Search Results - "Paull, Evan O"

Pathway-Based Genomics Prediction using Generalized Elastic Net by Sokolov, Artem, Carlin, Daniel E, Paull, Evan O, Baertsch, Robert, Stuart, Joshua M

“…We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The…”
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Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE) by Paull, Evan O, Carlin, Daniel E, Niepel, Mario, Sorger, Peter K, Haussler, David, Stuart, Joshua M

“…Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of…”
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Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling by Niepel, Mario, Hafner, Marc, Duan, Qiaonan, Wang, Zichen, Paull, Evan O., Chung, Mirra, Lu, Xiaodong, Stuart, Joshua M., Golub, Todd R., Subramanian, Aravind, Ma’ayan, Avi, Sorger, Peter K.

“…More effective use of targeted anti-cancer drugs depends on elucidating the connection between the molecular states induced by drug treatment and the cellular…”
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Prophetic Granger Causality to infer gene regulatory networks by Carlin, Daniel E, Paull, Evan O, Graim, Kiley, Wong, Christopher K, Bivol, Adrian, Ryabinin, Peter, Ellrott, Kyle, Sokolov, Artem, Stuart, Joshua M

“…We introduce a novel method called Prophetic Granger Causality (PGC) for inferring gene regulatory networks (GRNs) from protein-level time series data. The…”
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SJARACNe: a scalable software tool for gene network reverse engineering from big data by Khatamian, Alireza, Paull, Evan O, Califano, Andrea, Yu, Jiyang

“…Over the last two decades, we have observed an exponential increase in the number of generated array or sequencing-based transcriptomic profiles. Reverse…”
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Revealing cancer subtypes with higher-order correlations applied to imaging and omics data by Graim, Kiley, Liu, Tiffany Ting, Achrol, Achal S, Paull, Evan O, Newton, Yulia, Chang, Steven D, Harsh, 4th, Griffith R, Cordero, Sergio P, Rubin, Daniel L, Stuart, Joshua M

“…Patient stratification to identify subtypes with different disease manifestations, severity, and expected survival time is a critical task in cancer diagnosis…”
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ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES by Sokolov, Artem, Paull, Evan O, Stuart, Joshua M

“…The cellular composition of a tumor greatly influences the growth, spread, immune activity, drug response, and other aspects of the disease. Tumor cells are…”
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A modular master regulator landscape controls cancer transcriptional identity by Paull, Evan O., Aytes, Alvaro, Jones, Sunny J., Subramaniam, Prem S., Giorgi, Federico M., Douglass, Eugene F., Tagore, Somnath, Chu, Brennan, Vasciaveo, Alessandro, Zheng, Siyuan, Verhaak, Roel, Abate-Shen, Cory, Alvarez, Mariano J., Califano, Andrea

“…Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic…”
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Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer by Drake, Justin M., Paull, Evan O., Graham, Nicholas A., Lee, John K., Smith, Bryan A., Titz, Bjoern, Stoyanova, Tanya, Faltermeier, Claire M., Uzunangelov, Vladislav, Carlin, Daniel E., Fleming, Daniel Teo, Wong, Christopher K., Newton, Yulia, Sudha, Sud, Vashisht, Ajay A., Huang, Jiaoti, Wohlschlegel, James A., Graeber, Thomas G., Witte, Owen N., Stuart, Joshua M.

“…We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic,…”
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The number of titrated microRNA species dictates ceRNA regulation by Chiu, Hua-Sheng, Martínez, María Rodríguez, . Komissarova, Elena V, Llobet-Navas, David, Bansal, Mukesh, Paull, Evan O, Silva, José, Yang, Xuerui, Sumazin, Pavel, Califano, Andrea

“…Abstract microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently…”
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The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State by Arumugam, Karthik, Shin, William, Schiavone, Valentina, Vlahos, Lukas, Tu, Xiaochuan, Carnevali, Davide, Kesner, Jordan, Paull, Evan O., Romo, Neus, Subramaniam, Prem, Worley, Jeremy, Tan, Xiangtian, Califano, Andrea, Cosma, Maria Pia

“…Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1−/− murine…”
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Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses by Broyde, Joshua, Simpson, David R., Murray, Diana, Paull, Evan O., Chu, Brennan W., Tagore, Somnath, Jones, Sunny J., Griffin, Aaron T., Giorgi, Federico M., Lachmann, Alexander, Jackson, Peter, Sweet-Cordero, E. Alejandro, Honig, Barry, Califano, Andrea

“…Tumor-specific elucidation of physical and functional oncoprotein interactions could improve tumorigenic mechanism characterization and therapeutic response…”
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Molecular pathways: extracting medical knowledge from high-throughput genomic data by Goldstein, Theodore C, Paull, Evan O, Ellis, Matthew J, Stuart, Joshua M

“…High-throughput genomic data that measures RNA expression, DNA copy number, mutation status, and protein levels provide us with insights into the molecular…”
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Integrated Genomic Characterization of Papillary Thyroid Carcinoma by Akbani, Rehan, Aksoy, B. Arman, Ally, Adrian, Balasundaram, Miruna, Bernard, Brady, Beroukhim, Rameen, Black, Aaron D., Bodenheimer, Tom, Bowen, Jay, Bristow, Christopher A., Brookens, Robin, Buda, Elizabeth, Butterfield, Yaron S.N., Carty, Sally E., Chin, Lynda, Chuah, Eric, Cibulskis, Kristian, Clarke, Amanda, Clayman, Gary L., Cope, Leslie, Copland, John A., Davidsen, Tanja, Dhir, Rajiv, Dresdner, Gideon, Eldridge, Jonathan, Eley, Greg, El-Naggar, Adel K., Fisher, Sheila, Garraway, Levi A., Getz, Gad, Gehlenborg, Nils, Gibbs, Richard A., Gomez-Hernandez, Karen, Guin, Ranabir, Harper, Hollie A., Heiman, David I., Herman, James G., Hoadley, Katherine A., Hofree, Matan, Holt, Robert A., Hoyle, Alan P., Huang, Franklin W., Ideker, Trey, Kasaian, Katayoon, Khuri, Fadlo R., Kramer, Roger, Ladanyi, Marc, Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leraas, Kristen M., Ling, Shiyun, Liu, Wenbin, LiVolsi, Virginia A., Ma, Yussanne, Mahadeshwar, Harshad S., Mills, Gordon, Mose, Lisle E., Murray, Bradley A., Noble, Michael S., Owonikoko, Taofeek K., Pantazi, Angeliki, Pedamallu, Chandra Sekhar, Perou, Charles M., Prins, Jan F., Ren, Xiaojia, Reynolds, Sheila M., Robertson, A. Gordon, Rosenberg, Mara W., Rosenthal, Matthew, Schein, Jacqueline E., Seethala, Raja R., Shaw, Kenna R. Mills, Sheth, Margi, Shi, Yan, Sica, Gabriel L., Sipahimalani, Payal, Smallridge, Robert C., Sofia, Heidi J., Stuart, Joshua M., Sumer, S. Onur, Tam, Angela, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh, Thorsson, Vésteinn, Vandin, Fabio, Veluvolu, Umadevi, Vinco, Michelle, Voet, Doug, Weinhold, Nils, Wheeler, David, Wilson, Jocelyn, Williams, Michelle, Xu, Andrew W., Yang, Liming, Yang, Lixing, Zeng, Dong, Zhang, Jiashan (Julia), Zmuda, Erik

“…Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here, we describe the genomic landscape of 496 PTCs. We observed a low frequency…”
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Inferring causal molecular networks: empirical assessment through a community-based effort by Hill, Steven M, Heiser, Laura M, Cokelaer, Thomas, Unger, Michael, Nesser, Nicole K, Carlin, Daniel E, Zhang, Yang, Sokolov, Artem, Paull, Evan O, Wong, Chris K, Graim, Kiley, Bivol, Adrian, Wang, Haizhou, Zhu, Fan, Afsari, Bahman, Danilova, Ludmila V, Favorov, Alexander V, Lee, Wai Shing, Taylor, Dane, Hu, Chenyue W, Long, Byron L, Noren, David P, Bisberg, Alexander J, Mills, Gordon B, Gray, Joe W, Kellen, Michael, Norman, Thea, Friend, Stephen, Qutub, Amina A, Fertig, Elana J, Guan, Yuanfang, Song, Mingzhou, Stuart, Joshua M, Spellman, Paul T, Koeppl, Heinz, Stolovitzky, Gustavo, Saez-Rodriguez, Julio, Mukherjee, Sach

“…The HPN-DREAM community challenge assessed the ability of computational methods to infer causal molecular networks, focusing specifically on the task of…”
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Abstract 285: Uncovering the disorder of breast invasive carcinoma homeostasis proteins by Castro, Julia V., Paull, Evan O., Garzon, Jose I., Murray, Diana, Califano, Andrea, Honig, Barry

“…Breast cancer is one of the most common cancers among women worldwide. Recent studies suggest that cancer cell homeostatic stable phenotypes may be…”
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Abstract 3882: Patient-specific druggable networks in lethal prostate cancer through proteome-guided multi-omic integration by Drake, Justin M., Paull, Evan O., Graham, Nicholas A., Lee, John K., Smith, Bryan A., Stoyanova, Tanya, Faltermeier, Claire M., Carlin, Daniel E., Vashisht, Ajay, Huang, Jiaoti, Wohlschlegel, James A., Graeber, Thomas G., Witte, Owen N., Stuart, Joshua M.

“…Metastatic castration resistant prostate cancer (CRPC) remains incurable due to the lack of effective therapies. The need to identify new actionable targets in…”
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Sample-specific cancer pathway prediction from genomic, transcriptomic and phosphoproteomic data by Paull, Evan O

“…Cancer phenotypes such as invasion, evasion of programmed cell death, and rapid growth, arise from the complex interactions of genes, proteins and…”
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