Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings von Schubert, Benjamin, Maddamsetti, Rohan, Nyman, Jackson, Farhat, Maha R., Marks, Debora S.

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3-Aminobenzamide Blocks MAMP-Induced Callose Deposition Independently of Its Poly(ADPribosyl)ation Inhibiting Activity von Keppler, Brian D, Song, Junqi, Nyman, Jackson, Voigt, Christian A, Bent, Andrew F

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Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1−CD8+ Tumor-Infiltrating T Cells von Kurtulus, Sema, Madi, Asaf, Escobar, Giulia, Klapholz, Max, Nyman, Jackson, Christian, Elena, Pawlak, Mathias, Dionne, Danielle, Xia, Junrong, Rozenblatt-Rosen, Orit, Kuchroo, Vijay K., Regev, Aviv, Anderson, Ana C.

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Induction and transcriptional regulation of the co-inhibitory gene module in T cells von Chihara, Norio, Madi, Asaf, Kondo, Takaaki, Zhang, Huiyuan, Acharya, Nandini, Singer, Meromit, Nyman, Jackson, Marjanovic, Nemanja D., Kowalczyk, Monika S., Wang, Chao, Kurtulus, Sema, Law, Travis, Etminan, Yasaman, Nevin, James, Buckley, Christopher D., Burkett, Patrick R., Buenrostro, Jason D., Rozenblatt-Rosen, Orit, Anderson, Ana C., Regev, Aviv, Kuchroo, Vijay K.

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The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, Kuchroo, Vijay K.

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Spatially aware deep learning for clear cell renal cell carcinoma characterization and discovery von Nyman, Jackson

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A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells von Singer, Meromit, Wang, Chao, Cong, Le, Marjanovic, Nemanja D., Kowalczyk, Monika S., Zhang, Huiyuan, Nyman, Jackson, Sakuishi, Kaori, Kurtulus, Sema, Gennert, David, Xia, Junrong, Kwon, John Y.H., Nevin, James, Herbst, Rebecca H., Yanai, Itai, Rozenblatt-Rosen, Orit, Kuchroo, Vijay K., Regev, Aviv, Anderson, Ana C.

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Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma von Tirosh, Itay, Venteicher, Andrew S., Hebert, Christine, Escalante, Leah E., Patel, Anoop P., Yizhak, Keren, Fisher, Jonathan M., Rodman, Christopher, Mount, Christopher, Filbin, Mariella G., Neftel, Cyril, Desai, Niyati, Nyman, Jackson, Izar, Benjamin, Luo, Christina C., Francis, Joshua M., Patel, Aanand A., Onozato, Maristela L., Riggi, Nicolo, Livak, Kenneth J., Gennert, Dave, Satija, Rahul, Nahed, Brian V., Curry, William T., Martuza, Robert L., Mylvaganam, Ravindra, Iafrate, A. John, Frosch, Matthew P., Golub, Todd R., Rivera, Miguel N., Getz, Gad, Rozenblatt-Rosen, Orit, Cahill, Daniel P., Monje, Michelle, Bernstein, Bradley E., Louis, David N., Regev, Aviv, Suvà, Mario L.

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Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology von Rosenthal, Jacob, Carelli, Ryan, Omar, Mohamed, Brundage, David, Halbert, Ella, Nyman, Jackson, Hari, Surya N, Van Allen, Eliezer M, Marchionni, Luigi, Umeton, Renato, Loda, Massimo

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Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma von Bakouny, Ziad, Braun, David A., Shukla, Sachet A., Pan, Wenting, Gao, Xin, Hou, Yue, Flaifel, Abdallah, Tang, Stephen, Bosma-Moody, Alice, He, Meng Xiao, Vokes, Natalie, Nyman, Jackson, Xie, Wanling, Nassar, Amin H., Abou Alaiwi, Sarah, Flippot, Ronan, Bouchard, Gabrielle, Steinharter, John A., Nuzzo, Pier Vitale, Ficial, Miriam, Sant’Angelo, Miriam, Forman, Juliet, Berchuck, Jacob E., Dudani, Shaan, Bi, Kevin, Park, Jihye, Camp, Sabrina, Sticco-Ivins, Maura, Hirsch, Laure, Baca, Sylvan C., Wind-Rotolo, Megan, Ross-Macdonald, Petra, Sun, Maxine, Lee, Gwo-Shu Mary, Chang, Steven L., Wei, Xiao X., McGregor, Bradley A., Harshman, Lauren C., Genovese, Giannicola, Ellis, Leigh, Pomerantz, Mark, Hirsch, Michelle S., Freedman, Matthew L., Atkins, Michael B., Wu, Catherine J., Ho, Thai H., Linehan, W. Marston, McDermott, David F., Heng, Daniel Y. C., Viswanathan, Srinivas R., Signoretti, Sabina, Van Allen, Eliezer M., Choueiri, Toni K.

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Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling von Pawlak, Mathias, DeTomaso, David, Schnell, Alexandra, Meyer Zu Horste, Gerd, Lee, Youjin, Nyman, Jackson, Dionne, Danielle, Regan, Brianna M L, Singh, Vasundhara, Delorey, Toni, Schramm, Markus A, Wang, Chao, Wallrapp, Antonia, Burkett, Patrick R, Riesenfeld, Samantha J, Anderson, Ana C, Regev, Aviv, Xavier, Ramnik J, Yosef, Nir, Kuchroo, Vijay K

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An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets von Zhang, Huiyuan, Madi, Asaf, Yosef, Nir, Chihara, Norio, Awasthi, Amit, Pot, Caroline, Lambden, Conner, Srivastava, Amitabh, Burkett, Patrick R., Nyman, Jackson, Christian, Elena, Etminan, Yasaman, Lee, Annika, Stroh, Helene, Xia, Junrong, Karwacz, Katarzyna, Thakore, Pratiksha I., Acharya, Nandini, Schnell, Alexandra, Wang, Chao, Apetoh, Lionel, Rozenblatt-Rosen, Orit, Anderson, Ana C., Regev, Aviv, Kuchroo, Vijay K.

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Abstract 2063: Deep natural language processing for automated ascertainment of cancer outcomes from clinician progress notes von 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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Characterization of the Cellular Origin and Oncogenic Mechanisms of Chromophobe Renal Cell Carcinoma (ChRCC) and Renal Oncocytic Neoplasms von Labaki, Chris, Al-Choueiry, Michel, Nyman, Jackson, Hou, Yue, Bi, Kevin, Zhang, Long, Hobeika, Charbel, Bakouny, Ziad, Priolo, Carmen, Khabibullin, Damir, Schindler, Nicholas, Fu, Jingxin, Camp, Sabrina, Maria Saliby, Renee, Saad, Eddy, Van Allen, Eliezer M, Shukla, Sachet, Henske, Elizabeth P, Choueiri, Toni, Braun, David

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Integrative clinical and molecular characterization of translocation renal cell carcinoma von Bakouny, Ziad, Sadagopan, Ananthan, Ravi, Praful, Metaferia, Nebiyou Y, Li, Jiao, AbuHammad, Shatha, Tang, Stephen, Denize, Thomas, Garner, Emma R, Gao, Xin, Braun, David A, Hirsch, Laure, Steinharter, John A, Bouchard, Gabrielle, Walton, Emily, West, Destiny, Labaki, Chris, Dudani, Shaan, Gan, Chun-Loo, Sethunath, Vidyalakshmi, Carvalho, Filipe L F, Imamovic, Alma, Ricker, Cora, Vokes, Natalie I, Nyman, Jackson, Berchuck, Jacob E, Park, Jihye, Hirsch, Michelle S, Haq, Rizwan, Mary Lee, Gwo-Shu, McGregor, Bradley A, Chang, Steven L, Feldman, Adam S, Wu, Catherine J, McDermott, David F, Heng, Daniel Y C, Signoretti, Sabina, Van Allen, Eliezer M, Choueiri, Toni K, Viswanathan, Srinivas R

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A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells von Singer, Meromit, Wang, Chao, Cong, Le, Marjanovic, Nemanja D., Kowalczyk, Monika S., Zhang, Huiyuan, Nyman, Jackson, Sakuishi, Kaori, Kurtulus, Sema, Gennert, David, Xia, Junrong, Kwon, John Y.H., Nevin, James, Herbst, Rebecca H., Yanai, Itai, Rozenblatt-Rosen, Orit, Kuchroo, Vijay K., Regev, Aviv, Anderson, Ana C.

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Single-cell RNA-seq identifies the neuropeptide NMU as a novel regulator of ILC2 function von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, Kuchroo, Vijay K.

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Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states von Nyman, Jackson, Denize, Thomas, Bakouny, Ziad, Labaki, Chris, Titchen, Breanna M, Bi, Kevin, Hari, Surya Narayanan, Rosenthal, Jacob, Mehta, Nicita, Jiang, Bowen, Sharma, Bijaya, Felt, Kristen, Umeton, Renato, Braun, David A, Rodig, Scott, Choueiri, Toni K, Signoretti, Sabina, Van Allen, Eliezer M

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964 Dynamic immune landscapes during melanoma progression reveal a role for endogenous opioids in driving T cell dysfunction von Mangani, Davide, Huang, Linglin, Singer, Meromit, Li, Ruitong, Barilla, Rocky, Escobar, Giulia, Tooley, Katherine, Hanning Cheng, Delaney, Conor, Newcomer, Kathleen, Nyman, Jackson, Marjanovic, Nemanja, Nevin, James, Rozenblatt-Rosen, Orit, Kuchroo, Vijay, Regev, Aviv, Anderson, Ana

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Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, Kuchroo, Vijay K.

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