Ohcanbohtosat - Niknafs, Noushin

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing Dahkki Niknafs, Noushin, Beleva-Guthrie, Violeta, Naiman, Daniel Q., Karchin, Rachel

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Biomechanical Factors in Planning of Periacetabular Osteotomy Dahkki Niknafs, Noushin, Murphy, Ryan J., Armiger, Robert S., Lepistö, Jyri, Armand, Mehran

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Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors Dahkki Zheng, Lily, Niknafs, Noushin, Wood, Laura D, Karchin, Rachel, Scharpf, Robert B

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Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure Dahkki Tokheim, Collin, Bhattacharya, Rohit, Niknafs, Noushin, Gygax, Derek M., Kim, Rick, Ryan, Michael, Masica, David, Karchin, Rachel

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MuPIT Interactive: Webserver for mapping variant positions to annotated, interactive 3D structures Dahkki Niknafs, Noushin, Kim, Dewey, Kim, Ryang Guk, Diekhans, Mark, Ryan, Michael, Stenson, Peter D., Cooper, David N., Karchin, Rachel

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CRAVAT: cancer-related analysis of variants toolkit Dahkki Douville, Christopher, Carter, Hannah, Kim, Rick, Niknafs, Noushin, Diekhans, Mark, Stenson, Peter D., Cooper, David N., Ryan, Michael, Karchin, Rachel

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Characterization of genetic subclonal evolution in pancreatic cancer mouse models Dahkki Niknafs, Noushin, Zhong, Yi, Moral, John Alec, Zhang, Lance, Shao, Melody Xiaoshan, Lo, April, Makohon-Moore, Alvin, Iacobuzio-Donahue, Christine A., Karchin, Rachel

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A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing Dahkki Chen, Yun-Ching, Douville, Christopher, Wang, Cheng, Niknafs, Noushin, Yeo, Grace, Beleva-Guthrie, Violeta, Carter, Hannah, Stenson, Peter D., Cooper, David N., Li, Biao, Mooney, Sean, Karchin, Rachel

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Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing Dahkki Hoang, Margaret L., Chen, Chung-Hsin, Sidorenko, Viktoriya S., He, Jian, Dickman, Kathleen G., Yun, Byeong Hwa, Moriya, Masaaki, Niknafs, Noushin, Douville, Christopher, Karchin, Rachel, Turesky, Robert J., Pu, Yeong-Shiau, Vogelstein, Bert, Papadopoulos, Nickolas, Grollman, Arthur P., Kinzler, Kenneth W., Rosenquist, Thomas A.

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A machine learning approach for somatic mutation discovery Dahkki Wood, Derrick E., White, James R., Georgiadis, Andrew, Van Emburgh, Beth, Parpart-Li, Sonya, Mitchell, Jason, Anagnostou, Valsamo, Niknafs, Noushin, Karchin, Rachel, Papp, Eniko, McCord, Christine, LoVerso, Peter, Riley, David, Diaz, Luis A., Jones, Siân, Sausen, Mark, Velculescu, Victor E., Angiuoli, Samuel V.

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WHOLE-GENOME SEQUENCING OF SALIVARY GLAND ADENOID CYSTIC CARCINOMA Dahkki Rettig, Eleni M, Talbot, C Conover, Sausen, Mark, Jones, Sian, Bishop, Justin A, Wood, Laura D, Tokheim, Collin, Niknafs, Noushin, Karchin, Rachel, Fertig, Elana J, Wheelan, Sarah J, Marchionni, Luigi, Considine, Michael, Ling, Shizhang, Fakhry, Carole, Papadopoulos, Nickolas, Kinzler, Kenneth W, Vogelstein, Bert, Ha, Patrick K, Agrawal, Nishant

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Epigenetic Therapy Ties MYC Depletion to Reversing Immune Evasion and Treating Lung Cancer Dahkki Topper, Michael J., Vaz, Michelle, Chiappinelli, Katherine B., DeStefano Shields, Christina E., Niknafs, Noushin, Yen, Ray-Whay Chiu, Wenzel, Alyssa, Hicks, Jessica, Ballew, Matthew, Stone, Meredith, Tran, Phuoc T., Zahnow, Cynthia A., Hellmann, Matthew D., Anagnostou, Valsamo, Strissel, Pamela L., Strick, Reiner, Velculescu, Victor E., Baylin, Stephen B.

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Intraductal Papillary Mucinous Neoplasms Arise from Multiple Independent Clones, Each With Distinct Mutations Dahkki Fischer, Catherine G., Guthrie, Violeta Beleva, Braxton, Alicia M., Zheng, Lily, Wang, Pei, Song, Qianqian, Griffin, James F., Chianchiano, Peter E., Hosoda, Waki, Niknafs, Noushin, Springer, Simeon, Molin, Marco Dal, Masica, David, Scharpf, Robert B., Thompson, Elizabeth D., He, Jin, Wolfgang, Christopher L., Hruban, Ralph H., Roberts, Nicholas J., Lennon, Anne Marie, Jiao, Yuchen, Karchin, Rachel, Wood, Laura D.

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Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma Dahkki Anagnostou, Valsamo, Bruhm, Daniel C., Niknafs, Noushin, White, James R., Shao, Xiaoshan M., Sidhom, John William, Stein, Julie, Tsai, Hua-Ling, Wang, Hao, Belcaid, Zineb, Murray, Joseph, Balan, Archana, Ferreira, Leonardo, Ross-Macdonald, Petra, Wind-Rotolo, Megan, Baras, Alexander S., Taube, Janis, Karchin, Rachel, Scharpf, Robert B., Grasso, Catherine, Ribas, Antoni, Pardoll, Drew M., Topalian, Suzanne L., Velculescu, Victor E.

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High grade serous ovarian carcinomas originate in the fallopian tube Dahkki Labidi-Galy, S. Intidhar, Papp, Eniko, Hallberg, Dorothy, Niknafs, Noushin, Adleff, Vilmos, Noe, Michael, Bhattacharya, Rohit, Novak, Marian, Jones, Siân, Phallen, Jillian, Hruban, Carolyn A., Hirsch, Michelle S., Lin, Douglas I., Schwartz, Lauren, Maire, Cecile L., Tille, Jean-Christophe, Bowden, Michaela, Ayhan, Ayse, Wood, Laura D., Scharpf, Robert B., Kurman, Robert, Wang, Tian-Li, Shih, Ie-Ming, Karchin, Rachel, Drapkin, Ronny, Velculescu, Victor E.

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Peripheral blood immune cell dynamics reflect antitumor immune responses and predict clinical response to immunotherapy Dahkki Hwang, Michael, Canzoniero, Jenna Vanliere, Rosner, Samuel, Zhang, Guangfan, White, James R, Belcaid, Zineb, Cherry, Christopher, Balan, Archana, Pereira, Gavin, Curry, Alexandria, Niknafs, Noushin, Zhang, Jiajia, Smith, Kellie N, Sivapalan, Lavanya, Chaft, Jamie E, Reuss, Joshua E, Marrone, Kristen, Murray, Joseph C, Li, Qing Kay, Lam, Vincent, Levy, Benjamin P, Hann, Christine, Velculescu, Victor E, Brahmer, Julie R, Forde, Patrick M, Seiwert, Tanguy, Anagnostou, Valsamo

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Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer Dahkki Anagnostou, Valsamo, Smith, Kellie N., Forde, Patrick M., Niknafs, Noushin, Bhattacharya, Rohit, White, James, Zhang, Theresa, Adleff, Vilmos, Phallen, Jillian, Wali, Neha, Hruban, Carolyn, Guthrie, Violeta B., Rodgers, Kristen, Naidoo, Jarushka, Kang, Hyunseok, Sharfman, William, Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Gabrielson, Edward, Brock, Malcolm V., Zahnow, Cynthia A., Baylin, Stephen B., Scharpf, Rob, Brahmer, Julie R., Karchin, Rachel, Pardoll, Drew M., Velculescu, Victor E.

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Ipilimumab plus nivolumab and DNA-repair defects in AR-V7-expressing metastatic prostate cancer Dahkki Boudadi, Karim, Suzman, Daniel L., Anagnostou, Valsamo, Fu, Wei, Luber, Brandon, Wang, Hao, Niknafs, Noushin, White, James R., Silberstein, John L., Sullivan, Rana, Dowling, Donna, Harb, Rana, Nirschl, Thomas R., Veeneman, Brendan A., Tomlins, Scott A., Wang, Yipeng, Jendrisak, Adam, Graf, Ryon P., Dittamore, Ryan, Carducci, Michael A., Eisenberger, Mario A., Haffner, Michael C., Meeker, Alan K., Eshleman, James R., Luo, Jun, Velculescu, Victor E., Drake, Charles G., Antonarakis, Emmanuel S.

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Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial Dahkki Forde, Patrick M., Anagnostou, Valsamo, Sun, Zhuoxin, Dahlberg, Suzanne E., Kindler, Hedy L., Niknafs, Noushin, Purcell, Thomas, Santana-Davila, Rafael, Dudek, Arkadiusz Z., Borghaei, Hossein, Lanis, Mara, Belcaid, Zineb, Smith, Kellie N., Balan, Archana, White, James R., Cherry, Christopher, Ashok Sivakumar, I. K., Shao, Xiaoshan M., Chan, Hok Yee, Singh, Dipika, Thapa, Sampriti, Illei, Peter B., Pardoll, Drew M., Karchin, Rachel, Velculescu, Victor E., Brahmer, Julie R., Ramalingam, Suresh S.

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The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer Dahkki Bertotti, Andrea, Papp, Eniko, Jones, Siân, Adleff, Vilmos, Anagnostou, Valsamo, Lupo, Barbara, Sausen, Mark, Phallen, Jillian, Hruban, Carolyn A., Tokheim, Collin, Niknafs, Noushin, Nesselbush, Monica, Lytle, Karli, Sassi, Francesco, Cottino, Francesca, Migliardi, Giorgia, Zanella, Eugenia R., Ribero, Dario, Russolillo, Nadia, Mellano, Alfredo, Muratore, Andrea, Paraluppi, Gianluca, Salizzoni, Mauro, Marsoni, Silvia, Kragh, Michael, Lantto, Johan, Cassingena, Andrea, Li, Qing Kay, Karchin, Rachel, Scharpf, Robert, Sartore-Bianchi, Andrea, Siena, Salvatore, Diaz, Luis A., Trusolino, Livio, Velculescu, Victor E.

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