How Machine Learning Will Transform Biomedicine von Goecks, Jeremy, Jalili, Vahid, Heiser, Laura M., Gray, Joe W.

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Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics von Goodspeed, Andrew, Heiser, Laura M, Gray, Joe W, Costello, James C

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Metrics other than potency reveal systematic variation in responses to cancer drugs von Fallahi-Sichani, Mohammad, Honarnejad, Saman, Heiser, Laura M, Gray, Joe W, Sorger, Peter K

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MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms von Erdem, Cemal, Gross, Sean M., Heiser, Laura M., Birtwistle, Marc R.

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Inferring causal molecular networks: empirical assessment through a community-based effort von 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

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LSD1 activates a lethal prostate cancer gene network independently of its demethylase function von Sehrawat, Archana, Gao, Lina, Wang, Yuliang, Bankhead, Armand, McWeeney, Shannon K., King, Carly J., Schwartzman, Jacob, Urrutia, Joshua, Bisson, William H., Coleman, Daniel J., Joshi, Sunil K., Kim, Dae-Hwan, Sampson, David A., Weinmann, Sheila, Kallakury, Bhaskar V. S., Berry, Deborah L., Haque, Reina, Van Den Eeden, Stephen K., Sharma, Sunil, Bearss, Jared, Beer, Tomasz M., Thomas, George V., Heiser, Laura M., Alumkal, Joshi J.

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Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects von Gross, Sean M., Mohammadi, Farnaz, Sanchez-Aguila, Crystal, Zhan, Paulina J., Liby, Tiera A., Dane, Mark A., Meyer, Aaron S., Heiser, Laura M.

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A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma von Collisson, Eric A, Trejo, Christy L, Silva, Jillian M, Gu, Shenda, Korkola, James E, Heiser, Laura M, Charles, Roch-Philippe, Rabinovich, Brian A, Hann, Byron, Dankort, David, Spellman, Paul T, Phillips, Wayne A, Gray, Joe W, McMahon, Martin

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FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer von Fu, Xiaoyong, Jeselsohn, Rinath, Pereira, Resel, Hollingsworth, Emporia F., Creighton, Chad J., Li, Fugen, Shea, Martin, Nardone, Agostina, De Angelis, Carmine, Heiser, Laura M., Anur, Pavana, Wang, Nicholas, Grasso, Catherine S., Spellman, Paul T., Griffith, Obi L., Tsimelzon, Anna, Gutierrez, Carolina, Huang, Shixia, Edwards, Dean P., Trivedi, Meghana V., Rimawi, Mothaffar F., Lopez-Terrada, Dolores, Hilsenbeck, Susan G., Gray, Joe W., Brown, Myles, Osborne, C. Kent, Schiff, Rachel

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Combating subclonal evolution of resistant cancer phenotypes von Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

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HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2 + Breast Cancer von Xu, Xiaowei, De Angelis, Carmine, Burke, Kathleen A, Nardone, Agostina, Hu, Huizhong, Qin, Lanfang, Veeraraghavan, Jamunarani, Sethunath, Vidyalakshmi, Heiser, Laura M, Wang, Nicholas, Ng, Charlotte K Y, Chen, Edward S, Renwick, Alexander, Wang, Tao, Nanda, Sarmistha, Shea, Martin, Mitchell, Tamika, Rajendran, Mahitha, Waters, Ian, Zabransky, Daniel J, Scott, Kenneth L, Gutierrez, Carolina, Nagi, Chandandeep, Geyer, Felipe C, Chamness, Gary C, Park, Ben H, Shaw, Chad A, Hilsenbeck, Susan G, Rimawi, Mothaffar F, Gray, Joe W, Weigelt, Britta, Reis-Filho, Jorge S, Osborne, C Kent, Schiff, Rachel

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A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling von Erdem, Cemal, Mutsuddy, Arnab, Bensman, Ethan M., Dodd, William B., Saint-Antoine, Michael M., Bouhaddou, Mehdi, Blake, Robert C., Gross, Sean M., Heiser, Laura M., Feltus, F. Alex, Birtwistle, Marc R.

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MYC regulates ductal-neuroendocrine lineage plasticity in pancreatic ductal adenocarcinoma associated with poor outcome and chemoresistance von Farrell, Amy S., Joly, Meghan Morrison, Allen-Petersen, Brittany L., Worth, Patrick J., Lanciault, Christian, Sauer, David, Link, Jason, Pelz, Carl, Heiser, Laura M., Morton, Jennifer P., Muthalagu, Nathiya, Hoffman, Megan T., Manning, Sara L., Pratt, Erica D., Kendsersky, Nicholas D., Egbukichi, Nkolika, Amery, Taylor S., Thoma, Mary C., Jenny, Zina P., Rhim, Andrew D., Murphy, Daniel J., Sansom, Owen J., Crawford, Howard C., Sheppard, Brett C., Sears, Rosalie C.

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Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition von MIRZOEVA, Olga K, DAS, Debopriya, ZHI HU, KNIGHT, Zachary, FEILER, Heidi S, GASCARD, Philippe, PARVIN, Bahram, SPELLMAN, Paul T, SHOKAT, Kevan M, WYROBEK, Andrew J, BISSELL, Mina J, MCCORMICK, Frank, HEISER, Laura M, KUO, Wen-Lin, MILLS, Gordon B, GRAY, Joe W, KORN, W. Michael, BHATTACHARYA, Sanchita, SIWAK, Doris, GENDELMAN, Rina, BAYANI, Nora, WANG, Nicholas J, NEVE, Richard M, YINGHUI GUAN

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BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer von Coleman, Daniel J., Gao, Lina, King, Carly J., Schwartzman, Jacob, Urrutia, Joshua, Sehrawat, Archana, Tayou, Junior, Balter, Ariel, Burchard, Julja, Chiotti, Kami E., Derrick, Daniel S., Sun, Duanchen, Xia, Zheng, Heiser, Laura M., Alumkal, Joshi J.

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Maintenance of MYC expression promotes de novo resistance to BET bromodomain inhibition in castration-resistant prostate cancer von Coleman, Daniel J., Gao, Lina, Schwartzman, Jacob, Korkola, James E., Sampson, David, Derrick, Daniel S., Urrutia, Joshua, Balter, Ariel, Burchard, Julja, King, Carly J., Chiotti, Kami E., Heiser, Laura M., Alumkal, Joshi J.

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MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer von Doha, Zinab O., Wang, Xiaoyan, Calistri, Nicholas L., Eng, Jennifer, Daniel, Colin J., Ternes, Luke, Kim, Eun Na, Pelz, Carl, Munks, Michael, Betts, Courtney, Kwon, Sunjong, Bucher, Elmar, Li, Xi, Waugh, Trent, Tatarova, Zuzana, Blumberg, Dylan, Ko, Aaron, Kirchberger, Nell, Pietenpol, Jennifer A., Sanders, Melinda E., Langer, Ellen M., Dai, Mu-Shui, Mills, Gordon, Chin, Koei, Chang, Young Hwan, Coussens, Lisa M., Gray, Joe W., Heiser, Laura M., Sears, Rosalie C.

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Live Cell Lineage Tracing of Dormant Cancer Cells von Kim, Hyuna, Wirasaputra, Anna, Mohammadi, Farnaz, Kundu, Aritra Nath, Esteves, Jennifer A. E., Heiser, Laura M., Meyer, Aaron S., Peyton, Shelly R.

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Morphodynamical cell state description via live-cell imaging trajectory embedding von Copperman, Jeremy, Gross, Sean M., Chang, Young Hwan, Heiser, Laura M., Zuckerman, Daniel M.

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Annot: a Django-based sample, reagent, and experiment metadata tracking system von Bucher, Elmar, Claunch, Cheryl J, Hee, Derrick, Smith, Rebecca L, Devlin, Kaylyn, Thompson, Wallace, Korkola, James E, Heiser, Laura M

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