Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer von Rashid, Naim U, Peng, Xianlu L, Jin, Chong, Moffitt, Richard A, Volmar, Keith E, Belt, Brian A, Panni, Roheena Z, Nywening, Timothy M, Herrera, Silvia G, Moore, Kristin J, Hennessey, Sarah G, Morrison, Ashley B, Kawalerski, Ryan, Nayyar, Apoorve, Chang, Audrey E, Schmidt, Benjamin, Kim, Hong Jin, Linehan, David C, Yeh, Jen Jen

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Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex von Zawistowski, Jon S, Bevill, Samantha M, Goulet, Daniel R, Stuhlmiller, Timothy J, Beltran, Adriana S, Olivares-Quintero, Jose F, Singh, Darshan, Sciaky, Noah, Parker, Joel S, Rashid, Naim U, Chen, Xin, Duncan, James S, Whittle, Martin C, Angus, Steven P, Velarde, Sara Hanna, Golitz, Brian T, He, Xiaping, Santos, Charlene, Darr, David B, Gallagher, Kristalyn, Graves, Lee M, Perou, Charles M, Carey, Lisa A, Earp, H Shelton, Johnson, Gary L

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Pain modality- and sex-specific effects of COMT genetic functional variants von Belfer, Inna, Segall, Samantha K., Lariviere, William R., Smith, Shad B., Dai, Feng, Slade, Gary D., Rashid, Naim U., Mogil, Jeffrey S., Campbell, Claudia M., Edwards, Robert R., Liu, Qian, Bair, Eric, Maixner, William, Diatchenko, Luda

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glmmPen: High Dimensional Penalized Generalized Linear Mixed Models von Heiling, Hillary M, Rashid, Naim U, Li, Quefeng, Ibrahim, Joseph G

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A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability von 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.

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Mu Opioid Splice Variant MOR-1K Contributes to the Development of Opioid-Induced Hyperalgesia von Oladosu, Folabomi A, Conrad, Matthew S, O'Buckley, Sandra C, Rashid, Naim U, Slade, Gary D, Nackley, Andrea G

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Differential and limited expression of mutant alleles in multiple myeloma von Rashid, Naim U., Sperling, Adam S., Bolli, Niccolo, Wedge, David C., Van Loo, Peter, Tai, Yu-Tzu, Shammas, Masood A., Fulciniti, Mariateresa, Samur, Mehmet K., Richardson, Paul G., Magrangeas, Florence, Minvielle, Stephane, Futreal, P. Andrew, Anderson, Kenneth C., Avet-Loiseau, Herve, Campbell, Peter J., Parmigiani, Giovanni, Munshi, Nikhil C.

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Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model von Torre-Healy, Luke A., Kawalerski, Ryan R., Oh, Ki, Chrastecka, Lucie, Peng, Xianlu L., Aguirre, Andrew J., Rashid, Naim U., Yeh, Jen Jen, Moffitt, Richard A.

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Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma von Moffitt, Richard A, Marayati, Raoud, Flate, Elizabeth L, Volmar, Keith E, Loeza, S Gabriela Herrera, Hoadley, Katherine A, Rashid, Naim U, Williams, Lindsay A, Eaton, Samuel C, Chung, Alexander H, Smyla, Jadwiga K, Anderson, Judy M, Kim, Hong Jin, Bentrem, David J, Talamonti, Mark S, Iacobuzio-Donahue, Christine A, Hollingsworth, Michael A, Yeh, Jen Jen

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Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction von Rashid, Naim U., Li, Quefeng, Yeh, Jen Jen, Ibrahim, Joseph G.

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Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modeling von Young, Amber M, Van Buren, Scott, Rashid, Naim U

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FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036 von Angus, Steven P., Stuhlmiller, Timothy J., Mehta, Gaurav, Bevill, Samantha M., Goulet, Daniel R., Olivares-Quintero, J. Felix, East, Michael P., Tanioka, Maki, Zawistowski, Jon S., Singh, Darshan, Sciaky, Noah, Chen, Xin, He, Xiaping, Rashid, Naim U., Chollet-Hinton, Lynn, Fan, Cheng, Soloway, Matthew G., Spears, Patricia A., Jefferys, Stuart, Parker, Joel S., Gallagher, Kristalyn K., Forero-Torres, Andres, Krop, Ian E., Thompson, Alastair M., Murthy, Rashmi, Gatza, Michael L., Perou, Charles M., Earp, H. Shelton, Carey, Lisa A., Johnson, Gary L.

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DNA Mutational Profiling in Patients With Colorectal Cancer Treated With Standard of Care Reveals Differences in Outcome and Racial Distribution of Mutations von Innocenti, Federico, Mu, Wancen, Qu, Xueping, Ou, Fang-Shu, Kabbarah, Omar, Blanke, Charles David, Venook, Alan P, Lenz, Heinz-Josef, Rashid, Naim U

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Efficient detection and classification of epigenomic changes under multiple conditions von Baldoni, Pedro L., Rashid, Naim U., Ibrahim, Joseph G.

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ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions von Rashid, Naim U, Giresi, Paul G, Ibrahim, Joseph G, Sun, Wei, Lieb, Jason D

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Estimating cell type composition using isoform expression one gene at a time von Heiling, Hillary M., Wilson, Douglas R., Rashid, Naim U., Sun, Wei, Ibrahim, Joseph G.

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Compression of quantification uncertainty for scRNA-seq counts von Van Buren, Scott, Sarkar, Hirak, Srivastava, Avi, Rashid, Naim U, Patro, Rob, Love, Michael I

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Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing von Leary, Jack R, Xu, Yi, Morrison, Ashley B, Jin, Chong, Shen, Emily C, Kuhlers, Peyton C, Su, Ye, Rashid, Naim U, Yeh, Jen Jen, Peng, Xianlu Laura

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Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effects von Heiling, Hillary M, Rashid, Naim U, Li, Quefeng, Peng, Xianlu L, Yeh, Jen Jen, Ibrahim, Joseph G

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GSK2801, a BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer von Bevill, Samantha M, Olivares-Quintero, Jose F, Sciaky, Noah, Golitz, Brian T, Singh, Darshan, Beltran, Adriana S, Rashid, Naim U, Stuhlmiller, Timothy J, Hale, Andrew, Moorman, Nathaniel J, Santos, Charlene M, Angus, Steven P, Zawistowski, Jon S, Johnson, Gary L

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