Spatially interacting phosphorylation sites and mutations in cancer.
Nature Communications
Huang, Kuan-Lin KL; Scott, Adam D AD; Zhou, Daniel Cui DC; Wang, Liang-Bo LB; Weerasinghe, Amila A; Elmas, Abdulkadir A; Liu, Ruiyang R; Wu, Yige Y; Wendl, Michael C MC; Wyczalkowski, Matthew A MA; Baral, Jessika J; Sengupta, Sohini S; Lai, Chin-Wen CW; Ruggles, Kelly K; Payne, Samuel H SH; Raphael, Benjamin B; Fenyö, David D; Chen, Ken K; Mills, Gordon G; Ding, Li L
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Cell
Bailey, Matthew H MH; Tokheim, Collin C; Porta-Pardo, Eduard E; Sengupta, Sohini S; Bertrand, Denis D; Weerasinghe, Amila A; Colaprico, Antonio A; Wendl, Michael C MC; Kim, Jaegil J; Reardon, Brendan B; Ng, Patrick Kwok-Shing PK; Jeong, Kang Jin KJ; Cao, Song S; Wang, Zixing Z; Gao, Jianjiong J; Gao, Qingsong Q; Wang, Fang F; Liu, Eric Minwei EM; Mularoni, Loris L; Rubio-Perez, Carlota C; Nagarajan, Niranjan N; Cortés-Ciriano, Isidro I; Zhou, Daniel Cui DC; Liang, Wen-Wei WW; Hess, Julian M JM; Yellapantula, Venkata D VD; Tamborero, David D; Gonzalez-Perez, Abel A; Suphavilai, Chayaporn C; Ko, Jia Yu JY; Khurana, Ekta E; Park, Peter J PJ; Van Allen, Eliezer M EM; Liang, Han H; , ; , ; Lawrence, Michael S MS; Godzik, Adam A; Lopez-Bigas, Nuria N; Stuart, Josh J; Wheeler, David D; Getz, Gad G; Chen, Ken K; Lazar, Alexander J AJ; Mills, Gordon B GB; Karchin, Rachel R; Ding, Li L
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.
Cell Reports
Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Oncotarget
Fertig, Elana J EJ; Ozawa, Hiroyuki H; Thakar, Manjusha M; Howard, Jason D JD; Kagohara, Luciane T LT; Krigsfeld, Gabriel G; Ranaweera, Ruchira S RS; Hughes, Robert M RM; Perez, Jimena J; Jones, Siân S; Favorov, Alexander V AV; Carey, Jacob J; Stein-O'Brien, Genevieve G; Gaykalova, Daria A DA; Ochs, Michael F MF; Chung, Christine H CH
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
Cell Reports
Giannakis, Marios M; Mu, Xinmeng Jasmine XJ; Shukla, Sachet A SA; Qian, Zhi Rong ZR; Cohen, Ofir O; Nishihara, Reiko R; Bahl, Samira S; Cao, Yin Y; Amin-Mansour, Ali A; Yamauchi, Mai M; Sukawa, Yasutaka Y; Stewart, Chip C; Rosenberg, Mara M; Mima, Kosuke K; Inamura, Kentaro K; Nosho, Katsuhiko K; Nowak, Jonathan A JA; Lawrence, Michael S MS; Giovannucci, Edward L EL; Chan, Andrew T AT; Ng, Kimmie K; Meyerhardt, Jeffrey A JA; Van Allen, Eliezer M EM; Getz, Gad G; Gabriel, Stacey B SB; Lander, Eric S ES; Wu, Catherine J CJ; Fuchs, Charles S CS; Ogino, Shuji S; Garraway, Levi A LA