ATM Loss Confers Greater Sensitivity to ATR Inhibition than PARP Inhibition in Prostate Cancer by Rafiei, Shahrzad, Fitzpatrick, Kenyon, Liu, David, Cai, Mu-Yan, Elmarakeby, Haitham A, Park, Jihye, Ricker, Cora, Kochupurakkal, Bose S, Choudhury, Atish D, Hahn, William C, Balk, Steven P, Hwang, Justin H, Van Allen, Eliezer M, Mouw, Kent W

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

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Biologically informed deep neural network for prostate cancer discovery by 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.

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Systematic auditing is essential to debiasing machine learning in biology by Eid, Fatma-Elzahraa, Elmarakeby, Haitham A., Chan, Yujia Alina, Fornelos, Nadine, ElHefnawi, Mahmoud, Van Allen, Eliezer M., Heath, Lenwood S., Lage, Kasper

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A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to P... by Vinatzer, Boris A, Weisberg, Alexandra J, Monteil, Caroline L, Elmarakeby, Haitham A, Sheppard, Samuel K, Heath, Lenwood S

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Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis by Sieberts, Solveig K., Zhu, Fan, García-García, Javier, Stahl, Eli, Pratap, Abhishek, Pandey, Gaurav, Pappas, Dimitrios, Aguilar, Daniel, Anton, Bernat, Bonet, Jaume, Eksi, Ridvan, Fornés, Oriol, Guney, Emre, Li, Hongdong, Marín, Manuel Alejandro, Panwar, Bharat, Planas-Iglesias, Joan, Poglayen, Daniel, Cui, Jing, Falcao, Andre O., Suver, Christine, Hoff, Bruce, Balagurusamy, Venkat S. K., Dillenberger, Donna, Neto, Elias Chaibub, Norman, Thea, Aittokallio, Tero, Ammad-ud-din, Muhammad, Azencott, Chloe-Agathe, Bellón, Víctor, Boeva, Valentina, Bunte, Kerstin, Chheda, Himanshu, Cheng, Lu, Corander, Jukka, Dumontier, Michel, Goldenberg, Anna, Gopalacharyulu, Peddinti, Hajiloo, Mohsen, Hidru, Daniel, Jaiswal, Alok, Kaski, Samuel, Khalfaoui, Beyrem, Khan, Suleiman Ali, Kramer, Eric R., Marttinen, Pekka, Mezlini, Aziz M., Molparia, Bhuvan, Pirinen, Matti, Saarela, Janna, Samwald, Matthias, Stoven, Véronique, Tang, Hao, Tang, Jing, Torkamani, Ali, Vert, Jean-Phillipe, Wang, Bo, Wang, Tao, Wennerberg, Krister, Wineinger, Nathan E., Xiao, Guanghua, Xie, Yang, Yeung, Rae, Zhan, Xiaowei, Zhao, Cheng, Greenberg, Jeff, Kremer, Joel, Michaud, Kaleb, Barton, Anne, Coenen, Marieke, Mariette, Xavier, Miceli, Corinne, Shadick, Nancy, Weinblatt, Michael, de Vries, Niek, Tak, Paul P., Gerlag, Danielle, Huizinga, Tom W. J., Kurreeman, Fina, Allaart, Cornelia F., Louis Bridges Jr, S., Criswell, Lindsey, Moreland, Larry, Klareskog, Lars, Saevarsdottir, Saedis, Padyukov, Leonid, Gregersen, Peter K., Friend, Stephen, Plenge, Robert, Stolovitzky, Gustavo, Oliva, Baldo, Guan, Yuanfang, Mangravite, Lara M.

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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen by Menden, Michael P., Wang, Dennis, Mason, Mike J., Szalai, Bence, Bulusu, Krishna C., Guan, Yuanfang, Yu, Thomas, Kang, Jaewoo, Jeon, Minji, Wolfinger, Russ, Nguyen, Tin, Zaslavskiy, Mikhail, Jang, In Sock, Ghazoui, Zara, Ahsen, Mehmet Eren, Vogel, Robert, Neto, Elias Chaibub, Norman, Thea, Tang, Eric K. Y., Garnett, Mathew J., Veroli, Giovanni Y. Di, Fawell, Stephen, Stolovitzky, Gustavo, Guinney, Justin, Dry, Jonathan R., Saez-Rodriguez, Julio

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Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma by Tarantino, Giuseppe, Ricker, Cora A, Wang, Annette, Ge, William, Aprati, Tyler J, Huang, Amy Y, Madha, Shariq, Chen, Jiajia, Shi, Yingxiao, Glettig, Marc, Feng, Catherine H, Frederick, Dennie T, Freeman, Samuel, Holovatska, Marta M, Manos, Michael P, Zimmer, Lisa, Rösch, Alexander, Zaremba, Anne, Livingstone, Elisabeth, Jameson, Jacob C, Saghafian, Soroush, Lee, Andrew, Zhao, Karena, Morris, Luc G T, Reardon, Brendan, Park, Jihye, Elmarakeby, Haitham A, Schilling, Bastian, Giobbie-Hurder, Anita, Vokes, Natalie I, Buchbinder, Elizabeth I, Flaherty, Keith T, Haq, Rizwan, Wu, Catherine J, Boland, Genevieve M, Hodi, F Stephen, Van Allen, Eliezer M, Schadendorf, Dirk, Liu, David

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Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species membership, associated outbreaks, and transmission chains by Weisberg, Alexandra J, Elmarakeby, Haitham A, Heath, Lenwood S, Vinatzer, Boris A

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Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis by Sieberts, Solveig K., Zhu, Fan, García-García, Javier, Stahl, Eli, Pratap, Abhishek, Pandey, Gaurav, Pappas, Dimitrios, Aguilar, Daniel, Anton, Bernat, Bonet, Jaume, Eksi, Ridvan, Fornés, Oriol, Guney, Emre, Li, Hongdong, Marín, Manuel Alejandro, Panwar, Bharat, Planas-Iglesias, Joan, Poglayen, Daniel, Cui, Jing, Falcao, Andre O., Suver, Christine, Hoff, Bruce, Balagurusamy, Venkat S. K., Dillenberger, Donna, Neto, Elias Chaibub, Norman, Thea, Aittokallio, Tero, Ammad-ud-din, Muhammad, Azencott, Chloe-Agathe, Bellón, Víctor, Boeva, Valentina, Bunte, Kerstin, Chheda, Himanshu, Cheng, Lu, Corander, Jukka, Dumontier, Michel, Goldenberg, Anna, Gopalacharyulu, Peddinti, Hajiloo, Mohsen, Hidru, Daniel, Jaiswal, Alok, Kaski, Samuel, Khalfaoui, Beyrem, Khan, Suleiman Ali, Kramer, Eric R., Marttinen, Pekka, Mezlini, Aziz M., Molparia, Bhuvan, Pirinen, Matti, Saarela, Janna, Samwald, Matthias, Stoven, Véronique, Tang, Hao, Tang, Jing, Torkamani, Ali, Vert, Jean-Phillipe, Wang, Bo, Wang, Tao, Wennerberg, Krister, Wineinger, Nathan E., Xiao, Guanghua, Xie, Yang, Yeung, Rae, Zhan, Xiaowei, Zhao, Cheng, Greenberg, Jeff, Kremer, Joel, Michaud, Kaleb, Barton, Anne, Coenen, Marieke, Mariette, Xavier, Miceli, Corinne, Shadick, Nancy, Weinblatt, Michael, de Vries, Niek, Tak, Paul P., Gerlag, Danielle, Huizinga, Tom W. J., Kurreeman, Fina, Allaart, Cornelia F., Bridges Jr, S. Louis, Criswell, Lindsey, Moreland, Larry, Klareskog, Lars, Saevarsdottir, Saedis, Padyukov, Leonid, Gregersen, Peter K., Friend, Stephen, Plenge, Robert, Stolovitzky, Gustavo, Oliva, Baldo, Guan, Yuanfang, Mangravite, Lara M.

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Abstract 2062: Delta prognosis: A novel clinical outcome based on automated analysis of unstructured cancer EHR data by Kehl, Kenneth L., Elmarakeby, Haitham A., Hassett, Michael J., Van Allen, Eliezer M., Schrag, Deb

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Abstract 2063: Deep natural language processing for automated ascertainment of cancer outcomes from clinician progress notes by Kehl, Kenneth L., Xu, Wenxin, Elmarakeby, Haitham A., Hassett, Michael J., Nyman, Jackson, Johnson, Bruce E., Van Allen, Eliezer M., Schrag, Deb

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Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset by Kehl, Kenneth L., Xu, Wenxin, Gusev, Alexander, Bakouny, Ziad, Choueiri, Toni K., Riaz, Irbaz Bin, Elmarakeby, Haitham, Van Allen, Eliezer M., Schrag, Deborah

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Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine by Conway, Jake R, Kofman, Eric, Mo, Shirley S, Elmarakeby, Haitham, Van Allen, Eliezer

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A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis by Ni, Ying, Aghamirzaie, Delasa, Elmarakeby, Haitham, Collakova, Eva, Li, Song, Grene, Ruth, Heath, Lenwood S

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Abstract 5859: Genomic correlates of response to immune checkpoint inhibitors in advanced head and neck squamous cell carcinoma by Patel, Nisarg A., Vokes, Natalie I., Elmarakeby, Haitham, Hanna, Glenn J., Van Allen, Eliezer M.

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Potential targets of VIVIPAROUS1/ABI3‐LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos by Schneider, Andrew, Aghamirzaie, Delasa, Elmarakeby, Haitham, Poudel, Arati N, Koo, Abraham J, Heath, Lenwood S, Grene, Ruth, Collakova, Eva

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Abstract 1637: Biologically informed deep neural network for genomic discovery and clinical classification in prostate cancer by Elmarakeby, Haitham, Liu, David, Aldubayan, Saud H., Allen, Eliezer M. Van

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Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma by AlDubayan, Saud H, Conway, Jake R, Camp, Sabrina Y, Witkowski, Leora, Kofman, Eric, Reardon, Brendan, Han, Seunghun, Moore, Nicholas, Elmarakeby, Haitham, Salari, Keyan, Choudhry, Hani, Al-Rubaish, Abdullah M, Al-Sulaiman, Abdulsalam A, Al-Ali, Amein K, Taylor-Weiner, Amaro, Van Allen, Eliezer M

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Abstract CT050: Expansion cohort of Phase I study of oral sapacitabine and oral seliciclib in patients with metastatic breast cancer and BRCA1/2 mutations by Keenan, Tanya, Liu, David, Elmarakeby, Haitham, Stover, Daniel, Kochupurakkal, Bose, Tracy, Adam, Danielczyk, Elaine, Anderson, Leilani, Andrews, Chelsea, Reardon, Brendan, Overmoyer, Beth, Winer, Eric, Zheleva, Daniella, Chiao, Judy, Blake, David, Allen, Eliezer Van, Shapiro, Geoffrey I., Tolaney, Sara

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