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A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights Yu, Jing; Gui, Xiuqi; Zou, Yunhao; Liu, Qian; Yang, Zhicheng; An, Jusheng; Guo, Xuan; Wang, Kaihua; Guo, Jiaming; Huang, Manni; Zhou, Shuhan; Zuo, Jing; Chen, Yimin; Deng, Lu; Yuan, Guangwen; Li, Ning; Song, Yan; Jia, Jia; Zeng, Jia; Zhao, Yuxi; Liu, Xianming; Du, Xiaoxian; Liu, Yansheng; Wang, Pei; Zhang, Bing; Ding, Li; Robles, Ana I.; Rodriguez, Henry; Zhou, Hu; Shao, Zhen; Wu, Lingying; Gao, Daming Share Save
Resource requirements to accelerate clinical applications of next-generation sequencing and radiomics: workshop commentary and review Harris, Lyndsay; Shankar, Lalitha K.; Hildebrandt, Claire; Rubinstein, Wendy S.; Langlais, Kristofor; Rodriguez, Henry; Berger, Adam; Freymann, John; Huang, Erich P.; Williams, P. Mickey; Zenklusen, Jean Claude; Ochs, Robert; Tezak, Zivana; Sahiner, Berkman Share Save
Deciphering oncogenic dedifferentiation: A proteomic approach to quantifying stemness scores and unveiling druggable targets Kolodziejczak-Guglas, Iga; Simoes, Renan; Demicco, Elizabeth G.; Segura, Rossana L.; Lazar, Alexander J.; Ma, Weiping; Storrs, Erik; Petralia, Francesca; Colaprico, Antonio; da Leprevost, Felipe; Pugliese, Pietro; Ceccarelli, Michele; Nesvizhski, Alexey I.; Kaminska, Bozena; Zhang, Bing; Rodriguez, Henry; Mesri, Mehdi; Robles, Ana I.; Ding, Li; Malta, Tathiane M.; Wiznerowicz, Maciej Share Save
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NCI Cancer Research Data Commons: Resources to Share Key Cancer Data Wang, Zhining; Davidsen, Tanja M.; Kuffel, Gina R.; Addepalli, Kanakadurga; Bell, Amanda; Casas-Silva, Esmeralda; Dingerdissen, Hayley; Farahani, Keyvan; Fedorov, Andrey; Gaheen, Sharon; Grossman, Robert L.; Kikinis, Ron; Kim, Erika; Otridge, John; Pihl, Todd; Porter, Melissa; Rodriguez, Henry; Staudt, Louis M.; Thangudu, Ratna R.; Venkatachari, Sudha; Zenklusen, Jean Claude; Zhang, Xu; Barnholtz-Sloan, Jill S.; Kerlavage, Anthony R. Share Save
Deep learning integrates histopathology and proteogenomics at a pan-cancer level 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; Fenyo, David Share Save
Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology Ji, Shuyi; Feng, Li; Fu, Zile; Wu, Gaohua; Wu, Yingcheng; Lin, Youpei; Lu, Dayun; Song, Yuanli; Cui, Peng; Yang, Zijian; Sang, Chen; Song, Guohe; Cai, Shangli; Li, Yuanchuang; Lin, Hanqing; Zhang, Shu; Wang, Xiaoying; Qiu, Shuangjian; Zhang, Xiaoming; Hua, Guoqiang; Li, Junqiang; Zhou, Jian; Dai, Zhi; Wang, Xiangdong; Ding, Li; Wang, Pei; Gao, Daming; Zhang, Bing; Rodriguez, Henry; Fan, Jia; Clevers, Hans; Zhou, Hu; Sun, Yidi; Gao, Qiang Share Save
Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma (vol 14, 1681, 2023) Wu, Yige; Terekhanova, Nadezhda V.; Caravan, Wagma; Al Deen, Nataly Naser; Lal, Preet; Chen, Siqi; Mo, Chia-Kuei; Cao, Song; Li, Yize; Karpova, Alla; Liu, Ruiyang; Zhao, Yanyan; Shinkle, Andrew; Strunilin, Ilya; Weimholt, Cody; Sato, Kazuhito; Yao, Lijun; Serasanambati, Mamatha; Yang, Xiaolu; Wyczalkowski, Matthew; Zhu, Houxiang; Zhou, Daniel Cui; Jayasinghe, Reyka G.; Mendez, Daniel; Wendl, Michael C.; Clark, David; Newton, Chelsea; Ruan, Yijun; Reimers, Melissa A.; Pachynski, Russell K.; Kinsinger, Chris; Jewell, Scott; Chan, Daniel W.; Zhang, Hui; Chaudhuri, Aadel A.; Chheda, Milan G.; Humphreys, Benjamin D.; Mesri, Mehdi; Rodriguez, Henry; Hsieh, James J.; Ding, Li; Chen, Feng Share Save
Proteomic-based stemness score measure oncogenic dedifferentiation and enable the identification of druggable targets Malta, Tathiane M.; Kolodziejczak, Iga; Simoes, Renan; Colaprico, Antonio; Storrs, Erik; Petralia, Francesca; da von Leprevost, Felipe; Segura, Rossana L.; Demicco, Elizabeth; Lazar, Alexander J.; Ma, Weiping; Pugliese, Pietro; Ceccarelli, Michele; Kaminska, Bozena; Nesvizhski, Alexey I.; Zhang, Bing; Rodriguez, Henry; Mesri, Mehdi; Robles, Ana I.; Ding, Li; Wiznerowicz, Maciej Share Save
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Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma Wu, Yige; Terekhanova, Nadezhda V.; Caravan, Wagma; Al Deen, Nataly Naser; Lal, Preet; Chen, Siqi; Mo, Chia-Kuei; Cao, Song; Li, Yize; Karpova, Alla; Liu, Ruiyang; Zhao, Yanyan; Shinkle, Andrew; Strunilin, Ilya; Weimholt, Cody; Sato, Kazuhito; Yao, Lijun; Serasanambati, Mamatha; Yang, Xiaolu; Wyczalkowski, Matthew; Zhu, Houxiang; Zhou, Daniel Cui; Jayasinghe, Reyka G.; Mendez, Daniel; Wendl, Michael C.; Clark, David; Newton, Chelsea; Ruan, Yijun; Reimers, Melissa A.; Pachynski, Russell K.; Kinsinger, Chris; Jewell, Scott; Chan, Daniel W.; Zhang, Hui; Chaudhuri, Aadel A.; Chheda, Milan G.; Humphreys, Benjamin D.; Mesri, Mehdi; Rodriguez, Henry; Hsieh, James J.; Ding, Li; Chen, Feng Share Save
Proteogenomic profiling of fresh frozen core biopsies from CALGB 40601 Jaehnig, Eric J.; Fernandez-Martinez, Aranzazu; Vashist, Tanmayi; Holt, Matthew V.; Williams, LaTerrica; Lei, Jonathan; Kim, Beom-Jun; Dou, Yongchao; Korchina, Viktoriya; Gibbs, Richard; Muzny, Donna; Doddapaneni, Harshavardhan; Rodriguez, Henry; Robles, Ana; Hiltke, Tara; Mani, D. R.; Gillette, Michael; Hyslop, Terry; Wen, Yujia; McCart, Linda; Miles, George; Carr, Steven; Zhang, Bing; Satpathy, Shankha; Ellis, Matthew; Anurag, Meenakshi Share Save
Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling Adams, Lauren M.; DeHart, Caroline J.; Drown, Bryon S.; Anderson, Lissa C.; Bocik, William; Boja, Emily S.; Hiltke, Tara M.; Hendrickson, Christopher L.; Rodriguez, Henry; Caldwell, Michael; Vafabakhsh, Reza; Kelleher, Neil L. Share Save
Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer Anurag, Meenakshi; Jaehnig, Eric J.; Krug, Karsten; Lei, Jonathan T.; Bergstrom, Erik J.; Kim, Beom-Jun; Vashist, Tanmayi D.; Huynh, Anh Minh Tran; Dou, Yongchao; Gou, Xuxu; Huang, Chen; Shi, Zhiao; Wen, Bo; Korchina, Viktoriya; Gibbs, Richard A.; Muzny, Donna M.; Doddapaneni, Harshavardhan; Dobrolecki, Lacey E.; Rodriguez, Henry; Robles, Ana I.; Hiltke, Tara; Lewis, Michael T.; Nangia, Julie R.; Shafaee, Maryam Nemati; Li, Shunqiang; Hagemann, Ian S.; Hoog, Jeremy; Lim, Bora; Osborne, C. Kent; Mani, D. R.; Gillette, Michael A.; Zhang, Bing; Echeverria, Gloria V.; Miles, George; Rimawi, Mothaffar F.; Carr, Steven A.; Ademuyiwa, Foluso O.; Satpathy, Shankha; Ellis, Matthew J. Share Save
Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens Whiteaker, Jeffrey R.; Lundeen, Rachel A.; Zhao, Lei; Schoenherr, Regine M.; Burian, Aura; Huang, Dongqing; Voytovich, Ulianna; Wang, Tao; Kennedy, Jacob J.; Ivey, Richard G.; Lin, Chenwei; Murillo, Oscar D.; Lorentzen, Travis D.; Thiagarajan, Mathangi; Colantonio, Simona; Caceres, Tessa W.; Roberts, Rhonda R.; Knotts, Joseph G.; Reading, Joshua J.; Kaczmarczyk, Jan A.; Richardson, Christopher W.; Garcia-Buntley, Sandra S.; Bocik, William; Hewitt, Stephen M.; Murray, Karen E.; Do, Nhan; Brophy, Mary; Wilz, Stephen W.; Yu, Hongbo; Ajjarapu, Samuel; Boja, Emily; Hiltke, Tara; Rodriguez, Henry; Paulovich, Amanda G. Share Save
Targeted mass-spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP kinase, and AKT signaling Whiteaker, Jeffrey R.; Sharma, Kanika; Hoffman, Melissa A.; Kuhn, Eric; Zhao, Lei; Cocco, Alexandra R.; Schoenherr, Regine M.; Kennedy, Jacob J.; Voytovich, Ulianna; Lin, Chenwei; Fang, Bin; Bowers, Kiah; Whiteley, Gordon; Colantonio, Simona; Bocik, William; Roberts, Rhonda; Hiltke, Tara; Boja, Emily; Rodriguez, Henry; McCormick, Frank; Holderfield, Matthew; Carr, Steven A.; Koomen, John M.; Paulovich, Amanda G. Share Save
A community effort to identify and correct mislabeled samples in proteogenomic studies Yoo, Seungyeul; Shi, Zhiao; Wen, Bo; Kho, SoonJye; Pan, Renke; Feng, Hanying; Chen, Hong; Carlsson, Anders; Eden, Patrik; Ma, Weiping; Raymer, Michael; Maier, Ezekiel J.; Tezak, Zivana; Johanson, Elaine; Hinton, Denise; Rodriguez, Henry; Zhu, Jun; Boja, Emily; Wang, Pei; Zhang, Bing Share Save
A high-stringency blueprint of the human proteome Adhikari, Subash; Nice, Edouard C.; Deutsch, Eric W.; Lane, Lydie; Omenn, Gilbert S.; Pennington, Stephen R.; Paik, Young-Ki; Overall, Christopher M.; Corrales, Fernando J.; Cristea, Ileana M.; Van Eyk, Jennifer E.; Uhlen, Mathias; Lindskog, Cecilia; Chan, Daniel W.; Bairoch, Amos; Waddington, James C.; Justice, Joshua L.; LaBaer, Joshua; Rodriguez, Henry; He, Fuchu; Kostrzewa, Markus; Ping, Peipei; Gundry, Rebekah L.; Stewart, Peter; Srivastava, Sanjeeva; Srivastava, Sudhir; Nogueira, Fabio C. S.; Domont, Gilberto B.; Vandenbrouck, Yves; Lam, Maggie P. Y.; Wennersten, Sara; Vizcaino, Juan Antonio; Wilkins, Marc; Schwenk, Jochen M.; Lundberg, Emma; Bandeira, Nuno; Marko-Varga, Gyorgy; Weintraub, Susan T.; Pineau, Charles; Kusebauch, Ulrike; Moritz, Robert L.; Ahn, Seong Beom; Palmblad, Magnus; Snyder, Michael P.; Aebersold, Ruedi; Baker, Mark S. Share Save
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