Pathway-Based Genomics Prediction using Generalized Elastic Net
Sokolov, Artem, Carlin, Daniel E, Paull, Evan O, Baertsch, Robert, Stuart, Joshua M
Published in PLoS computational biology (01.03.2016)
Published in PLoS computational biology (01.03.2016)
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Journal Article
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
Paull, Evan O, Carlin, Daniel E, Niepel, Mario, Sorger, Peter K, Haussler, David, Stuart, Joshua M
Published in Bioinformatics (01.11.2013)
Published in Bioinformatics (01.11.2013)
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Journal Article
Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling
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.
Published in Nature communications (30.10.2017)
Published in Nature communications (30.10.2017)
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Journal Article
Prophetic Granger Causality to infer gene regulatory networks
Carlin, Daniel E, Paull, Evan O, Graim, Kiley, Wong, Christopher K, Bivol, Adrian, Ryabinin, Peter, Ellrott, Kyle, Sokolov, Artem, Stuart, Joshua M
Published in PloS one (06.12.2017)
Published in PloS one (06.12.2017)
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Journal Article
SJARACNe: a scalable software tool for gene network reverse engineering from big data
Khatamian, Alireza, Paull, Evan O, Califano, Andrea, Yu, Jiyang
Published in Bioinformatics (Oxford, England) (01.06.2019)
Published in Bioinformatics (Oxford, England) (01.06.2019)
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Journal Article
Revealing cancer subtypes with higher-order correlations applied to imaging and omics data
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
Published in BMC medical genomics (31.03.2017)
Published in BMC medical genomics (31.03.2017)
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Journal Article
A modular master regulator landscape controls cancer transcriptional identity
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
Published in Cell (21.01.2021)
Published in Cell (21.01.2021)
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Journal Article
Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer
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.
Published in Cell (11.08.2016)
Published in Cell (11.08.2016)
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Journal Article
The number of titrated microRNA species dictates ceRNA regulation
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
Published in Nucleic acids research (18.05.2018)
Published in Nucleic acids research (18.05.2018)
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Journal Article
The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State
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
Published in Cell reports (Cambridge) (08.12.2020)
Published in Cell reports (Cambridge) (08.12.2020)
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Journal Article
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses
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
Published in Nature biotechnology (01.02.2021)
Published in Nature biotechnology (01.02.2021)
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Journal Article
Molecular pathways: extracting medical knowledge from high-throughput genomic data
Goldstein, Theodore C, Paull, Evan O, Ellis, Matthew J, Stuart, Joshua M
Published in Clinical cancer research (15.06.2013)
Published in Clinical cancer research (15.06.2013)
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Journal Article
Integrated Genomic Characterization of Papillary Thyroid Carcinoma
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
Published in Cell (23.10.2014)
Published in Cell (23.10.2014)
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Journal Article
Inferring causal molecular networks: empirical assessment through a community-based effort
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
Published in Nature methods (01.04.2016)
Published in Nature methods (01.04.2016)
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Journal Article
Abstract 3882: Patient-specific druggable networks in lethal prostate cancer through proteome-guided multi-omic integration
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.
Published in Cancer research (Chicago, Ill.) (15.07.2016)
Published in Cancer research (Chicago, Ill.) (15.07.2016)
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Journal Article
Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity
Ding, Hongxu, Burgenske, Danielle M, Zhao, Wenting, Subramaniam, Prem S, Bakken, Katrina K, He, Lihong, Alvarez, Mariano J, Laise, Pasquale, Paull, Evan O, Spinazzi, Eleonora F, Dovas, Athanassios, Marie, Tamara, Upadhyayula, Pavan, Filemon Dela Cruz, Diolaiti, Daniel, Kung, Andrew, Bruce, Jeffrey N, Canoll, Peter, Sims, Peter A, Sarkaria, Jann N, Califano, Andrea
Published in bioRxiv (19.06.2019)
Published in bioRxiv (19.06.2019)
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