Search Results - "Mashl, R. Jay"

Protein-structure-guided discovery of functional mutations across 19 cancer types by Niu, Beifang, Scott, Adam D, Sengupta, Sohini, Bailey, Matthew H, Batra, Prag, Ning, Jie, Wyczalkowski, Matthew A, Liang, Wen-Wei, Zhang, Qunyuan, McLellan, Michael D, Sun, Sam Q, Tripathi, Piyush, Lou, Carolyn, Ye, Kai, Mashl, R Jay, Wallis, John, Wendl, Michael C, Chen, Feng, Ding, Li

“…Li Ding, Feng Chen and colleagues report a pan-cancer analysis using a new computational tool, HotSpot3D, to identify mutational hotspots in the encoded…”
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CharGer: clinical Characterization of Germline variants by Scott, Adam D, Huang, Kuan-Lin, Weerasinghe, Amila, Mashl, R Jay, Gao, Qingsong, Martins Rodrigues, Fernanda, Wyczalkowski, Matthew A, Ding, Li

“…Abstract Summary CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity of germline…”
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Database of evidence for precision oncology portal by Sun, Sam Q, Mashl, R Jay, Sengupta, Sohini, Scott, Adam D, Wang, Weihua, Batra, Prag, Wang, Liang-Bo, Wyczalkowski, Matthew A, Ding, Li

“…Abstract Summary A database of curated genomic variants with clinically supported drug therapies and other oncological annotations is described. The…”
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GenomeVIP: a cloud platform for genomic variant discovery and interpretation by Mashl, R Jay, Scott, Adam D, Huang, Kuan-Lin, Wyczalkowski, Matthew A, Yoon, Christopher J, Niu, Beifang, DeNardo, Erin, Yellapantula, Venkata D, Handsaker, Robert E, Chen, Ken, Koboldt, Daniel C, Ye, Kai, Fenyö, David, Raphael, Benjamin J, Wendl, Michael C, Ding, Li

“…Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating…”
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Cholesterol-Induced Modifications in Lipid Bilayers: A Simulation Study by Chiu, S.W., Jakobsson, Eric, Mashl, R. Jay, Scott, H. Larry

“…We present analysis of new configurational bias Monte Carlo and molecular dynamics simulation data for bilayers of dipalmitoyl phosphatidyl choline and…”
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Dynamic host immune response in virus-associated cancers by Cao, Song, Wylie, Kristine M., Wyczalkowski, Matt A., Karpova, Alla, Ley, Jessica, Sun, Sam, Mashl, R. Jay, Liang, Wen-Wei, Wang, Xiaowei, Johnson, Kimberly, DiPersio, John F., Gay, Hiram, Ratner, Lee, Chen, Feng, Adkins, Douglas R., Ding, Li

“…Viruses drive carcinogenesis in human cancers through diverse mechanisms that have not been fully elucidated but include promoting immune escape. Here we…”
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Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation by Pandit, Sagar A., Vasudevan, S., Chiu, S.W., Jay Mashl, R., Jakobsson, Eric, Scott, H.L.

“…We have carried out an atomic-level molecular dynamics simulation of a system of nanoscopic size containing a domain of 18:0 sphingomyelin and cholesterol…”
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Structure of Sphingomyelin Bilayers: A Simulation Study by Chiu, S.W., Vasudevan, S., Jakobsson, Eric, Mashl, R. Jay, Scott, H. Larry

“…We have carried out a molecular dynamics simulation of a hydrated 18:0 sphingomyelin lipid bilayer. The bilayer contained 1600 sphingomyelin (SM) molecules,…”
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Molecular Simulation of Dioleoylphosphatidylcholine Lipid Bilayers at Differing Levels of Hydration by Mashl, R. Jay, Scott, H. Larry, Subramaniam, Shankar, Jakobsson, Eric

“…The structure and dynamics of the lipid and water components of dioleoylphosphatidylcholine bilayers at various levels of hydration were studied using…”
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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer by Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S., Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C., Huang, Kuan-lin, Newberg, Justin Y., Mashl, R. Jay, Romanel, Alessandro, Sayaman, Rosalyn W., Demichelis, Francesca, Felau, Ina, Frampton, Garrett M., Han, Seunghun, Hoadley, Katherine A., Kemal, Anab, Laird, Peter W., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K., Zenklusen, Jean C., Ziv, Elad, Aguet, Francois, Ding, Li, Demchok, John A., Mensah, Michael K.A., Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J., MacArthur, Daniel G., Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M., Cherniack, Andrew D., Beroukhim, Rameen

“…We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer…”
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Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer by Cui Zhou, Daniel, Jayasinghe, Reyka G., Chen, Siqi, Herndon, John M., Iglesia, Michael D., Navale, Pooja, Wendl, Michael C., Caravan, Wagma, Sato, Kazuhito, Storrs, Erik, Mo, Chia-Kuei, Liu, Jingxian, Southard-Smith, Austin N., Wu, Yige, Naser Al Deen, Nataly, Baer, John M., Fulton, Robert S., Wyczalkowski, Matthew A., Liu, Ruiyang, Fronick, Catrina C., Fulton, Lucinda A., Shinkle, Andrew, Thammavong, Lisa, Zhu, Houxiang, Sun, Hua, Wang, Liang-Bo, Li, Yize, Zuo, Chong, McMichael, Joshua F., Davies, Sherri R., Appelbaum, Elizabeth L., Robbins, Keenan J., Chasnoff, Sara E., Yang, Xiaolu, Reeb, Ashley N., Oh, Clara, Serasanambati, Mamatha, Lal, Preet, Varghese, Rajees, Mashl, Jay R., Ponce, Jennifer, Terekhanova, Nadezhda V., Yao, Lijun, Wang, Fang, Chen, Lijun, Schnaubelt, Michael, Lu, Rita Jui-Hsien, Schwarz, Julie K., Puram, Sidharth V., Kim, Albert H., Song, Sheng-Kwei, Shoghi, Kooresh I., Lau, Ken S., Ju, Tao, Chen, Ken, Chatterjee, Deyali, Hawkins, William G., Zhang, Hui, Achilefu, Samuel, Chheda, Milan G., Oh, Stephen T., Gillanders, William E., Chen, Feng, DeNardo, David G., Fields, Ryan C., Ding, Li

“…Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11…”
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Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma by Wu, Yige, Chen, Siqi, Yang, Xiaolu, Sato, Kazuhito, Lal, Preet, Wang, Yuefan, Shinkle, Andrew T, Wendl, Michael C, Primeau, Tina M, Zhao, Yanyan, Gould, Alanna, Sun, Hua, Mudd, Jacqueline L, Hoog, Jeremy, Mashl, R Jay, Wyczalkowski, Matthew A, Mo, Chia-Kuei, Liu, Ruiyang, Herndon, John M, Davies, Sherri R, Liu, Di, Ding, Xi, Evrard, Yvonne A, Welm, Bryan E, Lum, David, Koh, Mei Yee, Welm, Alana L, Chuang, Jeffrey H, Moscow, Jeffrey A, Meric-Bernstam, Funda, Govindan, Ramaswamy, Li, Shunqiang, Hsieh, James, Fields, Ryan C, Lim, Kian-Huat, Ma, Cynthia X, Zhang, Hui, Ding, Li, Chen, Feng

“…Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug…”
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Anomalously Immobilized Water:  A New Water Phase Induced by Confinement in Nanotubes by Mashl, R. Jay, Joseph, Sony, Aluru, N. R, Jakobsson, Eric

“…Confinement can induce unusual behavior in the properties of matter. Using molecular dynamics simulations, we show here that water confined to carbon nanotubes…”
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Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models by Guo, Zhanfang, Luo, Jingqin, Mashl, R Jay, Hoog, Jeremy, Maiti, Piyush, Fettig, Nikki, Davies, Sherri R, Aft, Rebecca, Held, Jason M, Govindan, Ramaswamy, Ding, Li, Li, Shunqiang, von Morze, Cornelius, Wulf, Gerburg M, Shoghi, Kooresh I, Ma, Cynthia X

“…The PI3K pathway regulates essential cellular functions and promotes chemotherapy resistance. Activation of PI3K pathway signaling is commonly observed in…”
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Electrolytic Transport in Modified Carbon Nanotubes by Joseph, Sony, Mashl, R. Jay, Jakobsson, Eric, Aluru, N. R

“…Molecular dynamics simulations were used to study ionic flow in carbon nanotubes with the goal of using carbon nanotubes as artificial protein channels found…”
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Hierarchical Approach to Predicting Permeation in Ion Channels by Mashl, R. Jay, Tang, Yuzhou, Schnitzer, Jim, Jakobsson, Eric

“…A hierarchical computational strategy combining molecular modeling, electrostatics calculations, molecular dynamics, and Brownian dynamics simulations is…”
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Simulation of charge transport in ion channels and nanopores with anisotropic permittivity by Toghraee, Reza, Mashl, R. Jay, Lee, Kyu Il, Jakobsson, Eric, Ravaioli, Umberto

“…Ion channels are part of nature’s solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and…”
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Dynamic Protonation of Biomolecules in Molecular Simulation by Mashl, R. Jay

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Ancestry-specific predisposing germline variants in cancer by Oak, Ninad, Cherniack, Andrew D, Mashl, R Jay, Hirsch, Fred R, Ding, Li, Beroukhim, Rameen, Gümüş, Zeynep H, Plon, Sharon E, Huang, Kuan-Lin

“…Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of…”
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Abstract 3424: Genomic alterations in clonal hematopoiesis by Huang, Kuan-Lin, Xie, Mingchao, Wu, Yige, Jayasinghe, Reyka, Varghese, Rajees, Mashl, R. Jay, Cao, Song, Wyczalkowski, Matthew, Liang, Wen-wei, Wendel, Michael C., Fields, Ryan, McLellan, Michael D., Link, Daniel C., Chen, Feng, Ding, Li

“…Abstract Cancer development is an incremental process. Mutations that initiate clonal hematopoiesis often arise in individuals many years before disease…”
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