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  1. 1.   IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma
  2. Bolomsky, Arnold; Ceribelli, Michele; Scheich, Sebastian; Rinaldi, Kristina; Huang, Da Wei; Chakraborty, Papiya; Pham, Lisette; Wright, George W; Hsiao, Tony; Morris, Vivian; Choi, Jaewoo; Phelan, James D; Holewinski,Ronald; Andresson,Thorkell; Wisniewski, Jan; Riley, Deanna; Pittaluga, Stefania; Hill, Elizabeth; Thomas, Craig J; Muppidi, Jagan; Young, Ryan M
  3. Cancer Cell. 2024, Jul 8; 42(7): 1185-1201.
  1. 2.   Comprehensive proteogenomic characterization of rare kidney tumors
  2. 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
  3. Cell Reports. Medicine. 2024, May 21; 5(5): 101547.
  1. 3.   Proteogenomic insights suggest druggable pathways in endometrial carcinoma
  2. 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; Czekanski, 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; Jedryka, Marcin; Jewell, Scott D; Johnson, Isabelle; Kahn, Andrea G; Ku, Amy T; Kumar-Sinha, Chandan; Kurzawa, Pawel; 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, Rafal; 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; Fenyö, David
  3. Cancer Cell. 2023, Sep 11; 41(9): 1586-1605.e15.
  1. 4.   Proteogenomic data and resources for pan-cancer analysis
  2. 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; Colaprico, Antonio; Zhou, Daniel Cui; Day, Corbin; Domagalski, Marcin J; Esai Selvan, Myvizhi; Fenyö, David; Foltz, Steven M; Francis, Alicia; Gonzalez-Robles, Tania; Gümüs, 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; Pugliese, Pietro; 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, Hui; Zhang, Qing; Zuhl, Maya; Getz, Gad; Ding, Li; Nesvizhskii, Alexey I; Wang, Pei; Robles, Ana I; Zhang, Bing; Payne, Samuel H
  3. Cancer Cell. 2023, Aug 14; (8): 1397-1406.
  1. 5.   Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
  2. Li, Yize; Lih, Tung-Shing M; Dhanasekaran, Saravana M; Mannan, Rahul; Chen, Lijun; Cieslik, Marcin; Wu, Yige; Lu, Rita Jiu-Hsien; Clark, David J; Kolodziejczak, Iga; Hong, Runyu; Chen, Siqi; Zhao, Yanyan; Chugh, Seema; Caravan, Wagma; Naser Al Deen, Nataly; Hosseini, Noshad; Newton, Chelsea J; Krug, Karsten; Xu, Yuanwei; Cho, Kyung-Cho; Hu, Yingwei; Zhang, Yuping; Kumar-Sinha, Chandan; Ma, Weiping; Calinawan, Anna; Wyczalkowski, Matthew A; Wendl, Michael C; Wang, Yuefan; Guo, Shenghao; Zhang, Cissy; Le, Anne; Dagar, Aniket; Hopkins, Alex; Cho, Hanbyul; Leprevost, Felipe da Veiga; Jing, Xiaojun; Teo, Guo Ci; Liu, Wenke; Reimers, Melissa A; Pachynski, Russell; Lazar, Alexander J; Chinnaiyan, Arul M; Van Tine, Brian A; Zhang, Bing; Rodland, Karin D; Getz, Gad; Mani, D R; Wang, Pei; Chen, Feng; Hostetter, Galen; Thiagarajan,Mathangi; Linehan, W Marston; Fenyö, David; Jewell, Scott D; Omenn, Gilbert S; Mehra, Rohit; Wiznerowicz, Maciej; Robles, Ana I; Mesri, Mehdi; Hiltke, Tara; An, Eunkyung; Rodriguez, Henry; Chan, Daniel W; Ricketts, Christopher J; Nesvizhskii, Alexey I; Zhang, Hui; Ding, Li
  3. Cancer Cell. 2023, Jan 9; 41(1): 139-163.
  1. 6.   A proteogenomic portrait of lung squamous cell carcinoma
  2. Satpathy, Shankha; Krug, Karsten; Jean Beltran, Pierre M; Savage, Sara R; Petralia, Francesca; Kumar-Sinha, Chandan; Dou, Yongchao; Reva, Boris; Kane, M Harry; Avanessian, Shayan C; Vasaikar, Suhas V; Krek, Azra; Lei, Jonathan T; Jaehnig, Eric J; Omelchenko, Tatiana; Geffen, Yifat; Bergstrom, Erik J; Stathias, Vasileios; Christianson, Karen E; Heiman, David I; Cieslik, Marcin P; Cao, Song; Song, Xiaoyu; Ji, Jiayi; Liu, Wenke; Li, Kai; Wen, Bo; Li, Yize; Gümüs, Zeynep H; Selvan, Myvizhi Esai; Soundararajan, Rama; Visal, Tanvi H; Raso, Maria G; Parra, Edwin Roger; Babur, Özgün; Vats, Pankaj; Anand, Shankara; Schraink, Tobias; Cornwell, MacIntosh; Rodrigues, Fernanda Martins; Zhu, Houxiang; Mo, Chia-Kuei; Zhang, Yuping; da Veiga Leprevost, Felipe; Huang, Chen; Chinnaiyan, Arul M; Wyczalkowski, Matthew A; Omenn, Gilbert S; Newton, Chelsea J; Schurer, Stephan; Ruggles, Kelly V; Fenyö, David; Jewell, Scott D; Thiagarajan,Mathangi; Mesri, Mehdi; Rodriguez, Henry; Mani, Sendurai A; Udeshi, Namrata D; Getz, Gad; Suh,James; Li, Qing Kay; Hostetter, Galen; Paik, Paul K; Dhanasekaran, Saravana M; Govindan, Ramaswamy; Ding, Li; Robles, Ana I; Clauser, Karl R; Nesvizhskii, Alexey I; Wang, Pei; Carr, Steven A; Zhang, Bing; Mani, D R; Gillette, Michael A
  3. Cell. 2021, Aug 05; 184(16): 4348-4371.e40.
  1. 7.   Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy
  2. 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
  3. Cell. 2020, NOV 25; 183(5): 1436-+.
  1. 8.   Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
  2. Gillette, Michael A; Satpathy, Shankha; Cao, Song; Dhanasekaran, Saravana M; Vasaikar, Suhas V; Krug, Karsten; Petralia, Francesca; Li, Yize; Liang, Wen-Wei; Reva, Boris; Krek, Azra; Ji, Jiayi; Song, Xiaoyu; Liu, Wenke; Hong, Runyu; Yao, Lijun; Blumenberg, Lili; Savage, Sara R; Wendl, Michael C; Wen, Bo; Li, Kai; Tang, Lauren C; MacMullan, Melanie A; Avanessian, Shayan C; Kane, M Harry; Newton, Chelsea J; Cornwell, MacIntosh; Kothadia, Ramani B; Ma, Weiping; Yoo, Seungyeul; Mannan, Rahul; Vats, Pankaj; Kumar-Sinha, Chandan; Kawaler, Emily A; Omelchenko, Tatiana; Colaprico, Antonio; Geffen, Yifat; Maruvka, Yosef E; da Veiga Leprevost, Felipe; Wiznerowicz, Maciej; Gümüs, Zeynep H; Veluswamy, Rajwanth R; Hostetter, Galen; Heiman, David I; Wyczalkowski, Matthew A; Hiltke, Tara; Mesri, Mehdi; Kinsinger, Christopher R; Boja, Emily S; Omenn, Gilbert S; Chinnaiyan, Arul M; Rodriguez, Henry; Li, Qing Kay; Jewell, Scott D; Thiagarajan,Mathangi; Getz, Gad; Zhang, Bing; Fenyö, David; Ruggles, Kelly V; Cieslik, Marcin P; Robles, Ana I; Clauser, Karl R; Govindan, Ramaswamy; Wang, Pei; Nesvizhskii, Alexey I; Ding, Li; Mani, D R; Carr, Steven A
  3. Cell. 2020, Jul 09; 182(1): 200-225.e35.
  1. 9.   Proteogenomic Characterization of Endometrial Carcinoma
  2. Dou, Yongchao; Kawaler, Emily A; Cui Zhou, Daniel; Gritsenko, Marina A; Huang, Chen; Blumenberg, Lili; Karpova, Alla; Petyuk, Vladislav A; Savage, Sara R; Satpathy, Shankha; Liu, Wenke; Wu, Yige; Tsai, Chia-Feng; Wen, Bo; Li, Zhi; Cao, Song; Moon, Jamie; Shi, Zhiao; Cornwell, MacIntosh; Wyczalkowski, Matthew A; Chu, Rosalie K; Vasaikar, Suhas; Zhou, Hua; Gao, Qingsong; Moore, Ronald J; Li, Kai; Sethuraman, Sunantha; Monroe, Matthew E; Zhao, Rui; Heiman, David; Krug, Karsten; Clauser, Karl; Kothadia, Ramani; Maruvka, Yosef; Pico, Alexander R; Oliphant, Amanda E; Hoskins, Emily L; Pugh, Samuel L; Beecroft, Sean J I; Adams, David W; Jarman, Jonathan C; Kong, Andy; Chang, Hui-Yin; Reva, Boris; Liao, Yuxing; Rykunov, Dmitry; Colaprico, Antonio; Chen, Xi Steven; Czekanski, Andrzej; Jedryka, Marcin; Matkowski, Rafal; Wiznerowicz, Maciej; Hiltke, Tara; Boja, Emily; Kinsinger, Christopher R; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry; Mutch, David; Fuh, Katherine; Ellis, Matthew J; DeLair, Deborah; Thiagarajan,Mathangi; Mani, D R; Getz, Gad; Noble, Michael; Nesvizhskii, Alexey I; Wang, Pei; Anderson, Matthew L; Levine, Douglas A; Smith, Richard D; Payne, Samuel H; Ruggles, Kelly V; Rodland, Karin D; Ding, Li; Zhang, Bing; Liu, Tao; Fenyö, David
  3. Cell. 2020, Feb 20; 180(4): 729-748.e26.
  1. 10.   Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
  2. Clark, David J; Dhanasekaran, Saravana M; Petralia, Francesca; Pan, Jianbo; Song, Xiaoyu; Hu, Yingwei; da Veiga Leprevost, Felipe; Reva, Boris; Lih, Tung-Shing M; Chang, Hui-Yin; Ma, Weiping; Huang, Chen; Ricketts, Christopher J; Chen, Lijun; Krek, Azra; Li, Yize; Rykunov, Dmitry; Li, Qing Kay; Chen, Lin S; Ozbek, Umut; Vasaikar, Suhas; Wu, Yige; Yoo, Seungyeul; Chowdhury, Shrabanti; Wyczalkowski, Matthew A; Ji, Jiayi; Schnaubelt, Michael; Kong, Andy; Sethuraman, Sunantha; Avtonomov, Dmitry M; Ao, Minghui; Colaprico, Antonio; Cao, Song; Cho, Kyung-Cho; Kalayci, Selim; Ma, Shiyong; Liu, Wenke; Ruggles, Kelly; Calinawan, Anna; Gümüs, Zeynep H; Geizler, Daniel; Kawaler, Emily; Teo, Guo Ci; Wen, Bo; Zhang, Yuping; Keegan, Sarah; Li, Kai; Chen, Feng; Edwards, Nathan; Pierorazio, Phillip M; Chen, Xi Steven; Pavlovich, Christian P; Hakimi, A Ari; Brominski, Gabriel; Hsieh, James J; Antczak, Andrzej; Omelchenko, Tatiana; Lubinski, Jan; Wiznerowicz, Maciej; Linehan, W Marston; Kinsinger, Christopher R; Thiagarajan,Mathangi; Boja, Emily S; Mesri, Mehdi; Hiltke, Tara; Robles, Ana I; Rodriguez, Henry; Qian, Jiang; Fenyö, David; Zhang, Bing; Ding, Li; Schadt, Eric; Chinnaiyan, Arul M; Zhang, Zhen; Omenn, Gilbert S; Cieslik, Marcin; Chan, Daniel W; Nesvizhskii, Alexey I; Wang, Pei; Zhang, Hui
  3. Cell. 2019, Oct 31; 179(4): 964-983.e31.
  1. 11.   The Functional Comparison of Eukaryotic Proteomes: Implications for Choosing an Appropriate Model Organism to Probe Human Biology
  2. Karathia,Hiren; Hannenhalli, Sridhar; Alves, Rui
  3. Methods in Molecular Biology (Clifton, N.J.). 2025 2859: 163-179.
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