Author: "Thiagarajan, Mathangi" - Searchworks@Jio Institute Digital Library Search Results

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202 results on '"Thiagarajan, Mathangi"'

1. Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma

Author: Savage, Sara R., Wang, Yuefan, Chen, Lijun, Jewell, Scott, Newton, Chelsea, Dou, Yongchao, Li, Qing Kay, Bathe, Oliver F., Robles, Ana I., Omenn, Gilbert S., Thiagarajan, Mathangi, Zhang, Hui, Hostetter, Galen, and Zhang, Bing
Published: 2024
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2. Multi-scale signaling and tumor evolution in high-grade gliomas

Author: Liu, Jingxian, Cao, Song, Imbach, Kathleen J., Gritsenko, Marina A., Lih, Tung-Shing M., Kyle, Jennifer E., Yaron-Barir, Tomer M., Binder, Zev A., Li, Yize, Strunilin, Ilya, Wang, Yi-Ting, Tsai, Chia-Feng, Ma, Weiping, Chen, Lijun, Clark, Natalie M., Shinkle, Andrew, Naser Al Deen, Nataly, Caravan, Wagma, Houston, Andrew, Simin, Faria Anjum, Wyczalkowski, Matthew A., Wang, Liang-Bo, Storrs, Erik, Chen, Siqi, Illindala, Ritvik, Li, Yuping D., Jayasinghe, Reyka G., Rykunov, Dmitry, Cottingham, Sandra L., Chu, Rosalie K., Weitz, Karl K., Moore, Ronald J., Sagendorf, Tyler, Petyuk, Vladislav A., Nestor, Michael, Bramer, Lisa M., Stratton, Kelly G., Schepmoes, Athena A., Couvillion, Sneha P., Eder, Josie, Kim, Young-Mo, Gao, Yuqian, Fillmore, Thomas L., Zhao, Rui, Monroe, Matthew E., Southard-Smith, Austin N., Li, Yang E., Jui-Hsien Lu, Rita, Johnson, Jared L., Wiznerowicz, Maciej, Hostetter, Galen, Newton, Chelsea J., Ketchum, Karen A., Thangudu, Ratna R., Barnholtz-Sloan, Jill S., Wang, Pei, Fenyö, David, An, Eunkyung, Thiagarajan, Mathangi, Robles, Ana I., Mani, D.R., Smith, Richard D., Porta-Pardo, Eduard, Cantley, Lewis C., Iavarone, Antonio, Chen, Feng, Mesri, Mehdi, Nasrallah, MacLean P., Zhang, Hui, Resnick, Adam C., Chheda, Milan G., Rodland, Karin D., Liu, Tao, and Ding, Li
Published: 2024
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3. Comprehensive proteogenomic characterization of rare kidney tumors

Author: 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.
Published: 2024
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4. Pan-cancer proteogenomics characterization of tumor immunity

Author: 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
Published: 2024
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5. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author: Aguet, François, Akiyama, Yo, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cantley, Lewis C., Cao, Song, Carr, Steven A., Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Clauser, Karl R., Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Heiman, David I., Hiltke, Tara, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Johnson, Jared L., 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, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea J., Oldroyd, Robert, Paulovich, Amanda G., Payne, Samuel H., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Tignor, Nicole, Wang, Liang-Bo, Wang, Pei, Wang, Ying, Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Wang, Joshua M., Hong, Runyu, Demicco, Elizabeth G., Tan, Jimin, Lazcano, Rossana, Moreira, Andre L., Li, Yize, Calinawan, Anna, Razavian, Narges, Schraink, Tobias, Gillette, Michael A., Omenn, Gilbert S., An, Eunkyung, Rodriguez, Henry, Tsirigos, Aristotelis, Ruggles, Kelly V., Ding, Li, Robles, Ana I., Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Liu, Wenke, and Fenyö, David
Published: 2023
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6. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author: 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
Published: 2023
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7. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Author: 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
Published: 2023
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8. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author: 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
Published: 2023
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9. Proteogenomic data and resources for pan-cancer analysis

Author: 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, 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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10. Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Author: Li, Qing Kay, Hu, Yingwei, Chen, Lijun, Schnaubelt, Michael, Cui Zhou, Daniel, Li, Yize, Lu, Rita Jui-Hsien, Thiagarajan, Mathangi, Hostetter, Galen, Newton, Chelsea J., Jewell, Scott D., Omenn, Gil, Robles, Ana I., Mesri, Mehdi, Bathe, Oliver F., Zhang, Bing, Ding, Li, Hruban, Ralph H., Chan, Daniel W., and Zhang, Hui
Published: 2022
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11. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

Author: McDermott, Jason E., Arshad, Osama A., Petyuk, Vladislav A., Fu, Yi, Gritsenko, Marina A., Clauss, Therese R., Moore, Ronald J., Schepmoes, Athena A., Zhao, Rui, Monroe, Matthew E., Schnaubelt, Michael, Tsai, Chia-Feng, Payne, Samuel H., Huang, Chen, Wang, Liang-Bo, Foltz, Steven, Wyczalkowski, Matthew, Wu, Yige, Song, Ehwang, Brewer, Molly A., Thiagarajan, Mathangi, Kinsinger, Christopher R., Robles, Ana I., Boja, Emily S., Rodriguez, Henry, Chan, Daniel W., Zhang, Bing, Zhang, Zhen, Ding, Li, Smith, Richard D., Liu, Tao, and Rodland, Karin D.
Published: 2020
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12. Pan-cancer proteogenomics characterization of tumor immunity

Author: 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
Published: 2024
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13. EPCO-53. MULTI-SCALE REGULATION OF SIGNALING CASCADES AND TUMOR EVOLUTION IN HIGH GRADE ASTROCYTOMAS

Author: Chheda, Milan, primary, Liu, Jingxian, additional, Cao, Song, additional, Imbach, Kathleen, additional, Gritsenko, Marina, additional, Lih, Tung-Shing, additional, Kyle, Jennifer, additional, Yaron, Tomer, additional, Li, Yize, additional, Strunilin, Ilya, additional, Binder, Zev, additional, Wang, Yi-Ting, additional, Tsai, Chia-Feng, additional, Ma, Weiping, additional, Chen, Lijun, additional, Clark, Natalie, additional, Wyczalkowski, Matthew, additional, Wang, Liang-Bo, additional, Deen, Nataly Al, additional, Caravan, Wagma, additional, Houston, Andrew, additional, Rykunov, Dmitry, additional, Cottingham, Sandra, additional, Chu, Rosalie, additional, Weitz, Karl, additional, Moore, Ronald, additional, Wiznerowicz, Maciej, additional, Hostetter, Galen, additional, Jewell, Scott, additional, Newton, Chelsea, additional, Ketchum, Karen, additional, Thangudu, Ratna, additional, Barnholtz-Sloan, Jill, additional, Wang, Pei, additional, Fenyö, David, additional, An, Eunkyung, additional, Nasrallah, MacLean P, additional, Thiagarajan, Mathangi, additional, Robles, Ana, additional, Mani, D R, additional, Smith, Richard, additional, Porta-Pardo, Eduard, additional, Cantley, Lewis, additional, Iavarone, Antonio, additional, Mesri, Mehdi, additional, Zhang, Hui, additional, Resnick, Adam, additional, Rodland, Karin, additional, Liu, Tao, additional, and Ding, Li, additional
Published: 2023
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14. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author: 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
Published: 2023
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15. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author: 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
Published: 2023
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16. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Author: Liang, Wen-Wei, primary, Lu, Rita Jui-Hsien, additional, Jayasinghe, Reyka G., additional, Foltz, Steven M., additional, Porta-Pardo, Eduard, additional, Geffen, Yifat, additional, Wendl, Michael C., additional, Lazcano, Rossana, additional, Kolodziejczak, Iga, additional, Song, Yizhe, additional, Govindan, Akshay, additional, Demicco, Elizabeth G., additional, Li, Xiang, additional, Li, Yize, additional, Sethuraman, Sunantha, additional, Payne, Samuel H., additional, Fenyö, David, additional, Rodriguez, Henry, additional, Wiznerowicz, Maciej, additional, Shen, Hui, additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Robles, Ana I., additional, Ding, Li, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Ozgun, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael, additional, Calinawan, Anna, additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steve, additional, Ceccarelli, Michele, additional, Chan, Daniel, additional, Chinnaiyan, Arul, additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Mohan, additional, Domagalski, Marcin, additional, Dou, Yongchao, additional, Druker, Brian, additional, Edwards, Nathan, additional, Ellis, Matthew, additional, Selvan, Myvizhi Esai, additional, Francis, Alicia, additional, Getz, Gad, additional, Gillette, Michael A., additional, Robles, Tania Gonzalez, additional, Gosline, Sara, additional, Gümüş, Zeynep, additional, Heiman, David, additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric, additional, Jewel, Scott, additional, Ji, Jiayi, additional, Jiang, Wen, additional, Lee Johnson, Jared, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan, additional, Liao, Yuxing, additional, Lindgren, Caleb, additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert, additional, Paulovich, Amanda, additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Ruggles, Kelly, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara, additional, Schadt, Eric, additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Dick, additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik, additional, Tan, Jimin, additional, Terekhanova, Nadezhda, additional, Thangudu, Ratna, additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Joshua, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wu, Yige, 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
Published: 2023
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17. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author: 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
Published: 2023
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18. Proteogenomic data and resources for pan-cancer analysis

Author: 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
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19. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.

Author: Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, Cassidy-Hanley, Donna M, Wiley, Emily A, Smith, Joshua J, Collins, Kathleen, Lee, Suzanne R, Couvillion, Mary T, Liu, Yifan, Garg, Jyoti, Pearlman, Ronald E, Hamilton, Eileen P, Orias, Eduardo, Eisen, Jonathan A, and Methé, Barbara A
Subjects: Macronucleus, Micronucleus, Germline, Animals, Tetrahymena thermophila, Nucleic Acid Hybridization, Genes, Protozoan, Genome, Protozoan, Expressed Sequence Tags, Micronucleus, Germline, Genes, Protozoan, Genome, Genetics, Biotechnology, Human Genome, Generic Health Relevance, Bioinformatics, Biological Sciences, Medical and Health Sciences, Information and Computing Sciences
Abstract: BackgroundTetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of Tetrahymena's coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing.ResultsWe addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified.ConclusionWe report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes.
Published: 2008

20. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Author: Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, Badger, Jonathan H, Ren, Qinghu, Amedeo, Paolo, Jones, Kristie M, Tallon, Luke J, Delcher, Arthur L, Salzberg, Steven L, Silva, Joana C, Haas, Brian J, Majoros, William H, Farzad, Maryam, Carlton, Jane M, Smith, Roger K, Garg, Jyoti, Pearlman, Ronald E, Karrer, Kathleen M, Sun, Lei, Manning, Gerard, Elde, Nels C, Turkewitz, Aaron P, Asai, David J, Wilkes, David E, Wang, Yufeng, Cai, Hong, Collins, Kathleen, Stewart, B Andrew, Lee, Suzanne R, Wilamowska, Katarzyna, Weinberg, Zasha, Ruzzo, Walter L, Wloga, Dorota, Gaertig, Jacek, Frankel, Joseph, Tsao, Che-Chia, Gorovsky, Martin A, Keeling, Patrick J, Waller, Ross F, Patron, Nicola J, Cherry, J Michael, Stover, Nicholas A, Krieger, Cynthia J, del Toro, Christina, Ryder, Hilary F, Williamson, Sondra C, Barbeau, Rebecca A, Hamilton, Eileen P, and Orias, Eduardo
Abstract: The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
Published: 2006

21. Author Correction: The NCI Genomic Data Commons

Author: Heath, Allison P., Ferretti, Vincent, Agrawal, Stuti, An, Maksim, Angelakos, James C., Arya, Renuka, Bajari, Rosita, Baqar, Bilal, Barnowski, Justin H. B., Burt, Jeffrey, Catton, Ann, Chan, Brandon F., Chu, Fay, Cullion, Kim, Davidsen, Tanja, Do, Phuong-My, Dompierre, Christian, Ferguson, Martin L., Fitzsimons, Michael S., Ford, Michael, Fukuma, Miyuki, Gaheen, Sharon, Ganji, Gajanan L., Garcia, Tzintzuni I., George, Sameera S., Gerhard, Daniela S., Gerthoffert, Francois, Gomez, Fauzi, Han, Kang, Hernandez, Kyle M., Issac, Biju, Jackson, Richard, Jensen, Mark A., Joshi, Sid, Kadam, Ajinkya, Khurana, Aishmit, Kim, Kyle M. J., Kraft, Victoria E., Li, Shenglai, Lichtenberg, Tara M., Lodato, Janice, Lolla, Laxmi, Martinov, Plamen, Mazzone, Jeffrey A., Miller, Daniel P., Miller, Ian, Miller, Joshua S., Miyauchi, Koji, Murphy, Mark W., Nullet, Thomas, Ogwara, Rowland O., Ortuño, Francisco M., Pedrosa, Jesús, Pham, Phuong L., Popov, Maxim Y., Porter, James J., Powell, Raymond, Rademacher, Karl, Reid, Colin P., Rich, Samantha, Rogel, Bessie, Sahni, Himanso, Savage, Jeremiah H., Schmitt, Kyle A., Simmons, Trevar J., Sislow, Joseph, Spring, Jonathan, Stein, Lincoln, Sullivan, Sean, Tang, Yajing, Thiagarajan, Mathangi, Troyer, Heather D., Wang, Chang, Wang, Zhining, West, Bedford L., Wilmer, Alex, Wilson, Shane, Wu, Kaman, Wysocki, William P., Xiang, Linda, Yamada, Joseph T., Yang, Liming, Yu, Christine, Yung, Christina K., Zenklusen, Jean Claude, Zhang, Junjun, Zhang, Zhenyu, Zhao, Yuanheng, Zubair, Ariz, Staudt, Louis M., and Grossman, Robert L.
Published: 2021
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22. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Author: Li, Yize, primary, Lih, Tung-Shing M., additional, Dhanasekaran, Saravana M., additional, Mannan, Rahul, additional, Chen, Lijun, additional, Cieslik, Marcin, additional, Wu, Yige, additional, Lu, Rita Jiu-Hsien, additional, Clark, David J., additional, Kołodziejczak, Iga, additional, Hong, Runyu, additional, Chen, Siqi, additional, Zhao, Yanyan, additional, Chugh, Seema, additional, Caravan, Wagma, additional, Naser Al Deen, Nataly, additional, Hosseini, Noshad, additional, Newton, Chelsea J., additional, Krug, Karsten, additional, Xu, Yuanwei, additional, Cho, Kyung-Cho, additional, Hu, Yingwei, additional, Zhang, Yuping, additional, Kumar-Sinha, Chandan, additional, Ma, Weiping, additional, Calinawan, Anna, additional, Wyczalkowski, Matthew A., additional, Wendl, Michael C., additional, Wang, Yuefan, additional, Guo, Shenghao, additional, Zhang, Cissy, additional, Le, Anne, additional, Dagar, Aniket, additional, Hopkins, Alex, additional, Cho, Hanbyul, additional, Leprevost, Felipe da Veiga, additional, Jing, Xiaojun, additional, Teo, Guo Ci, additional, Liu, Wenke, additional, Reimers, Melissa A., additional, Pachynski, Russell, additional, Lazar, Alexander J., additional, Chinnaiyan, Arul M., additional, Van Tine, Brian A., additional, Zhang, Bing, additional, Rodland, Karin D., additional, Getz, Gad, additional, Mani, D.R., additional, Wang, Pei, additional, Chen, Feng, additional, Hostetter, Galen, additional, Thiagarajan, Mathangi, additional, Linehan, W. Marston, additional, Fenyö, David, additional, Jewell, Scott D., additional, Omenn, Gilbert S., additional, Mehra, Rohit, additional, Wiznerowicz, Maciej, additional, Robles, Ana I., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Chan, Daniel W., additional, Ricketts, Christopher J., additional, Nesvizhskii, Alexey I., additional, Zhang, Hui, additional, Ding, Li, additional, Francis, Alicia, additional, Paulovich, Amanda G., additional, Antczak, Andrzej, additional, Green, Anthony, additional, Colaprico, Antonio, additional, Hakimi, Ari, additional, Pruetz, Barb, additional, Hindenach, Barbara, additional, Yadav, Birendra Kumar, additional, Reva, Boris, additional, Fevrier-Sullivan, Brenda, additional, Druker, Brian J., additional, Szczylik, Cezary, additional, Goldthwaite, Charles A., additional, Birger, Chet, additional, Jones, Corbin D., additional, Rohrer, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Duffy, Elizabeth, additional, Schadt, Eri E., additional, Petralia, Francesca, additional, Bromiński, Gabriel, additional, Quiroga-Garza, Gabriela M., additional, Wilson, George D., additional, Li, Ginny Xiaohe, additional, Zhao, Grace, additional, Hsiao, Yi, additional, Hsieh, James, additional, Lubiński, Jan, additional, Bavarva, Jasmin, additional, Huang, Jasmine, additional, Hafron, Jason, additional, Eschbacher, Jennifer, additional, Hon, Jennifer, additional, Francis, Jesse, additional, Freymann, John, additional, Vo, Josh, additional, Wang, Joshua, additional, Kirby, Justin, additional, Zaalishvili, Kakhaber, additional, Ketchum, Karen A., additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Qi, Liqun, additional, Domagalski, Marcin J., additional, Tobin, Matt, additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ittmann, Michael M., additional, Roehrl, Michael H., additional, Schnaubelt, Michael, additional, Smith, Michael, additional, Fam, Mina, additional, Roche, Nancy, additional, Vatanian, Negin, additional, Maunganidze, Nicollette, additional, Potapova, Olga, additional, Paklina, Oxana V., additional, VanderKolk, Pamela, additional, Castro, Patricia, additional, Kurzawa, Paweł, additional, Hariharan, Pushpa, additional, Li, Qin, additional, Li, Qing Kay, additional, Dhir, Rajiv, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Smith, Richard D., additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cerda, Sandra, additional, Cottingham, Sandra, additional, Haynes, Sarah, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Singh, Shilpi, additional, Tsang, Shirley X., additional, Cai, Shuang, additional, Cao, Song, additional, Gabriel, Stacey, additional, Carr, Steven A., additional, Liu, Tao, additional, Bauer, Thomas, additional, Le, Toan, additional, Chen, Xi S., additional, Zhang, Xu, additional, Shutack, Yvonne, additional, and Zhang, Zhen, additional
Published: 2023
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23. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Author: Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A., Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, Zimmerman, Lisa J., Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A., Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, and Zimmerman, Lisa J.
Abstract: © 2020 The Authors The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this “proteogenomics” approach was applied to 122 treatment-naive primary breast cancers accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy, and allowed more accurate assessment of Rb status for prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomics profiles uncovered novel associations between tumor suppressor loss and targetable kinases. Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy.
Published: 2022

24. Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy

Author: Sedghizadeh, Parish P., Yooseph, Shibu, Fadrosh, Douglas W., Zeigler-Allen, Lisa, Thiagarajan, Mathangi, Salek, Hamid, Farahnik, Farid, and Williamson, Shannon J.
Published: 2012
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25. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

Author: Cuvelier, Marie L., Allen, Andrew E., Monier, Adam, McCrow, John P., Messié, Monique, Tringe, Susannah G., Woyke, Tanja, Welsh, Rory M., Ishoey, Thomas, Lee, Jae-Hyeok, Binder, Brian J., DuPont, Chris L., Latasa, Mikel, Guigand, Cédric, Buck, Kurt R., Hilton, Jason, Thiagarajan, Mathangi, Caler, Elisabet, Read, Betsy, Lasken, Roger S., Chavez, Francisco P., Worden, Alexandra Z., and Karl, David
Published: 2010

26. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

Author: Whiteaker, Jeffrey R., primary, Lundeen, Rachel A., additional, Zhao, Lei, additional, Schoenherr, Regine M., additional, Burian, Aura, additional, Huang, Dongqing, additional, Voytovich, Ulianna, additional, Wang, Tao, additional, Kennedy, Jacob J., additional, Ivey, Richard G., additional, Lin, Chenwei, additional, Murillo, Oscar D., additional, Lorentzen, Travis D., additional, Thiagarajan, Mathangi, additional, Colantonio, Simona, additional, Caceres, Tessa W., additional, Roberts, Rhonda R., additional, Knotts, Joseph G., additional, Reading, Joshua J., additional, Kaczmarczyk, Jan A., additional, Richardson, Christopher W., additional, Garcia-Buntley, Sandra S., additional, Bocik, William, additional, Hewitt, Stephen M., additional, Murray, Karen E., additional, Do, Nhan, additional, Brophy, Mary, additional, Wilz, Stephen W., additional, Yu, Hongbo, additional, Ajjarapu, Samuel, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, and Paulovich, Amanda G., additional
Published: 2021
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27. Proteogenomic characterization of pancreatic ductal adenocarcinoma

Author: Cao, Liwei, primary, Huang, Chen, additional, Cui Zhou, Daniel, additional, Hu, Yingwei, additional, Lih, T. Mamie, additional, Savage, Sara R., additional, Krug, Karsten, additional, Clark, David J., additional, Schnaubelt, Michael, additional, Chen, Lijun, additional, da Veiga Leprevost, Felipe, additional, Eguez, Rodrigo Vargas, additional, Yang, Weiming, additional, Pan, Jianbo, additional, Wen, Bo, additional, Dou, Yongchao, additional, Jiang, Wen, additional, Liao, Yuxing, additional, Shi, Zhiao, additional, Terekhanova, Nadezhda V., additional, Cao, Song, additional, Lu, Rita Jui-Hsien, additional, Li, Yize, additional, Liu, Ruiyang, additional, Zhu, Houxiang, additional, Ronning, Peter, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Easwaran, Hariharan, additional, Danilova, Ludmila, additional, Mer, Arvind Singh, additional, Yoo, Seungyeul, additional, Wang, Joshua M., additional, Liu, Wenke, additional, Haibe-Kains, Benjamin, additional, Thiagarajan, Mathangi, additional, Jewell, Scott D., additional, Hostetter, Galen, additional, Newton, Chelsea J., additional, Li, Qing Kay, additional, Roehrl, Michael H., additional, Fenyö, David, additional, Wang, Pei, additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Omenn, Gilbert S., additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Bathe, Oliver F., additional, Chan, Daniel W., additional, Hruban, Ralph H., additional, Ding, Li, additional, Zhang, Bing, additional, Zhang, Hui, additional, Amin, Mitual, additional, An, Eunkyung, additional, Ayad, Christina, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Boca, Simina M., additional, Bocik, William, additional, Borucki, Melissa, additional, Cai, Shuang, additional, Carr, Steven A., additional, Cerda, Sandra, additional, Chen, Huan, additional, Chen, Steven, additional, Chesla, David, additional, Chinnaiyan, Arul M., additional, Colaprico, Antonio, additional, Cottingham, Sandra, additional, Derejska, Magdalena, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Dyer, Maureen A., additional, Edwards, Nathan J., additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Francis, Alicia, additional, Francis, Jesse, additional, Gabriel, Stacey, additional, Gabrovski, Nikolay, additional, Gardner, Johanna, additional, Getz, Gad, additional, Gillette, Michael A., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Guo, Shuai, additional, Hariharan, Pushpa, additional, Hiltke, Tara, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kinsinger, Christopher R., additional, Koziak, Jennifer M., additional, Kusnierz, Katarzyna, additional, Liu, Tao, additional, Long, Jiang, additional, Mallery, David, additional, Mareedu, Sailaja, additional, Matteotti, Ronald, additional, Maunganidze, Nicollette, additional, McGarvey, Peter B., additional, Minoo, Parham, additional, Paklina, Oxana V., additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Potapova, Olga, additional, Pruetz, Barbara, additional, Qi, Liqun, additional, Roche, Nancy, additional, Rodland, Karin D., additional, Rohrer, Daniel C., additional, Schadt, Eric E., additional, Shabunin, Alexey V., additional, Shelton, Troy, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Smith, Richard D., additional, Sokoll, Lori J., additional, Suh, James, additional, Thangudu, Ratna R., additional, Tsang, Shirley X., additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vatanian, Negin, additional, Wang, Wenyi, additional, Wilson, George D., additional, Wiznerowicz, Maciej, additional, Zhang, Zhen, additional, and Zhao, Grace, additional
Published: 2021
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28. Proteogenomic and metabolomic characterization of human glioblastoma

Author: Wang, Liang-Bo, primary, Karpova, Alla, additional, Gritsenko, Marina A., additional, Kyle, Jennifer E., additional, Cao, Song, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Colaprico, Antonio, additional, Rothstein, Joseph H., additional, Hong, Runyu, additional, Stathias, Vasileios, additional, Cornwell, MacIntosh, additional, Petralia, Francesca, additional, Wu, Yige, additional, Reva, Boris, additional, Krug, Karsten, additional, Pugliese, Pietro, additional, Kawaler, Emily, additional, Olsen, Lindsey K., additional, Liang, Wen-Wei, additional, Song, Xiaoyu, additional, Dou, Yongchao, additional, Wendl, Michael C., additional, Caravan, Wagma, additional, Liu, Wenke, additional, Cui Zhou, Daniel, additional, Ji, Jiayi, additional, Tsai, Chia-Feng, additional, Petyuk, Vladislav A., additional, Moon, Jamie, additional, Ma, Weiping, additional, Chu, Rosalie K., additional, Weitz, Karl K., additional, Moore, Ronald J., additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Yang, Xiaolu, additional, Yoo, Seungyeul, additional, Krek, Azra, additional, Demopoulos, Alexis, additional, Zhu, Houxiang, additional, Wyczalkowski, Matthew A., additional, McMichael, Joshua F., additional, Henderson, Brittany L., additional, Lindgren, Caleb M., additional, Boekweg, Hannah, additional, Lu, Shuangjia, additional, Baral, Jessika, additional, Yao, Lijun, additional, Stratton, Kelly G., additional, Bramer, Lisa M., additional, Zink, Erika, additional, Couvillion, Sneha P., additional, Bloodsworth, Kent J., additional, Satpathy, Shankha, additional, Sieh, Weiva, additional, Boca, Simina M., additional, Schürer, Stephan, additional, Chen, Feng, additional, Wiznerowicz, Maciej, additional, Ketchum, Karen A., additional, Boja, Emily S., additional, Kinsinger, Christopher R., additional, Robles, Ana I., additional, Hiltke, Tara, additional, Thiagarajan, Mathangi, additional, Nesvizhskii, Alexey I., additional, Zhang, Bing, additional, Mani, D.R., additional, Ceccarelli, Michele, additional, Chen, Xi S., additional, Cottingham, Sandra L., additional, Li, Qing Kay, additional, Kim, Albert H., additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Rodriguez, Henry, additional, Mesri, Mehdi, additional, Payne, Samuel H., additional, Resnick, Adam C., additional, Wang, Pei, additional, Smith, Richard D., additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Barnholtz-Sloan, Jill S., additional, Rodland, Karin D., additional, Liu, Tao, additional, Ding, Li, additional, Agarwal, Anupriya, additional, Amin, Mitual, additional, An, Eunkyung, additional, Anderson, Matthew L., additional, Andrews, David W., additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Blumenberg, Lili, additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna P., additional, Carr, Steven A., additional, Cerda, Sandra, additional, Chan, Daniel W., additional, Charamut, Alyssa, additional, Chen, Lin S., additional, Chesla, David, additional, Chinnaiyan, Arul M., additional, Chowdhury, Shrabanti, additional, Cieślik, Marcin P., additional, Clark, David J., additional, Culpepper, Houston, additional, Czernicki, Tomasz, additional, D'Angelo, Fulvio, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Dhanasekaran, Saravana Mohan, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Elburn, Kimberly, additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Gabrovski, Nikolay, additional, Garofano, Luciano, additional, Getz, Gad, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Golbin, Denis, additional, Hanhan, Ziad, additional, Hannick, Linda I., additional, Hariharan, Pushpa, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hostetter, Galen, additional, Huang, Chen, additional, Jaehnig, Eric, additional, Jewell, Scott D., additional, Ji, Nan, additional, Jones, Corbin D., additional, Karz, Alcida, additional, Kaspera, Wojciech, additional, Kim, Lyndon, additional, Kothadia, Ramani B., additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan, additional, Leprevost, Felipe D., additional, Li, Kai, additional, Liao, Yuxing, additional, Lilly, Jena, additional, Liu, Hongwei, additional, Lubínski, Jan, additional, Madan, Rashna, additional, Maggio, William, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Martinez, Nina, additional, Maunganidze, Nicollette, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Migliozzi, Simona, additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Omenn, Gilbert S., additional, Ozbek, Umut, additional, Paklina, Oxana V., additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Pico, Alexander R., additional, Piehowski, Paul D., additional, Placantonakis, Dimitris G., additional, Polonskaya, Larisa, additional, Potapova, Olga, additional, Pruetz, Barbara, additional, Qi, Liqun, additional, Ramkissoon, Shakti, additional, Resnick, Adam, additional, Richey, Shannon, additional, Riggins, Gregory, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rohrer, Daniel C., additional, Rood, Brian R., additional, Rossell, Larissa, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Shi, Yan, additional, Shi, Zhiao, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Skelly, Tara, additional, Sokoll, Lori J., additional, Stawicki, Jakub, additional, Stein, Stephen E., additional, Suh, James, additional, Szopa, Wojciech, additional, Tabor, Dave, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tsang, Shirley, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vasaikar, Suhas, additional, Vatanian, Negin, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Wan, Weiqing, additional, Wang, Junmei, additional, Webster, Alex, additional, Wen, Bo, additional, Whiteaker, Jeffrey R., additional, Wilson, George D., additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhang, Hui, additional, Zhang, Liwei, additional, Zhang, Zhen, additional, Zhao, Grace, additional, and Zhu, Jun, additional
Published: 2021
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29. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Author: Huang, Chen, primary, Chen, Lijun, additional, Savage, Sara R., additional, Eguez, Rodrigo Vargas, additional, Dou, Yongchao, additional, Li, Yize, additional, da Veiga Leprevost, Felipe, additional, Jaehnig, Eric J., additional, Lei, Jonathan T., additional, Wen, Bo, additional, Schnaubelt, Michael, additional, Krug, Karsten, additional, Song, Xiaoyu, additional, Cieślik, Marcin, additional, Chang, Hui-Yin, additional, Wyczalkowski, Matthew A., additional, Li, Kai, additional, Colaprico, Antonio, additional, Li, Qing Kay, additional, Clark, David J., additional, Hu, Yingwei, additional, Cao, Liwei, additional, Pan, Jianbo, additional, Wang, Yuefan, additional, Cho, Kyung-Cho, additional, Shi, Zhiao, additional, Liao, Yuxing, additional, Jiang, Wen, additional, Anurag, Meenakshi, additional, Ji, Jiayi, additional, Yoo, Seungyeul, additional, Zhou, Daniel Cui, additional, Liang, Wen-Wei, additional, Wendl, Michael, additional, Vats, Pankaj, additional, Carr, Steven A., additional, Mani, D.R., additional, Zhang, Zhen, additional, Qian, Jiang, additional, Chen, Xi S., additional, Pico, Alexander R., additional, Wang, Pei, additional, Chinnaiyan, Arul M., additional, Ketchum, Karen A., additional, Kinsinger, Christopher R., additional, Robles, Ana I., additional, An, Eunkyung, additional, Hiltke, Tara, additional, Mesri, Mehdi, additional, Thiagarajan, Mathangi, additional, Weaver, Alissa M., additional, Sikora, Andrew G., additional, Lubiński, Jan, additional, Wierzbicka, Małgorzata, additional, Wiznerowicz, Maciej, additional, Satpathy, Shankha, additional, Gillette, Michael A., additional, Miles, George, additional, Ellis, Matthew J., additional, Omenn, Gilbert S., additional, Rodriguez, Henry, additional, Boja, Emily S., additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, El-Naggar, Adel K., additional, Chan, Daniel W., additional, Zhang, Hui, additional, Zhang, Bing, additional, Agarwal, Anupriya, additional, Anderson, Matthew L., additional, Avanessian, Shayan C., additional, Avtonomov, Dmitry, additional, Bathe, Oliver F., additional, Birger, Chet, additional, Birrer, Michael J., additional, Blumenberg, Lili, additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna Pamela, additional, Cerda, Sandra, additional, Charamut, Alyssa, additional, Chen, Lin S., additional, Chowdhury, Shrabanti, additional, Clauser, Karl R., additional, Culpepper, Houston, additional, Czernicki, Tomasz, additional, D'Angelo, Fulvio, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Ding, Fei, additional, Domagalski, Marcin J., additional, Dort, Joseph C., additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Elburn, Kimberly, additional, Ermakova, Tatiana S., additional, Fenyo, David, additional, Ferrarotto, Renata, additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Garofano, Luciano, additional, Geffen, Yifat, additional, Getz, Gad, additional, Goldthwaite, Charles A., additional, Hannick, Linda I., additional, Hariharan, Pushpa, additional, Hayes, David N., additional, Heiman, David, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hostetter, Galen, additional, Hyrcza, Martin, additional, Jewell, Scott D., additional, Jones, Corbin D., additional, Kane, M. Harry, additional, Karz, Alicia, additional, Kothadia, Ramani B., additional, Krek, Azra, additional, Kumar-Sinha, Chandan, additional, Liu, Tao, additional, Liu, Hongwei, additional, Ma, Weiping, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Maunganidze, Nicollette, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Migliozzi, Simona, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Ozbek, Umut, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Pazardzhikliev, Dimitar Dimitrov, additional, Perou, Amy M., additional, Petralia, Francesca, additional, Petrenko, Lyudmila, additional, Piehowski, Paul D., additional, Placantonakis, Dmitris, additional, Polonskaya, Larisa, additional, Ponomareva, Elena V., additional, Potapova, Olga, additional, Qi, Liqun, additional, Qu, Ning, additional, Ramkissoon, Shakti, additional, Reva, Boris, additional, Richey, Shannon, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rodland, Karin, additional, Rohrer, Daniel C., additional, Rykunov, Dmitry, additional, Schadt, Eric E., additional, Shi, Yan, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Skelly, Tara, additional, Smith, Richard, additional, Sokoll, Lori J., additional, Stawicki, Jakub, additional, Stein, Stephen E., additional, Suh, James, additional, Szopa, Wojciech, additional, Tabor, Dave, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Teo, Guo Ci, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tsang, Shirley, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vasilev, Lyubomir Valkov, additional, Vatanian, Negin, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Westbrook, Thomas F., additional, Whiteaker, Jeffrey R., additional, Wu, Yige, additional, Xu, Midie, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Yu, Fengchao, additional, Zaalishvili, Kakhaber, additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhao, Grace, additional, and Zhu, Jun, additional
Published: 2021
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30. The NCI Genomic Data Commons

Author: Heath, Allison P., primary, Ferretti, Vincent, additional, Agrawal, Stuti, additional, An, Maksim, additional, Angelakos, James C., additional, Arya, Renuka, additional, Bajari, Rosita, additional, Baqar, Bilal, additional, Barnowski, Justin H. B., additional, Burt, Jeffrey, additional, Catton, Ann, additional, Chan, Brandon F., additional, Chu, Fay, additional, Cullion, Kim, additional, Davidsen, Tanja, additional, Do, Phuong-My, additional, Dompierre, Christian, additional, Ferguson, Martin L., additional, Fitzsimons, Michael S., additional, Ford, Michael, additional, Fukuma, Miyuki, additional, Gaheen, Sharon, additional, Ganji, Gajanan L., additional, Garcia, Tzintzuni I., additional, George, Sameera S., additional, Gerhard, Daniela S., additional, Gerthoffert, Francois, additional, Gomez, Fauzi, additional, Han, Kang, additional, Hernandez, Kyle M., additional, Issac, Biju, additional, Jackson, Richard, additional, Jensen, Mark A., additional, Joshi, Sid, additional, Kadam, Ajinkya, additional, Khurana, Aishmit, additional, Kim, Kyle M. J., additional, Kraft, Victoria E., additional, Li, Shenglai, additional, Lichtenberg, Tara M., additional, Lodato, Janice, additional, Lolla, Laxmi, additional, Martinov, Plamen, additional, Mazzone, Jeffrey A., additional, Miller, Daniel P., additional, Miller, Ian, additional, Miller, Joshua S., additional, Miyauchi, Koji, additional, Murphy, Mark W., additional, Nullet, Thomas, additional, Ogwara, Rowland O., additional, Ortuño, Francisco M., additional, Pedrosa, Jesús, additional, Pham, Phuong L., additional, Popov, Maxim Y., additional, Porter, James J., additional, Powell, Raymond, additional, Rademacher, Karl, additional, Reid, Colin P., additional, Rich, Samantha, additional, Rogel, Bessie, additional, Sahni, Himanso, additional, Savage, Jeremiah H., additional, Schmitt, Kyle A., additional, Simmons, Trevar J., additional, Sislow, Joseph, additional, Spring, Jonathan, additional, Stein, Lincoln, additional, Sullivan, Sean, additional, Tang, Yajing, additional, Thiagarajan, Mathangi, additional, Troyer, Heather D., additional, Wang, Chang, additional, Wang, Zhining, additional, West, Bedford L., additional, Wilmer, Alex, additional, Wilson, Shane, additional, Wu, Kaman, additional, Wysocki, William P., additional, Xiang, Linda, additional, Yamada, Joseph T., additional, Yang, Liming, additional, Yu, Christine, additional, Yung, Christina K., additional, Zenklusen, Jean Claude, additional, Zhang, Junjun, additional, Zhang, Zhenyu, additional, Zhao, Yuanheng, additional, Zubair, Ariz, additional, Staudt, Louis M., additional, and Grossman, Robert L., additional
Published: 2021
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31. A framework for human microbiome research

Author: Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen
Published: 2012
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32. Structure, function and diversity of the healthy human microbiome

Author: Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen
Published: 2012
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33. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Author: Krug, Karsten, primary, Jaehnig, Eric J., additional, Satpathy, Shankha, additional, Blumenberg, Lili, additional, Karpova, Alla, additional, Anurag, Meenakshi, additional, Miles, George, additional, Mertins, Philipp, additional, Geffen, Yifat, additional, Tang, Lauren C., additional, Heiman, David I., additional, Cao, Song, additional, Maruvka, Yosef E., additional, Lei, Jonathan T., additional, Huang, Chen, additional, Kothadia, Ramani B., additional, Colaprico, Antonio, additional, Birger, Chet, additional, Wang, Jarey, additional, Dou, Yongchao, additional, Wen, Bo, additional, Shi, Zhiao, additional, Liao, Yuxing, additional, Wiznerowicz, Maciej, additional, Wyczalkowski, Matthew A., additional, Chen, Xi Steven, additional, Kennedy, Jacob J., additional, Paulovich, Amanda G., additional, Thiagarajan, Mathangi, additional, Kinsinger, Christopher R., additional, Hiltke, Tara, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Westbrook, Thomas F., additional, Ding, Li, additional, Getz, Gad, additional, Clauser, Karl R., additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Zhang, Bing, additional, Mani, D.R., additional, Carr, Steven A., additional, Ellis, Matthew J., additional, Gillette, Michael A., additional, Avanessian, Shayan C., additional, Cai, Shuang, additional, Chan, Daniel, additional, Chen, Xian, additional, Edwards, Nathan J., additional, Hoofnagle, Andrew N., additional, Kane, M. Harry, additional, Ketchum, Karen A., additional, Kuhn, Eric, additional, Levine, Douglas A., additional, Li, Shunqiang, additional, Liebler, Daniel C., additional, Liu, Tao, additional, Luo, Jingqin, additional, Madhavan, Subha, additional, Maher, Chris, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, Oberti, Mauricio, additional, Pandey, Akhilesh, additional, Payne, Samuel H., additional, Ransohoff, David F., additional, Rivers, Robert C., additional, Rodland, Karin D., additional, Rudnick, Paul, additional, Sanders, Melinda E., additional, Shaw, Kenna M., additional, Shih, Ie-Ming, additional, Slebos, Robbert J.C., additional, Smith, Richard D., additional, Snyder, Michael, additional, Stein, Stephen E., additional, Tabb, David L., additional, Thangudu, Ratna R., additional, Thomas, Stefani, additional, Wang, Yue, additional, White, Forest M., additional, Whiteaker, Jeffrey R., additional, Whiteley, Gordon A., additional, Zhang, Hui, additional, Zhang, Zhen, additional, Zhao, Yingming, additional, Zhu, Heng, additional, and Zimmerman, Lisa J., additional
Published: 2020
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34. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Author: Hu, Yingwei, primary, Pan, Jianbo, additional, Shah, Punit, additional, Ao, Minghui, additional, Thomas, Stefani N., additional, Liu, Yang, additional, Chen, Lijun, additional, Schnaubelt, Michael, additional, Clark, David J., additional, Rodriguez, Henry, additional, Boja, Emily S., additional, Hiltke, Tara, additional, Kinsinger, Christopher R., additional, Rodland, Karin D., additional, Li, Qing Kay, additional, Qian, Jiang, additional, Zhang, Zhen, additional, Chan, Daniel W., additional, Zhang, Hui, additional, Pandey, Akhilesh, additional, Paulovich, Amanda, additional, Hoofnagle, Andrew, additional, Zhang, Bing, additional, Mani, D.R., additional, Liebler, Daniel C., additional, Ransohoff, David F., additional, Fenyo, David, additional, Tabb, David L., additional, Levine, Douglas A., additional, Kuhn, Eric, additional, White, Forest M., additional, Whiteley, Gordon A., additional, Zhu, Heng, additional, Shih, Ie-Ming, additional, Bavarva, Jasmin, additional, McDermott, Jason E., additional, Whiteaker, Jeffrey, additional, Ketchum, Karen A., additional, Clauser, Karl R., additional, Ruggles, Kelly, additional, Elburn, Kimberly, additional, Ding, Li, additional, Hannick, Linda, additional, Zimmerman, Lisa J., additional, Watson, Mark, additional, Thiagarajan, Mathangi, additional, Ellis, Matthew J.C., additional, Oberti, Mauricio, additional, Mesri, Mehdi, additional, Sanders, Melinda E., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Snyder, Michael, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Rudnick, Paul A., additional, McGarvey, Peter B., additional, Mertins, Philip, additional, Townsend, R. Reid, additional, Thangudu, Ratna R., additional, Smith, Richard D., additional, Rivers, Robert C., additional, Slebos, Robert J.C., additional, Payne, Samuel H., additional, Davies, Sherri R., additional, Cai, Shuang, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Skates, Steven J., additional, Madhavan, Subha, additional, Liu, Tao, additional, Chen, Xian, additional, Zhao, Yingming, additional, Wang, Yue, additional, and Shi, Zhiao, additional
Published: 2020
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35. Abstract 5123: Proteogenomic characterization reveals mitotic kinase and replication stress implicated in ovarian high-grade serous cancer

Author: McDermott, Jason, primary, Arshad, Osama, additional, Petyuk, Vladislav, additional, Fu, Yi, additional, Gritsenko, Marina, additional, Tsai, Chia-Feng, additional, Payne, Samuel, additional, Thiagarajan, Mathangi, additional, Kinsinger, Christopher, additional, Robles, Ana, additional, Boja, Emily, additional, Rodriguez, Henry, additional, Chan, Daniel, additional, Zhang, Bing, additional, Zhang, Zhen, additional, Ding, Li, additional, Smith, Richard, additional, Liu, Tao, additional, and Rodland, Karin, additional
Published: 2020
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36. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Author: Gillette, Michael A., primary, Satpathy, Shankha, additional, Cao, Song, additional, Dhanasekaran, Saravana M., additional, Vasaikar, Suhas V., additional, Krug, Karsten, additional, Petralia, Francesca, additional, Li, Yize, additional, Liang, Wen-Wei, additional, Reva, Boris, additional, Krek, Azra, additional, Ji, Jiayi, additional, Song, Xiaoyu, additional, Liu, Wenke, additional, Hong, Runyu, additional, Yao, Lijun, additional, Blumenberg, Lili, additional, Savage, Sara R., additional, Wendl, Michael C., additional, Wen, Bo, additional, Li, Kai, additional, Tang, Lauren C., additional, MacMullan, Melanie A., additional, Avanessian, Shayan C., additional, Kane, M. Harry, additional, Newton, Chelsea J., additional, Cornwell, MacIntosh, additional, Kothadia, Ramani B., additional, Ma, Weiping, additional, Yoo, Seungyeul, additional, Mannan, Rahul, additional, Vats, Pankaj, additional, Kumar-Sinha, Chandan, additional, Kawaler, Emily A., additional, Omelchenko, Tatiana, additional, Colaprico, Antonio, additional, Geffen, Yifat, additional, Maruvka, Yosef E., additional, da Veiga Leprevost, Felipe, additional, Wiznerowicz, Maciej, additional, Gümüş, Zeynep H., additional, Veluswamy, Rajwanth R., additional, Hostetter, Galen, additional, Heiman, David I., additional, Wyczalkowski, Matthew A., additional, Hiltke, Tara, additional, Mesri, Mehdi, additional, Kinsinger, Christopher R., additional, Boja, Emily S., additional, Omenn, Gilbert S., additional, Chinnaiyan, Arul M., additional, Rodriguez, Henry, additional, Li, Qing Kay, additional, Jewell, Scott D., additional, Thiagarajan, Mathangi, additional, Getz, Gad, additional, Zhang, Bing, additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Cieslik, Marcin P., additional, Robles, Ana I., additional, Clauser, Karl R., additional, Govindan, Ramaswamy, additional, Wang, Pei, additional, Nesvizhskii, Alexey I., additional, Ding, Li, additional, Mani, D.R., additional, Carr, Steven A., additional, Webster, Alex, additional, Francis, Alicia, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Godwin, Andrew K., additional, Karnuta, Andrii, additional, Marrero-Oliveras, Annette, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kubisa, Bartosz, additional, Druker, Brian J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel Cui, additional, Chan, Daniel W., additional, Chesla, David, additional, Clark, David J., additional, Rykunov, Dmitry, additional, Tan, Donghui, additional, Ponomareva, Elena V., additional, Duffy, Elizabeth, additional, Burks, Eric J., additional, Schadt, Eric E., additional, Bergstrom, Erik J., additional, Fedorov, Eugene S., additional, Malc, Ewa, additional, Wilson, George D., additional, Chen, Hai-Quan, additional, Krzystek, Halina M., additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhang, Hui, additional, Day, Jacob, additional, Suh, James, additional, Whiteaker, Jeffrey R., additional, Eschbacher, Jennifer, additional, McGee, John, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Robinson, Karna, additional, Hoadley, Katherine A., additional, Suzuki, Kei, additional, Um, Ki Sung, additional, Elburn, Kim, additional, Wang, Liang-Bo, additional, Chen, Lijun, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Wojtyś, Małgorzata, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Beasley, Mary B., additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Sun, Meng-Hong, additional, Roehrl, Michael H., additional, Birrer, Michael J., additional, Noble, Michael, additional, Schnaubelt, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Krotevich, Mikhail, additional, Khan, Munziba, additional, Selvan, Myvizhi Esai, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Potapova, Olga, additional, Grady, Pamela, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Madan, Rashna, additional, Thangudu, Ratna R., additional, Smith, Richard D., additional, Welsh, Robert J., additional, Zelt, Robert, additional, Mehra, Rohit, additional, Matteotti, Ronald, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Chugh, Seema, additional, Smith, Shaleigh, additional, Tsang, Shirley, additional, Cai, Shuang, additional, Boca, Simina M., additional, Carter, Sonya, additional, Gabriel, Stacey, additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Shankar, Sunita, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Bauer, Thomas, additional, Velvulou, Uma, additional, Ozbek, Umut, additional, Petyuk, Vladislav A., additional, Sovenko, Volodymyr, additional, Bocik, William E., additional, Maggio, William W., additional, Chen, Xi, additional, Shi, Yan, additional, Wu, Yige, additional, Hu, Yingwei, additional, Liao, Yuxing, additional, Zhang, Zhen, additional, and Shi, Zhiao, additional
Published: 2020
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37. Proteogenomic Characterization of Endometrial Carcinoma

Author: Dou, Yongchao, primary, Kawaler, Emily A., additional, Cui Zhou, Daniel, additional, Gritsenko, Marina A., additional, Huang, Chen, additional, Blumenberg, Lili, additional, Karpova, Alla, additional, Petyuk, Vladislav A., additional, Savage, Sara R., additional, Satpathy, Shankha, additional, Liu, Wenke, additional, Wu, Yige, additional, Tsai, Chia-Feng, additional, Wen, Bo, additional, Li, Zhi, additional, Cao, Song, additional, Moon, Jamie, additional, Shi, Zhiao, additional, Cornwell, MacIntosh, additional, Wyczalkowski, Matthew A., additional, Chu, Rosalie K., additional, Vasaikar, Suhas, additional, Zhou, Hua, additional, Gao, Qingsong, additional, Moore, Ronald J., additional, Li, Kai, additional, Sethuraman, Sunantha, additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Heiman, David, additional, Krug, Karsten, additional, Clauser, Karl, additional, Kothadia, Ramani, additional, Maruvka, Yosef, additional, Pico, Alexander R., additional, Oliphant, Amanda E., additional, Hoskins, Emily L., additional, Pugh, Samuel L., additional, Beecroft, Sean J.I., additional, Adams, David W., additional, Jarman, Jonathan C., additional, Kong, Andy, additional, Chang, Hui-Yin, additional, Reva, Boris, additional, Liao, Yuxing, additional, Rykunov, Dmitry, additional, Colaprico, Antonio, additional, Chen, Xi Steven, additional, Czekański, Andrzej, additional, Jędryka, Marcin, additional, Matkowski, Rafał, additional, Wiznerowicz, Maciej, additional, Hiltke, Tara, additional, Boja, Emily, additional, Kinsinger, Christopher R., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Mutch, David, additional, Fuh, Katherine, additional, Ellis, Matthew J., additional, DeLair, Deborah, additional, Thiagarajan, Mathangi, additional, Mani, D.R., additional, Getz, Gad, additional, Noble, Michael, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Anderson, Matthew L., additional, Levine, Douglas A., additional, Smith, Richard D., additional, Payne, Samuel H., additional, Ruggles, Kelly V., additional, Rodland, Karin D., additional, Ding, Li, additional, Zhang, Bing, additional, Liu, Tao, additional, Fenyö, David, additional, Agarwal, Anupriya, additional, Anurag, Meenakshi, additional, Avtonomov, Dmitry, additional, Birger, Chet, additional, Birrer, Michael J., additional, Boca, Simina M., additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna, additional, Carr, Steven A., additional, Carter, Sonya, additional, Castro, Patricia, additional, Cerda, Sandra, additional, Chaikin, Michelle, additional, Chan, Daniel W., additional, Chan, Doug, additional, Charamut, Alyssa, additional, Chen, Feng, additional, Chen, Jin, additional, Chen, Lijun, additional, Chen, Lin S., additional, Chesla, David, additional, Chheda, Milan G., additional, Chinnaiyan, Arul M., additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clark, David J., additional, Cottingham, Sandra, additional, Culpepper, Houston, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Dhanasekaran, Saravana Mohan, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Dottino, Peter, additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Elburn, Kim, additional, Field, Jayson B., additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Geffen, Yifat, additional, Geiszler, Daniel, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Grady, Pamela, additional, Hannick, Linda, additional, Hariharan, Pushpa, additional, Hilsenbeck, Sue, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hsieh, James J., additional, Hu, Yingwei, additional, Ittmann, Michael M., additional, Jaehnig, Eric, additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jones, Corbin D., additional, Karabon, Renee, additional, Ketchum, Karen A., additional, Khan, Munziba, additional, Kim, Beom-Jun, additional, Krek, Azra, additional, Krubit, Tanya, additional, Kumar-Sinha, Chandan, additional, Leprevost, Felipe D., additional, Lewis, Michael, additional, Li, Qing Kay, additional, Li, Yize, additional, Liu, Hongwei, additional, Lubinski, Jan, additional, Ma, Weiping, additional, Madan, Rashna, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Martignetti, John, additional, McDermott, Jason, additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Petralia, Francesca, additional, Piehowski, Paul, additional, Polonskaya, Larisa, additional, Qi, Liqun, additional, Richey, Shannon, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rohrer, Daniel C., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Shi, Yan, additional, Skelly, Tara, additional, Sokoll, Lori J., additional, Song, Xiaoyu, additional, Stein, Stephen E., additional, Suh, James, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Teo, Guo Ci, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vatanian, Negin, additional, Vats, Pankaj, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Wang, Liang-Bo, additional, Wang, Ying, additional, Webster, Alex, additional, Westbrook, Thomas, additional, Wheeler, David, additional, Whiteaker, Jeffrey R., additional, Wilson, George D., additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhang, Hui, additional, Zhang, Yuping, additional, Zhang, Zhen, additional, and Zhao, Grace, additional
Published: 2020
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38. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author: Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional
Published: 2020
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39. METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

Author: Goll, Johannes, Rusch, Douglas B., Tanenbaum, David M., Thiagarajan, Mathangi, Li, Kelvin, Methé, Barbara A., and Yooseph, Shibu
Published: 2010
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40. Pathema: a clade-specific bioinformatics resource center for pathogen research

Author: Brinkac, Lauren M., Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Caler, Elisabet, Dodson, Robert J., Durkin, A. Scott, Harkins, Derek M., Lorenzi, Hernan, Madupu, Ramana, Sebastian, Yinong, Shrivastava, Susmita, Thiagarajan, Mathangi, Orvis, Joshua, Sundaram, Jaideep P., Crabtree, Jonathon, Galens, Kevin, Zhao, Yongmei, Inman, Jason M., Montgomery, Robert, Schobel, Seth, Galinsky, Kevin, Tanenbaum, David M., Resnick, Adam, Zafar, Nikhat, White, Owen, and Sutton, Granger
Published: 2010
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41. [9] TM4 Microarray Software Suite

Author: Saeed, Alexander I., primary, Bhagabati, Nirmal K., additional, Braisted, John C., additional, Liang, Wei, additional, Sharov, Vasily, additional, Howe, Eleanor A., additional, Li, Jianwei, additional, Thiagarajan, Mathangi, additional, White, Joseph A., additional, and Quackenbush, John, additional
Published: 2006
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42. Microbial community function and biomarker discovery in the human microbiome

Author: Segata, Nicola, Abubucker, Sahar, Goll, Johannes, Schubert, Alyxandria M, Izard, Jacques, Cantarel, Brandi L, Rodriguez-Mueller, Beltran, Waldron, Levi, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T, Methé, Barbara, Schloss, Patrick D, Garrett, Wendy S, Gevers, Dirk, Mitreva, Makedonka, and Huttenhower, Curtis
Published: 2011
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43. Comparative genomic analysis and phylogenetic position of Theileria equi

Author: Kappmeyer Lowell S, Thiagarajan Mathangi, Herndon David R, Ramsay Joshua D, Caler Elisabet, Djikeng Appolinaire, Gillespie Joseph J, Lau Audrey OT, Roalson Eric H, Silva Joana C, Silva Marta G, Suarez Carlos E, Ueti Massaro W, Nene Vishvanath M, Mealey Robert H, Knowles Donald P, and Brayton Kelly A
Subjects: Apicomplexa, Parasite, Vaccine, Horse, Vector-borne disease, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms.
Published: 2012
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44. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author: Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional
Published: 2019
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45. Abstract 2129: CPTAC: Biospecimen accrual for proteogenomics

Author: Thiagarajan, Mathangi, primary
Published: 2019
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46. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Author: Vasaikar, Suhas, primary, Huang, Chen, additional, Wang, Xiaojing, additional, Petyuk, Vladislav A., additional, Savage, Sara R., additional, Wen, Bo, additional, Dou, Yongchao, additional, Zhang, Yun, additional, Shi, Zhiao, additional, Arshad, Osama A., additional, Gritsenko, Marina A., additional, Zimmerman, Lisa J., additional, McDermott, Jason E., additional, Clauss, Therese R., additional, Moore, Ronald J., additional, Zhao, Rui, additional, Monroe, Matthew E., additional, Wang, Yi-Ting, additional, Chambers, Matthew C., additional, Slebos, Robbert J.C., additional, Lau, Ken S., additional, Mo, Qianxing, additional, Ding, Li, additional, Ellis, Matthew, additional, Thiagarajan, Mathangi, additional, Kinsinger, Christopher R., additional, Rodriguez, Henry, additional, Smith, Richard D., additional, Rodland, Karin D., additional, Liebler, Daniel C., additional, Liu, Tao, additional, Zhang, Bing, additional, Pandey, Akhilesh, additional, Paulovich, Amanda, additional, Hoofnagle, Andrew, additional, Mani, D.R., additional, Chan, Daniel W., additional, Ransohoff, David F., additional, Fenyo, David, additional, Tabb, David L., additional, Levine, Douglas A., additional, Boja, Emily S., additional, Kuhn, Eric, additional, White, Forest M., additional, Whiteley, Gordon A., additional, Zhu, Heng, additional, Zhang, Hui, additional, Shih, Ie-Ming, additional, Bavarva, Jasmin, additional, Whiteaker, Jeffrey, additional, Ketchum, Karen A., additional, Clauser, Karl R., additional, Ruggles, Kelly, additional, Elburn, Kimberly, additional, Hannick, Linda, additional, Watson, Mark, additional, Oberti, Mauricio, additional, Mesri, Mehdi, additional, Sanders, Melinda E., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Snyder, Michael, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Rudnick, Paul A., additional, McGarvey, Peter B., additional, Mertins, Philip, additional, Townsend, R. Reid, additional, Thangudu, Ratna R., additional, Rivers, Robert C., additional, Payne, Samuel H., additional, Davies, Sherri R., additional, Cai, Shuang, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Skates, Steven J., additional, Madhavan, Subha, additional, Hiltke, Tara, additional, Chen, Xian, additional, Zhao, Yingming, additional, Wang, Yue, additional, and Zhang, Zhen, additional
Published: 2019
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47. Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

Author: Wortman Jennifer, Haas Brian, Thiagarajan Mathangi, Lorenzi Hernan, Hall Neil, and Caler Elisabet
Subjects: Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba genomes, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens, we performed comparative sequence analysis to identify and map all class I and class II transposable elements in their sequences. Results Here, we report the identification of two novel Entamoeba-specific repeats: ERE1 and ERE2; ERE1 is spread across the three genomes and associated with different repeats in a species-specific manner, while ERE2 is unique to E. histolytica. We also report the identification of two novel subfamilies of LINE and SINE retrotransposons in E. dispar and provide evidence for how the different LINE and SINE subfamilies evolved in these species. Additionally, we found a putative transposase-coding gene in E. histolytica and E. dispar related to the mariner transposon Hydargos from E. invadens. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters. More than 70% of the three genomes have a repeat density below their corresponding average value indicating that transposable elements are not evenly distributed. We show that repeats and repeat-clusters are found at syntenic break points between E. histolytica and E. dispar and hence, could work as recombination hot spots promoting genome rearrangements. Conclusion The mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. LINE, ERE1 and mariner elements were present in the common ancestor to the three Entamoeba species while ERE2 was likely acquired by E. histolytica after its separation from E. dispar. We demonstrate that E. histolytica and E. dispar share their entire repertoire of LINE and SINE retrotransposons and that Eh_SINE3/Ed_SINE1 originated as a chimeric SINE from Eh/Ed_SINE2 and Eh_SINE1/Ed_SINE3. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites.
Published: 2008
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48. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

Author: Lee Suzanne R, Collins Kathleen, Smith Joshua J, Wiley Emily A, Cassidy-Hanley Donna M, Haas Brian J, Tallon Luke J, Wortman Jennifer R, Jones Kristie M, Thiagarajan Mathangi, Coyne Robert S, Couvillion Mary T, Liu Yifan, Garg Jyoti, Pearlman Ronald E, Hamilton Eileen P, Orias Eduardo, Eisen Jonathan A, and Methé Barbara A
Subjects: Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Tetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of Tetrahymena's coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing. Results We addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified. Conclusion We report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes.
Published: 2008
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49. Comprehensive proteogenomic characterization of rare kidney tumors

Author: 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, Nesvizhskii, Alexey I., 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., 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, and Zhang, Zhen
Abstract: Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
Published: 2024
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50. Abstract 784: NCI CPTAC phase III, proteogenomic analysis of 10 cancers

Author: Thiagarajan, Mathangi, primary
Published: 2018
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