Historical perspective and future directions: computational science in immuno-oncology by Eliezer M Van Allen, Cora A Ricker, Kevin Meli

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Genome-guided discovery of cancer therapeutic targets by Prathyusha Konda, Simon Garinet, Eliezer M. Van Allen, Srinivas R. Viswanathan

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Germline Features Associated with Immune Infiltration in Solid Tumors by Sahar Shahamatdar, Meng Xiao He, Matthew A. Reyna, Alexander Gusev, Saud H. AlDubayan, Eliezer M. Van Allen, Sohini Ramachandran

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Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports by Haitham A. Elmarakeby, Pavel S. Trukhanov, Vidal M. Arroyo, Irbaz Bin Riaz, Deborah Schrag, Eliezer M. Van Allen, Kenneth L. Kehl

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Scaling computational genomics to millions of individuals with GPUs by Amaro Taylor-Weiner, François Aguet, Nicholas J. Haradhvala, Sager Gosai, Shankara Anand, Jaegil Kim, Kristin Ardlie, Eliezer M. Van Allen, Gad Getz

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Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics by Shreya Johri, Kevin Bi, Breanna M. Titchen, Jingxin Fu, Jake Conway, Jett P. Crowdis, Natalie I. Vokes, Zenghua Fan, Lawrence Fong, Jihye Park, David Liu, Meng Xiao He, Eliezer M. Van Allen

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Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients by Mohammed Al-Jumaan, Hoyin Chu, Abdullah Alsulaiman, Sabrina Y. Camp, Seunghun Han, Riaz Gillani, Yousef Al Marzooq, Fatmah Almulhim, Chittibabu Vatte, Areej Al Nemer, Afnan Almuhanna, Eliezer M. Van Allen, Amein Al-Ali, Saud H. AlDubayan

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Phase Ib study of pembrolizumab in combination with trastuzumab emtansine for metastatic HER2-positive breast cancer by Sara M Tolaney, Tianyu Li, Edward T Richardson, Judith Agudo, Elizabeth A Mittendorf, Beth Overmoyer, Eric P Winer, Adrienne G Waks, Tanya E Keenan, Nabihah Tayob, Gerburg M Wulf, Victoria Attaya, Leilani Anderson, Ian E Krop, Eliezer M Van Allen

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Change in neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma by Aly-Khan A. Lalani, Wanling Xie, Dylan J. Martini, John A. Steinharter, Craig K. Norton, Katherine M. Krajewski, Audrey Duquette, Dominick Bossé, Joaquim Bellmunt, Eliezer M. Van Allen, Bradley A. McGregor, Chad J. Creighton, Lauren C. Harshman, Toni K. Choueiri

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Integrative Analysis of Germline Rare Variants in Clear and Non–clear Cell Renal Cell Carcinoma by Seung Hun Han, Sabrina Y. Camp, Hoyin Chu, Ryan Collins, Riaz Gillani, Jihye Park, Ziad Bakouny, Cora A. Ricker, Brendan Reardon, Nicholas Moore, Eric Kofman, Chris Labaki, David Braun, Toni K. Choueiri, Saud H. AlDubayan, Eliezer M. Van Allen

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Patterns of structural variation define prostate cancer across disease states by Meng Zhou, Minjeong Ko, Anna C.H. Hoge, Kelsey Luu, Yuzhen Liu, Magdalena L. Russell, William W. Hannon, Zhenwei Zhang, Jian Carrot-Zhang, Rameen Beroukhim, Eliezer M. Van Allen, Atish D. Choudhury, Peter S. Nelson, Matthew L. Freedman, Mary-Ellen Taplin, Matthew Meyerson, Srinivas R. Viswanathan, Gavin Ha

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Somatic cancer variant curation and harmonization through consensus minimum variant level data by Deborah I. Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J. Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F. Davis, Reece K. Hart, Christine Micheel, Meredith Weaver, Eliezer M. Van Allen, Donald W. Parsons, Howard L. McLeod, Michael S. Watson, Sharon E. Plon, Shashikant Kulkarni, Subha Madhavan, on behalf of the ClinGen Somatic Cancer Working Group

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CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies by Justin H Hwang, Rand Arafeh, Ji-Heui Seo, Sylvan C Baca, Megan Ludwig, Taylor E Arnoff, Lydia Sawyer, Camden Richter, Sydney Tape, Hannah E Bergom, Sean McSweeney, Jonathan P Rennhack, Sarah A Klingenberg, Alexander TM Cheung, Jason Kwon, Jonathan So, Steven Kregel, Eliezer M Van Allen, Justin M Drake, Matthew L Freedman, William C Hahn

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The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma by Yuji Mishima, Bruno Paiva, Jiantao Shi, Jihye Park, Salomon Manier, Satoshi Takagi, Mira Massoud, Adriana Perilla-Glen, Yosra Aljawai, Daisy Huynh, Aldo M. Roccaro, Antonio Sacco, Marzia Capelletti, Alexandre Detappe, Diego Alignani, Kenneth C. Anderson, Nikhil C. Munshi, Felipe Prosper, Jens G. Lohr, Gavin Ha, Samuel S. Freeman, Eliezer M. Van Allen, Viktor A. Adalsteinsson, Franziska Michor, Jesus F. San Miguel, Irene M. Ghobrial

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Ten challenges and opportunities in computational immuno-oncology by Hong Zhang, Riyue Bao, Song Liu, Mark Long, Sacha Gnjatic, Yi Xing, Elana J Fertig, Alan Hutson, Martin Morgan, Eytan Ruppin, Anant Madabhushi, Natalie Vokes, Daoud Meerzaman, Edgar Gonzalez-Kozlova, Vanessa D Jonsson, Eliezer M Van Allen, Spencer R Rosario, Jennifer Altreuter, Himangi Marathe, Jill S Barnholtz-Sloan, Lyndsay Harris, Qingrong Chen, James Dignam, Andrew J Gentles, Erika Kim, David Van Valen

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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma by Marios Giannakis, Xinmeng Jasmine Mu, Sachet A. Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A. Nowak, Michael S. Lawrence, Edward L. Giovannucci, Andrew T. Chan, Kimmie Ng, Jeffrey A. Meyerhardt, Eliezer M. Van Allen, Gad Getz, Stacey B. Gabriel, Eric S. Lander, Catherine J. Wu, Charles S. Fuchs, Shuji Ogino, Levi A. Garraway

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CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer by Justin H. Hwang, Ji-Heui Seo, Michael L. Beshiri, Stephanie Wankowicz, David Liu, Alexander Cheung, Ji Li, Xintao Qiu, Andrew L. Hong, Ginevra Botta, Lior Golumb, Camden Richter, Jonathan So, Gabriel J. Sandoval, Andrew O. Giacomelli, Seav Huong Ly, Celine Han, Chao Dai, Hubert Pakula, Anjali Sheahan, Federica Piccioni, Ole Gjoerup, Massimo Loda, Adam G. Sowalsky, Leigh Ellis, Henry Long, David E. Root, Kathleen Kelly, Eliezer M. Van Allen, Matthew L. Freedman, Atish D. Choudhury, William C. Hahn

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Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders by Jeffrey A Meyerhardt, Sunil Kumar, Jessica A Zerillo, Aparna Parikh, James M Cleary, Scott Rodig, Benjamin Schlechter, Kimmie Ng, Stephanie K Dougan, Nora Horick, Glenn J Hanna, Andrew L Coveler, Anuj K Patel, Nadine J McCleary, Douglas A Rubinson, Jeffrey W Clark, Kent Mouw, Kathleen Pfaff, Thomas A Abrams, Matthew B Yurgelun, Eliezer M Van Allen, S Jennifer Wang, Leah H Biller, Harshabad Singh, Emma L Welsh, Brandon M Huffman, Lestat R Ali, Megan T Hoffman, Katherine A Metayer, Shayla Murray, Alexandra Bird, Jennifer A Chan, Wolfram Goessling, Jeffrey S Wisch, Brendan Reardon, Robert J Mayer, Catherine Del Vecchio Fitz, Charlotte Kuperwasser

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Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma by Talal El Zarif, Karl Semaan, Marc Eid, Ji-Heui Seo, Simon Garinet, Matthew P. Davidsohn, Pranshu Sahgal, Brad Fortunato, John Canniff, Amin H. Nassar, Sarah Abou Alaiwi, Ziad Bakouny, Gitanjali Lakshminarayanan, Hunter Savignano, Kevin Lyons, Sayed Matar, Atef Ali, Eddy Saad, Renee Maria Saliby, Paulo Cordeiro, Ziwei Zhang, Nourhan El Ahmar, Yasmin Nabil Laimon, Chris Labaki, Valisha Shah, Dory Freeman, Jillian O’Toole, Gwo-Shu Mary Lee, Justin Hwang, Mark Pomerantz, Sabina Signoretti, Eliezer M. Van Allen, Wanling Xie, Jacob E. Berchuck, Srinivas R. Viswanathan, David A. Braun, Toni K. Choueiri, Matthew L. Freedman, Sylvan C. Baca

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