Next-Generation Machine Learning for Biological Networks von Camacho, Diogo M., Collins, Katherine M., Powers, Rani K., Costello, James C., Collins, James J.

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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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Crowdsourcing biomedical research: leveraging communities as innovation engines von Saez-Rodriguez, Julio, Costello, James C., Friend, Stephen H., Kellen, Michael R., Mangravite, Lara, Meyer, Pablo, Norman, Thea, Stolovitzky, Gustavo

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Metastatic cells are preferentially vulnerable to lysosomal inhibition von Morgan, Michael J., Fitzwalter, Brent E., Owens, Charles R., Powers, Rani K., Sottnik, Joseph L., Gamez, Graciela, Costello, James C., Theodorescu, Dan, Thorburn, Andrew

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Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes von Stern, Josh Lewis, Paucek, Richard D., Huang, Franklin W., Ghandi, Mahmoud, Nwumeh, Ronald, Costello, James C., Cech, Thomas R.

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Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy von Tu, Megan M., Abdel-Hafiz, Hany A., Jones, Robert T., Jean, Annie, Hoff, Katelyn J., Duex, Jason E., Chauca-Diaz, Ana, Costello, James C., Dancik, Garrett M., Tamburini, Beth A. Jirón, Czerniak, Bogdan, Kaye, Jonathan, Theodorescu, Dan

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ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer von Orman, Michael V, Sreekanth, Varsha, Laajala, Teemu D, Cramer, Scott D, Costello, James C

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A Whole-genome CRISPR Screen Identifies a Role of MSH2 in Cisplatin-mediated Cell Death in Muscle-invasive Bladder Cancer von Goodspeed, Andrew, Jean, Annie, Costello, James C.

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Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression von Wang, Chu-An, Drasin, David, Pham, Catherine, Jedlicka, Paul, Zaberezhnyy, Vadym, Guney, Michelle, Li, Howard, Nemenoff, Raphael, Costello, James C, Tan, Aik-Choon, Ford, Heide L

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Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth von Tarca, Adi L., Pataki, Bálint Ármin, Romero, Roberto, Sirota, Marina, Guan, Yuanfang, Kutum, Rintu, Gomez-Lopez, Nardhy, Done, Bogdan, Bhatti, Gaurav, Yu, Thomas, Andreoletti, Gaia, Chaiworapongsa, Tinnakorn, Hassan, Sonia S., Hsu, Chaur-Dong, Aghaeepour, Nima, Stolovitzky, Gustavo, Csabai, Istvan, Costello, James C.

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SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses von Lee, Alexandra J., Mould, Dallas L., Crawford, Jake, Hu, Dongbo, Powers, Rani K., Doing, Georgia, Costello, James C., Hogan, Deborah A., Greene, Casey S.

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A harmonized resource of integrated prostate cancer clinical, -omic, and signature features von Laajala, Teemu D., Sreekanth, Varsha, Soupir, Alex C., Creed, Jordan H., Halkola, Anni S., Calboli, Federico C. F., Singaravelu, Kalaimathy, Orman, Michael V., Colin-Leitzinger, Christelle, Gerke, Travis, Fridley, Brooke L., Tyekucheva, Svitlana, Costello, James C.

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Improved inference of chromosome conformation from images of labeled loci [version 3; peer review: 2 approved] von Ross, Brian C, Costello, James C

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Biologically Informed Neural Networks Predict Drug Responses von Greene, Casey S., Costello, James C.

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Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma von Kwong, Lawrence N, Costello, James C, Liu, Huiyun, Jiang, Shan, Helms, Timothy L, Langsdorf, Aliete E, Jakubosky, David, Genovese, Giannicola, Muller, Florian L, Jeong, Joseph H, Bender, Ryan P, Chu, Gerald C, Flaherty, Keith T, Wargo, Jennifer A, Collins, James J, Chin, Lynda

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Down syndrome is associated with altered frequency and functioning of tracheal multiciliated cells, and response to influenza virus infection von Thomas, Samantha N., Niemeyer, Brian F., Jimenez-Valdes, Rocio J., Kaiser, Alexander J., Espinosa, Joaquin M., Sullivan, Kelly D., Goodspeed, Andrew, Costello, James C., Alder, Jonathan K., Cañas-Arranz, Rodrigo, García-Sastre, Adolfo, Benam, Kambez H.

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Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia von Pei, Shanshan, Pollyea, Daniel A., Gustafson, Annika, Stevens, Brett M., Minhajuddin, Mohammad, Fu, Rui, Riemondy, Kent A., Gillen, Austin E., Sheridan, Ryan M., Kim, Jihye, Costello, James C., Amaya, Maria L., Inguva, Anagha, Winters, Amanda, Ye, Haobin, Krug, Anna, Jones, Courtney L., Adane, Biniam, Khan, Nabilah, Ponder, Jessica, Schowinsky, Jeffrey, Abbott, Diana, Hammes, Andrew, Myers, Jason R., Ashton, John M., Nemkov, Travis, D'Alessandro, Angelo, Gutman, Jonathan A., Ramsey, Haley E., Savona, Michael R., Smith, Clayton A., Jordan, Craig T.

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PRDM paralogs antagonistically balance Wnt/β-catenin activity during craniofacial chondrocyte differentiation von Shull, Lomeli C, Lencer, Ezra S, Kim, Hyun Min, Goyama, Susumu, Kurokawa, Mineo, Costello, James C, Jones, Kenneth, Artinger, Kristin B

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SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program von Oliphant, Michael U J, Vincent, Melanie Y, Galbraith, Matthew D, Pandey, Ahwan, Zaberezhnyy, Vadym, Rudra, Pratyaydipta, Johnson, Katherine R, Costello, James C, Ghosh, Debashis, DeGregori, James, Espinosa, Joaquin M, Ford, Heide L

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The Capacity of the Ovarian Cancer Tumor Microenvironment to Integrate Inflammation Signaling Conveys a Shorter Disease-free Interval von Jordan, Kimberly R., Sikora, Matthew J., Slansky, Jill E., Minic, Angela, Richer, Jennifer K., Moroney, Marisa R., Hu, Junxiao, Wolsky, Rebecca J., Watson, Zachary L., Yamamoto, Tomomi M., Costello, James C., Clauset, Aaron, Behbakht, Kian, Kumar, T. Rajendra, Bitler, Benjamin G.

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