430 results on '"Dhanasekaran, Saravana M."'
Search Results
2. Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies
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He, Tongchen, Xiao, Lanbo, Qiao, Yuanyuan, Klingbeil, Olaf, Young, Eleanor, Wu, Xiaoli S., Mannan, Rahul, Mahapatra, Somnath, Redin, Esther, Cho, Hanbyul, Bao, Yi, Kandarpa, Malathi, Ching-Yi Tien, Jean, Wang, Xiaoju, Eyunni, Sanjana, Zheng, Yang, Kim, NamHoon, Zheng, Heng, Hou, Siyu, Su, Fengyun, Miner, Stephanie J., Mehra, Rohit, Cao, Xuhong, Abbineni, Chandrasekhar, Samajdar, Susanta, Ramachandra, Murali, Dhanasekaran, Saravana M., Talpaz, Moshe, Parolia, Abhijit, Rudin, Charles M., Vakoc, Christopher R., and Chinnaiyan, Arul M.
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- 2024
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3. Expression of L1 Cell Adhesion Molecule, a Nephronal Principal Cell Marker, in Nephrogenic Adenoma
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Mannan, Rahul, Wang, Xiaoming, Mahapatra, Somnath, Wang, Susanna, Chinnaiyan, Anya K., Skala, Stephanie L., Zhang, Yuping, McMurry, Lisa M., Zelenka-Wang, Sylvia, Cao, Xuhong, Sangoi, Ankur R., Dadhania, Vipulkumar, Picken, Maria M., Menon, Santosh, Al-Ahmadie, Hikmat, Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
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- 2024
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4. Comprehensive proteogenomic characterization of rare kidney tumors
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Lazar, Alexander J., Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Ma’ayan, Avi, Pruetz, Barb, Zhang, Bing, Reva, Boris, Druker, Brian J., Goldthwaite, Charles A., Jr., Birger, Chet, Mani, D.R., Chesla, David, Fenyö, David, Schadt, Eric E., Wilson, George, Kołodziejczak, Iga, John, Ivy, Hafron, Jason, Vo, Josh, Zaalishvili, Kakhaber, Ketchum, Karen A., Rodland, Karin D., Nyce, Kristen, Wiznerowicz, Maciej, Domagalski, Marcin J., Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Edwards, Nathan J., Vatanian, Negin, VanderKolk, Pamela, McGarvey, Peter B., Dhir, Rajiv, Thangudu, Ratna R., Crispen, Reese, Smith, Richard D., Payne, Samuel H., Cottingham, Sandra, Cai, Shuang, Carr, Steven A., Liu, Tao, Le, Toan, Ma, Weiping, Zhang, Xu, Lu, Yin, Shutack, Yvonne, Zhang, Zhen, Li, Ginny Xiaohe, Chen, Lijun, Hsiao, Yi, Mannan, Rahul, Zhang, Yuping, Luo, Jie, Petralia, Francesca, Cho, Hanbyul, Hosseini, Noshad, Leprevost, Felipe da Veiga, Calinawan, Anna, Li, Yize, Anand, Shankara, Dagar, Aniket, Geffen, Yifat, Kumar-Sinha, Chandan, Chugh, Seema, Le, Anne, Ponce, Sean, Guo, Shenghao, Zhang, Cissy, Schnaubelt, Michael, Al Deen, Nataly Naser, Chen, Feng, Caravan, Wagma, Houston, Andrew, Hopkins, Alex, Newton, Chelsea J., Wang, Xiaoming, Polasky, Daniel A., Haynes, Sarah, Yu, Fengchao, Jing, Xiaojun, Chen, Siqi, Robles, Ana I., Mesri, Mehdi, Thiagarajan, Mathangi, An, Eunkyung, Getz, Gad A., Linehan, W. Marston, Hostetter, Galen, Jewell, Scott D., Chan, Daniel W., Wang, Pei, Omenn, Gilbert S., Mehra, Rohit, Ricketts, Christopher J., Ding, Li, Chinnaiyan, Arul M., Cieslik, Marcin P., Dhanasekaran, Saravana M., Zhang, Hui, and Nesvizhskii, Alexey I.
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- 2024
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5. Evaluation of TRIM63 RNA in situ hybridization (RNA-ISH) as a potential biomarker for alveolar soft-part sarcoma (ASPS)
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Taylor, Alexander S., Mannan, Rahul, Pantanowitz, Liron, Chinnaiyan, Arul M., Dhanasekaran, Saravana M., Hrycaj, Steven, Cao, Xuhong, Chan, May P., Lucas, David, Wang, Xiao-Ming, and Mehra, Rohit
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- 2024
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6. Pan-cancer proteogenomics characterization of tumor immunity
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Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei
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- 2024
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7. Discovery and Validation of a 15-Gene Prognostic Signature for Clear Cell Renal Cell Carcinoma
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Mehra, Rohit, Nallandhighal, Srinivas, Cotta, Brittney, Knuth, Zayne, Su, Fengyun, Kasputis, Amy, Zhang, Yuping, Wang, Rui, Cao, Xuhong, Udager, Aaron M., Dhanasekaran, Saravana M., Cieslik, Marcin P., Morgan, Todd M., and Salami, Simpa S.
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- 2024
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8. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
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Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Ozgun, Bavarva, Jasmin, Birger, Chet, Birrer, Michael, Calinawan, Anna, Cantley, Lewis C., Cao, Song, Carr, Steve, Ceccarelli, Michele, Chan, Daniel, Chinnaiyan, Arul, Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Mohan, Domagalski, Marcin, Dou, Yongchao, Druker, Brian, Edwards, Nathan, Ellis, Matthew, Selvan, Myvizhi Esai, Francis, Alicia, Getz, Gad, Gillette, Michael A., Robles, Tania Gonzalez, Gosline, Sara, Gümüş, Zeynep, Heiman, David, Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric, Jewel, Scott, Ji, Jiayi, Jiang, Wen, Lee Johnson, Jared, Katsnelson, Lizabeth, Ketchum, Karen, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan, Liao, Yuxing, Lindgren, Caleb, Liu, Tao, Liu, Wenke, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert, Paulovich, Amanda, Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Ruggles, Kelly, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara, Schadt, Eric, Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Dick, Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik, Tan, Jimin, Terekhanova, Nadezhda, Thangudu, Ratna, Thiagarajan, Mathangi, Tignor, Nicole, Wang, Joshua, Wang, Liang-Bo, Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Chan, Daniel W., Dhanasekaran, Saravana M., Schürer, Stephan, Smith, Richard D., Wyczalkowski, Matthew A., Liang, Wen-Wei, Lu, Rita Jui-Hsien, Jayasinghe, Reyka G., Foltz, Steven M., Porta-Pardo, Eduard, Geffen, Yifat, Wendl, Michael C., Lazcano, Rossana, Kolodziejczak, Iga, Song, Yizhe, Govindan, Akshay, Demicco, Elizabeth G., Li, Xiang, Li, Yize, Sethuraman, Sunantha, Payne, Samuel H., Fenyö, David, Rodriguez, Henry, Wiznerowicz, Maciej, Shen, Hui, Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Robles, Ana I., and Ding, Li
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- 2023
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9. Proteogenomic insights suggest druggable pathways in endometrial carcinoma
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Antczak, Andrzej, Anurag, Meenakshi, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Borucki, Melissa, Cai, Shuang, Calinawan, Anna, Carr, Steven A., Castro, Patricia, Cerda, Sandra, Chan, Daniel W., Chesla, David, Cieslik, Marcin P., Cottingham, Sandra, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Edwards, Nathan J., Edwards, Robert, Ellis, Matthew J., Eschbacher, Jennifer, Fam, Mina, Fevrier-Sullivan, Brenda, Francis, Jesse, Freymann, John, Gabriel, Stacey, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Goldthwaite, Charles A., Grady, Pamela, Hafron, Jason, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Ittmann, Michael M., Johnson, Ashlie, Jones, Corbin D., Ketchum, Karen A., Kirby, Justin, Le, Toan, Ma'ayan, Avi, Madan, Rashna, Mareedu, Sailaja, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Nyce, Kristen, Paulovich, Amanda G., Pruetz, Barbara L., Qi, Liqun, Richey, Shannon, Schadt, Eric E., Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Tansil, Darlene, Thangudu, Ratna R., Tobin, Matt, Um, Ki Sung, Vatanian, Negin, Webster, Alex, Wilson, George D., Wright, Jason, Zaalishvili, Kakhaber, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Katsnelson, Lizabeth, Gritsenko, Marina A., Hu, Yingwei, Reva, Boris, Hong, Runyu, Wang, Yi-Ting, Kolodziejczak, Iga, Lu, Rita Jui-Hsien, Tsai, Chia-Feng, Bu, Wen, Liu, Wenke, Guo, Xiaofang, An, Eunkyung, Arend, Rebecca C., Bavarva, Jasmin, Chen, Lijun, Chu, Rosalie K., Czekański, Andrzej, Davoli, Teresa, Demicco, Elizabeth G., DeLair, Deborah, Devereaux, Kelly, Dhanasekaran, Saravana M., Dottino, Peter, Dover, Bailee, Fillmore, Thomas L., Foxall, McKenzie, Hermann, Catherine E., Hiltke, Tara, Hostetter, Galen, Jędryka, Marcin, Jewell, Scott D., Johnson, Isabelle, Kahn, Andrea G., Ku, Amy T., Kumar-Sinha, Chandan, Kurzawa, Paweł, Lazar, Alexander J., Lazcano, Rossana, Lei, Jonathan T., Li, Yi, Liao, Yuxing, Lih, Tung-Shing M., Lin, Tai-Tu, Martignetti, John A., Masand, Ramya P., Matkowski, Rafał, McKerrow, Wilson, Mesri, Mehdi, Monroe, Matthew E., Moon, Jamie, Moore, Ronald J., Nestor, Michael D., Newton, Chelsea, Omelchenko, Tatiana, Omenn, Gilbert S., Payne, Samuel H., Petyuk, Vladislav A., Robles, Ana I., Rodriguez, Henry, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schepmoes, Athena A., Shi, Tujin, Shi, Zhiao, Tan, Jimin, Taylor, Mason, Thiagarajan, Mathangi, Wang, Joshua M., Weitz, Karl K., Wen, Bo, Williams, C.M., Wu, Yige, Wyczalkowski, Matthew A., Yi, Xinpei, Zhang, Xu, Zhao, Rui, Mutch, David, Chinnaiyan, Arul M., Smith, Richard D., Nesvizhskii, Alexey I., Wang, Pei, Wiznerowicz, Maciej, Ding, Li, Mani, D.R., Zhang, Hui, Anderson, Matthew L., Rodland, Karin D., Zhang, Bing, Liu, Tao, and Fenyö, David
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- 2023
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10. Pan-cancer proteogenomics connects oncogenic drivers to functional states
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li
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- 2023
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11. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad
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- 2023
- Full Text
- View/download PDF
12. Proteogenomic data and resources for pan-cancer analysis
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Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, Chan, Daniel W., Li, Yize, Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Akiyama, Yo, Anand, Shankara, Birger, Chet, Cao, Song, Chaudhary, Rekha, Chilappagari, Padmini, Cieslik, Marcin, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Esai Selvan, Myvizhi, Fenyö, David, Foltz, Steven M., Francis, Alicia, Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Holck, Michael, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Klein, Robert J., Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, McKerrow, Wilson, Nguyen, Ngoc, Oldroyd, Robert, Pilozzi, Alexander, Reva, Boris, Rudnick, Paul, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Song, Xiaoyu, Storrs, Erik, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wang, Ying, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Yi, Xinpei, Zhang, Qing, Zuhl, Maya, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Wang, Pei, Robles, Ana I., Zhang, Bing, and Payne, Samuel H.
- Published
- 2023
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13. Hybrid Oncocytic Tumors (HOTs) in Birt-Hogg-Dubé Syndrome Patients—A Tale of Two Cities: Sequencing Analysis Reveals Dual Lineage Markers Capturing the 2 Cellular Populations of HOT
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Wang, Xiao-Ming, Mannan, Rahul, Zhang, Yuping, Chinnaiyan, Anya, Rangaswamy, Roshni, Chugh, Seema, Su, Fengyun, Cao, Xuhong, Wang, Rui, Skala, Stephanie L., Hafez, Khaled S., Vaishampayan, Ulka, Mckenney, Jesse, Picken, Maria M., Gupta, Sounak, Alaghehbandan, Reza, Tretiakova, Maria, Argani, Pedram, Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
- Published
- 2024
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14. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
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Francis, Alicia, Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Colaprico, Antonio, Hakimi, Ari, Pruetz, Barb, Hindenach, Barbara, Yadav, Birendra Kumar, Reva, Boris, Fevrier-Sullivan, Brenda, Druker, Brian J., Szczylik, Cezary, Goldthwaite, Charles A., Jr., Birger, Chet, Jones, Corbin D., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Duffy, Elizabeth, Schadt, Eri E., Petralia, Francesca, Bromiński, Gabriel, Quiroga-Garza, Gabriela M., Wilson, George D., Li, Ginny Xiaohe, Zhao, Grace, Hsiao, Yi, Hsieh, James, Lubiński, Jan, Bavarva, Jasmin, Huang, Jasmine, Hafron, Jason, Eschbacher, Jennifer, Hon, Jennifer, Francis, Jesse, Freymann, John, Vo, Josh, Wang, Joshua, Kirby, Justin, Zaalishvili, Kakhaber, Ketchum, Karen A., Hoadley, Katherine A., Um, Ki Sung, Qi, Liqun, Domagalski, Marcin J., Tobin, Matt, Dyer, Maureen, Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Ittmann, Michael M., Roehrl, Michael H., Schnaubelt, Michael, Smith, Michael, Fam, Mina, Roche, Nancy, Vatanian, Negin, Maunganidze, Nicollette, Potapova, Olga, Paklina, Oxana V., VanderKolk, Pamela, Castro, Patricia, Kurzawa, Paweł, Hariharan, Pushpa, Li, Qin, Li, Qing Kay, Dhir, Rajiv, Thangudu, Ratna R., Montgomery, Rebecca, Smith, Richard D., Mareedu, Sailaja, Payne, Samuel H., Cerda, Sandra, Cottingham, Sandra, Haynes, Sarah, Satpathy, Shankha, Richey, Shannon, Singh, Shilpi, Tsang, Shirley X., Cai, Shuang, Cao, Song, Gabriel, Stacey, Carr, Steven A., Liu, Tao, Bauer, Thomas, Le, Toan, Chen, Xi S., Zhang, Xu, Shutack, Yvonne, Zhang, Zhen, Li, Yize, Lih, Tung-Shing M., Dhanasekaran, Saravana M., Mannan, Rahul, Chen, Lijun, Cieslik, Marcin, Wu, Yige, Lu, Rita Jiu-Hsien, Clark, David J., Kołodziejczak, Iga, Hong, Runyu, Chen, Siqi, Zhao, Yanyan, Chugh, Seema, Caravan, Wagma, Naser Al Deen, Nataly, Hosseini, Noshad, Newton, Chelsea J., Krug, Karsten, Xu, Yuanwei, Cho, Kyung-Cho, Hu, Yingwei, Zhang, Yuping, Kumar-Sinha, Chandan, Ma, Weiping, Calinawan, Anna, Wyczalkowski, Matthew A., Wendl, Michael C., Wang, Yuefan, Guo, Shenghao, Zhang, Cissy, Le, Anne, Dagar, Aniket, Hopkins, Alex, Cho, Hanbyul, Leprevost, Felipe da Veiga, Jing, Xiaojun, Teo, Guo Ci, Liu, Wenke, Reimers, Melissa A., Pachynski, Russell, Lazar, Alexander J., Chinnaiyan, Arul M., Van Tine, Brian A., Zhang, Bing, Rodland, Karin D., Getz, Gad, Mani, D.R., Wang, Pei, Chen, Feng, Hostetter, Galen, Thiagarajan, Mathangi, Linehan, W. Marston, Fenyö, David, Jewell, Scott D., Omenn, Gilbert S., Mehra, Rohit, Wiznerowicz, Maciej, Robles, Ana I., Mesri, Mehdi, Hiltke, Tara, An, Eunkyung, Rodriguez, Henry, Chan, Daniel W., Ricketts, Christopher J., Nesvizhskii, Alexey I., Zhang, Hui, and Ding, Li
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- 2023
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15. Deciphering intratumor heterogeneity in clear cell renal cell carcinoma utilizing clinicopathologic and molecular platforms
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Vormittag-Nocito, Erica, Mannan, Rahul, Wang, Xiaoming, Chinnaiyan, Anya, Zhang, Yuping, Zelenka-Wang, Sylvia, Cao, Xuhong, Morgan, Todd M., Hafez, Khaled, Vaishampayan, Ulka, Abdulfatah, Eman, Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
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- 2022
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16. Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response
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Zhang, Yuping, Narayanan, Sathiya P., Mannan, Rahul, Raskind, Gregory, Wang, Xiaoming, Vats, Pankaj, Su, Fengyun, Hosseini, Noshad, Cao, Xuhong, Kumar-Sinha, Chandan, Ellison, Stephanie J., Giordano, Thomas J., Morgan, Todd M., Pitchiaya, Sethuramasundaram, Alva, Ajjai, Mehra, Rohit, Cieslik, Marcin, Dhanasekaran, Saravana M., and Chinnaiyan, Arul M.
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- 2021
17. Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression
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Zhang, Yajia, Pitchiaya, Sethuramasundaram, Cieślik, Marcin, Niknafs, Yashar S, Tien, Jean C-Y, Hosono, Yasuyuki, Iyer, Matthew K, Yazdani, Sahr, Subramaniam, Shruthi, Shukla, Sudhanshu K, Jiang, Xia, Wang, Lisha, Liu, Tzu-Ying, Uhl, Michael, Gawronski, Alexander R, Qiao, Yuanyuan, Xiao, Lanbo, Dhanasekaran, Saravana M, Juckette, Kristin M, Kunju, Lakshmi P, Cao, Xuhong, Patel, Utsav, Batish, Mona, Shukla, Girish C, Paulsen, Michelle T, Ljungman, Mats, Jiang, Hui, Mehra, Rohit, Backofen, Rolf, Sahinalp, Cenk S, Freier, Susan M, Watt, Andrew T, Guo, Shuling, Wei, John T, Feng, Felix Y, Malik, Rohit, and Chinnaiyan, Arul M
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Genetics ,Prostate Cancer ,Aging ,Cancer ,Urologic Diseases ,2.1 Biological and endogenous factors ,Androgens ,Cell Line ,Tumor ,Disease Progression ,Gene Expression Regulation ,Neoplastic ,Humans ,Male ,Prostate ,Prostatic Neoplasms ,RNA ,Long Noncoding ,Receptors ,Androgen ,Signal Transduction ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
The androgen receptor (AR) plays a critical role in the development of the normal prostate as well as prostate cancer. Using an integrative transcriptomic analysis of prostate cancer cell lines and tissues, we identified ARLNC1 (AR-regulated long noncoding RNA 1) as an important long noncoding RNA that is strongly associated with AR signaling in prostate cancer progression. Not only was ARLNC1 induced by the AR protein, but ARLNC1 stabilized the AR transcript via RNA-RNA interaction. ARLNC1 knockdown suppressed AR expression, global AR signaling and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARLNC1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression and identify ARLNC1 as a novel therapeutic target.
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- 2018
18. Viral Status Predicts the Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma
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Harms, Paul W., Verhaegen, Monique E., Vo, Josh N., Tien, Jean C., Pratt, Drew, Su, Fengyun, Dhanasekaran, Saravana M., Cao, Xuhong, Mangelberger, Doris, VanGoor, Julia, Choi, Jae Eun, Ma, Vincent T., Dlugosz, Andrzej A., and Chinnaiyan, Arul M.
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- 2022
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19. Leveraging artificial intelligence to predict ERG gene fusion status in prostate cancer
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Dadhania, Vipulkumar, Gonzalez, Daniel, Yousif, Mustafa, Cheng, Jerome, Morgan, Todd M., Spratt, Daniel E., Reichert, Zachery R., Mannan, Rahul, Wang, Xiaoming, Chinnaiyan, Anya, Cao, Xuhong, Dhanasekaran, Saravana M., Chinnaiyan, Arul M., Pantanowitz, Liron, and Mehra, Rohit
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- 2022
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20. Proteogenomic characterization of pancreatic ductal adenocarcinoma
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Amin, Mitual, An, Eunkyung, Ayad, Christina, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Boca, Simina M., Bocik, William, Borucki, Melissa, Cai, Shuang, Carr, Steven A., Cerda, Sandra, Chen, Huan, Chen, Steven, Chesla, David, Chinnaiyan, Arul M., Colaprico, Antonio, Cottingham, Sandra, Derejska, Magdalena, Dhanasekaran, Saravana M., Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Dyer, Maureen A., Edwards, Nathan J., Ellis, Matthew J., Eschbacher, Jennifer, Francis, Alicia, Francis, Jesse, Gabriel, Stacey, Gabrovski, Nikolay, Gardner, Johanna, Getz, Gad, Gillette, Michael A., Goldthwaite, Charles A., Jr., Grady, Pamela, Guo, Shuai, Hariharan, Pushpa, Hiltke, Tara, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Jones, Corbin D., Ketchum, Karen A., Kinsinger, Christopher R., Koziak, Jennifer M., Kusnierz, Katarzyna, Liu, Tao, Long, Jiang, Mallery, David, Mareedu, Sailaja, Matteotti, Ronald, Maunganidze, Nicollette, McGarvey, Peter B., Minoo, Parham, Paklina, Oxana V., Paulovich, Amanda G., Payne, Samuel H., Potapova, Olga, Pruetz, Barbara, Qi, Liqun, Roche, Nancy, Rodland, Karin D., Rohrer, Daniel C., Schadt, Eric E., Shabunin, Alexey V., Shelton, Troy, Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Smith, Richard D., Sokoll, Lori J., Suh, James, Thangudu, Ratna R., Tsang, Shirley X., Um, Ki Sung, Valley, Dana R., Vatanian, Negin, Wang, Wenyi, Wilson, George D., Wiznerowicz, Maciej, Zhang, Zhen, Zhao, Grace, Cao, Liwei, Huang, Chen, Cui Zhou, Daniel, Hu, Yingwei, Lih, T. Mamie, Savage, Sara R., Krug, Karsten, Clark, David J., Schnaubelt, Michael, Chen, Lijun, da Veiga Leprevost, Felipe, Eguez, Rodrigo Vargas, Yang, Weiming, Pan, Jianbo, Wen, Bo, Dou, Yongchao, Jiang, Wen, Liao, Yuxing, Shi, Zhiao, Terekhanova, Nadezhda V., Cao, Song, Lu, Rita Jui-Hsien, Li, Yize, Liu, Ruiyang, Zhu, Houxiang, Ronning, Peter, Wu, Yige, Wyczalkowski, Matthew A., Easwaran, Hariharan, Danilova, Ludmila, Mer, Arvind Singh, Yoo, Seungyeul, Wang, Joshua M., Liu, Wenke, Haibe-Kains, Benjamin, Thiagarajan, Mathangi, Jewell, Scott D., Hostetter, Galen, Newton, Chelsea J., Li, Qing Kay, Roehrl, Michael H., Fenyö, David, Wang, Pei, Nesvizhskii, Alexey I., Mani, D.R., Omenn, Gilbert S., Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Bathe, Oliver F., Chan, Daniel W., Hruban, Ralph H., Ding, Li, Zhang, Bing, and Zhang, Hui
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- 2021
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21. A proteogenomic portrait of lung squamous cell carcinoma
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Green, Alex, Molinolo, Alfredo, Francis, Alicia, Paulovich, Amanda G., Karnuta, Andrii, Colaprico, Antonio, Hindenach, Barbara, Pruetz, Barbara L., Kubisa, Bartosz, Druker, Brian J., Huynh, Carissa, Goldthwaite, Charles A., Jr., Birger, Chet, Kinsinger, Christopher R., Jones, Corbin D., Rohrer, Dan, Valley, Dana R., Chan, Daniel W., Chesla, David, Hansel, Donna, Ponomareva, Elena V., Duffy, Elizabeth, Burks, Eric, Schadt, Eric E., Fedorov, Eugene S., An, Eunkyung, Ding, Fei, Wilson, George D., Batra, Harsh, Zhang, Hui, Maas, Jennifer E., Eschbacher, Jennifer, Ketchum, Karen A., Rodland, Karin D., Hoadley, Katherine A., Suzuki, Kei, Um, Ki Sung, Qi, Liqun, Bernard, Lori, Wiznerowicz, Maciej, Wojtyś, Małgorzata, Domagalski, Marcin J., Ellis, Matthew J., Dyer, Maureen A., Borucki, Melissa, Anurag, Meenakshi, Birrer, Michael J., Xu, Midie, Krotevich, Mikhail, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Mucci, Neil R., Maunganidze, Nicollette, Gabrovski, Nikolay, Potapova, Olga, Fadare, Oluwole, Grady, Pamela, McGarvey, Peter B., Hariharan, Pushpa, Thangudu, Ratna R., Montgomery, Rebecca, Pandurengan, Renganayaki, Smith, Richard D., Welsh, Robert J., Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Singh, Shilpi, Tsang, Shirley X., Cai, Shuang, Gabriel, Stacey, Liu, Tao, Hiltke, Tara, Vashist, Tanmayi, Bauer, Thomas, Sovenko, Volodymyr, Tourtellotte, Warren G., Ma, Weiping, Bocik, William, Hasan, Wohaib, Jing, Xiaojun, Tang, Ximing, Liao, Yuxing, Yvonne, Shutack, Zhang, Zhen, Hanhan, Ziad, Satpathy, Shankha, Krug, Karsten, Jean Beltran, Pierre M., Savage, Sara R., Petralia, Francesca, Kumar-Sinha, Chandan, Dou, Yongchao, Reva, Boris, Kane, M. Harry, Avanessian, Shayan C., Vasaikar, Suhas V., Krek, Azra, Lei, Jonathan T., Jaehnig, Eric J., Omelchenko, Tatiana, Geffen, Yifat, Bergstrom, Erik J., Stathias, Vasileios, Christianson, Karen E., Heiman, David I., Cieslik, Marcin P., Cao, Song, Song, Xiaoyu, Ji, Jiayi, Liu, Wenke, Li, Kai, Wen, Bo, Li, Yize, Gümüş, Zeynep H., Selvan, Myvizhi Esai, Soundararajan, Rama, Visal, Tanvi H., Raso, Maria G., Parra, Edwin Roger, Babur, Özgün, Vats, Pankaj, Anand, Shankara, Schraink, Tobias, Cornwell, MacIntosh, Rodrigues, Fernanda Martins, Zhu, Houxiang, Mo, Chia-Kuei, Zhang, Yuping, da Veiga Leprevost, Felipe, Huang, Chen, Chinnaiyan, Arul M., Wyczalkowski, Matthew A., Omenn, Gilbert S., Newton, Chelsea J., Schurer, Stephan, Ruggles, Kelly V., Fenyö, David, Jewell, Scott D., Thiagarajan, Mathangi, Mesri, Mehdi, Rodriguez, Henry, Mani, Sendurai A., Udeshi, Namrata D., Getz, Gad, Suh, James, Li, Qing Kay, Hostetter, Galen, Paik, Paul K., Dhanasekaran, Saravana M., Govindan, Ramaswamy, Ding, Li, Robles, Ana I., Clauser, Karl R., Nesvizhskii, Alexey I., Wang, Pei, Carr, Steven A., Zhang, Bing, Mani, D.R., and Gillette, Michael A.
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- 2021
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22. TRIM63 is a sensitive and specific biomarker for MiT family aberration-associated renal cell carcinoma
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Wang, Xiao-Ming, Zhang, Yuping, Mannan, Rahul, Skala, Stephanie L., Rangaswamy, Roshni, Chinnaiyan, Anya, Su, Fengyun, Cao, Xuhong, Zelenka-Wang, Sylvia, McMurry, Lisa, Xiao, Hong, Spratt, Daniel E., Sangoi, Ankur R., Shao, Lina, Betz, Bryan L., Brown, Noah, Tickoo, Satish K., McKenney, Jesse K., Argani, Pedram, Gupta, Sounak, Reuter, Victor E., Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
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- 2021
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23. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
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Agarwal, Anupriya, Anderson, Matthew L., Avanessian, Shayan C., Avtonomov, Dmitry, Bathe, Oliver F., Birger, Chet, Birrer, Michael J., Blumenberg, Lili, Bocik, William E., Borate, Uma, Borucki, Melissa, Burke, Meghan C., Cai, Shuang, Calinawan, Anna Pamela, Cerda, Sandra, Charamut, Alyssa, Chen, Lin S., Chowdhury, Shrabanti, Clauser, Karl R., Culpepper, Houston, Czernicki, Tomasz, D'Angelo, Fulvio, Day, Jacob, De Young, Stephanie, Demir, Emek, Ding, Fei, Domagalski, Marcin J., Dort, Joseph C., Druker, Brian, Duffy, Elizabeth, Dyer, Maureen, Edwards, Nathan J., Elburn, Kimberly, Ermakova, Tatiana S., Fenyo, David, Ferrarotto, Renata, Francis, Alicia, Gabriel, Stacey, Garofano, Luciano, Geffen, Yifat, Getz, Gad, Goldthwaite, Charles A., Hannick, Linda I., Hariharan, Pushpa, Hayes, David N., Heiman, David, Hindenach, Barbara, Hoadley, Katherine A., Hostetter, Galen, Hyrcza, Martin, Jewell, Scott D., Jones, Corbin D., Kane, M. Harry, Karz, Alicia, Kothadia, Ramani B., Krek, Azra, Kumar-Sinha, Chandan, Liu, Tao, Liu, Hongwei, Ma, Weiping, Malc, Ewa, Malovannaya, Anna, Mareedu, Sailaja, Markey, Sanford P., Marrero-Oliveras, Annette, Maunganidze, Nicollette, McDermott, Jason E., McGarvey, Peter B., McGee, John, Mieczkowski, Piotr, Migliozzi, Simona, Montgomery, Rebecca, Newton, Chelsea J., Ozbek, Umut, Paulovich, Amanda G., Payne, Samuel H., Pazardzhikliev, Dimitar Dimitrov, Perou, Amy M., Petralia, Francesca, Petrenko, Lyudmila, Piehowski, Paul D., Placantonakis, Dmitris, Polonskaya, Larisa, Ponomareva, Elena V., Potapova, Olga, Qi, Liqun, Qu, Ning, Ramkissoon, Shakti, Reva, Boris, Richey, Shannon, Robinson, Karna, Roche, Nancy, Rodland, Karin, Rohrer, Daniel C., Rykunov, Dmitry, Schadt, Eric E., Shi, Yan, Shutack, Yvonne, Singh, Shilpi, Skelly, Tara, Smith, Richard, Sokoll, Lori J., Stawicki, Jakub, Stein, Stephen E., Suh, James, Szopa, Wojciech, Tabor, Dave, Tan, Donghui, Tansil, Darlene, Teo, Guo Ci, Thangudu, Ratna R., Tognon, Cristina, Traer, Elie, Tsang, Shirley, Tyner, Jeffrey, Um, Ki Sung, Valley, Dana R., Vasilev, Lyubomir Valkov, Vatanian, Negin, Velvulou, Uma, Vernon, Michael, Westbrook, Thomas F., Whiteaker, Jeffrey R., Wu, Yige, Xu, Midie, Yao, Lijun, Yi, Xinpei, Yu, Fengchao, Zaalishvili, Kakhaber, Zakhartsev, Yuriy, Zelt, Robert, Zhao, Grace, Zhu, Jun, Huang, Chen, Chen, Lijun, Savage, Sara R., Eguez, Rodrigo Vargas, Dou, Yongchao, Li, Yize, da Veiga Leprevost, Felipe, Jaehnig, Eric J., Lei, Jonathan T., Wen, Bo, Schnaubelt, Michael, Krug, Karsten, Song, Xiaoyu, Cieślik, Marcin, Chang, Hui-Yin, Wyczalkowski, Matthew A., Li, Kai, Colaprico, Antonio, Li, Qing Kay, Clark, David J., Hu, Yingwei, Cao, Liwei, Pan, Jianbo, Wang, Yuefan, Cho, Kyung-Cho, Shi, Zhiao, Liao, Yuxing, Jiang, Wen, Anurag, Meenakshi, Ji, Jiayi, Yoo, Seungyeul, Zhou, Daniel Cui, Liang, Wen-Wei, Wendl, Michael, Vats, Pankaj, Carr, Steven A., Mani, D.R., Zhang, Zhen, Qian, Jiang, Chen, Xi S., Pico, Alexander R., Wang, Pei, Chinnaiyan, Arul M., Ketchum, Karen A., Kinsinger, Christopher R., Robles, Ana I., An, Eunkyung, Hiltke, Tara, Mesri, Mehdi, Thiagarajan, Mathangi, Weaver, Alissa M., Sikora, Andrew G., Lubiński, Jan, Wierzbicka, Małgorzata, Wiznerowicz, Maciej, Satpathy, Shankha, Gillette, Michael A., Miles, George, Ellis, Matthew J., Omenn, Gilbert S., Rodriguez, Henry, Boja, Emily S., Dhanasekaran, Saravana M., Ding, Li, Nesvizhskii, Alexey I., El-Naggar, Adel K., Chan, Daniel W., Zhang, Hui, and Zhang, Bing
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- 2021
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24. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
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Webster, Alex, Francis, Alicia, Charamut, Alyssa, Paulovich, Amanda G., Perou, Amy M., Godwin, Andrew K., Karnuta, Andrii, Marrero-Oliveras, Annette, Hindenach, Barbara, Pruetz, Barbara, Kubisa, Bartosz, Druker, Brian J., Birger, Chet, Jones, Corbin D., Valley, Dana R., Rohrer, Daniel C., Zhou, Daniel Cui, Chan, Daniel W., Chesla, David, Clark, David J., Rykunov, Dmitry, Tan, Donghui, Ponomareva, Elena V., Duffy, Elizabeth, Burks, Eric J., Schadt, Eric E., Bergstrom, Erik J., Fedorov, Eugene S., Malc, Ewa, Wilson, George D., Chen, Hai-Quan, Krzystek, Halina M., Liu, Hongwei, Culpepper, Houston, Sun, Hua, Zhang, Hui, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, McGee, John, Ketchum, Karen A., Rodland, Karin D., Robinson, Karna, Hoadley, Katherine A., Suzuki, Kei, Um, Ki Sung, Elburn, Kim, Wang, Liang-Bo, Chen, Lijun, Hannick, Linda, Qi, Liqun, Sokoll, Lori J., Wojtyś, Małgorzata, Domagalski, Marcin J., Gritsenko, Marina A., Beasley, Mary B., Monroe, Matthew E., Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Sun, Meng-Hong, Roehrl, Michael H., Birrer, Michael J., Noble, Michael, Schnaubelt, Michael, Vernon, Michael, Chaikin, Michelle, Krotevich, Mikhail, Khan, Munziba, Selvan, Myvizhi Esai, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Potapova, Olga, Grady, Pamela, McGarvey, Peter B., Mieczkowski, Piotr, Hariharan, Pushpa, Madan, Rashna, Thangudu, Ratna R., Smith, Richard D., Welsh, Robert J., Zelt, Robert, Mehra, Rohit, Matteotti, Ronald, Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Markey, Sanford P., Chugh, Seema, Smith, Shaleigh, Tsang, Shirley, Cai, Shuang, Boca, Simina M., Carter, Sonya, Gabriel, Stacey, De Young, Stephanie, Stein, Stephen E., Shankar, Sunita, Krubit, Tanya, Liu, Tao, Skelly, Tara, Bauer, Thomas, Velvulou, Uma, Ozbek, Umut, Petyuk, Vladislav A., Sovenko, Volodymyr, Bocik, William E., Maggio, William W., Chen, Xi, Shi, Yan, Wu, Yige, Hu, Yingwei, Liao, Yuxing, Zhang, Zhen, Shi, Zhiao, Gillette, Michael A., Satpathy, Shankha, Cao, Song, Dhanasekaran, Saravana M., Vasaikar, Suhas V., Krug, Karsten, Petralia, Francesca, Li, Yize, Liang, Wen-Wei, Reva, Boris, Krek, Azra, Ji, Jiayi, Song, Xiaoyu, Liu, Wenke, Hong, Runyu, Yao, Lijun, Blumenberg, Lili, Savage, Sara R., Wendl, Michael C., Wen, Bo, Li, Kai, Tang, Lauren C., MacMullan, Melanie A., Avanessian, Shayan C., Kane, M. Harry, Newton, Chelsea J., Cornwell, MacIntosh, Kothadia, Ramani B., Ma, Weiping, Yoo, Seungyeul, Mannan, Rahul, Vats, Pankaj, Kumar-Sinha, Chandan, Kawaler, Emily A., Omelchenko, Tatiana, Colaprico, Antonio, Geffen, Yifat, Maruvka, Yosef E., da Veiga Leprevost, Felipe, Wiznerowicz, Maciej, Gümüş, Zeynep H., Veluswamy, Rajwanth R., Hostetter, Galen, Heiman, David I., Wyczalkowski, Matthew A., Hiltke, Tara, Mesri, Mehdi, Kinsinger, Christopher R., Boja, Emily S., Omenn, Gilbert S., Chinnaiyan, Arul M., Rodriguez, Henry, Li, Qing Kay, Jewell, Scott D., Thiagarajan, Mathangi, Getz, Gad, Zhang, Bing, Fenyö, David, Ruggles, Kelly V., Cieslik, Marcin P., Robles, Ana I., Clauser, Karl R., Govindan, Ramaswamy, Wang, Pei, Nesvizhskii, Alexey I., Ding, Li, Mani, D.R., and Carr, Steven A.
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- 2020
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25. Next-generation RNA Sequencing–based Biomarker Characterization of Chromophobe Renal Cell Carcinoma and Related Oncocytic Neoplasms
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Skala, Stephanie L., Wang, Xiaoming, Zhang, Yuping, Mannan, Rahul, Wang, Lisha, Narayanan, Sathiya P., Vats, Pankaj, Su, Fengyun, Chen, Jin, Cao, Xuhong, Siddiqui, Javed, Argani, Pedram, Cieślik, Marcin P., Giordano, Thomas J., Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
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- 2020
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26. KRAS Engages AGO2 to Enhance Cellular Transformation
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Shankar, Sunita, Pitchiaya, Sethuramasundaram, Malik, Rohit, Kothari, Vishal, Hosono, Yasuyuki, Yocum, Anastasia K, Gundlapalli, Harika, White, Yasmine, Firestone, Ari, Cao, Xuhong, Dhanasekaran, Saravana M, Stuckey, Jeanne A, Bollag, Gideon, Shannon, Kevin, Walter, Nils G, Kumar-Sinha, Chandan, and Chinnaiyan, Arul M
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Cancer ,Aetiology ,2.1 Biological and endogenous factors ,Animals ,Argonaute Proteins ,Base Sequence ,Carboxypeptidases ,Cell Transformation ,Neoplastic ,Endoplasmic Reticulum ,Gene Expression Regulation ,Neoplastic ,Gene Silencing ,Humans ,Mice ,MicroRNAs ,Molecular Sequence Data ,Mutation ,NIH 3T3 Cells ,Phosphatidylinositol 3-Kinases ,Protein Binding ,Proto-Oncogene Proteins p21(ras) ,RNA ,Small Interfering ,Transgenes ,Argonaute 2 ,EIF2C2 ,KRAS ,RNA silencing ,cancer ,Medical Physiology ,Biological sciences - Abstract
Oncogenic mutations in RAS provide a compelling yet intractable therapeutic target. Using co-immunoprecipitation mass spectrometry, we uncovered an interaction between RAS and Argonaute 2 (AGO2). Endogenously, RAS and AGO2 co-sediment and co-localize in the endoplasmic reticulum. The AGO2 N-terminal domain directly binds the Switch II region of KRAS, agnostic of nucleotide (GDP/GTP) binding. Functionally, AGO2 knockdown attenuates cell proliferation in mutant KRAS-dependent cells and AGO2 overexpression enhances KRAS(G12V)-mediated transformation. Using AGO2-/- cells, we demonstrate that the RAS-AGO2 interaction is required for maximal mutant KRAS expression and cellular transformation. Mechanistically, oncogenic KRAS attenuates AGO2-mediated gene silencing. Overall, the functional interaction with AGO2 extends KRAS function beyond its canonical role in signaling.
- Published
- 2016
27. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
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Hashimi, Abdul Samad, Pico, Alexander R., Karpova, Alla, Charamut, Alyssa, Paulovich, Amanda G., Perou, Amy M., Malovannaya, Anna, Marrero-Oliveras, Annette, Agarwal, Anupriya, Hindenach, Barbara, Pruetz, Barbara, Kim, Beom-Jun, Druker, Brian J., Newton, Chelsea J., Birger, Chet, Jones, Corbin D., Tognon, Cristina, Mani, D.R., Valley, Dana R., Rohrer, Daniel C., Zhou, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Tan, Donghui, Chan, Doug, Demir, Emek, Malc, Ewa, Modugno, Francesmary, Getz, Gaddy, Hostetter, Galen, Wilson, George D., Hart, Gerald W., Zhu, Heng, Liu, Hongwei, Culpepper, Houston, Sun, Hua, Zhou, Hua, Day, Jacob, Suh, James, Huang, Jasmine, McDermott, Jason, Whiteaker, Jeffrey R., Tyner, Jeffrey W., Eschbacher, Jennifer, Chen, Jin, McGee, John, Zhu, Jun, Ketchum, Karen A., Rodland, Karin D., Clauser, Karl, Robinson, Karna, Krug, Karsten, Hoadley, Katherine A., Um, Ki Sung, Elburn, Kim, Holloway, Kimberly, Wang, Liang-Bo, Blumenberg, Lili, Hannick, Linda, Qi, Liqun, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Domagalski, Marcin J., Gritsenko, Marina A., Anderson, Matthew, Monroe, Matthew E., Ellis, Matthew J., Dyer, Maureen, Anurag, Meenakshi, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Lewis, Michael, Ittmann, Michael M., Smith, Michael, Vernon, Michael, Chaikin, Michelle, Chheda, Milan G., Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Beckmann, Noam, Grady, Pamela, Castro, Patricia, Piehowski, Paul, McGarvey, Peter B., Mieczkowski, Piotr, Hariharan, Pushpa, Gao, Qingsong, Dhir, Rajiv, Kothadia, Ramani Bhupendra, Thangudu, Ratna R., Montgomery, Rebecca, Jayasinghe, Reyka G., Smith, Richard D., Edwards, Robert, Zelt, Robert, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Markey, Sanford P., Jewell, Scott D., Patel, Shalin, Satpathy, Shankha, Richey, Shannon, Davies, Sherri R., Cai, Shuang, Boca, Simina M., Patil, Snehal, Sengupta, Sohini, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., De Young, Stephanie, Stein, Stephen E., Carr, Steven A., Foltz, Steven M., Hilsenbeck, Sue, Krubit, Tanya, Liu, Tao, Skelly, Tara, Westbrook, Thomas, Borate, Uma, Velvulou, Uma, Petyuk, Vladislav A., Bocik, William E., Chen, Xi, Shi, Yan, Geffen, Yifat, Lu, Yihao, Wang, Ying, Maruvka, Yosef, Li, Zhi, Shi, Zhiao, Tu, Zhidong, Clark, David J., Dhanasekaran, Saravana M., Petralia, Francesca, Pan, Jianbo, Song, Xiaoyu, Hu, Yingwei, da Veiga Leprevost, Felipe, Reva, Boris, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Huang, Chen, Ricketts, Christopher J., Chen, Lijun, Krek, Azra, Li, Yize, Rykunov, Dmitry, Li, Qing Kay, Chen, Lin S., Ozbek, Umut, Vasaikar, Suhas, Wu, Yige, Yoo, Seungyeul, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Ji, Jiayi, Schnaubelt, Michael, Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Ao, Minghui, Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Liu, Wenke, Ruggles, Kelly, Calinawan, Anna, Gümüş, Zeynep H., Geiszler, Daniel, Kawaler, Emily, Teo, Guo Ci, Wen, Bo, Zhang, Yuping, Keegan, Sarah, Li, Kai, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Chen, Xi Steven, Pavlovich, Christian P., Hakimi, A. Ari, Brominski, Gabriel, Hsieh, James J., Antczak, Andrzej, Omelchenko, Tatiana, Lubinski, Jan, Wiznerowicz, Maciej, Linehan, W. Marston, Kinsinger, Christopher R., Thiagarajan, Mathangi, Boja, Emily S., Mesri, Mehdi, Hiltke, Tara, Robles, Ana I., Rodriguez, Henry, Qian, Jiang, Fenyö, David, Zhang, Bing, Ding, Li, Schadt, Eric, Chinnaiyan, Arul M., Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Wang, Pei, and Zhang, Hui
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- 2019
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28. The landscape of long noncoding RNAs in the human transcriptome
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Iyer, Matthew K, Niknafs, Yashar S, Malik, Rohit, Singhal, Udit, Sahu, Anirban, Hosono, Yasuyuki, Barrette, Terrence R, Prensner, John R, Evans, Joseph R, Zhao, Shuang, Poliakov, Anton, Cao, Xuhong, Dhanasekaran, Saravana M, Wu, Yi-Mi, Robinson, Dan R, Beer, David G, Feng, Felix Y, Iyer, Hariharan K, and Chinnaiyan, Arul M
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Generic health relevance ,Cell Line ,Cell Line ,Tumor ,Gene Expression ,Humans ,Neoplasms ,RNA ,Long Noncoding ,Sequence Analysis ,RNA ,Transcriptome ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes including cancer. To delineate genome-wide lncRNA expression, we curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. We applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes. Over 68% (58,648) of genes were classified as lncRNAs, of which 79% were previously unannotated. About 1% (597) of the lncRNAs harbored ultraconserved elements, and 7% (3,900) overlapped disease-associated SNPs. To prioritize lineage-specific, disease-associated lncRNA expression, we employed non-parametric differential expression testing and nominated 7,942 lineage- or cancer-associated lncRNA genes. The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.
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- 2015
29. Pan-cancer proteogenomics characterization of tumor immunity
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Petralia, Francesca, primary, Ma, Weiping, additional, Yaron, Tomer M., additional, Caruso, Francesca Pia, additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Charytonowicz, Daniel, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Marino, Giacomo B., additional, Calinawan, Anna, additional, Evangelista, John Erol, additional, Selvan, Myvizhi Esai, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Song, Xiaoyu, additional, Turhan, Berk, additional, Christianson, Karen E., additional, Lewis, David A., additional, Deng, Eden Z., additional, Clarke, Daniel J.B., additional, Whiteaker, Jeffrey R., additional, Kennedy, Jacob J., additional, Zhao, Lei, additional, Segura, Rossana Lazcano, additional, Batra, Harsh, additional, Raso, Maria Gabriela, additional, Parra, Edwin Roger, additional, Soundararajan, Rama, additional, Tang, Ximing, additional, Li, Yize, additional, Yi, Xinpei, additional, Satpathy, Shankha, additional, Wang, Ying, additional, Wiznerowicz, Maciej, additional, González-Robles, Tania J., additional, Iavarone, Antonio, additional, Gosline, Sara J.C., additional, Reva, Boris, additional, Robles, Ana I., additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Gillette, Michael A., additional, Klein, Robert J., additional, Cieslik, Marcin, additional, Zhang, Bing, additional, Paulovich, Amanda G., additional, Sebra, Robert, additional, Gümüş, Zeynep H., additional, Hostetter, Galen, additional, Fenyö, David, additional, Omenn, Gilbert S., additional, Cantley, Lewis C., additional, Ma'ayan, Avi, additional, Lazar, Alexander J., additional, Ceccarelli, Michele, additional, Wang, Pei, additional, Abelin, Jennifer, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cao, Song, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Heiman, David I., additional, Hong, Runyu, additional, Hu, Yingwei, additional, Huang, Chen, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, McDermott, Jason, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Mumphrey, Michael Brodie, additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Payne, Samuel H., additional, Pugliese, Pietro, additional, Rodland, Karin D., additional, Rodrigues, Fernanda Martins, additional, Ruggles, Kelly V., additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Feng, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Li, Qing Kay, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2024
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30. Therapeutic benefit of the dual ALK/FAK inhibitor ESK440 in ALK-driven neuroblastoma
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Chugh, Seema, primary, Tien, Jean C., additional, Hon, Jennifer, additional, Kenum, Carson, additional, Mannan, Rahul, additional, Cheng, Yunhui, additional, Li, Chi Chiang, additional, Taher, Zainab I., additional, Delekta, Andrew D., additional, Bawa, Pushpinder Singh, additional, Apel, Ingrid J., additional, Miner, Stephanie J., additional, Cao, Xuhong, additional, Mehra, Rohit, additional, Dhanasekaran, Saravana M., additional, Qiao, Yuanyuan, additional, Mody, Rajen, additional, and Chinnaiyan, Arul M., additional
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- 2024
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31. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1
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Prensner, John R, Zhao, Shuang, Erho, Nicholas, Schipper, Matthew, Iyer, Matthew K, Dhanasekaran, Saravana M, Magi-Galluzzi, Cristina, Mehra, Rohit, Sahu, Anirban, Siddiqui, Javed, Davicioni, Elai, Den, Robert B, Dicker, Adam P, Karnes, R Jeffrey, Wei, John T, Klein, Eric A, Jenkins, Robert B, Chinnaiyan, Arul M, and Feng, Felix Y
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Aging ,Urologic Diseases ,Prostate Cancer ,Cancer ,Genetics ,Biotechnology ,Clinical Research ,Detection ,screening and diagnosis ,4.1 Discovery and preclinical testing of markers and technologies ,Aetiology ,2.1 Biological and endogenous factors ,Aged ,Biomarkers ,Tumor ,Case-Control Studies ,Disease Progression ,Follow-Up Studies ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Humans ,Lymphatic Metastasis ,Male ,Middle Aged ,Neoplasm Grading ,Neoplasm Invasiveness ,Neoplasm Recurrence ,Local ,Neoplasm Staging ,Prognosis ,Prostate-Specific Antigen ,Prostatectomy ,Prostatic Neoplasms ,RNA ,Long Noncoding ,Retrospective Studies ,Survival Rate ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundImproved clinical predictors for disease progression are needed for localised prostate cancer, since only a subset of patients develop recurrent or refractory disease after first-line treatment. Therefore, we undertook an unbiased analysis to identify RNA biomarkers associated with metastatic progression after prostatectomy.MethodsProstate cancer samples from patients treated with radical prostatectomy at three academic institutions were analysed for gene expression by a high-density Affymetrix GeneChip platform, encompassing more than 1 million genomic loci. In a discovery cohort, all protein-coding genes and known long non-coding RNAs were ranked by fold change in expression between tumours that subsequently metastasised versus those that did not. The top ranked gene was then validated for its prognostic value for metastatic progression in three additional independent cohorts. 95% of the gene expression assays were done in a Clinical Laboratory Improvements Amendments certified laboratory facility. All genes were assessed for their ability to predict metastatic progression by receiver-operating-curve area-under-the-curve analyses. Multivariate analyses were done for the primary endpoint of metastatic progression, with variables including Gleason score, preoperative prostate-specific antigen concentration, seminal vesicle invasion, surgical margin status, extracapsular extension, lymph node invasion, and expression of the highest ranked gene.Findings1008 patients were included in the study: 545 in the discovery cohort and 463 in the validation cohorts. The long non-coding RNA SChLAP1 was identified as the highest-ranked overexpressed gene in cancers with metastatic progression. Validation in three independent cohorts confirmed the prognostic value of SChLAP1 for metastatic progression. On multivariate modelling, SChLAP1 expression (high vs low) independently predicted metastasis within 10 years (odds ratio [OR] 2·45, 95% CI 1·70-3·53; p
- Published
- 2014
32. The lncRNA PCAT29 Inhibits Oncogenic Phenotypes in Prostate Cancer
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Malik, Rohit, Patel, Lalit, Prensner, John R, Shi, Yang, Iyer, Matthew K, Subramaniyan, Shruthi, Carley, Alexander, Niknafs, Yashar S, Sahu, Anirban, Han, Sumin, Ma, Teng, Liu, Meilan, Asangani, Irfan A, Jing, Xiaojun, Cao, Xuhong, Dhanasekaran, Saravana M, Robinson, Dan R, Feng, Felix Y, and Chinnaiyan, Arul M
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Urologic Diseases ,Prostate Cancer ,Aging ,Cancer ,2.1 Biological and endogenous factors ,Aetiology ,Animals ,Cell Line ,Tumor ,Cell Movement ,Cell Proliferation ,Disease Progression ,Gene Expression Regulation ,Neoplastic ,Genes ,Tumor Suppressor ,Humans ,Male ,Mice ,Mice ,Inbred BALB C ,Mice ,Nude ,Phenotype ,Prostatic Neoplasms ,RNA ,Long Noncoding ,Tumor Suppressor Proteins ,Developmental Biology ,Oncology & Carcinogenesis ,Biochemistry and cell biology ,Oncology and carcinogenesis - Abstract
UnlabelledLong noncoding RNAs (lncRNA) have recently been associated with the development and progression of a variety of human cancers. However, to date, the interplay between known oncogenic or tumor-suppressive events and lncRNAs has not been well described. Here, the novel lncRNA, prostate cancer-associated transcript 29 (PCAT29), is characterized along with its relationship to the androgen receptor. PCAT29 is suppressed by DHT and upregulated upon castration therapy in a prostate cancer xenograft model. PCAT29 knockdown significantly increased proliferation and migration of prostate cancer cells, whereas PCAT29 overexpression conferred the opposite effect and suppressed growth and metastases of prostate tumors in chick chorioallantoic membrane assays. Finally, in prostate cancer patient specimens, low PCAT29 expression correlated with poor prognostic outcomes. Taken together, these data expose PCAT29 as an androgen-regulated tumor suppressor in prostate cancer.ImplicationsThis study identifies PCAT29 as the first androgen receptor-repressed lncRNA that functions as a tumor suppressor and that its loss may identify a subset of patients at higher risk for disease recurrence. Visual Overview: http://mcr.aacrjournals.org/content/early/2014/07/31/1541-7786.MCR-14-0257/F1.large.jpg.
- Published
- 2014
33. The Landscape of Circular RNA in Cancer
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Vo, Josh N., Cieslik, Marcin, Zhang, Yajia, Shukla, Sudhanshu, Xiao, Lanbo, Zhang, Yuping, Wu, Yi-Mi, Dhanasekaran, Saravana M., Engelke, Carl G., Cao, Xuhong, Robinson, Dan R., Nesvizhskii, Alexey I., and Chinnaiyan, Arul M.
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- 2019
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34. Somatic Bi-allelic Loss of TSC Genes in Eosinophilic Solid and Cystic Renal Cell Carcinoma
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Mehra, Rohit, Vats, Pankaj, Cao, Xuhong, Su, Fengyun, Lee, Nicole D., Lonigro, Robert, Premkumar, Kumpati, Trpkov, Kiril, McKenney, Jesse K., Dhanasekaran, Saravana M., and Chinnaiyan, Arul M.
- Published
- 2018
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35. Contemporary Renal Tumor Categorization With Biomarker and Translational Updates: A Practical Review
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Taylor, Alexander S., Spratt, Daniel E., Dhanasekaran, Saravana M., and Mehra, Rohit
- Subjects
World Health Organization ,Development and progression ,Genetic aspects ,Cancer -- Genetic aspects -- Development and progression ,Criminal investigation ,Technology ,Carcinoma ,Biological markers ,Clinical trials ,Health ,Renal cell carcinoma ,Tumors ,Public health - Abstract
The 2016 update to the World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs (1-3) continued the recent trend of an evolutionary increase in our [...], Context.--Renal tumor classification has evolved in recent decades, as evidenced by the comparable complexity of the 2016 revision to the World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs. A recent expansion of the knowledge base surrounding the cells of origin and evolutionary genomic characteristics of renal tumors has led to molecular characterization of novel entities and enriched understanding of established entities. This pace of research and its implementation into clinical practice has again begun to surpass that of our own classification schemata, with significant discoveries having been made since the introduction of the 2016 revision to the World Health Organization classification. In particular, biomarkers for renal tumor diagnosis and prognosis are in translation for future clinical application. Objectives.--To provide a brief framework for clinical characterization of renal tumors rooted in morphologic assessment, to briefly review the current and future status of renal tumor biomarkers with an emphasis on practical use of these ancillary tools for accurate diagnosis, and to discuss the impact of emerging technologies and clinical trials relevant to renal cell carcinoma classification and biomarker development. Data Sources.--We review recent literature relevant to renal tumor classification (including established and proposed entities), focusing on molecular characterization and biomarker assessment. Conclusions.--Accurate renal tumor diagnosis requires an up-to-date understanding of renal tumor classification, including an awareness of morphologic clues that should stimulate consideration of molecularly defined entities, as well as the ancillary biomarker testing required to confirm diagnoses. doi: 10.5858/arpa.2019-0442-RA
- Published
- 2019
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36. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex
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Prensner, John R, Iyer, Matthew K, Sahu, Anirban, Asangani, Irfan A, Cao, Qi, Patel, Lalit, Vergara, Ismael A, Davicioni, Elai, Erho, Nicholas, Ghadessi, Mercedeh, Jenkins, Robert B, Triche, Timothy J, Malik, Rohit, Bedenis, Rachel, McGregor, Natalie, Ma, Teng, Chen, Wei, Han, Sumin, Jing, Xiaojun, Cao, Xuhong, Wang, Xiaoju, Chandler, Benjamin, Yan, Wei, Siddiqui, Javed, Kunju, Lakshmi P, Dhanasekaran, Saravana M, Pienta, Kenneth J, Feng, Felix Y, and Chinnaiyan, Arul M
- Subjects
Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Agricultural Biotechnology ,Prostate Cancer ,Urologic Diseases ,Aging ,Cancer ,Animals ,Cell Line ,Tumor ,Cell Proliferation ,Chromosomal Proteins ,Non-Histone ,DNA-Binding Proteins ,Female ,Gene Expression Profiling ,Humans ,Male ,Mice ,Molecular Sequence Data ,Neoplasm Invasiveness ,Neoplasm Metastasis ,Promoter Regions ,Genetic ,Prostatic Neoplasms ,RNA Interference ,RNA ,Long Noncoding ,RNA ,Small Interfering ,SMARCB1 Protein ,Transcription Factors ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Prostate cancers remain indolent in the majority of individuals but behave aggressively in a minority. The molecular basis for this clinical heterogeneity remains incompletely understood. Here we characterize a long noncoding RNA termed SChLAP1 (second chromosome locus associated with prostate-1; also called LINC00913) that is overexpressed in a subset of prostate cancers. SChLAP1 levels independently predict poor outcomes, including metastasis and prostate cancer-specific mortality. In vitro and in vivo gain-of-function and loss-of-function experiments indicate that SChLAP1 is critical for cancer cell invasiveness and metastasis. Mechanistically, SChLAP1 antagonizes the genome-wide localization and regulatory functions of the SWI/SNF chromatin-modifying complex. These results suggest that SChLAP1 contributes to the development of lethal cancer at least in part by antagonizing the tumor-suppressive functions of the SWI/SNF complex.
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- 2013
37. Detection of 6 TFEB-amplified renal cell carcinomas and 25 renal cell carcinomas with MITF translocations: systematic morphologic analysis of 85 cases evaluated by clinical TFE3 and TFEB FISH assays
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Skala, Stephanie L, Xiao, Hong, Udager, Aaron M, Dhanasekaran, Saravana M, Shukla, Sudhanshu, Zhang, Yang, Landau, Carrie, Shao, Lina, Roulston, Diane, Wang, Lisha, Siddiqui, Javed, Cao, Xuhong, Magi-Galluzzi, Cristina, Zhang, Miao, Osunkoya, Adeboye O, Smith, Steven C, McKenney, Jesse K, Betz, Bryan L, Myers, Jeffrey L, Chinnaiyan, Arul M, Tomlins, Scott A, and Mehra, Rohit
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- 2018
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38. Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer
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Tomlins, Scott A., Rhodes, Daniel R., Perner, Sven, Dhanasekaran, Saravana M., Mehra, Rohit, Sun, Xiao-Wei, Varambally, Sooryanarayana, Cao, Xuhong, Tchinda, Joelle, Kuefer, Rainer, Lee, Charles, Montie, James E., Shah, Rajal B., Pienta, Kenneth J., Rubin, Mark A., and Chinnaiyan, Arul M.
- Published
- 2005
39. Gene of the month:VSTM2A
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Wang, Lisha, primary, Yilmaz, Osman, additional, Veeneman, Brendan A, additional, Zhang, Yuping, additional, Dhanasekaran, Saravana M, additional, and Mehra, Rohit, additional
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- 2023
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40. Hybrid Oncocytic Tumors (HOTs) in Birt-Hogg-Dubé Syndrome Patients—A Tale of Two Cities
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Wang, Xiao-Ming, primary, Mannan, Rahul, additional, Zhang, Yuping, additional, Chinnaiyan, Anya, additional, Rangaswamy, Roshni, additional, Chugh, Seema, additional, Su, Fengyun, additional, Cao, Xuhong, additional, Wang, Rui, additional, Skala, Stephanie L., additional, Hafez, Khaled S., additional, Vaishampayan, Ulka, additional, Mckenney, Jesse, additional, Picken, Maria M., additional, Gupta, Sounak, additional, Alaghehbandan, Reza, additional, Tretiakova, Maria, additional, Argani, Pedram, additional, Chinnaiyan, Arul M., additional, Dhanasekaran, Saravana M., additional, and Mehra, Rohit, additional
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- 2023
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41. Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA
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Hosono, Yasuyuki, Niknafs, Yashar S., Prensner, John R., Iyer, Matthew K., Dhanasekaran, Saravana M., Mehra, Rohit, Pitchiaya, Sethuramasundaram, Tien, Jean, Escara-Wilke, June, Poliakov, Anton, Chu, Shih-Chun, Saleh, Sahal, Sankar, Keerthana, Su, Fengyun, Guo, Shuling, Qiao, Yuanyuan, Freier, Susan M., Bui, Huynh-Hoa, Cao, Xuhong, Malik, Rohit, Johnson, Timothy M., Beer, David G., Feng, Felix Y., Zhou, Weibin, and Chinnaiyan, Arul M.
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- 2017
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42. Hereditary Leiomyomatosis and Renal Cell Carcinoma Syndrome (HLRCC): A Contemporary Review and Practical Discussion of the Differential Diagnosis for HLRCC-Associated Renal Cell Carcinoma
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Skala, Stephanie L., Dhanasekaran, Saravana M., and Mehra, Rohit
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Care and treatment ,Development and progression ,Research ,Immunohistochemistry -- Research ,Renal cell carcinoma -- Development and progression -- Care and treatment - Abstract
Hereditary leiomyomatosis and renal cell carcinoma syndrome (HLRCC), also referred to as Reed syndrome, (1-4) is a rare familial cancer disorder caused by a germline mutation in the fumarate hydratase [...], Context.--Hereditary leiomyomatosis and renal cell carcinoma syndrome (HLRCC) is an uncommon disorder with germline-inactivating mutations in the fumarate hydratase (FH) gene. The kidney cancers that develop in patients with HLRCC are often unilateral and solitary, with a potentially aggressive clinical course; morphologic identification of suspicious cases is of the utmost importance. Objective.--To review classic morphologic features of HLRCC-associated renal cell carcinoma, the reported morphologic spectrum of these tumors and their mimics, and the evidence for use of immunohistochemistry and molecular testing in diagnosis of these tumors. Data Sources.--University of Michigan cases and review of pertinent literature about HLRCC and the morphologic spectrum of HLRCC-associated renal cell carcinoma. Conclusions.--Histologic features, such as prominent nucleoli with perinucleolar halos and multiple architectural patterns within one tumor, are suggestive of HLRCC-associated renal cell carcinoma. However, the morphologic spectrum is broad. Appropriate use of FH immunohistochemistry and referral to genetic counseling is important for detection of this syndrome. doi: 10.5858/arpa.2018-0216-RA
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- 2018
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43. Deep learning integrates histopathology and proteogenomics at a pan-cancer level
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Wang, Joshua M., primary, Hong, Runyu, additional, Demicco, Elizabeth G., additional, Tan, Jimin, additional, Lazcano, Rossana, additional, Moreira, Andre L., additional, Li, Yize, additional, Calinawan, Anna, additional, Razavian, Narges, additional, Schraink, Tobias, additional, Gillette, Michael A., additional, Omenn, Gilbert S., additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Tsirigos, Aristotelis, additional, Ruggles, Kelly V., additional, Ding, Li, additional, Robles, Ana I., additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Liu, Wenke, additional, Fenyö, David, additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steven A., additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clauser, Karl R., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Heiman, David I., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Johnson, Jared L., additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying, additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yaron, Tomer M., additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2023
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44. Proteogenomic insights suggest druggable pathways in endometrial carcinoma
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Dou, Yongchao, primary, Katsnelson, Lizabeth, additional, Gritsenko, Marina A., additional, Hu, Yingwei, additional, Reva, Boris, additional, Hong, Runyu, additional, Wang, Yi-Ting, additional, Kolodziejczak, Iga, additional, Lu, Rita Jui-Hsien, additional, Tsai, Chia-Feng, additional, Bu, Wen, additional, Liu, Wenke, additional, Guo, Xiaofang, additional, An, Eunkyung, additional, Arend, Rebecca C., additional, Bavarva, Jasmin, additional, Chen, Lijun, additional, Chu, Rosalie K., additional, Czekański, Andrzej, additional, Davoli, Teresa, additional, Demicco, Elizabeth G., additional, DeLair, Deborah, additional, Devereaux, Kelly, additional, Dhanasekaran, Saravana M., additional, Dottino, Peter, additional, Dover, Bailee, additional, Fillmore, Thomas L., additional, Foxall, McKenzie, additional, Hermann, Catherine E., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Jędryka, Marcin, additional, Jewell, Scott D., additional, Johnson, Isabelle, additional, Kahn, Andrea G., additional, Ku, Amy T., additional, Kumar-Sinha, Chandan, additional, Kurzawa, Paweł, additional, Lazar, Alexander J., additional, Lazcano, Rossana, additional, Lei, Jonathan T., additional, Li, Yi, additional, Liao, Yuxing, additional, Lih, Tung-Shing M., additional, Lin, Tai-Tu, additional, Martignetti, John A., additional, Masand, Ramya P., additional, Matkowski, Rafał, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Monroe, Matthew E., additional, Moon, Jamie, additional, Moore, Ronald J., additional, Nestor, Michael D., additional, Newton, Chelsea, additional, Omelchenko, Tatiana, additional, Omenn, Gilbert S., additional, Payne, Samuel H., additional, Petyuk, Vladislav A., additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schepmoes, Athena A., additional, Shi, Tujin, additional, Shi, Zhiao, additional, Tan, Jimin, additional, Taylor, Mason, additional, Thiagarajan, Mathangi, additional, Wang, Joshua M., additional, Weitz, Karl K., additional, Wen, Bo, additional, Williams, C.M., additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yi, Xinpei, additional, Zhang, Xu, additional, Zhao, Rui, additional, Mutch, David, additional, Chinnaiyan, Arul M., additional, Smith, Richard D., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Wiznerowicz, Maciej, additional, Ding, Li, additional, Mani, D.R., additional, Zhang, Hui, additional, Anderson, Matthew L., additional, Rodland, Karin D., additional, Zhang, Bing, additional, Liu, Tao, additional, Fenyö, David, additional, Antczak, Andrzej, additional, Anurag, Meenakshi, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Borucki, Melissa, additional, Cai, Shuang, additional, Calinawan, Anna, additional, Carr, Steven A., additional, Castro, Patricia, additional, Cerda, Sandra, additional, Chan, Daniel W., additional, Chesla, David, additional, Cieslik, Marcin P., additional, Cottingham, Sandra, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Fam, Mina, additional, Fevrier-Sullivan, Brenda, additional, Francis, Jesse, additional, Freymann, John, additional, Gabriel, Stacey, additional, Getz, Gad, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Hafron, Jason, additional, Hariharan, Pushpa, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Ittmann, Michael M., additional, Johnson, Ashlie, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kirby, Justin, additional, Le, Toan, additional, Ma'ayan, Avi, additional, Madan, Rashna, additional, Mareedu, Sailaja, additional, McGarvey, Peter B., additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Nyce, Kristen, additional, Paulovich, Amanda G., additional, Pruetz, Barbara L., additional, Qi, Liqun, additional, Richey, Shannon, additional, Schadt, Eric E., additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Tansil, Darlene, additional, Thangudu, Ratna R., additional, Tobin, Matt, additional, Um, Ki Sung, additional, Vatanian, Negin, additional, Webster, Alex, additional, Wilson, George D., additional, Wright, Jason, additional, Zaalishvili, Kakhaber, additional, Zhang, Zhen, additional, and Zhao, Grace, additional
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- 2023
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45. Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA
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Hosono, Yasuyuki, primary, Niknafs, Yashar S., additional, Prensner, John R., additional, Iyer, Matthew K., additional, Dhanasekaran, Saravana M., additional, Mehra, Rohit, additional, Pitchiaya, Sethuramasundaram, additional, Tien, Jean, additional, Escara-Wilke, June, additional, Poliakov, Anton, additional, Chu, Shih-Chun, additional, Saleh, Sahal, additional, Sankar, Keerthana, additional, Su, Fengyun, additional, Guo, Shuling, additional, Qiao, Yuanyuan, additional, Freier, Susan M., additional, Bui, Huynh-Hoa, additional, Cao, Xuhong, additional, Malik, Rohit, additional, Johnson, Timothy M., additional, Beer, David G., additional, Feng, Felix Y., additional, Zhou, Weibin, additional, and Chinnaiyan, Arul M., additional
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- 2023
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46. Pan-cancer proteogenomics connects oncogenic drivers to functional states
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Li, Yize, primary, Porta-Pardo, Eduard, additional, Tokheim, Collin, additional, Bailey, Matthew H., additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Geffen, Yifat, additional, Imbach, Kathleen J., additional, Cao, Song, additional, Anand, Shankara, additional, Akiyama, Yo, additional, Liu, Wenke, additional, Wyczalkowski, Matthew A., additional, Song, Yizhe, additional, Storrs, Erik P., additional, Wendl, Michael C., additional, Zhang, Wubing, additional, Sibai, Mustafa, additional, Ruiz-Serra, Victoria, additional, Liang, Wen-Wei, additional, Terekhanova, Nadezhda V., additional, Rodrigues, Fernanda Martins, additional, Clauser, Karl R., additional, Heiman, David I., additional, Zhang, Qing, additional, Aguet, Francois, additional, Calinawan, Anna P., additional, Dhanasekaran, Saravana M., additional, Birger, Chet, additional, Satpathy, Shankha, additional, Zhou, Daniel Cui, additional, Wang, Liang-Bo, additional, Baral, Jessika, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Pugliese, Pietro, additional, Colaprico, Antonio, additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Ricketts, Christopher J., additional, Fenyö, David, additional, Payne, Samuel H., additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Gillette, Michael A., additional, Kumar-Sinha, Chandan, additional, Lazar, Alexander J., additional, Cantley, Lewis C., additional, Getz, Gad, additional, Ding, Li, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Calinawan, Anna, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Lei, Jonathan T., additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Tan, Jimin, additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
- Published
- 2023
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47. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
- Author
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Geffen, Yifat, primary, Anand, Shankara, additional, Akiyama, Yo, additional, Yaron, Tomer M., additional, Song, Yizhe, additional, Johnson, Jared L., additional, Govindan, Akshay, additional, Babur, Özgün, additional, Li, Yize, additional, Huntsman, Emily, additional, Wang, Liang-Bo, additional, Birger, Chet, additional, Heiman, David I., additional, Zhang, Qing, additional, Miller, Mendy, additional, Maruvka, Yosef E., additional, Haradhvala, Nicholas J., additional, Calinawan, Anna, additional, Belkin, Saveliy, additional, Kerelsky, Alexander, additional, Clauser, Karl R., additional, Krug, Karsten, additional, Satpathy, Shankha, additional, Payne, Samuel H., additional, Mani, D.R., additional, Gillette, Michael A., additional, Dhanasekaran, Saravana M., additional, Thiagarajan, Mathangi, additional, Mesri, Mehdi, additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Carr, Steven A., additional, Lazar, Alexander J., additional, Aguet, François, additional, Cantley, Lewis C., additional, Ding, Li, additional, Getz, Gad, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Cao, Song, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Fenyo, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2023
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48. Proteogenomic data and resources for pan-cancer analysis
- Author
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Li, Yize, primary, Dou, Yongchao, additional, Da Veiga Leprevost, Felipe, additional, Geffen, Yifat, additional, Calinawan, Anna P., additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Birger, Chet, additional, Cao, Song, additional, Chaudhary, Rekha, additional, Chilappagari, Padmini, additional, Cieslik, Marcin, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Esai Selvan, Myvizhi, additional, Fenyö, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez-Robles, Tania, additional, Gümüş, Zeynep H., additional, Heiman, David, additional, Holck, Michael, additional, Hong, Runyu, additional, Hu, Yingwei, additional, Jaehnig, Eric J., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Klein, Robert J., additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Ma, Weiping, additional, Ma, Lei, additional, MacCoss, Michael J., additional, Martins Rodrigues, Fernanda, additional, McKerrow, Wilson, additional, Nguyen, Ngoc, additional, Oldroyd, Robert, additional, Pilozzi, Alexander, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rudnick, Paul, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Singhal, Deepak, additional, Song, Xiaoyu, additional, Storrs, Erik, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Wang, Ying, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Xin, Yi, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zuhl, Maya, additional, Getz, Gad, additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Robles, Ana I., additional, Zhang, Bing, additional, Payne, Samuel H., additional, Lazar, Alexander J., additional, Paulovich, Amanda G., additional, Iavarone, Antonio, additional, Chinnaiyan, Arul M., additional, Druker, Brian J., additional, Kumar-Sinha, Chandan, additional, Newton, Chelsea J., additional, Huang, Chen, additional, Mani, D.R., additional, Smith, Richard D., additional, Huntsman, Emily, additional, Schadt, Eric E., additional, An, Eunkyung, additional, Petralia, Francesca, additional, Hostetter, Galen, additional, Omenn, Gilbert S., additional, Cho, Hanbyul, additional, Rodriguez, Henry, additional, Kolodziejczak, Iga, additional, Johnson, Jared L., additional, Bavarva, Jasmin, additional, Tan, Jimin, additional, Rodland, Karin D., additional, Clauser, Karl R., additional, Krug, Karsten, additional, Cantley, Lewis C., additional, Wiznerowicz, Maciej, additional, Ellis, Matthew J., additional, Anurag, Meenakshi, additional, Mesri, Mehdi, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ceccarelli, Michele, additional, Dhanasekaran, Saravana M., additional, Edwards, Nathan, additional, Tignor, Nicole, additional, Babur, Özgün, additional, Gosline, Sara J.C., additional, Jewell, Scott D., additional, Satpathy, Shankha, additional, Chowdhury, Shrabanti, additional, Schürer, Stephan, additional, Carr, Steven A., additional, Liu, Tao, additional, Hiltke, Tara, additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Liu, Wenke, additional, Zhang, Xu, additional, Song, Yizhe, additional, and Zhang, Zhen, additional
- Published
- 2023
- Full Text
- View/download PDF
49. Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer
- Author
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Shukla, Sudhanshu, Zhang, Xiang, Niknafs, Yashar S., Xiao, Lanbo, Mehra, Rohit, Cieślik, Marcin, Ross, Ashley, Schaeffer, Edward, Malik, Bhavna, Guo, Shuling, Freier, Susan M., Bui, Huynh-Hoa, Siddiqui, Javed, Jing, Xiaojun, Cao, Xuhong, Dhanasekaran, Saravana M., Feng, Felix Y., Chinnaiyan, Arul M., and Malik, Rohit
- Published
- 2016
- Full Text
- View/download PDF
50. VSTM2A Overexpression is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney
- Author
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Wang, Lisha, Zhang, Yuping, Chen, Ying-Bei, Skala, Stephanie L., Al-Ahmadie, Hikmat A., Wang, Xiaoming, Cao, Xuhong, Veeneman, Brendan A., Chen, Jin, Cieślik, Marcin, Qiao, Yuanyuan, Su, Fengyun, Vats, Pankaj, Siddiqui, Javed, Xiao, Hong, Sadimin, Evita T., Epstein, Jonathan I., Zhou, Ming, Sangoi, Ankur R., Trpkov, Kiril, Osunkoya, Adeboye O., Giannico, Giovanna A., McKenney, Jesse K., Argani, Pedram, Tickoo, Satish K., Reuter, Victor E., Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit
- Published
- 2018
- Full Text
- View/download PDF
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