Not logged in Combining chemoproteomics with machine learning identifies functionally active covalent fragments for hard-to-drug cancer drivers Hermann, Johannes C.; Everley, Robert; Marholz, Laura; Berberich, Matthew; Yang, Tzu-Yi; Chao, Yu-Hsin; Awol, Abduselam K.; Shaghafi, Michael; Yoon, Han; Varma, Rohan; Stein, Reed; Krug, Karsten; Lachtara, Emily; Erlanson, Daniel; Varma, Chris; Webster, Kevin R. Share Save
ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling Gentili, Matteo; Liu, Bingxu; Papanastasiou, Malvina; Dele-Oni, Deborah; Schwartz, Marc A.; Carlson, Rebecca J.; Al'Khafaji, Aziz M.; Krug, Karsten; Brown, Adam; Doench, John G.; Carr, Steven A.; Hacohen, Nir 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
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PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation Khadka, Prasidda; Reitman, Zachary J.; Lu, Sophie; Buchan, Graham; Gionet, Gabrielle; Dubois, Frank; Carvalho, Diana M.; Shih, Juliann; Zhang, Shu; Greenwald, Noah F.; Zack, Travis; Shapira, Ofer; Pelton, Kristine; Hartley, Rachel; Bear, Heather; Georgis, Yohanna; Jarmale, Spandana; Melanson, Randy; Bonanno, Kevin; Schoolcraft, Kathleen; Miller, Peter G.; Condurat, Alexandra L.; Gonzalez, Elizabeth M.; Qian, Kenin; Morin, Eric; Langhnoja, Jaldeep; Lupien, Leslie E.; Rendo, Veronica; Digiacomo, Jeromy; Wang, Dayle; Zhou, Kevin; Kumbhani, Rushil; Garcia, Maria E. Guerra; Sinai, Claire E.; Becker, Sarah; Schneider, Rachel; Vogelzang, Jayne; Krug, Karsten; Goodale, Amy; Abid, Tanaz; Kalani, Zohra; Piccioni, Federica; Beroukhim, Rameen; Persky, Nicole S.; Root, David E.; Carcaboso, Angel M.; Ebert, Benjamin L.; Fuller, Christine; Babur, Ozgun; Kieran, Mark W.; Jones, Chris; Keshishian, Hasmik; Ligon, Keith L.; Carr, Steven A.; Phoenix, Timothy N.; Bandopadhayay, Pratiti Share Save
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies Keshishian, Hasmik; McDonald, E. Robert; Mundt, Filip; Melanson, Randy; Krug, Karsten; Porter, Dale A.; Wallace, Luke; Forestier, Dominique; Rabasha, Bokang; Marlow, Sara E.; Jane-Valbuena, Judit; Todres, Ellen; Specht, Harrison; Robinson, Margaret Lea; Beltran, Pierre M. Jean; Babur, Ozgun; Olive, Meagan E.; Golji, Javad; Kuhn, Eric; Burgess, Michael; MacMullan, Melanie A.; Rejtar, Tomas; Wang, Karen; Mani, D. R.; Satpathy, Shankha; Gillette, Michael A.; Sellers, William R.; Carr, Steven A. Share Save
PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis Mani, D. R.; Maynard, Myranda; Kothadia, Ramani; Krug, Karsten; Christianson, Karen E.; Heiman, David; Clauser, Karl R.; Birger, Chet; Getz, Gad; Carr, Steven A. Share Save
Noncanonical open reading frames encode functional proteins essential for cancer cell survival Prensner, John R.; Enache, Oana M.; Luria, Victor; Krug, Karsten; Clauser, Karl R.; Dempster, Joshua M.; Karger, Amir; Wang, Li; Stumbraite, Karolina; Wang, Vickie M.; Botta, Ginevra; Lyons, Nicholas J.; Goodale, Amy; Kalani, Zohra; Fritchman, Briana; Brown, Adam; Alan, Douglas; Green, Thomas; Yang, Xiaoping; Jaffe, Jacob D.; Roth, Jennifer A.; Piccioni, Federica; Kirschner, Marc W.; Ji, Zhe; Root, David E.; Golub, Todd R. Share Save
Avant-garde: an automated data-driven DIA data curation tool Vaca Jacome, Alvaro Sebastian; Peckner, Ryan; Shulman, Nicholas; Krug, Karsten; DeRuff, Katherine C.; Officer, Adam; Christianson, Karen E.; MacLean, Brendan; MacCoss, Michael J.; Carr, Steven A.; Jaffe, Jacob D. Share Save
Proteogenomics characterization of HPV-negative head and neck squamous cell carcinomas Huang, Chen; Chen, Lijun; Li, Yize; Savage, Sara; Schnaubelt, Michael; Leprevost, Felipe, V; Cieslik, Marcin; Dou, Yongchao; Wen, Bo; Lei, Jonathan T.; Li, Kai; Jaehnig, Eric; Shi, Zhiao; Anurag, Meenakshi; Pan, Jianbo; Hu, Yingwei; Eguez, Rodrigo, V; Clark, David J.; Wyczalkowski, Matthew; Dhanasekaran, Saravana M.; Kumar, Chandan; Colaprico, Antonio; Krug, Karsten; Gillette, Michael; Mani, D. R.; Yoo, Seungyeul; Ji, Jiayi; Song, Xiaoyu; Ma, Weiping; Chen, Xi Steven; Pico, Alex; Edwards, Nathan J.; Jewell, Scott D.; Thiagarajan, Mathangi; Boja, Emily S.; Rodriguez, Henry; Sikora, Andrew; Wang, Pei; Ellis, Matthew; Omenn, Gilbert S.; Ding, Li; Nesvizhskii, Alexey, I; EI-Naggar, Adel K.; Chan, Daniel W.; Zhang, Hui; Zhang, Bing Share Save
Microscaled proteogenomic methods for precision oncology Satpathy, Shankha; Jaehnig, Eric; Karsten, Krug; Kim, Beom-Jun; Saltzman, Alexander; Chan, Doug; Holloway, Kimberly; Anurag, Meenakshi; Huang, Chen; Singh, Purba; Gao, Ari; Namai, Noel; Dou, Yongchao; Wen, Bo; Vasaikar, Suhas; Mutch, David; Watson, Mark; Ma, Cynthia; Ademuyiwa, Foluso; Rimawi, Mothaffar; Hoog, Jeremy; Jacobs, Samuel; Malovannaya, Anna; Hyslop, Terry; Mani, D. R.; Perou, Charles; Miles, George; Zhang, Bing; Gillette, Michael; Carr, Steven; Ellis, Matthew Share Save
Proteogenomic Landscape of Prospectively Collected Breast Cancer Gillette, M.; Krug, K.; Satpathy, S.; Jaehnig, E.; Karpova, A.; Clauser, K.; Tang, L.; Blumenberg, L.; Kothadia, R.; Ruggles, K.; Zhang, B.; Ding, L.; Mertins, P.; Mani, D. R.; Ellis, M.; Carr, S. Share Save
Microscaled proteogenomic methods for precision oncology Satpathy, Shankha; Jaehnig, Eric J.; Krug, Karsten; Kim, Beom-Jun; Saltzman, Alexander B.; Chan, Doug W.; Holloway, Kimberly R.; Anurag, Meenakshi; Huang, Chen; Singh, Purba; Gao, Ari; Namai, Noel; Dou, Yongchao; Wen, Bo; Vasaikar, Suhas V.; Mutch, David; Watson, Mark A.; Ma, Cynthia; Ademuyiwa, Foluso O.; Rimawi, Mothaffar F.; Schiff, Rachel; Hoog, Jeremy; Jacobs, Samuel; Malovannaya, Anna; Hyslop, Terry; Clauser, Karl R.; Mani, D. R.; Perou, Charles M.; Miles, George; Zhang, Bing; Gillette, Michael A.; Carr, Steven A.; Ellis, Matthew J. Share Save
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Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells Myers, Samuel A.; Rhoads, Andrew; Cocco, Alexandra R.; Peckner, Ryan; Haber, Adam L.; Schweitzer, Lawrence D.; Krug, Karsten; Mani, D. R.; Clauser, Karl R.; Rozenblatt-Rosen, Orit; Hacohen, Nir; Regev, Aviv; Carr, Steven A. Share Save
A Curated Resource for Phosphosite- specific Signature Analysis Krug, Karsten; Mertins, Philipp; Zhang, Bin; Hornbeck, Peter; Raju, Rajesh; Ahmad, Rushdy; Szucs, Matthew; Mund, Filip; Forestier, Dominique; Jane-Valbuena, Judit; Keshishian, Hasmik; Gillette, Michael A.; Tamayo, Pablo; Mesirov, Jill P.; Jaffe, Jacob D.; Carr, Steven A.; Mani, D. R. Share Save
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Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry Mertins, Philipp; Tang, Lauren C.; Krug, Karsten; Clark, David J.; Gritsenko, Marina A.; Chen, Lijun; Clauser, Karl R.; Clauss, Therese R.; Shah, Punit; Gillette, Michael A.; Petyuk, Vladislav A.; Thomas, Stefani N.; Mani, D. R.; Mundt, Filip; Moore, Ronald J.; Hui, Yingwei; Zhao, Rui; Schnaubelt, Michael; Keshishian, Hasmik; Monroe, Matthew E.; Zhang, Zhen; Udeshi, Namrata D.; Mani, Deepak; Davies, Sherri R.; Townsend, R. Reid; Chan, Daniel W.; Smith, Richard D.; Zhang, Hui; Liu, Tao; Carr, Steven A. Share Save
Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V.; Mooradian, Arshag D.; Mertins, Philipp; Gillette, Michael A.; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P.; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D. R.; Clauser, Karl R.; Gao, Feng; Luo, Jingqin; Davies, Sherri R.; Johnson, Gary L.; Huang, Kuan-Lin; Yoon, Christopher J.; Ding, Li; Fenyoe, David; Ellis, Matthew J.; Townsend, R. Reid; Held, Jason M.; Carr, Steven A.; Ma, Cynthia X. Share Save
TORC1 and TORC2 converge to regulate the SAGA co-activator in response to nutrient availability Laboucarie, Thomas; Detilleux, Dylane; Rodriguez-Mias, Ricard A.; Faux, Celine; Romeo, Yves; Franz-Wachtel, Mirita; Krug, Karsten; Macek, Boris; Villen, Judit; Petersen, Janni; Helmlinger, Dominique Share Save
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