Predicting cancer outcomes from histology and genomics using convolutional networks von Mobadersany, Pooya, Yousefi, Safoora, Amgad, Mohamed, Gutman, David A., Barnholtz-Sloan, Jill S., Vega, José E. Velázquez, Brat, Daniel J., Cooper, Lee A. D.

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Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization von Khosravi, Pegah, Kazemi, Ehsan, Zhan, Qiansheng, Malmsten, Jonas E., Toschi, Marco, Zisimopoulos, Pantelis, Sigaras, Alexandros, Lavery, Stuart, Cooper, Lee A. D., Hickman, Cristina, Meseguer, Marcos, Rosenwaks, Zev, Elemento, Olivier, Zaninovic, Nikica, Hajirasouliha, Iman

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MR imaging predictors of molecular profile and survival: multi-institutional study of the TCGA glioblastoma data set von Gutman, David A, Cooper, Lee A D, Hwang, Scott N, Holder, Chad A, Gao, Jingjing, Aurora, Tarun D, Dunn, Jr, William D, Scarpace, Lisa, Mikkelsen, Tom, Jain, Rajan, Wintermark, Max, Jilwan, Manal, Raghavan, Prashant, Huang, Erich, Clifford, Robert J, Mongkolwat, Pattanasak, Kleper, Vladimir, Freymann, John, Kirby, Justin, Zinn, Pascal O, Moreno, Carlos S, Jaffe, Carl, Colen, Rivka, Rubin, Daniel L, Saltz, Joel, Flanders, Adam, Brat, Daniel J

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GestAltNet: aggregation and attention to improve deep learning of gestational age from placental whole-slide images von Mobadersany, Pooya, Cooper, Lee A.D., Goldstein, Jeffery A.

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Learning from crowds in digital pathology using scalable variational Gaussian processes von López-Pérez, Miguel, Amgad, Mohamed, Morales-Álvarez, Pablo, Ruiz, Pablo, Cooper, Lee A. D., Molina, Rafael, Katsaggelos, Aggelos K.

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Tumor-Infiltrating Lymphocytes in Glioblastoma Are Associated with Specific Genomic Alterations and Related to Transcriptional Class von CALEB RUTLEDGE, W, JUN KONG, ALDAPE, Kenneth D, MCLENDON, Roger E, LEHMAN, Norman L, RYAN MILLER, C, SCHNIEDERJAN, Matthew J, BRENNAN, Cameron W, SALTZ, Joel H, MORENO, Carlos S, BRAT, Daniel J, JINGJING GAO, GUTMAN, David A, COOPER, Lee A. D, APPIN, Christina, PARK, Yuna, SCARPACE, Lisa, MIKKELSEN, Tom, COHEN, Mark L

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A population-level digital histologic biomarker for enhanced prognosis of invasive breast cancer von Amgad, Mohamed, Hodge, James M., Elsebaie, Maha A. T., Bodelon, Clara, Puvanesarajah, Samantha, Gutman, David A., Siziopikou, Kalliopi P., Goldstein, Jeffery A., Gaudet, Mia M., Teras, Lauren R., Cooper, Lee A. D.

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The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas von Cooper, Lee A D, Gutman, David A, Long, Qi, Johnson, Brent A, Cholleti, Sharath R, Kurc, Tahsin, Saltz, Joel H, Brat, Daniel J, Moreno, Carlos S

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The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies von Li, Zenggang, Ivanov, Andrei A., Su, Rina, Gonzalez-Pecchi, Valentina, Qi, Qi, Liu, Songlin, Webber, Philip, McMillan, Elizabeth, Rusnak, Lauren, Pham, Cau, Chen, Xiaoqian, Mo, Xiulei, Revennaugh, Brian, Zhou, Wei, Marcus, Adam, Harati, Sahar, Chen, Xiang, Johns, Margaret A., White, Michael A., Moreno, Carlos S., Cooper, Lee A. D., Du, Yuhong, Khuri, Fadlo R., Fu, Haian

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The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research von Gutman, David A, Khalilia, Mohammed, Lee, Sanghoon, Nalisnik, Michael, Mullen, Zach, Beezley, Jonathan, Chittajallu, Deepak R, Manthey, David, Cooper, Lee A D

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A convolutional neural network to filter artifacts in spectroscopic MRI von Gurbani, Saumya S., Schreibmann, Eduard, Maudsley, Andrew A., Cordova, James Scott, Soher, Brian J., Poptani, Harish, Verma, Gaurav, Barker, Peter B., Shim, Hyunsuk, Cooper, Lee A. D.

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Whole-brain spectroscopic MRI biomarkers identify infiltrating margins in glioblastoma patients von Cordova, James S, Shu, Hui-Kuo G, Liang, Zhongxing, Gurbani, Saumya S, Cooper, Lee A D, Holder, Chad A, Olson, Jeffrey J, Kairdolf, Brad, Schreibmann, Eduard, Neill, Stewart G, Hadjipanayis, Constantinos G, Shim, Hyunsuk

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Somatic mutations associated with MRI-derived volumetric features in glioblastoma von Gutman, David A., Dunn, William D., Grossmann, Patrick, Cooper, Lee A. D., Holder, Chad A., Ligon, Keith L., Alexander, Brian M., Aerts, Hugo J. W. L.

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Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data von Gutman, David A, Cobb, Jake, Somanna, Dhananjaya, Park, Yuna, Wang, Fusheng, Kurc, Tahsin, Saltz, Joel H, Brat, Daniel J, Cooper, Lee A D

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The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma von Cooper, Lee A.D, Gutman, David A, Chisolm, Candace, Appin, Christina, Kong, Jun, Rong, Yuan, Kurc, Tahsin, Van Meir, Erwin G, Saltz, Joel H, Moreno, Carlos S, Brat, Daniel J

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High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients von Yang, Xuan, Amgad, Mohamed, Cooper, Lee A D, Du, Yuhong, Fu, Haian, Ivanov, Andrey A

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TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics von Hou, Yue, Konen, Jessica, Brat, Daniel J., Marcus, Adam I., Cooper, Lee A. D.

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Incorporation of a spectral model in a convolutional neural network for accelerated spectral fitting von Gurbani, Saumya S., Sheriff, Sulaiman, Maudsley, Andrew A., Shim, Hyunsuk, Cooper, Lee A.D.

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Interactive Classification of Whole-Slide Imaging Data for Cancer Researchers von Lee, Sanghoon, Amgad, Mohamed, Mobadersany, Pooya, McCormick, Matt, Pollack, Brian P, Elfandy, Habiba, Hussein, Hagar, Gutman, David A, Cooper, Lee A D

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PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective von Cooper, Lee AD, Demicco, Elizabeth G, Saltz, Joel H, Powell, Reid T, Rao, Arvind, Lazar, Alexander J

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