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Coté, Allison, O'Farrell, Aoife, Dardani, Ian, Dunagin, Margaret, Coté, Chris, Wan, Yihan, Bayatpour, Sareh, Drexler, Heather L, Alexander, Katherine A, Chen, Fei, Wassie, Asmamaw T, Patel, Rohan, Pham, Kenneth, Boyden, Edward S, Berger, Shelly, Phillips-Cremins, Jennifer, Churchman, L Stirling, Raj, Arjun (April 2024) Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife, 12. ISSN 2050-084X (Public Dataset)

Alexander, Katherine A, Yu, Ruofan, Skuli, Nicolas, Coffey, Nathan J, Nguyen, Son, Faunce, Christine, Huang, Hua, Dardani, Ian P, Good, Austin L, Lim, Joan, Li, Catherine, Biddle, Nicholas, Joyce, Eric F, Raj, Arjun, Lee, Daniel, Keith, Brian, Simon, M Celeste, Berger, Shelley L (September 2023) Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer. bioRxiv. (Submitted)

Yu, Ruofan, Roseman, Shelby, Siegenfeld, Allison P, Nguyen, Son C, Joyce, Eric F, Liau, Brian B, Krantz, Ian D, Alexander, Katherine A, Berger, Shelley L (July 2023) CTCF/cohesin organize the ground state of chromatin-nuclear speckle association. bioRxiv. (Submitted)

Collins, Sierra M, Alexander, Katherine A, Lundh, Stefan, Dimitri, Alexander J, Zhang, Zhen, Good, Charly R, Fraietta, Joseph A, Berger, Shelley L (July 2023) TOX2 coordinates with TET2 to positively regulate central memory differentiation in human CAR T cells. Science Advances, 9 (29). ISSN 2375-2548

Rajurkar, Mihir, Parikh, Aparna R, Solovyov, Alexander, You, Eunae, Kulkarni, Anupriya S, Chu, Chong, Xu, Katherine H, Jaicks, Christopher, Taylor, Martin S, Wu, Connie, Alexander, Katherine A, Good, Charly R, Szabolcs, Annamaria, Gerstberger, Stefanie, Tran, Antuan V, Xu, Nova, Ebright, Richard Y, Van Seventer, Emily E, Vo, Kevin D, Tai, Eric C, Lu, Chenyue, Joseph-Chazan, Jasmin, Raabe, Michael J, Nieman, Linda T, Desai, Niyati, Arora, Kshitij S, Ligorio, Matteo, Thapar, Vishal, Cohen, Limor, Garden, Padric M, Senussi, Yasmeen, Zheng, Hui, Allen, Jill N, Blaszkowsky, Lawrence S, Clark, Jeffrey W, Goyal, Lipika, Wo, Jennifer Y, Ryan, David P, Corcoran, Ryan B, Deshpande, Vikram, Rivera, Miguel N, Aryee, Martin J, Hong, Theodore S, Berger, Shelley L, Walt, David R, Burns, Kathleen H, Park, Peter J, Greenbaum, Benjamin D, Ting, David T (June 2022) Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discovery, 12 (6). pp. 1462-1481. ISSN 2159-8274

Good, Charly R, Aznar, M Angela, Kuramitsu, Shunichiro, Samareh, Parisa, Agarwal, Sangya, Donahue, Greg, Ishiyama, Kenichi, Wellhausen, Nils, Rennels, Austin K, Ma, Yujie, Tian, Lifeng, Guedan, Sonia, Alexander, Katherine A, Zhang, Zhen, Rommel, Philipp C, Singh, Nathan, Glastad, Karl M, Richardson, Max W, Watanabe, Keisuke, Tanyi, Janos L, O’Hara, Mark H, Ruella, Marco, Lacey, Simon F, Moon, Edmund K, Schuster, Stephen J, Albelda, Steven M, Lanier, Lewis L, Young, Regina M, Berger, Shelley L, June, Carl H (December 2021) An NK-like CAR T cell transition in CAR T cell dysfunction. Cell, 184 (25). 6081-6100.e26. ISSN 0092-8674

Alexander, Katherine A, Coté, Allison, Nguyen, Son C, Zhang, Liguo, Gholamalamdari, Omid, Agudelo-Garcia, Paula, Lin-Shiao, Enrique, Tanim, KMA, Lim, Joan, Biddle, Nicolas, Dunagin, Margaret C, Good, Charly R, Mendoza, Mariel R, Little, Shawn C, Belmont, Andrew, Joyce, Eric F, Raj, Arjun, Berger, Shelley L (April 2021) p53 mediates target gene association with nuclear speckles for amplified RNA expression. Molecular Cell, 81 (8). 1666-1681.e6. ISSN 1097-2765

Khan, Omar, Giles, Josephine R, McDonald, Sierra, Manne, Sasikanth, Ngiow, Shin Foong, Patel, Kunal P, Werner, Michael T, Huang, Alexander C, Alexander, Katherine A, Wu, Jennifer E, Attanasio, John, Yan, Patrick, George, Sangeeth M, Bengsch, Bertram, Staupe, Ryan P, Donahue, Greg, Xu, Wei, Amaravadi, Ravi K, Xu, Xiaowei, Karakousis, Giorgos C, Mitchell, Tara C, Schuchter, Lynn M, Kaye, Jonathan, Berger, Shelley L, Wherry, E John (June 2019) TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature, 571 (7764). pp. 211-218. ISSN 0028-0836

Lin-Shiao, Enrique, Lan, Yemin, Welzenbach, Julia, Alexander, Katherine A, Zhang, Zhen, Knapp, Michael, Mangold, Elisabeth, Sammons, Morgan, Ludwig, Kerstin U, Berger, Shelley L (May 2019) p63 establishes epithelial enhancers at critical craniofacial development genes. Science Advances, 5 (5). ISSN 2375-2548

Catizone, Allison N, Good, Charly Ryan, Alexander, Katherine A, Berger, Shelley L, Sammons, Morgan A (April 2019) Comparison of genotoxic versus nongenotoxic stabilization of p53 provides insight into parallel stress-responsive transcriptional networks. Cell Cycle, 18 (8). pp. 809-823. ISSN 1538-4101

Alexander, Katherine A, García-García, María J (January 2019) Imprinted gene expression at the Dlk1-Dio3 cluster is controlled by both maternal and paternal IG-DMRs in a tissue-specific fashion. bioRxiv. (Submitted)

Fraietta, Joseph A, Nobles, Christopher L, Sammons, Morgan A, Lundh, Stefan, Carty, Shannon A, Reich, Tyler J, Cogdill, Alexandria P, Morrissette, Jennifer JD, DeNizio, Jamie E, Reddy, Shantan, Hwang, Young, Gohil, Mercy, Kulikovskaya, Irina, Nazimuddin, Farzana, Gupta, Minnal, Chen, Fang, Everett, John K, Alexander, Katherine A, Lin-Shiao, Enrique, Gee, Marvin H, Liu, Xiaojun, Young, Regina M, Ambrose, David, Wang, Yan, Xu, Jun, Jordan, Martha S, Marcucci, Katherine T, Levine, Bruce L, Garcia, K Christopher, Zhao, Yangbing, Kalos, Michael, Porter, David L, Kohli, Rahul M, Lacey, Simon F, Berger, Shelley L, Bushman, Frederic D, June, Carl H, Melenhorst, J Joseph (June 2018) Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature, 558 (7709). pp. 307-312. ISSN 0028-0836

Guo, Yu, Alexander, Katherine, Clark, Andrew G, Grimson, Andrew, Yu, Haiyuan (November 2016) Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. RNA: A publication of the RNA Society, 22 (11). pp. 1663-1672. ISSN 1355-8382

Murphy, Kristin E, Shylo, Natalia A, Alexander, Katherine A, Churchill, Angela J, Copperman, Cecilia, García-García, María J (September 2016) The Transcriptional Repressive Activity of KRAB Zinc Finger Proteins Does Not Correlate with Their Ability to Recruit TRIM28. PLoS ONE, 11 (9). e0163555-e0163555. ISSN 1932-6203

Alexander, Katherine A, Wang, Xu, Shibata, Maho, Clark, Andrew G, García-García, María J (November 2015) TRIM28 Controls Genomic Imprinting through Distinct Mechanisms during and after Early Genome-wide Reprogramming. Cell Reports, 13 (6). pp. 1194-1205. ISSN 2211-1247