Cancer proteogenomics: current impact and future prospects von Mani, D. R., Krug, Karsten, Zhang, Bing, Satpathy, Shankha, Clauser, Karl R., Ding, Li, Ellis, Matthew, Gillette, Michael A., Carr, Steven A.

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Microscaled proteogenomic methods for precision oncology von 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.

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

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A Curated Resource for Phosphosite-specific Signature Analysis[S] von Krug, Karsten, Mertins, Philipp, Zhang, Bin, Hornbeck, Peter, Raju, Rajesh, Ahmad, Rushdy, Szucs, Matthew, Mundt, Filip, Forestier, Dominique, Jane-Valbuena, Judit, Keshishian, Hasmik, Gillette, Michael A., Tamayo, Pablo, Mesirov, Jill P., Jaffe, Jacob D., Carr, StevenA, Mani, D.R.

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PPM1D-truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells von Kahn, Josephine D., Miller, Peter G., Silver, Alexander J., Sellar, Rob S., Bhatt, Shruti, Gibson, Christopher, McConkey, Marie, Adams, Dylan, Mar, Brenton, Mertins, Philipp, Fereshetian, Shaunt, Krug, Karsten, Zhu, Haoling, Letai, Anthony, Carr, Steven A., Doench, John, Jaiswal, Siddhartha, Ebert, Benjamin L.

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Noncanonical open reading frames encode functional proteins essential for cancer cell survival von 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.

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Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry von 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., Hu, 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.

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Methods, Tools and Current Perspectives in Proteogenomics von Ruggles, Kelly V., Krug, Karsten, Wang, Xiaojing, Clauser, Karl R., Wang, Jing, Payne, Samuel H., Fenyö, David, Zhang, Bing, Mani, D.R.

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ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling von 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

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Absolute Proteome and Phosphoproteome Dynamics during the Cell Cycle of Schizosaccharomyces pombe (Fission Yeast) von Carpy, Alejandro, Krug, Karsten, Graf, Sabine, Koch, André, Popic, Sasa, Hauf, Silke, Macek, Boris

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Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells von 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.

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Avant-garde: an automated data-driven DIA data curation tool von 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.

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A bidirectional switch in the Shank3 phosphorylation state biases synapses toward up- or downscaling von Wu, Chi-Hong, Tatavarty, Vedakumar, Jean Beltran, Pierre M, Guerrero, Andrea A, Keshishian, Hasmik, Krug, Karsten, MacMullan, Melanie A, Li, Li, Carr, Steven A, Cottrell, Jeffrey R, Turrigiano, Gina G

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Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models von Borchert, Nadine, Dieterich, Christoph, Krug, Karsten, Schütz, Wolfgang, Jung, Stephan, Nordheim, Alfred, Sommer, Ralf J, Macek, Boris

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Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments von Krug, Karsten, Carpy, Alejandro, Behrends, Gesa, Matic, Katarina, Soares, Nelson C., Macek, Boris

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PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis von Mani, D. R., Maynard, Myranda, Kothadia, Ramani, Krug, Karsten, Christianson, Karen E., Heiman, David, Clauser, Karl R., Birger, Chet, Getz, Gad, Carr, Steven A.

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Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers von 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, Fenyö, David, Ellis, Matthew J, Townsend, R Reid, Held, Jason M, Carr, Steven A, Ma, Cynthia X

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TORC1 and TORC2 converge to regulate the SAGA co‐activator in response to nutrient availability von Laboucarié, Thomas, Detilleux, Dylane, Rodriguez‐Mias, Ricard A, Faux, Céline, Romeo, Yves, Franz‐Wachtel, Mirita, Krug, Karsten, Maček, Boris, Villén, Judit, Petersen, Janni, Helmlinger, Dominique

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Global Detection of Protein Kinase D-dependent Phosphorylation Events in Nocodazole-treated Human Cells von Franz-Wachtel, Mirita, Eisler, Stephan A., Krug, Karsten, Wahl, Silke, Carpy, Alejandro, Nordheim, Alfred, Pfizenmaier, Klaus, Hausser, Angelika, Macek, Boris

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A highly multiplexed quantitative phosphosite assay for biology and preclinical studies von 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, Jean Beltran, Pierre M, Babur, Ozgun, Olive, Meagan E, Golji, Javad, Kuhn, Eric, Burgess, Michael, MacMullan, Melanie A, Rejtar, Tomas, Wang, Karen, Mani, DR, Satpathy, Shankha, Gillette, Michael A, Sellers, William R, Carr, Steven A

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