Nirali M, Parker, Joel S, Hoyle, Alan P, Mose, Lisle E, Marron, Andrew, Hayward, Michele C, Bizon, Christopher, Wilhelmsen, Kirk C, Evans, James P, Earp, 3rd, H Shelton, Sharpless, Norman E, Hayes, D Neil, Berg, Jonathan S

“…To evaluate germline variants in hereditary cancer susceptibility genes among unselected cancer patients undergoing tumor-germline sequencing. Germline…”
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Virus expression detection reveals RNA-sequencing contamination in TCGA by Selitsky, Sara R, Marron, David, Hollern, Daniel, Mose, Lisle E, Hoadley, Katherine A, Jones, Corbin, Parker, Joel S, Dittmer, Dirk P, Perou, Charles M

“…Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous,…”
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Integrated RNA and DNA sequencing improves mutation detection in low purity tumors by Wilkerson, Matthew D, Cabanski, Christopher R, Sun, Wei, Hoadley, Katherine A, Walter, Vonn, Mose, Lisle E, Troester, Melissa A, Hammerman, Peter S, Parker, Joel S, Perou, Charles M, Hayes, D Neil

“…Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is…”
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SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling by Silva, Grace O, Siegel, Marni B, Mose, Lisle E, Parker, Joel S, Sun, Wei, Perou, Charles M, Chen, Mengjie

“…Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs…”
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A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability by Fagan-Solis, Katerina D., Simpson, Dennis A., Kumar, Rashmi J., Martelotto, Luciano G., Mose, Lisle E., Rashid, Naim U., Ho, Alice Y., Powell, Simon N., Wen, Y. Hannah, Parker, Joel S., Reis-Filho, Jorge S., Petrini, John H.J., Gupta, Gaorav P.

“…The Mre11-Rad50-Nbs1 complex is a DNA double-strand break sensor that mediates a tumor-suppressive DNA damage response (DDR) in cells undergoing oncogenic…”
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Translating transcriptomic findings from cancer model systems to humans through joint dimension reduction by Price, Brandon A., Marron, J. S., Mose, Lisle E., Perou, Charles M., Parker, Joel S.

“…Model systems are an essential resource in cancer research. They simulate effects that we can infer into humans, but come at a risk of inaccurately…”
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Genomic characterization of rare molecular subclasses of hepatocellular carcinoma by Damrauer, Jeffrey S., Smith, Markia A., Walter, Vonn, Thennavan, Aatish, Mose, Lisle E., Selitsky, Sara R., Hoadley, Katherine A.

“…Primary liver cancer, consisting of both cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC), is the second leading cause of cancer deaths worldwide…”
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Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality by Selitsky, Sara R, Marron, David, Mose, Lisle E, Parker, Joel S, Dittmer, Dirk P

“…Epstein-Barr virus (EBV) is convincingly associated with gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types…”
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Improved indel detection in DNA and RNA via realignment with ABRA2 by Mose, Lisle E, Perou, Charles M, Parker, Joel S

“…Genomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both…”
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Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer by Mose, Lisle E, Selitsky, Sara R, Bixby, Lisa M, Marron, David L, Iglesia, Michael D, Serody, Jonathan S, Perou, Charles M, Vincent, Benjamin G, Parker, Joel S

“…B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing…”
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Claudin-low bladder tumors are immune infiltrated and actively immune suppressed by Kardos, Jordan, Chai, Shengjie, Mose, Lisle E, Selitsky, Sara R, Krishnan, Bhavani, Saito, Ryoichi, Iglesia, Michael D, Milowsky, Matthew I, Parker, Joel S, Kim, William Y, Vincent, Benjamin G

“…We report the discovery of a claudin-low molecular subtype of high-grade bladder cancer that shares characteristics with the homonymous subtype of breast…”
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Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo by Lou, Jitong, Yang, Yang, Gu, Qisheng, Price, Brandon A, Qiu, Yuheng, Fedoriw, Yuri, Desai, Siddhi, Mose, Lisle E, Chen, Brian, Tateishi, Satoshi, Parker, Joel S, Vaziri, Cyrus, Wu, Di

“…The E3 ubiquitin ligase Rad18 promotes a damage-tolerant and error-prone mode of DNA replication termed trans-lesion synthesis that is pathologically activated…”
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Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer by Ciriello, Giovanni, Gatza, Michael L., Wilkerson, Matthew D., Rhie, Suhn K., Pastore, Alessandro, McLellan, Michael, Bowlby, Reanne, Lester, Susan C., Tse, Gary M.K., Chen, Yunn-Yi, Jensen, Kristin, Johnson, Nicole B., Mills, Gordon B., Robertson, Gordon, Benz, Christopher, Sander, Chris, Hoadley, Katherine A., King, Tari A., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Barr, Thomas, Beck, Andrew, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Cherniack, Andrew D., Chin, Lynda, Davidsen, Tanja, Demchok, John A., Dennison, Jennifer B., Ding, Li, Ferguson, Martin L., Gabriel, Stacey B., Gao, JianJiong, Gastier-Foster, Julie M., Gatza, Michael L., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gibson, William J., Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holbrook, Andrea, Hoyle, Alan P., Hu, Hai, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Ju, Zhenlin, Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lin, Pei, Liu, Jia, Liu, Wenbin, Maglinte, Dennis T., Mardis, Elaine, Marra, Marco A., McAllister, Cynthia, McLellan, Michael, Meng, Shaowu, Mills, Gordon B., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Noble, Michael S., Olopade, Olufunmilayo, Perou, Charles M., Saksena, Gordon, Schumacher, Steven E., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Sander, Chris, Sheth, Margi, Shi, Yan, Shih, Juliann, Shelley, Carl Simon, Simons, Janae V., Sofia, Heidi J., Sougnez, Carrie, Sun, Charlie, Van Den Berg, David J., Wan, Yunhu, Wang, Zhining, Wise, Lisa, Wiznerowicz, Maciej, Wu, Junyuan, Yang, Liming, Yau, Christina, Zack, Travis I., Zhang, Hailei, Zhang, Jiashan, Perou, Charles M.

“…Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast…”
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Abstract 1678: Accurate detection of expressed variation in RNA-seq by Mose, Lisle E., Marron, David, Parker, Joel S.

“…Abstract Somatic variant detection has long been an area of great interest and critical importance in cancer research and treatment. DNA-Seq based somatic…”
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Integrative Molecular Characterization of Malignant Pleural Mesothelioma by Hmeljak, Julija, Sanchez-Vega, Francisco, Hoadley, Katherine A, Shih, Juliann, Stewart, Chip, Heiman, David, Tarpey, Patrick, Danilova, Ludmila, Drill, Esther, Gibb, Ewan A, Bowlby, Reanne, Kanchi, Rupa, Osmanbeyoglu, Hatice U, Sekido, Yoshitaka, Takeshita, Jumpei, Newton, Yulia, Graim, Kiley, Gupta, Manaswi, Gay, Carl M, Diao, Lixia, Gibbs, David L, Thorsson, Vesteinn, Iype, Lisa, Kantheti, Havish, Severson, David T, Ravegnini, Gloria, Desmeules, Patrice, Jungbluth, Achim A, Travis, William D, Dacic, Sanja, Chirieac, Lucian R, Galateau-Sallé, Françoise, Fujimoto, Junya, Husain, Aliya N, Silveira, Henrique C, Rusch, Valerie W, Rintoul, Robert C, Pass, Harvey, Kindler, Hedy, Zauderer, Marjorie G, Kwiatkowski, David J, Bueno, Raphael, Tsao, Anne S, Creaney, Jenette, Lichtenberg, Tara, Leraas, Kristen, Bowen, Jay, Felau, Ina, Zenklusen, Jean Claude, Akbani, Rehan, Cherniack, Andrew D, Byers, Lauren A, Noble, Michael S, Fletcher, Jonathan A, Robertson, A Gordon, Shen, Ronglai, Aburatani, Hiroyuki, Robinson, Bruce W, Campbell, Peter, Ladanyi, Marc

“…Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a…”
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Integrated Molecular Characterization of Uterine Carcinosarcoma by Cherniack, Andrew D., Murray, Bradley A., Hu, Xin, Ling, Shiyun, Soslow, Robert A., Zuna, Rosemary E., Laird, Peter W., Kucherlapati, Raju, Mills, Gordon B., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Bodenheimer, Tom, Bogomolniy, Faina, Brooks, Denise, Carlsen, Rebecca, Cherniack, Andrew D., Cho, Juok, Chuah, Eric, Chudamani, Sudha, David, Mutch, Ferguson, Martin L., Frick, Jessica, Gabriel, Stacey, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Heiman, David I., Hess, Julian, Hoffmann, Robert, Holt, Robert A., Hu, Xin, Hutter, Carolyn M., Jefferys, Stuart R., Kanchi, Rupa S., Kandoth, Cyriac, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leshchiner, Ignaty, Levine, Douglas A., Lichtenberg, Tara M., Ling, Shiyun, Liu, Jia, Liu, Wenbin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Moore, Richard A., Mose, Lisle E., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Parker, Joel S., Perou, Charles M., Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salvesen, Helga B., Sheth, Margi, Shi, Yan, Shih, Juliann, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Sun, Charlie, Tan, Donghui, Tarnuzzer, Roy, Thorne, Leigh B., Tseng, Jill, Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Chen, Weisenberger, Daniel J., Wilkerson, Matthew D., Winterhoff, Boris, Wong, Tina, Yang, Liming, Zhang, Hailei, Zhu, Jing-chun, Zuna, Rosemary E., Weinstein, John N.

“…We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number…”
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Abstract 3592: Improved indel detection in RNA-seq data via assembly based re-alignment reveals expressed Epidermal Growth Factor Receptor indels in Lung Adenocarcinoma by Mose, Lisle E., Hayes, D. Neil, Perou, Charles M., Parker, Joel S.

“…Abstract Insertions and deletions in the transcriptome can potentially have significant impact on function and can be clinically actionable. A number of…”
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