477 results on '"Rodland, Karin D."'
Search Results
2. Multi-scale signaling and tumor evolution in high-grade gliomas
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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
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- 2024
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3. New views of old proteins: clarifying the enigmatic proteome
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Functional, Participants in a NIH Workshop on, Proteomics, Integrative, Johnson, Kristin E. Burnum, Conrads, Thomas P., Drake, Richard R., Herr, Amy E., Iyengar, Ravi, Kelly, Ryan T., Lundberg, Emma, MacCoss, Michael J., Naba, Alexandra, Nolan, Garry P., Pevzner, Pavel A., Rodland, Karin D., Sechi, Salvatore, Slavov, Nikolai, Spraggins, Jeffrey M., Van Eyk, Jennifer E., Vidal, Marc, Vogel, Christine, Walt, David R., and Kelleher, Neil L.
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Quantitative Biology - Biomolecules - Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we offer potential futures for a next generation of disruptive approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade., Comment: Submitted to Nature. 22 Pages. 6 Figures. Corresponding author Neil L. Kelleher
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- 2021
4. Comprehensive proteogenomic characterization of rare kidney tumors
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Lazar, Alexander J., Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Ma’ayan, Avi, Pruetz, Barb, Zhang, Bing, Reva, Boris, Druker, Brian J., Goldthwaite, Charles A., Jr., Birger, Chet, Mani, D.R., Chesla, David, Fenyö, David, Schadt, Eric E., Wilson, George, Kołodziejczak, Iga, John, Ivy, Hafron, Jason, Vo, Josh, Zaalishvili, Kakhaber, Ketchum, Karen A., Rodland, Karin D., Nyce, Kristen, Wiznerowicz, Maciej, Domagalski, Marcin J., Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Edwards, Nathan J., Vatanian, Negin, VanderKolk, Pamela, McGarvey, Peter B., Dhir, Rajiv, Thangudu, Ratna R., Crispen, Reese, Smith, Richard D., Payne, Samuel H., Cottingham, Sandra, Cai, Shuang, Carr, Steven A., Liu, Tao, Le, Toan, Ma, Weiping, Zhang, Xu, Lu, Yin, Shutack, Yvonne, Zhang, Zhen, Li, Ginny Xiaohe, Chen, Lijun, Hsiao, Yi, Mannan, Rahul, Zhang, Yuping, Luo, Jie, Petralia, Francesca, Cho, Hanbyul, Hosseini, Noshad, Leprevost, Felipe da Veiga, Calinawan, Anna, Li, Yize, Anand, Shankara, Dagar, Aniket, Geffen, Yifat, Kumar-Sinha, Chandan, Chugh, Seema, Le, Anne, Ponce, Sean, Guo, Shenghao, Zhang, Cissy, Schnaubelt, Michael, Al Deen, Nataly Naser, Chen, Feng, Caravan, Wagma, Houston, Andrew, Hopkins, Alex, Newton, Chelsea J., Wang, Xiaoming, Polasky, Daniel A., Haynes, Sarah, Yu, Fengchao, Jing, Xiaojun, Chen, Siqi, Robles, Ana I., Mesri, Mehdi, Thiagarajan, Mathangi, An, Eunkyung, Getz, Gad A., Linehan, W. Marston, Hostetter, Galen, Jewell, Scott D., Chan, Daniel W., Wang, Pei, Omenn, Gilbert S., Mehra, Rohit, Ricketts, Christopher J., Ding, Li, Chinnaiyan, Arul M., Cieslik, Marcin P., Dhanasekaran, Saravana M., Zhang, Hui, and Nesvizhskii, Alexey I.
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- 2024
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5. A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics
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Tsai, Chia-Feng, Wang, Yi-Ting, Hsu, Chuan-Chih, Kitata, Reta Birhanu, Chu, Rosalie K., Velickovic, Marija, Zhao, Rui, Williams, Sarah M., Chrisler, William B., Jorgensen, Marda L., Moore, Ronald J., Zhu, Ying, Rodland, Karin D., Smith, Richard D., Wasserfall, Clive H., Shi, Tujin, and Liu, Tao
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- 2023
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6. Pan-cancer proteogenomics characterization of tumor immunity
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Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei
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- 2024
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7. Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells
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Martin, Kendall, Zhang, Tong, Lin, Tai-Tu, Habowski, Amber N, Zhao, Rui, Tsai, Chia-Feng, Chrisler, William B, Sontag, Ryan L, Orton, Daniel J, Lu, Yong-Jie, Rodland, Karin D, Yang, Bin, Liu, Tao, Smith, Richard D, Qian, Wei-Jun, Waterman, Marian L, Wiley, H Steven, and Shi, Tujin
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Biotechnology ,Animals ,Chromatography ,Liquid ,Gene Expression Profiling ,Mass Spectrometry ,Mice ,Proteome ,Proteomics ,SOPs-MS ,nanoproteomics ,small numbers of cells ,surfactant DDM ,colon crypt cells ,Chemical Sciences ,Biological Sciences ,Biochemistry & Molecular Biology - Abstract
Recent advances in sample preparation enable label-free mass spectrometry (MS)-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 μL to sub-μL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by the proteomics research community. Herein, we report a facile one-pot nanoproteomics method termed SOPs-MS (surfactant-assisted one-pot sample processing at the standard volume coupled with MS) for convenient robust proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOPs-MS for label-free single-cell proteomics at a low μL volume, we have systematically evaluated its processing volume at 10-200 μL using 100 human cells. The processing volume of 50 μL that is in the range of volume for standard proteomics sample preparation has been selected for easy sample handling with a benchtop micropipette. SOPs-MS allows for reliable label-free quantification of ∼1200-2700 protein groups from 50 to 1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS has revealed protein signatures between distinct subpopulation cells with identification of ∼1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells and low-input samples.
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- 2021
8. Deep learning integrates histopathology and proteogenomics at a pan-cancer level
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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
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- 2023
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9. Proteogenomic insights suggest druggable pathways in endometrial carcinoma
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Antczak, Andrzej, Anurag, Meenakshi, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Borucki, Melissa, Cai, Shuang, Calinawan, Anna, Carr, Steven A., Castro, Patricia, Cerda, Sandra, Chan, Daniel W., Chesla, David, Cieslik, Marcin P., Cottingham, Sandra, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Edwards, Nathan J., Edwards, Robert, Ellis, Matthew J., Eschbacher, Jennifer, Fam, Mina, Fevrier-Sullivan, Brenda, Francis, Jesse, Freymann, John, Gabriel, Stacey, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Goldthwaite, Charles A., Grady, Pamela, Hafron, Jason, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Ittmann, Michael M., Johnson, Ashlie, Jones, Corbin D., Ketchum, Karen A., Kirby, Justin, Le, Toan, Ma'ayan, Avi, Madan, Rashna, Mareedu, Sailaja, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Nyce, Kristen, Paulovich, Amanda G., Pruetz, Barbara L., Qi, Liqun, Richey, Shannon, Schadt, Eric E., Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Tansil, Darlene, Thangudu, Ratna R., Tobin, Matt, Um, Ki Sung, Vatanian, Negin, Webster, Alex, Wilson, George D., Wright, Jason, Zaalishvili, Kakhaber, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Katsnelson, Lizabeth, Gritsenko, Marina A., Hu, Yingwei, Reva, Boris, Hong, Runyu, Wang, Yi-Ting, Kolodziejczak, Iga, Lu, Rita Jui-Hsien, Tsai, Chia-Feng, Bu, Wen, Liu, Wenke, Guo, Xiaofang, An, Eunkyung, Arend, Rebecca C., Bavarva, Jasmin, Chen, Lijun, Chu, Rosalie K., Czekański, Andrzej, Davoli, Teresa, Demicco, Elizabeth G., DeLair, Deborah, Devereaux, Kelly, Dhanasekaran, Saravana M., Dottino, Peter, Dover, Bailee, Fillmore, Thomas L., Foxall, McKenzie, Hermann, Catherine E., Hiltke, Tara, Hostetter, Galen, Jędryka, Marcin, Jewell, Scott D., Johnson, Isabelle, Kahn, Andrea G., Ku, Amy T., Kumar-Sinha, Chandan, Kurzawa, Paweł, Lazar, Alexander J., Lazcano, Rossana, Lei, Jonathan T., Li, Yi, Liao, Yuxing, Lih, Tung-Shing M., Lin, Tai-Tu, Martignetti, John A., Masand, Ramya P., Matkowski, Rafał, McKerrow, Wilson, Mesri, Mehdi, Monroe, Matthew E., Moon, Jamie, Moore, Ronald J., Nestor, Michael D., Newton, Chelsea, Omelchenko, Tatiana, Omenn, Gilbert S., Payne, Samuel H., Petyuk, Vladislav A., Robles, Ana I., Rodriguez, Henry, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schepmoes, Athena A., Shi, Tujin, Shi, Zhiao, Tan, Jimin, Taylor, Mason, Thiagarajan, Mathangi, Wang, Joshua M., Weitz, Karl K., Wen, Bo, Williams, C.M., Wu, Yige, Wyczalkowski, Matthew A., Yi, Xinpei, Zhang, Xu, Zhao, Rui, Mutch, David, Chinnaiyan, Arul M., Smith, Richard D., Nesvizhskii, Alexey I., Wang, Pei, Wiznerowicz, Maciej, Ding, Li, Mani, D.R., Zhang, Hui, Anderson, Matthew L., Rodland, Karin D., Zhang, Bing, Liu, Tao, and Fenyö, David
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- 2023
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10. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
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Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Ozgun, Bavarva, Jasmin, Birger, Chet, Birrer, Michael, Calinawan, Anna, Cantley, Lewis C., Cao, Song, Carr, Steve, Ceccarelli, Michele, Chan, Daniel, Chinnaiyan, Arul, Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Mohan, Domagalski, Marcin, Dou, Yongchao, Druker, Brian, Edwards, Nathan, Ellis, Matthew, Selvan, Myvizhi Esai, Francis, Alicia, Getz, Gad, Gillette, Michael A., Robles, Tania Gonzalez, Gosline, Sara, Gümüş, Zeynep, Heiman, David, Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric, Jewel, Scott, Ji, Jiayi, Jiang, Wen, Lee Johnson, Jared, Katsnelson, Lizabeth, Ketchum, Karen, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan, Liao, Yuxing, Lindgren, Caleb, Liu, Tao, Liu, Wenke, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert, Paulovich, Amanda, Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Ruggles, Kelly, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara, Schadt, Eric, Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Dick, Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik, Tan, Jimin, Terekhanova, Nadezhda, Thangudu, Ratna, Thiagarajan, Mathangi, Tignor, Nicole, Wang, Joshua, Wang, Liang-Bo, Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Chan, Daniel W., Dhanasekaran, Saravana M., Schürer, Stephan, Smith, Richard D., Wyczalkowski, Matthew A., Liang, Wen-Wei, Lu, Rita Jui-Hsien, Jayasinghe, Reyka G., Foltz, Steven M., Porta-Pardo, Eduard, Geffen, Yifat, Wendl, Michael C., Lazcano, Rossana, Kolodziejczak, Iga, Song, Yizhe, Govindan, Akshay, Demicco, Elizabeth G., Li, Xiang, Li, Yize, Sethuraman, Sunantha, Payne, Samuel H., Fenyö, David, Rodriguez, Henry, Wiznerowicz, Maciej, Shen, Hui, Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Robles, Ana I., and Ding, Li
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- 2023
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11. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad
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- 2023
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12. Pan-cancer proteogenomics connects oncogenic drivers to functional states
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li
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- 2023
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13. Proteogenomic data and resources for pan-cancer analysis
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Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, 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.
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- 2023
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14. Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection
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Madda, Rashmi, primary, Petyuk, Vladislav A., additional, Wang, Yi-Ting, additional, Shi, Tujin, additional, Shriver, Craig D., additional, Rodland, Karin D., additional, and Liu, Tao, additional
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- 2023
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15. Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence
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Gosline, Sara J.C., Velickovic, Marija, Pino, James, Day, Le Z., Attah, Isaac K., Swensen, Adam C., Danna, Vincent, Posso, Camilo, Rodland, Karin D., Chen, Jing, Matthews, Clayton E., Campbell-Thompson, Martha, Laskin, Julia, Burnum-Johnson, Kristin, Zhu, Ying, and Piehowski, Paul D.
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- 2023
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16. A prognostic risk model for glioma patients by systematic evaluation of genomic variations
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Zhang, Baifeng, Wan, Weiqing, Li, Zibo, Gao, Zhixian, Ji, Nan, Xie, Jian, Wang, Junmei, Wang, Bin, Lai-Wan Kwong, Dora, Guan, Xinyuan, Gao, Shengjie, Zhao, Yuanli, Lu, Youyong, Zhang, Liwei, Rodland, Karin D., and Tsang, Shirley X.
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- 2022
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17. Abstract B039: Identification of ovarian cancer protein biomarkers in liquid-based Pap tests
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Skubitz, Amy P.N., primary, Boylan, Kristin L.M., additional, Petersen, Ashley J., additional, Hansen, Joshua R., additional, Liu, Tao, additional, Gao, Yuqian, additional, Wang, Yi-Ting, additional, Rodland, Karin D., additional, Geller, Melissa A., additional, Argenta, Peter A., additional, Hoffman, Samantha L., additional, and Piehowski, Paul D., additional
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- 2024
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18. Pan-cancer proteogenomics characterization of tumor immunity
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Petralia, Francesca, primary, Ma, Weiping, additional, Yaron, Tomer M., additional, Caruso, Francesca Pia, additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Charytonowicz, Daniel, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Marino, Giacomo B., additional, Calinawan, Anna, additional, Evangelista, John Erol, additional, Selvan, Myvizhi Esai, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Song, Xiaoyu, additional, Turhan, Berk, additional, Christianson, Karen E., additional, Lewis, David A., additional, Deng, Eden Z., additional, Clarke, Daniel J.B., additional, Whiteaker, Jeffrey R., additional, Kennedy, Jacob J., additional, Zhao, Lei, additional, Segura, Rossana Lazcano, additional, Batra, Harsh, additional, Raso, Maria Gabriela, additional, Parra, Edwin Roger, additional, Soundararajan, Rama, additional, Tang, Ximing, additional, Li, Yize, additional, Yi, Xinpei, additional, Satpathy, Shankha, additional, Wang, Ying, additional, Wiznerowicz, Maciej, additional, González-Robles, Tania J., additional, Iavarone, Antonio, additional, Gosline, Sara J.C., additional, Reva, Boris, additional, Robles, Ana I., additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Gillette, Michael A., additional, Klein, Robert J., additional, Cieslik, Marcin, additional, Zhang, Bing, additional, Paulovich, Amanda G., additional, Sebra, Robert, additional, Gümüş, Zeynep H., additional, Hostetter, Galen, additional, Fenyö, David, additional, Omenn, Gilbert S., additional, Cantley, Lewis C., additional, Ma'ayan, Avi, additional, Lazar, Alexander J., additional, Ceccarelli, Michele, additional, Wang, Pei, additional, Abelin, Jennifer, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cao, Song, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Heiman, David I., additional, Hong, Runyu, additional, Hu, Yingwei, additional, Huang, Chen, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, McDermott, Jason, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Mumphrey, Michael Brodie, additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Payne, Samuel H., additional, Pugliese, Pietro, additional, Rodland, Karin D., additional, Rodrigues, Fernanda Martins, additional, Ruggles, Kelly V., additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Feng, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Li, Qing Kay, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2024
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19. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia
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Pino, James C., primary, Posso, Camilo, additional, Joshi, Sunil K., additional, Nestor, Michael, additional, Moon, Jamie, additional, Hansen, Joshua R., additional, Hutchinson-Bunch, Chelsea, additional, Gritsenko, Marina A., additional, Weitz, Karl K., additional, Watanabe-Smith, Kevin, additional, Long, Nicola, additional, McDermott, Jason E., additional, Druker, Brian J., additional, Liu, Tao, additional, Tyner, Jeffrey W., additional, Agarwal, Anupriya, additional, Traer, Elie, additional, Piehowski, Paul D., additional, Tognon, Cristina E., additional, Rodland, Karin D., additional, and Gosline, Sara J.C., additional
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- 2024
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20. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability
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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.
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- 2020
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21. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
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Zhang, Hui, Liu, Tao, Zhang, Zhen, Payne, Samuel H, Zhang, Bai, McDermott, Jason E, Zhou, Jian-Ying, Petyuk, Vladislav A, Chen, Li, Ray, Debjit, Sun, Shisheng, Yang, Feng, Chen, Lijun, Wang, Jing, Shah, Punit, Cha, Seong Won, Aiyetan, Paul, Woo, Sunghee, Tian, Yuan, Gritsenko, Marina A, Clauss, Therese R, Choi, Caitlin, Monroe, Matthew E, Thomas, Stefani, Nie, Song, Wu, Chaochao, Moore, Ronald J, Yu, Kun-Hsing, Tabb, David L, Fenyö, David, Bafna, Vineet, Wang, Yue, Rodriguez, Henry, Boja, Emily S, Hiltke, Tara, Rivers, Robert C, Sokoll, Lori, Zhu, Heng, Shih, Ie-Ming, Cope, Leslie, Pandey, Akhilesh, Zhang, Bing, Snyder, Michael P, Levine, Douglas A, Smith, Richard D, Chan, Daniel W, Rodland, Karin D, Investigators, the CPTAC, Carr, Steven A, Gillette, Michael A, Klauser, Karl R, Kuhn, Eric, Mani, DR, Mertins, Philipp, Ketchum, Karen A, Thangudu, Ratna, Cai, Shuang, Oberti, Mauricio, Paulovich, Amanda G, Whiteaker, Jeffrey R, Edwards, Nathan J, McGarvey, Peter B, Madhavan, Subha, Wang, Pei, Whiteley, Gordon A, Skates, Steven J, White, Forest M, Kinsinger, Christopher R, Mesri, Mehdi, Shaw, Kenna M, Stein, Stephen E, Fenyo, David, Rudnick, Paul, Snyder, Michael, Zhao, Yingming, Chen, Xian, Ransohoff, David F, Hoofnagle, Andrew N, Liebler, Daniel C, Sanders, Melinda E, Shi, Zhiao, and Slebos, Robbert JC
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Human Genome ,Genetics ,Biotechnology ,Ovarian Cancer ,Rare Diseases ,Cancer ,Acetylation ,Chromosomal Instability ,DNA Repair ,DNA ,Neoplasm ,Female ,Gene Dosage ,Humans ,Mass Spectrometry ,Neoplasm Proteins ,Neoplasms ,Cystic ,Mucinous ,and Serous ,Ovarian Neoplasms ,Phosphoproteins ,Protein Processing ,Post-Translational ,Proteome ,Survival Analysis ,CPTAC Investigators ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC. VIDEO ABSTRACT.
- Published
- 2016
22. Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics
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Tsai, Chia-Feng, Zhang, Pengfei, Scholten, David, Martin, Kendall, Wang, Yi-Ting, Zhao, Rui, Chrisler, William B., Patel, Dhwani B., Dou, Maowei, Jia, Yuzhi, Reduzzi, Carolina, Liu, Xia, Moore, Ronald J., Burnum-Johnson, Kristin E., Lin, Miao-Hsia, Hsu, Chuan-Chih, Jacobs, Jon M., Kagan, Jacob, Srivastava, Sudhir, Rodland, Karin D., Steven Wiley, H., Qian, Wei-Jun, Smith, Richard D., Zhu, Ying, Cristofanilli, Massimo, Liu, Tao, Liu, Huiping, and Shi, Tujin
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- 2021
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23. Proteogenomic strategies for identification of aberrant cancer peptides using large‐scale next‐generation sequencing data
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Woo, Sunghee, Cha, Seong Won, Na, Seungjin, Guest, Clark, Liu, Tao, Smith, Richard D, Rodland, Karin D, Payne, Samuel, and Bafna, Vineet
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Cancer ,Aetiology ,2.1 Biological and endogenous factors ,Databases ,Protein ,High-Throughput Nucleotide Sequencing ,Humans ,Neoplasms ,Peptides ,Proteomics ,MS ,Mutated peptide identification ,Ovarian cancer ,Proteogenomics ,Information and Computing Sciences ,Medical and Health Sciences ,Biochemistry & Molecular Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular subtyping of cancers, understanding cancer progression, and the discovery of novel biomarkers. The advances of genomics technologies (whole-genome exome, and transcript sequencing, collectively referred to as NGS (next-generation sequencing)) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome translated portion of aberrant genes using only genomic approaches. Combination of proteomic and genomic technologies are increasingly being employed. Various strategies have been employed to allow the usage of large-scale NGS data for conventional MS/MS searches. This paper provides a discussion of applying different strategies relating to large database search, and FDR (false discovery rate) -based error control, and their implication to cancer proteogenomics. Moreover, it extends and develops the idea of a unified genomic variant database that can be searched by any MS sample. A total of 879 BAM files downloaded from TCGA repository were used to create a 4.34 GB unified FASTA database that contained 2787062 novel splice junctions, 38,464 deletions, 1,105 insertions, and 182,302 substitutions. Proteomic data from a single ovarian carcinoma sample (439,858 spectra) was searched against the database. By applying the most conservative FDR measure, we have identified 524 novel peptides and 65,578 known peptides at 1% FDR threshold. The novel peptides include interesting examples of doubly mutated peptides, frame-shifts, and nonsample-recruited mutations, which emphasize the strength of our approach.
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- 2014
24. Mass Spectrometry–Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.
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Joshi, Sunil K., Piehowski, Paul, Liu, Tao, Gosline, Sara J.C., McDermott, Jason E., Druker, Brian J., Traer, Elie, Tyner, Jeffrey W., Agarwal, Anupriya, Tognon, Cristina E., and Rodland, Karin D.
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TUMOR genetics ,GENETIC mutation ,INDIVIDUALIZED medicine ,PROTEOMICS ,MASS spectrometry ,GENOMICS ,GENOTYPES ,SYMPTOMS ,TUMORS ,DRUG resistance in cancer cells ,PHENOTYPES ,CANCER patient medical care - Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools. [ABSTRACT FROM AUTHOR]
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- 2024
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25. Validation of a Proteomic Signature of Lung Cancer Risk from Bronchial Specimens of Risk-Stratified Individuals
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Rahman, S.M. Jamshedur, primary, Chen, Sheau-Chiann, additional, Wang, Yi-Ting, additional, Gao, Yuqian, additional, Schepmoes, Athena A., additional, Fillmore, Thomas L., additional, Shi, Tujin, additional, Chen, Heidi, additional, Rodland, Karin D., additional, Massion, Pierre P., additional, Grogan, Eric L., additional, and Liu, Tao, additional
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- 2023
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26. Deep learning integrates histopathology and proteogenomics at a pan-cancer level
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Wang, Joshua M., primary, Hong, Runyu, additional, Demicco, Elizabeth G., additional, Tan, Jimin, additional, Lazcano, Rossana, additional, Moreira, Andre L., additional, Li, Yize, additional, Calinawan, Anna, additional, Razavian, Narges, additional, Schraink, Tobias, additional, Gillette, Michael A., additional, Omenn, Gilbert S., additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Tsirigos, Aristotelis, additional, Ruggles, Kelly V., additional, Ding, Li, additional, Robles, Ana I., additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Liu, Wenke, additional, Fenyö, David, additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steven A., additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clauser, Karl R., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Heiman, David I., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Johnson, Jared L., additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying, additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yaron, Tomer M., additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2023
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27. Proteogenomic insights suggest druggable pathways in endometrial carcinoma
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Dou, Yongchao, primary, Katsnelson, Lizabeth, additional, Gritsenko, Marina A., additional, Hu, Yingwei, additional, Reva, Boris, additional, Hong, Runyu, additional, Wang, Yi-Ting, additional, Kolodziejczak, Iga, additional, Lu, Rita Jui-Hsien, additional, Tsai, Chia-Feng, additional, Bu, Wen, additional, Liu, Wenke, additional, Guo, Xiaofang, additional, An, Eunkyung, additional, Arend, Rebecca C., additional, Bavarva, Jasmin, additional, Chen, Lijun, additional, Chu, Rosalie K., additional, Czekański, Andrzej, additional, Davoli, Teresa, additional, Demicco, Elizabeth G., additional, DeLair, Deborah, additional, Devereaux, Kelly, additional, Dhanasekaran, Saravana M., additional, Dottino, Peter, additional, Dover, Bailee, additional, Fillmore, Thomas L., additional, Foxall, McKenzie, additional, Hermann, Catherine E., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Jędryka, Marcin, additional, Jewell, Scott D., additional, Johnson, Isabelle, additional, Kahn, Andrea G., additional, Ku, Amy T., additional, Kumar-Sinha, Chandan, additional, Kurzawa, Paweł, additional, Lazar, Alexander J., additional, Lazcano, Rossana, additional, Lei, Jonathan T., additional, Li, Yi, additional, Liao, Yuxing, additional, Lih, Tung-Shing M., additional, Lin, Tai-Tu, additional, Martignetti, John A., additional, Masand, Ramya P., additional, Matkowski, Rafał, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Monroe, Matthew E., additional, Moon, Jamie, additional, Moore, Ronald J., additional, Nestor, Michael D., additional, Newton, Chelsea, additional, Omelchenko, Tatiana, additional, Omenn, Gilbert S., additional, Payne, Samuel H., additional, Petyuk, Vladislav A., additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schepmoes, Athena A., additional, Shi, Tujin, additional, Shi, Zhiao, additional, Tan, Jimin, additional, Taylor, Mason, additional, Thiagarajan, Mathangi, additional, Wang, Joshua M., additional, Weitz, Karl K., additional, Wen, Bo, additional, Williams, C.M., additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yi, Xinpei, additional, Zhang, Xu, additional, Zhao, Rui, additional, Mutch, David, additional, Chinnaiyan, Arul M., additional, Smith, Richard D., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Wiznerowicz, Maciej, additional, Ding, Li, additional, Mani, D.R., additional, Zhang, Hui, additional, Anderson, Matthew L., additional, Rodland, Karin D., additional, Zhang, Bing, additional, Liu, Tao, additional, Fenyö, David, additional, Antczak, Andrzej, additional, Anurag, Meenakshi, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Borucki, Melissa, additional, Cai, Shuang, additional, Calinawan, Anna, additional, Carr, Steven A., additional, Castro, Patricia, additional, Cerda, Sandra, additional, Chan, Daniel W., additional, Chesla, David, additional, Cieslik, Marcin P., additional, Cottingham, Sandra, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Fam, Mina, additional, Fevrier-Sullivan, Brenda, additional, Francis, Jesse, additional, Freymann, John, additional, Gabriel, Stacey, additional, Getz, Gad, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Hafron, Jason, additional, Hariharan, Pushpa, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Ittmann, Michael M., additional, Johnson, Ashlie, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kirby, Justin, additional, Le, Toan, additional, Ma'ayan, Avi, additional, Madan, Rashna, additional, Mareedu, Sailaja, additional, McGarvey, Peter B., additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Nyce, Kristen, additional, Paulovich, Amanda G., additional, Pruetz, Barbara L., additional, Qi, Liqun, additional, Richey, Shannon, additional, Schadt, Eric E., additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Tansil, Darlene, additional, Thangudu, Ratna R., additional, Tobin, Matt, additional, Um, Ki Sung, additional, Vatanian, Negin, additional, Webster, Alex, additional, Wilson, George D., additional, Wright, Jason, additional, Zaalishvili, Kakhaber, additional, Zhang, Zhen, additional, and Zhao, Grace, additional
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- 2023
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28. Pan-cancer proteogenomics connects oncogenic drivers to functional states
- Author
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Li, Yize, primary, Porta-Pardo, Eduard, additional, Tokheim, Collin, additional, Bailey, Matthew H., additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Geffen, Yifat, additional, Imbach, Kathleen J., additional, Cao, Song, additional, Anand, Shankara, additional, Akiyama, Yo, additional, Liu, Wenke, additional, Wyczalkowski, Matthew A., additional, Song, Yizhe, additional, Storrs, Erik P., additional, Wendl, Michael C., additional, Zhang, Wubing, additional, Sibai, Mustafa, additional, Ruiz-Serra, Victoria, additional, Liang, Wen-Wei, additional, Terekhanova, Nadezhda V., additional, Rodrigues, Fernanda Martins, additional, Clauser, Karl R., additional, Heiman, David I., additional, Zhang, Qing, additional, Aguet, Francois, additional, Calinawan, Anna P., additional, Dhanasekaran, Saravana M., additional, Birger, Chet, additional, Satpathy, Shankha, additional, Zhou, Daniel Cui, additional, Wang, Liang-Bo, additional, Baral, Jessika, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Pugliese, Pietro, additional, Colaprico, Antonio, additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Ricketts, Christopher J., additional, Fenyö, David, additional, Payne, Samuel H., additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Gillette, Michael A., additional, Kumar-Sinha, Chandan, additional, Lazar, Alexander J., additional, Cantley, Lewis C., additional, Getz, Gad, additional, Ding, Li, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Calinawan, Anna, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Lei, Jonathan T., additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Tan, Jimin, additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2023
- Full Text
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29. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
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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
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- 2023
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30. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
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Geffen, Yifat, primary, Anand, Shankara, additional, Akiyama, Yo, additional, Yaron, Tomer M., additional, Song, Yizhe, additional, Johnson, Jared L., additional, Govindan, Akshay, additional, Babur, Özgün, additional, Li, Yize, additional, Huntsman, Emily, additional, Wang, Liang-Bo, additional, Birger, Chet, additional, Heiman, David I., additional, Zhang, Qing, additional, Miller, Mendy, additional, Maruvka, Yosef E., additional, Haradhvala, Nicholas J., additional, Calinawan, Anna, additional, Belkin, Saveliy, additional, Kerelsky, Alexander, additional, Clauser, Karl R., additional, Krug, Karsten, additional, Satpathy, Shankha, additional, Payne, Samuel H., additional, Mani, D.R., additional, Gillette, Michael A., additional, Dhanasekaran, Saravana M., additional, Thiagarajan, Mathangi, additional, Mesri, Mehdi, additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Carr, Steven A., additional, Lazar, Alexander J., additional, Aguet, François, additional, Cantley, Lewis C., additional, Ding, Li, additional, Getz, Gad, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Cao, Song, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Fenyo, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional
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- 2023
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31. Proteogenomic data and resources for pan-cancer analysis
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Li, Yize, primary, Dou, Yongchao, additional, Da Veiga Leprevost, Felipe, additional, Geffen, Yifat, additional, Calinawan, Anna P., additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Birger, Chet, additional, Cao, Song, additional, Chaudhary, Rekha, additional, Chilappagari, Padmini, additional, Cieslik, Marcin, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Esai Selvan, Myvizhi, additional, Fenyö, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez-Robles, Tania, additional, Gümüş, Zeynep H., additional, Heiman, David, additional, Holck, Michael, additional, Hong, Runyu, additional, Hu, Yingwei, additional, Jaehnig, Eric J., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Klein, Robert J., additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Ma, Weiping, additional, Ma, Lei, additional, MacCoss, Michael J., additional, Martins Rodrigues, Fernanda, additional, McKerrow, Wilson, additional, Nguyen, Ngoc, additional, Oldroyd, Robert, additional, Pilozzi, Alexander, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rudnick, Paul, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Singhal, Deepak, additional, Song, Xiaoyu, additional, Storrs, Erik, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Wang, Ying, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Xin, Yi, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zuhl, Maya, additional, Getz, Gad, additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Robles, Ana I., additional, Zhang, Bing, additional, Payne, Samuel H., additional, Lazar, Alexander J., additional, Paulovich, Amanda G., additional, Iavarone, Antonio, additional, Chinnaiyan, Arul M., additional, Druker, Brian J., additional, Kumar-Sinha, Chandan, additional, Newton, Chelsea J., additional, Huang, Chen, additional, Mani, D.R., additional, Smith, Richard D., additional, Huntsman, Emily, additional, Schadt, Eric E., additional, An, Eunkyung, additional, Petralia, Francesca, additional, Hostetter, Galen, additional, Omenn, Gilbert S., additional, Cho, Hanbyul, additional, Rodriguez, Henry, additional, Kolodziejczak, Iga, additional, Johnson, Jared L., additional, Bavarva, Jasmin, additional, Tan, Jimin, additional, Rodland, Karin D., additional, Clauser, Karl R., additional, Krug, Karsten, additional, Cantley, Lewis C., additional, Wiznerowicz, Maciej, additional, Ellis, Matthew J., additional, Anurag, Meenakshi, additional, Mesri, Mehdi, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ceccarelli, Michele, additional, Dhanasekaran, Saravana M., additional, Edwards, Nathan, additional, Tignor, Nicole, additional, Babur, Özgün, additional, Gosline, Sara J.C., additional, Jewell, Scott D., additional, Satpathy, Shankha, additional, Chowdhury, Shrabanti, additional, Schürer, Stephan, additional, Carr, Steven A., additional, Liu, Tao, additional, Hiltke, Tara, additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Liu, Wenke, additional, Zhang, Xu, additional, Song, Yizhe, additional, and Zhang, Zhen, additional
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- 2023
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32. Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection
- Author
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Stevens, Susan L., Liu, Tao, Bahjat, Frances Rena, Petyuk, Vladislav A., Schepmoes, Athena A., Sontag, Ryan L., Gritsenko, Marina A., Wu, Chaochao, Wang, Sheng, Shukla, Anil K., Jacobs, Jon M., Smith, Richard D., Rodland, Karin D., Alexander West, G., Kohama, Steven G., Glynn, Christine, and Stenzel-Poore, Mary P.
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- 2019
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33. Clinical potential of mass spectrometry-based proteogenomics
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Zhang, Bing, Whiteaker, Jeffrey R., Hoofnagle, Andrew N., Baird, Geoffrey S., Rodland, Karin D., and Paulovich, Amanda G.
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- 2019
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34. Inhibition of interleukin-1 receptor-associated kinase-1 is a therapeutic strategy for acute myeloid leukemia subtypes
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Hosseini, Mona M., Kurtz, Stephen E., Abdelhamed, Sherif, Mahmood, Shawn, Davare, Monika A., Kaempf, Andy, Elferich, Johannes, McDermott, Jason E., Liu, Tao, Payne, Samuel H., Shinde, Ujwal, Rodland, Karin D., Mori, Motomi, Druker, Brian J., Singer, Jack W., and Agarwal, Anupriya
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- 2018
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35. Abstract 3172: Mapping the molecular landscape of acute myeloid leukemia enables prediction of drug response from proteogenomic data
- Author
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Pino, James C., primary, Posso, Camilo, additional, Joshi, Sunil K., additional, Nestor, Michael, additional, Moon, Jamie, additional, Hansen, Joshua R., additional, Gritsenko, Marina A., additional, Hutchinson-Bunch, Chelsea, additional, Weitz, Karl K., additional, Watanabe-Smith, Kevin, additional, McDermott, Jason E., additional, Druker, Brian J., additional, Liu, Tao, additional, Tyner, Jeffrey W., additional, Agarwal, Anupriya, additional, Traer, Elie, additional, Piehowski, Paul D., additional, Tognon, Cristina E., additional, Rodland, Karin D., additional, and Gosline, Sara J., additional
- Published
- 2023
- Full Text
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36. Mass Spectrometry for Biomarker Development
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Wu, Chaochao, Liu, Tao, Baker, Erin S., Rodland, Karin D., Smith, Richard D., Preedy, Victor R., Series editor, and Patel, Vinood B., editor
- Published
- 2015
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37. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
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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
- Full Text
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38. Characterization of the Ovarian Tumor Peptidome
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Liu, Tao, primary, Rodland, Karin D., additional, and Smith, Richard D., additional
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- 2018
- Full Text
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39. Oncoproteomic profiling of AML: moving beyond genomics
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Joshi, Sunil K., primary, Tognon, Cristina E., additional, Druker, Brian J., additional, and Rodland, Karin D., additional
- Published
- 2022
- Full Text
- View/download PDF
40. Proteome mapping of the human pancreatic islet microenvironment reveals endocrine-exocrine signaling sphere of influence
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Gosline, Sara JC, primary, Velickovic, Marija, additional, Pino, James, additional, Day, Le Z., additional, Attah, Isaac K., additional, Swensen, Adam C., additional, Danna, Vincent, additional, Rodland, Karin D., additional, Chen, Jing, additional, Matthews, Clayton E., additional, Campbell-Thompson, Martha, additional, Laskin, Julia, additional, Burnum-Johnson, Kristin, additional, Zhu, Ying, additional, and Piehowski, Paul D., additional
- Published
- 2022
- Full Text
- View/download PDF
41. New Views of Old Proteins: Clarifying the Enigmatic Proteome
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Burnum-Johnson, Kristin E., primary, Conrads, Thomas P., additional, Drake, Richard R., additional, Herr, Amy E., additional, Iyengar, Ravi, additional, Kelly, Ryan T., additional, Lundberg, Emma, additional, MacCoss, Michael J., additional, Naba, Alexandra, additional, Nolan, Garry P., additional, Pevzner, Pavel A., additional, Rodland, Karin D., additional, Sechi, Salvatore, additional, Slavov, Nikolai, additional, Spraggins, Jeffrey M., additional, Van Eyk, Jennifer E., additional, Vidal, Marc, additional, Vogel, Christine, additional, Walt, David R., additional, and Kelleher, Neil L., additional
- Published
- 2022
- Full Text
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42. Moonshot Objectives: Catalyze New Scientific Breakthroughs—Proteogenomics
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Rodland, Karin D., Piehowski, Paul, and Smith, Richard D.
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- 2018
- Full Text
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43. Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells
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Shi, Tujin, Gaffrey, Matthew J., Fillmore, Thomas L., Nicora, Carrie D., Yi, Lian, Zhang, Pengfei, Shukla, Anil K., Wiley, H. Steven, Rodland, Karin D., Liu, Tao, Smith, Richard D., and Qian, Wei-Jun
- Published
- 2018
- Full Text
- View/download PDF
44. Residual tissue repositories as a resource for population-based cancer proteomic studies
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Piehowski, Paul D., Petyuk, Vladislav A., Sontag, Ryan L., Gritsenko, Marina A., Weitz, Karl K., Fillmore, Thomas L., Moon, Jamie, Makhlouf, Hala, Chuaqui, Rodrigo F., Boja, Emily S., Rodriguez, Henry, Lee, Jerry S. H., Smith, Richard D., Carrick, Danielle M., Liu, Tao, and Rodland, Karin D.
- Published
- 2018
- Full Text
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45. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics
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Wu, Chaochao, Monroe, Matthew E., Xu, Zhe, Slysz, Gordon W., Payne, Samuel H., Rodland, Karin D., Liu, Tao, and Smith, Richard D.
- Published
- 2015
- Full Text
- View/download PDF
46. Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma
- Author
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Kennedy, Jacob J., primary, Whiteaker, Jeffrey R., additional, Ivey, Richard G., additional, Burian, Aura, additional, Chowdhury, Shrabanti, additional, Tsai, Chia-Feng, additional, Liu, Tao, additional, Lin, ChenWei, additional, Murillo, Oscar D., additional, Lundeen, Rachel A., additional, Jones, Lisa A., additional, Gafken, Philip R., additional, Longton, Gary, additional, Rodland, Karin D., additional, Skates, Steven J., additional, Landua, John, additional, Wang, Pei, additional, Lewis, Michael T., additional, and Paulovich, Amanda G., additional
- Published
- 2022
- Full Text
- View/download PDF
47. A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics
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Tsai, Chia-Feng, primary, Wang, Yi-Ting, additional, Hsu, Chuan-Chih, additional, Kitata, Reta Birhanu, additional, Chu, Rosalie K., additional, Velickovic, Marija, additional, Zhao, Rui, additional, Williams, Sarai M., additional, Chrisler, William B., additional, Jorgensen, Marda L., additional, Moore, Ronald J., additional, Zhu, Ying, additional, Rodland, Karin D., additional, Smith, Richard D., additional, Wasserfall, Clive H., additional, Shi, Tujin, additional, and Liu, Tao, additional
- Published
- 2022
- Full Text
- View/download PDF
48. Calcium Receptor-mediated Signaling
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Rodland, Karin D., Melmed, Shlomo, editor, Chattopadhyay, Naibedya, editor, and Brown, Edward M., editor
- Published
- 2003
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49. Quantitative proteomics identifies altered O‐GlcNAcylation of structural, synaptic and memory‐associated proteins in Alzheimerʼs disease
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Wang, Sheng, Yang, Feng, Petyuk, Vladislav A, Shukla, Anil K, Monroe, Matthew E, Gritsenko, Marina A, Rodland, Karin D, Smith, Richard D, Qian, Wei‐Jun, Gong, Cheng‐Xin, and Liu, Tao
- Published
- 2017
- Full Text
- View/download PDF
50. Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum
- Author
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Shi, Tujin, Fillmore, Thomas L., Sun, Xuefei, Zhao, Rui, Schepmoes, Athena A., Hossain, Mahmud, Xie, Fang, Wu, Si, Kim, Jong-Seo, Jones, Nathan, Moore, Ronald J., Paša-Tolić, Ljiljana, Kagan, Jacob, Rodland, Karin D., Liu, Tao, Tang, Keqi, Camp, David G., Smith, Richard D., and Qian, Wei-Jun
- Published
- 2012
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