Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

por Zhu, Yitan, Brettin, Thomas, Evrard, Yvonne A., Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Doroshow, James H., Stevens, Rick L.
Publicado 2020

Ensemble transfer learning for the prediction of anti-cancer drug response

por Zhu, Yitan, Brettin, Thomas, Evrard, Yvonne A., Partin, Alexander, Xia, Fangfang, Shukla, Maulik, Yoo, Hyunseung, Doroshow, James H., Stevens, Rick L.
Publicado 2020

Converting tabular data into images for deep learning with convolutional neural networks

por Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2021

Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks

por Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2021

Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images

por Partin, Alexander, Brettin, Thomas, Zhu, Yitan, Dolezal, James M., Kochanny, Sara, Pearson, Alexander T., Shukla, Maulik, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2023

Learning curves for drug response prediction in cancer cell lines

por Partin, Alexander, Brettin, Thomas, Evrard, Yvonne A., Zhu, Yitan, Yoo, Hyunseung, Xia, Fangfang, Jiang, Songhao, Clyde, Austin, Shukla, Maulik, Fonstein, Michael, Doroshow, James H., Stevens, Rick L.
Publicado 2021

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository

por Zhao, Yingdong, Li, Ming-Chung, Konaté, Mariam M., Chen, Li, Das, Biswajit, Karlovich, Chris, Williams, P. Mickey, Evrard, Yvonne A., Doroshow, James H., McShane, Lisa M.
Publicado 2021

Predicting tumor cell line response to drug pairs with deep learning

por Xia, Fangfang, Shukla, Maulik, Brettin, Thomas, Garcia-Cardona, Cristina, Cohn, Judith, Allen, Jonathan E., Maslov, Sergei, Holbeck, Susan L., Doroshow, James H., Evrard, Yvonne A., Stahlberg, Eric A., Stevens, Rick L.
Publicado 2018

AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing

por Bhattacharya, Tanmoy, Brettin, Thomas, Doroshow, James H., Evrard, Yvonne A., Greenspan, Emily J., Gryshuk, Amy L., Hoang, Thuc T., Lauzon, Carolyn B. Vea, Nissley, Dwight, Penberthy, Lynne, Stahlberg, Eric, Stevens, Rick, Streitz, Fred, Tourassi, Georgia, Xia, Fangfang, Zaki, George
Publicado 2019

Development and Validation of an Immunoassay for Quantification of Topoisomerase I in Solid Tumor Tissues

por Pfister, Thomas D., Hollingshead, Melinda, Kinders, Robert J., Zhang, Yiping, Evrard, Yvonne A., Ji, Jiuping, Khin, Sonny A., Borgel, Suzanne, Stotler, Howard, Carter, John, Divelbiss, Raymond, Kummar, Shivaani, Pommier, Yves, Parchment, Ralph E., Tomaszewski, Joseph E., Doroshow, James H.
Publicado 2012

PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery

por Koc, Soner, Lloyd, Michael W, Grover, Jeffrey W, Xiao, Nan, Seepo, Sara, Subramanian, Sai Lakshmi, Ray, Manisha, Frech, Christian, DiGiovanna, John, Webster, Phillip, Neuhauser, Steven, Srivastava, Anuj, Woo, Xing Yi, Sanderson, Brian J, White, Brian, Lott, Paul, Dobrolecki, Lacey E, Dowst, Heidi, Evrard, Yvonne A, Wallace, Tiffany A, Moscow, Jeffrey A, Doroshow, James H, Mitsiades, Nicholas, Kaochar, Salma, Pan, Chong-xian, Chen, Moon S, Carvajal-Carmona, Luis, Welm, Alana L, Welm, Bryan E, Lewis, Michael T, Govindan, Ramaswamy, Ding, Li, Li, Shunqiang, Herlyn, Meenhard, Davies, Michael A, Roth, Jack, Meric-Bernstam, Funda, Robinson, Peter N, Bult, Carol J, Davis-Dusenbery, Brandi, Dean, Dennis A, Chuang, Jeffrey H
Publicado 2022

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

por Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., Ding, Li
Publicado 2021

Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

por Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., Ding, Li
Publicado 2022

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

por Woo, Xing Yi, Giordano, Jessica, Srivastava, Anuj, Zhao, Zi-Ming, Lloyd, Michael W., de Bruijn, Roebi, Suh, Yun-Suhk, Patidar, Rajesh, Chen, Li, Scherer, Sandra, Bailey, Matthew H., Yang, Chieh-Hsiang, Cortes-Sanchez, Emilio, Xi, Yuanxin, Wang, Jing, Wickramasinghe, Jayamanna, Kossenkov, Andrew V., Rebecca, Vito W., Sun, Hua, Mashl, R. Jay, Davies, Sherri R., Jeon, Ryan, Frech, Christian, Randjelovic, Jelena, Rosains, Jacqueline, Galimi, Francesco, Bertotti, Andrea, Lafferty, Adam, O’Farrell, Alice C., Modave, Elodie, Lambrechts, Diether, ter Brugge, Petra, Serra, Violeta, Marangoni, Elisabetta, El Botty, Rania, Kim, Hyunsoo, Kim, Jong-Il, Yang, Han-Kwang, Lee, Charles, Dean, Dennis A., Davis-Dusenbery, Brandi, Evrard, Yvonne A., Doroshow, James H., Welm, Alana L., Welm, Bryan E., Lewis, Michael T., Fang, Bingliang, Roth, Jack A., Meric-Bernstam, Funda, Herlyn, Meenhard, Davies, Michael A., Ding, Li, Li, Shunqiang, Govindan, Ramaswamy, Isella, Claudio, Moscow, Jeffrey A., Trusolino, Livio, Byrne, Annette T., Jonkers, Jos, Bult, Carol J., Medico, Enzo, Chuang, Jeffrey H.
Publicado 2021

Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

por Woo, Xing Yi, Giordano, Jessica, Srivastava, Anuj, Zhao, Zi-Ming, Lloyd, Michael W., de Bruijn, Roebi, Suh, Yun-Suhk, Patidar, Rajesh, Chen, Li, Scherer, Sandra, Bailey, Matthew H., Yang, Chieh-Hsiang, Cortes-Sanchez, Emilio, Xi, Yuanxin, Wang, Jing, Wickramasinghe, Jayamanna, Kossenkov, Andrew V., Rebecca, Vito W., Sun, Hua, Mashl, R. Jay, Davies, Sherri R., Jeon, Ryan, Frech, Christian, Randjelovic, Jelena, Rosains, Jacqueline, Galimi, Francesco, Bertotti, Andrea, Lafferty, Adam, O’Farrell, Alice C., Modave, Elodie, Lambrechts, Diether, ter Brugge, Petra, Serra, Violeta, Marangoni, Elisabetta, El Botty, Rania, Kim, Hyunsoo, Kim, Jong-Il, Yang, Han-Kwang, Lee, Charles, Dean, Dennis A., Davis-Dusenbery, Brandi, Evrard, Yvonne A., Doroshow, James H., Welm, Alana L., Welm, Bryan E., Lewis, Michael T., Fang, Bingliang, Roth, Jack A., Meric-Bernstam, Funda, Herlyn, Meenhard, Davies, Michael A., Ding, Li, Li, Shunqiang, Govindan, Ramaswamy, Isella, Claudio, Moscow, Jeffrey A., Trusolino, Livio, Byrne, Annette T., Jonkers, Jos, Bult, Carol J., Medico, Enzo, Chuang, Jeffrey H.
Publicado 2021