Search Results - "Shen, John P"

Network-based stratification of tumor mutations by Hofree, Matan, Shen, John P, Carter, Hannah, Gross, Andrew, Ideker, Trey

“…This paper reports a strategy for combining somatic mutation profiles of human tumors with gene networks to stratify tumors into biologically and clinically…”
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Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss by Gross, Andrew M, Orosco, Ryan K, Shen, John P, Egloff, Ann Marie, Carter, Hannah, Hofree, Matan, Choueiri, Michel, Coffey, Charles S, Lippman, Scott M, Hayes, D Neil, Cohen, Ezra E, Grandis, Jennifer R, Nguyen, Quyen T, Ideker, Trey

“…Trey Ideker and colleagues report a comprehensive genome-wide analysis of head and neck squamous cell carcinoma, reporting that TP53 mutations are frequently…”
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Prognostic significance of acellular mucin in patients undergoing cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CRS/HIPEC) for appendiceal neoplasms by Erstad, Derek J., Robinson, Kristen A., Beaty, Karen, Rafeeq, Safia, Chiang, Yi-Ju, Raghav, Kanwal, Shen, John P., Overman, Michael J., Foo, Wai Chin, Taggart, Melissa W., Mansfield, Paul. F., Royal, Richard E., Fournier, Keith F., Scally, Christopher P.

“…Introduction Appendiceal neoplasms have a propensity for peritoneal dissemination. The standard of care for select individuals is CRS/HIPEC. In the current 8…”
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Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy in RAS/RAF Wild-Type Colorectal Cancer Vary by Regimen and Line of Therapy by Parseghian, Christine M, Sun, Ryan, Woods, Melanie, Napolitano, Stefania, Lee, Hey Min, Alshenaifi, Jumanah, Willis, Jason, Nunez, Shakayla, Raghav, Kanwal P, Morris, Van K, Shen, John P, Eluri, Madhulika, Sorokin, Alexey, Kanikarla, Preeti, Vilar, Eduardo, Rehn, Marko, Ang, Agnes, Troiani, Teresa, Kopetz, Scott

“…Acquired resistance to anti-epidermal growth factor receptor (EGFR) inhibitor (EGFRi) therapy in colorectal cancer (CRC) has previously been explained by the…”
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Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer by Raghav, Kanwal, Shen, John P., Jácome, Alexandre A., Guerra, Jennifer L., Scally, Christopher P., Taggart, Melissa W., Foo, Wai C., Matamoros, Aurelio, Shaw, Kenna R., Fournier, Keith, Overman, Michael J., Eng, Cathy

“…Background Appendiceal adenocarcinoma (AA) is an orphan disease with unique clinical attributes but often treated as colorectal cancer (CRC). Understanding key…”
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Clinical and molecular characteristics of patients with brain metastasis secondary to pancreatic ductal adenocarcinoma by Yousef, Mahmoud, Hurd, Mark W, Yousef, Abdelrahman, Ludmir, Ethan B, Pillai, Ashwathy B, Peterson, Jennifer, Koay, Eugene J, Albarouki, Sali, Tzeng, Ching-Wei, Snyder, Rebecca, Katz, Matthew H G, Wang, Huamin, Overman, Michael J, Maitra, Anirban, Pant, Shubham, Smaglo, Brandon G, Wolff, Robert A, Yao, James, Shen, John P, Zhao, Dan

“…The prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) is poor. Secondary brain metastasis (Br-M) occurs in less than 1% of patients. Clinical…”
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Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers by Klomp, Jeffrey A, Klomp, Jennifer E, Stalnecker, Clint A, Bryant, Kirsten L, Edwards, A Cole, Drizyte-Miller, Kristina, Hibshman, Priya S, Diehl, J Nathaniel, Lee, Ye S, Morales, Alexis J, Taylor, Khalilah E, Peng, Sen, Tran, Nhan L, Herring, Laura E, Prevatte, Alex W, Barker, Natalie K, Hover, Laura D, Hallin, Jill, Chowdhury, Saikat, Coker, Oluwadara, Lee, Hey Min, Goodwin, Craig M, Gautam, Prson, Olson, Peter, Christensen, James G, Shen, John P, Kopetz, Scott, Graves, Lee M, Lim, Kian-Huat, Wang-Gillam, Andrea, Wennerberg, Krister, Cox, Adrienne D, Der, Channing J

“…How the oncogene drives cancer growth remains poorly understood. Therefore, we established a systemwide portrait of KRAS- and extracellular signal-regulated…”
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Dynamic speculative precomputation by Collins, J.D., Tullsen, D.M., Wang, Hong, Shen, J.P.

“…A large number of memory accesses in memory-bound applications are irregular, such as pointer dereferences, and can be effectively targeted by thread-based…”
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Theoretical modeling of superscalar processor performance by Noonburg, Derek B., Shen, John P.

“…The current trace-driven simulation approach to determine superscalar processor performance is widely used but has some shortcomings. Modern benchmarks…”
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Speculative precomputation: long-range prefetching of delinquent loads by Collins, Jamison D., Wang, Hong, Tullsen, Dean M., Hughes, Christopher, Lee, Yong-Fong, Lavery, Dan, Shen, John P.

“…This paper explores Speculative Precomputation, a technique that uses idle thread context in a multithreaded architecture to improve performance of…”
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Somatic mutation landscape of appendiceal cancer by Shen, John P., Jacobs, Miriam T., Fuh, Ingrid L, Baumgartner, Joel Micah, Fanta, Paul T., Lowy, Andrew M., Harismendy, Olivier

“…Abstract only 671 Background: Appendiceal cancers are rare, comprising just 0.5% of all intestinal neoplasia, which has prevented the systematic study of these…”
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Physical Experimentation with Prefetching Helper Threads on Intel's Hyper-Threaded Processors by Kim, Dongkeun, Liao, Steve Shih-wei, Wang, Perry H., Cuvillo, Juan del, Tian, Xinmin, Zou, Xiang, Wang, Hong, Yeung, Donald, Girkar, Milind, Shen, John P.

“…Pre-execution techniques have received much attention as aneffective way of prefetching cache blocks to tolerate the ever-increasingmemory latency. A number of…”
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Abstract 822: Oncogene addiction to GNAS in GNASR201 mutant tumors by More, Aditya, Haridas, Valsala, Ito, Ichiaki, Chowdhury, Saikat, Gu, Yue, Fowlkes, Natalie W., Shen, John P.

“…Abstract Background: The GNASR201 mutation is the single most frequent cancer-causing mutation across all heterotrimeric G proteins. This gain of function…”
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Abstract 6546: Peritoneal microenvironment promotes appendiceal adenocarcinoma tumor formation in PDX models by Pattalachinti, Vinay K., Ito, Ichiaki, Chowdhury, Saikat, Yousef, Abdelrahman, Gu, Yue, Fournier, Keith F., Shen, John P.

“…Abstract Background: Few preclinical models of appendiceal adenocarcinomas (AAs) exist. Orthotopic patient-derived xenografts (PDXs) better recapitulate the…”
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Hardware Support for Prescient Instruction Prefetch by Aamodt, T.M., Chow, P., Hammarlund, P., Wang, Hong, Shen, J.P.

“…This paper proposes and evaluates hardware mechanisms for supporting prescient instruction prefetch - an approach to improving single-threaded application…”
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Abstract 6040: Orthotopic patient-derived xenograft models of appendiceal adenocarcinoma identify intraperitoneal paclitaxel treatment as an active therapeutic agent by Ito, Ichiaki, White, Michael G., Yousef, Abdelrahman M., Dickson, Princess N., Gu, Yue, Fournier, Keith F., Shen, John P.

“…Abstract Background Appendiceal adenocarcinomas (AAs) are a rare and heterogeneous mix of tumors for which only few preclinical models exist for drug…”
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A platinum-resistant subtype of high-grade serous ovarian cancer identified by a network of somatic mutations by Shen, John P., Bojorquez-Gomez, Ana, Huang, Justin, Hofree, Matan, Kurnit, Katie, Klepper, Kristin, Beckett, Alex, Kreisberg, Jason F, Saenz, Cheryl C., Ideker, Trey

“…Abstract only 5561 Background: High-grade serous ovarian carcinoma (HGS-OvCa) is a heterogeneous entity with a widely variable clinical course even among…”
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A Robust Small-Molecule Microarray Platform for Screening Cell Lysates by Bradner, James E., McPherson, Olivia M., Mazitschek, Ralph, Barnes-Seeman, David, Shen, John P., Dhaliwal, Jasmeet, Stevenson, Kristen E., Duffner, Jay L., Park, Seung Bum, Neuberg, Donna S., Nghiem, Paul, Schreiber, Stuart L., Koehler, Angela N.

“…Herein we report the expanded functional group compatibility of small-molecule microarrays to include immobilization of primary alcohols, secondary alcohols,…”
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Abstract CT148: Efficacy, safety, and biomarker analysis of combined MEK (Cobimetinib) and PD-L1 (Atezolizumab) inhibition (COTEZO) in advanced small bowel adenocarcinoma (SBA) by Hornstein, Nicholas, Shen, John P., Pellatt, Andrew J., Liu, Suyu, Knafl, Mark, Willett, Anneleis F., Zhu, Haifeng, Maru, Dipen M., Darbonne, Walter, Wistuba, Ignacio I., Futreal, Andy, Yao, James C., Woodman, Scott E., Overman, Michael J., Raghav, Kanwal P.

“…Abstract Purpose: Preclinical evidence supporting immunomodulatory effect of MEK inhibition that augments anti-tumor activity of PD-1 inhibitors is a…”
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Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma by Gross, Andrew, Choueiri, Michel, Shen, John P., Randall, James Michael, Ideker, Trey, Hofree, Matan

“…Abstract only e15562 Background: Epigenetic silencing of genes associated with the taurine/hypotaurine pathway has been associated with worse outcome in…”
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