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Braun, David A., Hou, Yue, Bakouny, Ziad, Ficial, Miriam, Sant’ Angelo, Miriam, Forman, Juliet, Ross-Macdonald, Petra, Berger, Ashton C., Jegede, Opeyemi A., Elagina, Liudmilla, Steinharter, John, Sun, Maxine, Wind-Rotolo, Megan, Pignon, Jean-Christophe, Cherniack, Andrew D., Lichtenstein, Lee, Neuberg, Donna, Catalano, Paul, Freeman, Gordon J., Sharpe, Arlene H., McDermott, David F., Van Allen, Eliezer M., Signoretti, Sabina, Wu, Catherine J., Shukla, Sachet A., Choueiri, Toni K.
Published in Nature medicine (01.06.2020)
Published in Nature medicine (01.06.2020)
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Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma
Miao, Diana, Margolis, Claire A, Gao, Wenhua, Voss, Martin H, Li, Wei, Martini, Dylan J, Norton, Craig, Bossé, Dominick, Wankowicz, Stephanie M, Cullen, Dana, Horak, Christine, Wind-Rotolo, Megan, Tracy, Adam, Giannakis, Marios, Hodi, Frank Stephen, Drake, Charles G, Ball, Mark W, Allaf, Mohamad E, Snyder, Alexandra, Hellmann, Matthew D, Ho, Thai, Motzer, Robert J, Signoretti, Sabina, Kaelin, Jr, William G, Choueiri, Toni K, Van Allen, Eliezer M
Published in Science (American Association for the Advancement of Science) (16.02.2018)
Published in Science (American Association for the Advancement of Science) (16.02.2018)
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Response and Acquired Resistance to Everolimus in Anaplastic Thyroid Cancer
Wagle, Nikhil, Grabiner, Brian C, Van Allen, Eliezer M, Amin-Mansour, Ali, Taylor-Weiner, Amaro, Rosenberg, Mara, Gray, Nathanael, Barletta, Justine A, Guo, Yanan, Swanson, Scott J, Ruan, Daniel T, Hanna, Glenn J, Haddad, Robert I, Getz, Gad, Kwiatkowski, David J, Carter, Scott L, Sabatini, David M, Jänne, Pasi A, Garraway, Levi A, Lorch, Jochen H
Published in The New England journal of medicine (09.10.2014)
Published in The New England journal of medicine (09.10.2014)
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Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset
Kehl, Kenneth L., Xu, Wenxin, Gusev, Alexander, Bakouny, Ziad, Choueiri, Toni K., Riaz, Irbaz Bin, Elmarakeby, Haitham, Van Allen, Eliezer M., Schrag, Deborah
Published in Nature communications (15.12.2021)
Published in Nature communications (15.12.2021)
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A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma
Nassar, Amin H., Mouw, Kent W., Jegede, Opeyemi, Shinagare, Atul B., Kim, Jaegil, Liu, Chia-Jen, Pomerantz, Mark, Harshman, Lauren C., Van Allen, Eliezer M., Wei, Xiao X., McGregor, Bradley, Choudhury, Atish D., Preston, Mark A., Dong, Fei, Signoretti, Sabina, Lindeman, Neal I., Bellmunt, Joaquim, Choueiri, Toni K., Sonpavde, Guru, Kwiatkowski, David J.
Published in British journal of cancer (01.02.2020)
Published in British journal of cancer (01.02.2020)
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Dissecting the immunogenomic biology of cancer for biomarker development
Van Allen, Eliezer M., Choueiri, Toni K.
Published in Nature reviews. Clinical oncology (01.03.2021)
Published in Nature reviews. Clinical oncology (01.03.2021)
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Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer
Keenan, Tanya E., Guerriero, Jennifer L., Barroso-Sousa, Romualdo, Li, Tianyu, O’Meara, Tess, Giobbie-Hurder, Anita, Tayob, Nabihah, Hu, Jiani, Severgnini, Mariano, Agudo, Judith, Vaz-Luis, Ines, Anderson, Leilani, Attaya, Victoria, Park, Jihye, Conway, Jake, He, Meng Xiao, Reardon, Brendan, Shannon, Erin, Wulf, Gerburg, Spring, Laura M., Jeselsohn, Rinath, Krop, Ian, Lin, Nancy U., Partridge, Ann, Winer, Eric P., Mittendorf, Elizabeth A., Liu, David, Van Allen, Eliezer M., Tolaney, Sara M.
Published in Nature communications (21.09.2021)
Published in Nature communications (21.09.2021)
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Biologically informed deep neural network for prostate cancer discovery
Elmarakeby, Haitham A., Hwang, Justin, Arafeh, Rand, Crowdis, Jett, Gang, Sydney, Liu, David, AlDubayan, Saud H., Salari, Keyan, Kregel, Steven, Richter, Camden, Arnoff, Taylor E., Park, Jihye, Hahn, William C., Van Allen, Eliezer M.
Published in Nature (London) (14.10.2021)
Published in Nature (London) (14.10.2021)
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Intron retention is a source of neoepitopes in cancer
Smart, Alicia C, Margolis, Claire A, Pimentel, Harold, He, Meng Xiao, Miao, Diana, Adeegbe, Dennis, Fugmann, Tim, Wong, Kwok-Kin, Van Allen, Eliezer M
Published in Nature biotechnology (01.12.2018)
Published in Nature biotechnology (01.12.2018)
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Identification of cancer driver genes based on nucleotide context
Dietlein, Felix, Weghorn, Donate, Taylor-Weiner, Amaro, Richters, André, Reardon, Brendan, Liu, David, Lander, Eric S., Van Allen, Eliezer M., Sunyaev, Shamil R.
Published in Nature genetics (01.02.2020)
Published in Nature genetics (01.02.2020)
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FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues
Font-Tello, Alba, Kesten, Nikolas, Xie, Yingtian, Taing, Len, Varešlija, Damir, Young, Leonie S., Hamid, Anis A., Van Allen, Eliezer M., Sweeney, Christopher J., Gjini, Evisa, Lako, Ana, Hodi, F. Steven, Bellmunt, Joaquim, Brown, Myles, Cejas, Paloma, Long, Henry W.
Published in Nature protocols (01.08.2020)
Published in Nature protocols (01.08.2020)
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Genomic Approaches to Understanding Response and Resistance to Immunotherapy
Braun, David A, Burke, Kelly P, Van Allen, Eliezer M
Published in Clinical cancer research (01.12.2016)
Published in Clinical cancer research (01.12.2016)
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Genomic correlates of response to CTLA-4 blockade in metastatic melanoma
Van Allen, Eliezer M., Miao, Diana, Schilling, Bastian, Shukla, Sachet A., Blank, Christian, Zimmer, Lisa, Sucker, Antje, Hillen, Uwe, Foppen, Marnix H. Geukes, Goldinger, Simone M., Utikal, Jochen, Hassel, Jessica C., Weide, Benjamin, Kaehler, Katharina C., Loquai, Carmen, Mohr, Peter, Gutzmer, Ralf, Dummer, Reinhard, Gabriel, Stacey, Wu, Catherine J., Schadendorf, Dirk, Garraway, Levi A.
Published in Science (American Association for the Advancement of Science) (09.10.2015)
Published in Science (American Association for the Advancement of Science) (09.10.2015)
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Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma
Mouw, Kent W, Cleary, James M, Reardon, Brendan, Pike, Jonathan, Braunstein, Lior Z, Kim, Jaegil, Amin-Mansour, Ali, Miao, Diana, Damish, Alexis, Chin, Joanna, Ott, Patrick A, Fuchs, Charles S, Martin, Neil E, Getz, Gad, Carter, Scott, Mamon, Harvey J, Hornick, Jason L, Van Allen, Eliezer M, D'Andrea, Alan D
Published in Clinical cancer research (15.06.2017)
Published in Clinical cancer research (15.06.2017)
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Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer
Beltran, Himisha, Prandi, Davide, Mosquera, Juan Miguel, Benelli, Matteo, Puca, Loredana, Cyrta, Joanna, Marotz, Clarisse, Giannopoulou, Eugenia, Chakravarthi, Balabhadrapatruni V S K, Varambally, Sooryanarayana, Tomlins, Scott A, Nanus, David M, Tagawa, Scott T, Van Allen, Eliezer M, Elemento, Olivier, Sboner, Andrea, Garraway, Levi A, Rubin, Mark A, Demichelis, Francesca
Published in Nature medicine (01.03.2016)
Published in Nature medicine (01.03.2016)
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Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma
El Zarif, Talal, Semaan, Karl, Eid, Marc, Seo, Ji-Heui, Garinet, Simon, Davidsohn, Matthew P., Sahgal, Pranshu, Fortunato, Brad, Canniff, John, Nassar, Amin H., Abou Alaiwi, Sarah, Bakouny, Ziad, Lakshminarayanan, Gitanjali, Savignano, Hunter, Lyons, Kevin, Matar, Sayed, Ali, Atef, Saad, Eddy, Saliby, Renee Maria, Cordeiro, Paulo, Zhang, Ziwei, El Ahmar, Nourhan, Laimon, Yasmin Nabil, Labaki, Chris, Shah, Valisha, Freeman, Dory, O’Toole, Jillian, Lee, Gwo-Shu Mary, Hwang, Justin, Pomerantz, Mark, Signoretti, Sabina, Van Allen, Eliezer M., Xie, Wanling, Berchuck, Jacob E., Viswanathan, Srinivas R., Braun, David A., Choueiri, Toni K., Freedman, Matthew L., Baca, Sylvan C.
Published in Cell reports (Cambridge) (25.06.2024)
Published in Cell reports (Cambridge) (25.06.2024)
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Scaling computational genomics to millions of individuals with GPUs
Taylor-Weiner, Amaro, Aguet, François, Haradhvala, Nicholas J, Gosai, Sager, Anand, Shankara, Kim, Jaegil, Ardlie, Kristin, Van Allen, Eliezer M, Getz, Gad
Published in Genome Biology (01.11.2019)
Published in Genome Biology (01.11.2019)
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Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer
Hamid, Anis A., Gray, Kathryn P., Shaw, Grace, MacConaill, Laura E., Evan, Carolyn, Bernard, Brandon, Loda, Massimo, Corcoran, Niall M., Van Allen, Eliezer M., Choudhury, Atish D., Sweeney, Christopher J.
Published in European urology (01.07.2019)
Published in European urology (01.07.2019)
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Beyond conventional immune-checkpoint inhibition — novel immunotherapies for renal cell carcinoma
Braun, David A., Bakouny, Ziad, Hirsch, Laure, Flippot, Ronan, Van Allen, Eliezer M., Wu, Catherine J., Choueiri, Toni K.
Published in Nature reviews. Clinical oncology (01.04.2021)
Published in Nature reviews. Clinical oncology (01.04.2021)
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