Browse by CSHL Author

Paper

Bhattacharya, Swarnabh, Tie, Guodong, Singh, Pratik NP, Malagola, Ermanno, Eskiocak, Onur, He, Ruiyang, Kraiczy, Judith, Gu, Wei, Perlov, Yakov, Alici-Garipcan, Aybuke, Beyaz, Semir, Wang, Timothy C, Zhou, Qiao, Shivdasani, Ramesh A (April 2025) Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell. Cell Stem Cell. ISSN 1934-5909 (Public Dataset)

Bhattacharya, Swarnabh, Tei, Guodong, Singh, Pratik Narendra Pratap, Malagola, Ermanno, Eskiocak, Onur, He, Ruiyang, Kraiczy, Judith, Gu, Wei, Perlov, Yakov, Beyaz, Semir, Wang, Timothy Cragin, Zhou, Qiao, Shivdasani, Ramesh Arjun (February 2025) Niche-driven phenotypic plasticity and cis-regulatory dynamics of a revised model for intestinal secretory differentiation. bioRxiv. ISSN 2692-8205 (Public Dataset)

Barbi, Mali, Gowthaman, Divya, Katcher, Arielle, Gorman, Megan, Yueh, Brian, Nizam, Aaron, Chung, Charlie, Akyildiz, Erdogan Oguzhan, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (October 2024) Generation and Maintenance of Patient-Derived Endometrial Cancer Organoids. Bio-protocol, 14 (20). e5093. ISSN 2331-8325

Soula, Mariluz, Unlu, Gokhan, Welch, Rachel, Chudnovskiy, Aleksey, Uygur, Beste, Shah, Vyom, Alwaseem, Hanan, Bunk, Paul, Subramanyam, Vishvak, Yeh, Hsi-Wen, Khan, Artem, Heissel, Søren, Goodarzi, Hani, Victora, Gabriel D, Beyaz, Semir, Birsoy, Kıvanç (August 2024) Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer. Nature. ISSN 0028-0836 (Public Dataset)

Tierney, Braden T, Kim, JangKeun, Overbey, Eliah G, Ryon, Krista A, Foox, Jonathan, Sierra, Maria A, Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, J Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hirschberg, Jeremy, Qiu, Jake, Kleinman, Ashley S, Al-Ghalith, Gabriel A, MacKay, Matthew, Afshin, Evan E, Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Benjamin P, Beyaz, Semir, Venkateswaran, Kasthuri J, Wiseman, Kelly, Moreno, Juan, Boddicker, Andrew M, Zhao, Junhua, Lajoie, Bryan R, Scott, Ryan T, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George M, Mason, Christopher E (June 2024) Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nature Microbiology. ISSN 2058-5276

Eskiocak, Onur, Chowdhury, Saria, Shah, Vyom, Nnuji-John, Emmanuella, Chung, Charlie, Boyer, Jacob A, Harris, Alexander S, Habel, Jill, Sadelain, Michel, Beyaz, Semir, Amor, Corina (March 2024) Senolytic CAR T cells reverse aging-associated defects in intestinal regeneration and fitness. bioRxiv. (Submitted)

Gaudino, Stephen J, Singh, Ankita, Huang, Huakang, Padiadpu, Jyothi, Jean-Pierre, Makheni, Kempen, Cody, Bahadur, Tej, Shiomitsu, Kiyoshi, Blumberg, Richard, Shroyer, Kenneth R, Beyaz, Semir, Shulzhenko, Natalia, Morgun, Andrey, Kumar, Pawan (February 2024) Intestinal IL-22RA1 signaling regulates intrinsic and systemic lipid and glucose metabolism to alleviate obesity-associated disorders. Nature Communications, 15 (1). p. 1597. ISSN 2041-1723 (Public Dataset)

Karakaya, Eda, Oleinik, Natalia, Edwards, Jazlyn, Tomberlin, Jensen, Barker, Randy Bent, Berber, Burak, Ericsson, Maria, Alsudani, Habeeb, Ergul, Adviye, Beyaz, Semir, Lemasters, John J, Ogretmen, Besim, Albayram, Onder (February 2024) p17/C18-ceramide-mediated mitophagy is an endogenous neuroprotective response in preclinical and clinical brain injury. PNAS Nexus, 3 (2). ISSN 2752-6542

Rogava, Meri, Aprati, Tyler J, Chi, Wei-Yu, Melms, Johannes C, Hug, Clemens, Davis, Stephanie H, Earlie, Ethan M, Chung, Charlie, Deshmukh, Sachin K, Wu, Sharon, Sledge, George, Tang, Stephen, Ho, Patricia, Amin, Amit Dipak, Caprio, Lindsay, Gurjao, Carino, Tagore, Somnath, Ngo, Bryan, Lee, Michael J, Zanetti, Giorgia, Wang, Yiping, Chen, Sean, Ge, William, Melo, Luiza Martins Nascentes, Allies, Gabriele, Rösler, Jonas, Gibney, Goeffrey T, Schmitz, Oliver J, Sykes, Megan, Creusot, Rémi J, Tüting, Thomas, Schadendorf, Dirk, Röcken, Martin, Eigentler, Thomas K, Molotkov, Andrei, Mintz, Akiva, Bakhoum, Samuel F, Beyaz, Semir, Cantley, Lewis C, Sorger, Peter K, Meckelmann, Sven W, Tasdogan, Alpaslan, Liu, David, Laughney, Ashley M, Izar, Benjamin (January 2024) Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nature Cancer. ISSN 2662-1347 (Public Dataset)

Hu, Thomas, Allam, Mayar, Cai, Shuangyi, Henderson, Walter, Yueh, Brian, Garipcan, Aybuke, Ievlev, Anton V, Afkarian, Maryam, Beyaz, Semir, Coskun, Ahmet F (December 2023) Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology. Nature Communications, 14 (1). p. 8260. ISSN 2041-1723

Tierney, Braden T, Kim, JangKeun, Overbey, Eliah G, Ryon, Krista A, Foox, Jonathan, Sierra, Maria, Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hershberg, Jeremy, Qiu, Jake, Kleinman, Ashley, Al Ghalith, Gabe, MacKay, Matthew, Afshin, Evan E, Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Ben, Beyaz, Semir, Venkateswaran, Kasthuri J, Blease, Kelly, Moreno, Juan, Boddicker, Andrew, Zhao, Junhua, Lajoie, Bryan, Scott, Ryan T, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George, Mason, Christopher E (October 2023) Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation. (Submitted)

Lei, Pin-Ji, Pereira, Ethel R, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William W, Posada, Jessica M, Kumar, Ashwin S, Morita, Satoru, Menzel, Lutz, Chung, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (September 2023) Cancer cell plasticity and MHC-II-mediated immune tolerance promote breast cancer metastasis to lymph nodes. Journal of Experimental Medicine, 220 (9). e20221847. ISSN 0022-1007 (Public Dataset)

Zilbauer, Matthias, James, Kylie R, Kaur, Mandeep, Pott, Sebastian, Li, Zhixin, Burger, Albert, Thiagarajah, Jay R, Burclaff, Joseph, Jahnsen, Frode L, Perrone, Francesca, Ross, Alexander D, Matteoli, Gianluca, Stakenborg, Nathalie, Sujino, Tomohisa, Moor, Andreas, Bartolome-Casado, Raquel, Bækkevold, Espen S, Zhou, Ran, Xie, Bingqing, Lau, Ken S, Din, Shahida, Magness, Scott T, Yao, Qiuming, Beyaz, Semir, Arends, Mark, Denadai-Souza, Alexandre, Coburn, Lori A, Gaublomme, Jellert T, Baldock, Richard, Papatheodorou, Irene, Ordovas-Montanes, Jose, Boeckxstaens, Guy, Hupalowska, Anna, Teichmann, Sarah A, Regev, Aviv, Xavier, Ramnik J, Simmons, Alison, Snyder, Michael P, Wilson, Keith T, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium (September 2023) A Roadmap for the Human Gut Cell Atlas. Nature Reviews Gastroenterology & Hepatology, 20 (9). pp. 597-614. ISSN 1759-5045

Cable, Jennifer, Rathmell, Jeffrey C, Pearce, Erika L, Ho, Ping-Chih, Haigis, Marcia C, Mamedov, Murad R, Wu, Meng-Ju, Kaech, Susan M, Lynch, Lydia, Febbraio, Mark A, Bapat, Sagar P, Hong, Hanna S, Zou, Weiping, Belkaid, Yasmine, Sullivan, Zuri A, Keller, Andrea, Wculek, Stefanie K, Green, Douglas R, Postic, Catherine, Amit, Ido, Benitah, Salvador Aznar, Jones, Russell G, Reina-Campos, Miguel, Torres, Santiago Valle, Beyaz, Semir, Brennan, Donal, O'Neill, Luke AJ, Perry, Rachel J, Brenner, Dirk (May 2023) Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report. Annals of the New York Academy of Sciences, 1523 (1). pp. 38-50. ISSN 0077-8923

Mou, Haiwei, Eskiocak, Onur, Özler, Kadir A, Gorman, Megan, Yue, Junjiayu, Jin, Ying, Wang, Zhikai, Gao, Ya, Janowitz, Tobias, Meyer, Hannah V, Yu, Tianxiong, Wilkinson, John E, Kucukural, Alper, Ozata, Deniz M, Beyaz, Semir (January 2023) CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer. Journal of Pathology. ISSN 0022-3417

Katcher, Arielle, Yueh, Brian, Ozler, Kadir, Nizam, Aaron, Kredentser, Ariel, Chung, Charlie, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) Establishing patient-derived organoids from human endometrial cancer and normal endometrium. Frontiers in Endocrinology, 14. p. 1059228. ISSN 1664-2392

Burr, Ansen HP, Ji, Junyi, Ozler, Kadir, Mentrup, Heather L, Eskiocak, Onur, Yueh, Brian, Cumberland, Rachel, Menk, Ashley V, Rittenhouse, Natalie, Marshall, Chris W, Chiaranunt, Pailin, Zhang, Xiaoyi, Mullinax, Lauren, Overacre-Delgoffe, Abigail, Cooper, Vaughn S, Poholek, Amanda C, Delgoffe, Greg M, Mollen, Kevin P, Beyaz, Semir, Hand, Timothy W (2023) Excess Dietary Sugar Alters Colonocyte Metabolism and Impairs the Proliferative Response to Damage. Cellular and Molecular Gastroenterology and Hepatology, 16 (2). pp. 287-316. ISSN 2352-345X (Public Dataset)

Furlan, Alessandro, Corona, Alberto, Boyle, Sara, Sharma, Radhashree, Rubino, Rachel, Habel, Jill, Gablenz, Eva Carlotta, Giovanniello, Jacqueline, Beyaz, Semir, Janowitz, Tobias, Shea, Stephen David, Li, Bo (October 2022) Neurotensin neurons in the extended amygdala control dietary choice and energy homeostasis. Nature Neuroscience. ISSN 1097-6256

Chu, Timothy H, Khairallah, Camille, Shieh, Jason, Cho, Rhea, Qiu, Zhijuan, Zhang, Yue, Eskiocak, Onur, Thanassi, David G, Kaplan, Mark H, Beyaz, Semir, Yang, Vincent W, Bliska, James B, Sheridan, Brian S (May 2022) Correction: γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathogens, 18 (5). e1010586. ISSN 1553-7366

Dmitrieva-Posocco, Oxana, Wong, Andrea C, Lundgren, Patrick, Golos, Aleksandra M, Descamps, Hélène C, Dohnalová, Lenka, Cramer, Zvi, Tian, Yuhua, Yueh, Brian, Eskiocak, Onur, Egervari, Gabor, Lan, Yemin, Liu, Jinping, Fan, Jiaxin, Kim, Jihee, Madhu, Bhoomi, Schneider, Kai Markus, Khoziainova, Svetlana, Andreeva, Natalia, Wang, Qiaohong, Li, Ning, Furth, Emma E, Bailis, Will, Kelsen, Judith R, Hamilton, Kathryn E, Kaestner, Klaus H, Berger, Shelley L, Epstein, Jonathan A, Jain, Rajan, Li, Mingyao, Beyaz, Semir, Lengner, Christopher J, Katona, Bryson W, Grivennikov, Sergei I, Thaiss, Christoph A, Levy, Maayan (April 2022) β-Hydroxybutyrate suppresses colorectal cancer. Nature, 605 (7908). pp. 160-165. ISSN 0028-0836

Lin, Xun, Gaudino, Stephen J, Jang, Kyung Ku, Bahadur, Tej, Singh, Ankita, Banerjee, Anirban, Beaupre, Michael, Chu, Timothy, Wong, Hoi Tong, Kim, Chang-Kyung, Kempen, Cody, Axelrad, Jordan, Huang, Huakang, Khalid, Saba, Shah, Vyom, Eskiocak, Onur, Parks, Olivia B, Berisha, Artan, McAleer, Jeremy P, Good, Misty, Hoshino, Miko, Blumberg, Richard, Bialkowska, Agnieszka B, Gaffen, Sarah L, Kolls, Jay K, Yang, Vincent W, Beyaz, Semir, Cadwell, Ken, Kumar, Pawan (January 2022) IL-17RA-signaling in Lgr5+ intestinal stem cells induces expression of transcription factor ATOH1 to promote secretory cell lineage commitment. Immunity. ISSN 1074-7613

Hanasoge Somasundara, Amritha Varshini, Moss, Matthew A, Feigman, Mary J, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael F, Trousdell, Marygrace C, Vollbrecht, Macy, Li, Siran, Kendall, Jude, Beyaz, Semir, Wilkinson, John E, Dos Santos, Camila O (December 2021) Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell Reports, 37 (10). p. 110099. ISSN 2211-1247

Chu, Timothy H, Khairallah, Camille, Shieh, Jason, Cho, Rhea, Qiu, Zhijuan, Zhang, Yue, Eskiocak, Onur, Thanassi, David G, Kaplan, Mark H, Beyaz, Semir, Yang, Vincent W, Bliska, James B, Sheridan, Brian S (December 2021) γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathogens, 17 (12). e1010103. ISSN 1553-7374

Beyaz, Semir, Chung, Charlie, Mou, Haiwei, Bauer-Rowe, Khristian E, Xifaras, Michael E, Ergin, Ilgin, Dohnalova, Lenka, Biton, Moshe, Shekhar, Karthik, Eskiocak, Onur, Papciak, Katherine, Ozler, Kadir, Almeqdadi, Mohammad, Yueh, Brian, Fein, Miriam, Annamalai, Damodaran, Valle-Encinas, Eider, Erdemir, Aysegul, Dogum, Karoline, Shah, Vyom, Alici-Garipcan, Aybuke, Meyer, Hannah V, Özata, Deniz M, Elinav, Eran, Kucukural, Alper, Kumar, Pawan, McAleer, Jeremy P, Fox, James G, Thaiss, Christoph A, Regev, Aviv, Roper, Jatin, Orkin, Stuart H, Yilmaz, Ömer H (September 2021) Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. ISSN 1934-5909

Furlan, Alessandro, Corona, Alberto, Boyle, Sara, Sharma, Radhashree, Rubino, Rachel, Habel, Jill, Gablenz, Eva Carlotta, Giovanniello, Jacqueline, Beyaz, Semir, Janowitz, Tobias, Shea, Stephen D, Li, Bo (August 2021) Neurotensin neurons in the central extended amygdala control energy balance. bioRxiv. (Unpublished)

Beyaz, Semir, Mana, Miyeko D, Yilmaz, Ömer H (April 2021) High-fat diet activates a PPAR-δ program to enhance intestinal stem cell function. Cell Stem Cell, 28 (4). pp. 598-599. ISSN 1934-5909

Gaudino, S. J., Beaupre, M., Lin, X., Joshi, P., Rathi, S., McLaughlin, P. A., Kempen, C., Mehta, N., Eskiocak, O., Yueh, B., Blumberg, R. S., van der Velden, A. W. M., Shroyer, K. R., Bialkowska, A. B., Beyaz, S., Kumar, P. (October 2020) IL-22 receptor signaling in Paneth cells is critical for their maturation, microbiota colonization, Th17-related immune responses, and anti-Salmonella immunity. Mucosal Immunol. ISSN 1933-0219

Beyaz, S., Roper, J., Bauer-Rowe, K. E., Xifaras, M. E., Ergin, I., Dohnalova, L., Biton, M., Shekar, K., Mou, H. W., Eskiocak, O., Ozata, D., Papciak, K., Chung, C., Almeqdadi, M., Fein, M., Valle-Encinas, E., Erdemir, A., Dogum, K, Garipcan, A., Meyer, H., Fox, J.G., Elinav, E., Kucukural, A., Kumar, P., McAleer, J., Thaiss, C.A., Regev, A., Orkin, S. H., Yilmaz, O. H. (September 2020) Dietary suppression of MHC-II expression in intestinal stem cells enhances intestinal tumorigenesis. bioRxiv. (Unpublished)

Ordovas-Montanes, J., Beyaz, S., Rakoff-Nahoum, S., Shalek, A. K. (February 2020) Distribution and storage of inflammatory memory in barrier tissues. Nat Rev Immunol, 20 (5). pp. 308-320. ISSN 1474-1733

Luo, Y., Yang, Y., Liu, M., Wang, D., Wang, F., Bi, Y., Ji, J., Li, S., Liu, Y., Chen, R., Huang, H., Wang, X., Swidnicka-Siergiejko, A. K., Janowitz, T., Beyaz, S., Wang, G., Xu, S., Bialkowska, A. B., Luo, C. K., Pin, C. L., Liang, G., Lu, X., Wu, M., Shroyer, K. R., Wolff, R. A., Plunkett, W., Ji, B., Li, Z., Li, E., Li, X., Yang, V. W., Logsdon, C. D., Abbruzzese, J. L., Lu, W. (July 2019) Oncogenic KRAS Reduces Expression of FGF21 in Acinar Cells to Promote Pancreatic Tumorigenesis in Mice on a High-Fat Diet. Gastroenterology, 157 (5). ISSN 0016-5085

Michelet, Xavier, Dyck, Lydia, Hogan, Andrew, Loftus, Roisin M, Duquette, Danielle, Wei, Kevin, Beyaz, Semir, Tavakkoli, Ali, Foley, Cathriona, Donnelly, Raymond, O'Farrelly, Cliona, Raverdeau, Mathilde, Vernon, Ashley, Pettee, William, O'Shea, Donal, Nikolajczyk, Barbara S, Mills, Kingston HG, Brenner, Michael B, Finlay, David, Lynch, Lydia (December 2018) Metabolic reprogramming of natural killer cells in obesity limits antitumor responses. Nature Immunology, 19 (12). pp. 1330-1340. ISSN 1529-2908

Biton, M., Haber, A. L., Rogel, N., Burgin, G., Beyaz, S., Schnell, A., Ashenberg, O., Su, C. W., Smillie, C., Shekhar, K., Chen, Z., Wu, C., Ordovas-Montanes, J., Alvarez, D., Herbst, R. H., Zhang, M., Tirosh, I., Dionne, D., Nguyen, L. T., Xifaras, M. E., Shalek, A. K., von Andrian, U. H., Graham, D. B., Rozenblatt-Rosen, O., Shi, H. N., Kuchroo, V., Yilmaz, O. H., Regev, A., Xavier, R. J. (October 2018) T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell, 175 (5). pp. 1307-1320. ISSN 0092-8674

Haber, A. L., Biton, M., Rogel, N., Herbst, R. H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T. M., Howitt, M. R., Katz, Y., Tirosh, I., Beyaz, S., Dionne, D., Zhang, M., Raychowdhury, R., Garrett, W. S., Rozenblatt-Rosen, O., Shi, H. N., Yilmaz, O., Xavier, R. J., Regev, A. (November 2017) A single-cell survey of the small intestinal epithelium. Nature, 551 (7680). pp. 333-339. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Roper, J., Tammela, T., Cetinbas, N. M., Akkad, A., Roghanian, A., Rickelt, S., Almeqdadi, M., Wu, K., Oberli, M. A., Sanchez-Rivera, F., Park, Y. K., Liang, X., Eng, G., Taylor, M. S., Azimi, R., Kedrin, D., Neupane, R., Beyaz, S., Sicinska, E. T., Suarez, Y., Yoo, J., Chen, L., Zukerberg, L., Katajisto, P., Deshpande, V., Bass, A. J., Tsichlis, P. N., Lees, J., Langer, R., Hynes, R. O., Chen, J., Bhutkar, A., Jacks, T., Yilmaz, O. H. (June 2017) In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis. Nat Biotechnol, 35 (6). pp. 569-576. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Beyaz, S., Kim, J. H., Pinello, L., Xifaras, M. E., Hu, Y., Huang, J., Kerenyi, M. A., Das, P. P., Barnitz, R. A., Herault, A., Dogum, R., Haining, W. N., Yilmaz, O. H., Passegue, E., Yuan, G. C., Orkin, S. H., Winau, F. (February 2017) The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol, 18 (2). pp. 184-195. ISSN 1529-2916 (Electronic)1529-2908 (Linking)

Beyaz, S., Yilmaz, O. H. (December 2016) Molecular Pathways: Dietary Regulation of Stemness and Tumor Initiation by the PPAR-delta Pathway. Clin Cancer Res, 22 (23). pp. 5636-5641. ISSN 1078-0432 (Print)1078-0432 (Linking)

Beyaz, S., Mana, M. D., Roper, J., Kedrin, D., Saadatpour, A., Hong, S. J., Bauer-Rowe, K. E., Xifaras, M. E., Akkad, A., Arias, E., Pinello, L., Katz, Y., Shinagare, S., Abu-Remaileh, M., Mihaylova, M. M., Lamming, D. W., Dogum, R., Guo, G., Bell, G. W., Selig, M., Nielsen, G. P., Gupta, N., Ferrone, C. R., Deshpande, V., Yuan, G. C., Orkin, S. H., Sabatini, D. M., Yilmaz, O. H. (March 2016) High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature, 531 (7592). pp. 53-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Das, P. P., Hendrix, D. A., Apostolou, E., Buchner, A. H., Canver, M. C., Beyaz, S., Ljuboja, D., Kuintzle, R., Kim, W., Karnik, R., Shao, Z., Xie, H., Xu, J., De Los Angeles, A., Zhang, Y., Choe, J., Jun, D. L., Shen, X., Gregory, R. I., Daley, G. Q., Meissner, A., Kellis, M., Hochedlinger, K., Kim, J., Orkin, S. H. (September 2015) PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep, 12 (9). pp. 1456-70. ISSN 2211-1247 (Electronic)

Das, P. P., Shao, Z., Beyaz, S., Apostolou, E., Pinello, L., Angeles, A. L., O'Brien, K., Atsma, J. M., Fujiwara, Y., Nguyen, M., Ljuboja, D., Guo, G., Woo, A., Yuan, G. C., Onder, T., Daley, G., Hochedlinger, K., Kim, J., Orkin, S. H. (January 2014) Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell, 53 (1). pp. 32-48. ISSN 1097-4164 (Electronic)1097-2765 (Linking)

Haspot, F., Li, H. W., Lucas, C. L., Fehr, T., Beyaz, S., Sykes, M. (January 2014) Allospecific rejection of MHC class I-deficient bone marrow by CD8 T cells. Am J Transplant, 14 (1). pp. 49-58. ISSN 1600-6143 (Electronic)1600-6135 (Linking)

Guo, G., Luc, S., Marco, E., Lin, T. W., Peng, C., Kerenyi, M. A., Beyaz, S., Kim, W., Xu, J., Das, P. P., Neff, T., Zou, K., Yuan, G. C., Orkin, S. H. (October 2013) Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell, 13 (4). pp. 492-505. ISSN 1875-9777 (Electronic)1875-9777 (Linking)

Lucas, C. L., Workman, C. J., Beyaz, S., LoCascio, S., Zhao, G., Vignali, D. A., Sykes, M. (May 2011) LAG-3, TGF-beta, and cell-intrinsic PD-1 inhibitory pathways contribute to CD8 but not CD4 T-cell tolerance induced by allogeneic BMT with anti-CD40L. Blood, 117 (20). pp. 5532-40. ISSN 1528-0020 (Electronic)0006-4971 (Linking)

Book Section

Xu, M., Ergin, I., Beyaz, S. (April 2020) Advances in Diagnostic Procedures and Their Applications in the Era of Cancer Immunotherapy. In: Immunotherapy. Springer, pp. 37-50.

Conference or Workshop Item

Sivetz, Nicole, Cunniff, Patrick J, Vakoc, Christopher R, Beyaz, Semir, Egeblad, Mikala (November 2024) Sepsis-induced inflammation alters natural killer cell-mediated surveillance of liver metastasis. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer, 2024 Nov 17-20, Boston, Massachusetts.

Gorman, Megan, Katcher, Arielle, Gowthaman, Divya, Chung, Charlie, Yueh, Brian, Garcia, Libia, Kapedani, Arisa, Frimer, Marina, Goldberg, Gary, Beyaz, Semir (November 2024) Development of a clinically relevant orthotopic uterine carcinosarcoma mouse model using patient-derived organoids. In: Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer and 2024 Winter Meeting.

Gholami, S, Gazzara, E, Adrover, J, Liu, A, Han, S, Aminzada, Z, Rishi, A, Chung, C, Devoe, C, Huang, H, Vitiello, G, Deperalta, D, Weiss, M, Beyaz, S, Lou, E, Grothey, A, Tuveson, D, Westcott, P, Egeblad, M (June 2024) Overcoming therapeutic resistance in colorectal cancer by inhibiting neutrophil extracellular traps. In: UNSPECIFIED.

Eskiocak, Onur, Subhash, Santhilal, Shah, Vyom, Moresco, Phill, Beyaz, Semir (May 2024) Divergent coactivator usage and CREB1 activity controls tuft lineage commitment. In: UNSPECIFIED.

Bunk, Paul, Maher, Timothy, Beyaz, Semir (May 2024) PPAR delta promotes tumor-infiltrating Treg plasticity. In: UNSPECIFIED.

Gazzara, Emma, Adrover, Jose, Liu, Alex, Han, Song, Rishi, Arvind, Chung, Charlie, Devoe, Craig, Huang, Hai, DePeralta, Danielle, Weiss, Matthew, Beyaz, Semir, Westcott, Peter, Taveson, Dave, Egeblad, Mikala, Gholami, Sepideh (2024) Neutrophil extracellular traps are an immunotherapeutic target in colorectal cancer. In: Annals of Surgical Oncology.

Chung, Charlie, Nizam, Aaron, Yueh, Brian, Subhash, Santhilal, Eskiocak, Onur, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) Autologous patient-derived organoid-immune cell co-culture platform for therapeutic discovery in high-grade endometrial cancer. In: 114th Annual Meeting of the American Association for Cancer Research (AACR), APR 14-19, 2023, Orlando, FL.

Garipcan, Aybuke, Eskiocak, Onur, Subhash, Santhilal, Ozler, Kadir, Yueh, Brian, Chung, Charlie, Ergin, Ilgin, Gautier, Nelson, Habel, Jill, Rubino, Rachel, Van der Velden, Adrianus WM, Beyaz, Semir (2023) Epigenetic mechanisms of epithelial - immune interactions that shape immune surveillance in the intestinal epithelium. In: UNSPECIFIED.

Burr, Ansen, Ji, Junyi, Ozler, Kadir, Mentrup, Heather, Eskiocak, Onur, Cumberland, Rachel, Menk, Ashley, Zhang, Xiaoyi, Overacre-Delgoffe, Abigail, Rittenhouse, Natalie, Marshall, Chris, Cooper, Vaughn, Poholek, Amanda, Delgoffe, Greg, Beyaz, Semir, Hand, Timothy (2023) Excess dietary sugar alters colonocyte metabolism and impairs the early proliferative response to damage. In: Crohns and Colitis Congress, JAN 19-21, 2023, Denver, CO.

Chung, Charlie, Ozcelik, Elif, Habel, Jill, Zhang, Jialin, Qin, Yihan, Garcia, Libia, Merrill, Joseph, Chung, Taemoon, Lyons, Scott, Shen, Zeli, Fox, James G, Westcott, Peter, Beyaz, Semir (2023) Microbial regulation of anti-tumor immunity in colorectal cancer. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024, 2024 Apr 5-10, San Diego, CA.

Lei, Pin-Ji, Pereira, Ethel, Andersson, Patrik, Amoozgar, Zohreh, Van Wijnbergen, Jan Willem, O'Melia, Meghan J, Zhou, Hengbo, Chatterjee, Sampurna, Ho, William Wee, Posada, Jessica M, Kumar, Ashwin Srinivasan, Morita, Satoru, Chuang, Charlie, Ergin, Ilgin, Jones, Dennis, Huang, Peigen, Beyaz, Semir, Padera, Timothy P (2023) Single cell analysis of breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation. In: 114th Annual Meeting of the American Association for Cancer Research (AACR), APR 14-19, 2023, Orlando, FL.

Katcher, Arielle, Chung, Charlie, Gorman, Megan, Yueh, Brian, Lyons, Scott, Merrill, Joseph, Garcia, Libia, Frimer, Marina, Goldberg, Gary L, Beyaz, Semir (2023) A clinically-relevant orthotopic endometrial carcinosarcoma mouse model using human patient-derived organoids. In: American Association for Cancer Research Annual Meeting 2023, 2023 Apr 14-19, Orlando, FL.

Almeqdadi, Mohammad, Yueh, Brian S, Chung, Charlie, Spagnardi, Marzia, Zeng, Jianying, Paredes, Jenny, Akadri, Mubarak, Martello-Rooney, Laura, Beyaz, Semir (2022) Novel colon cancer organoid models from african american patients: new resource for mechanistic studies. In: Digestive Disease Week (DDW), MAY 21-24, 2022, San Diego, CA.

Brownridge, Stephanie R, Beyaz, Semir, Noyes, Nicole, Goldberg, Gary L (September 2021) DEVELOPMENT OF ENDOMETRIAL ORGANOIDS FROM AN ENDOMETRIAL BIOPSY. In: 77th Scientific Congress of the American Society for Reproductive Medicine.

Nizam, Aaron, Chung, Charlie, Goldberg, Gary L, Beyaz, Semir (July 2021) Abstract LB236: Utilizing endometrial tumor organoids to model cancer immunomodulation. In: AACR Annual Meeting 2021.

Nizam, Aaron, Chung, Charlie, Goldberg, Gary L, Beyaz, Semir (July 2021) Utilizing endometrial tumor organoids to model cancer immunomodulation. In: AACR Annual Meeting 2021.

Almeqdadi, Mohammad, Yueh, Brian, Paredes, Jenny, Akadri, Mubarak, Spagnardi, Marzia, Chung, Charlie, Martello-Rooney, Laura, Beyaz, Semir (May 2021) EXPLORING THE RACIAL DISPARITIES OF COLON CANCER OUTCOMES IN THE SETTING OF OBESITY. In: Digestive Disease Week 2021.

Gaudino, Stephen, Beaupre, Michael, Lin, Xun, Rathi, Sonika, McLaughlin, Patrick, Mehta, Neil, Eskiocak, Onur, Yueh, Brian, Van der Velden, Adrianus, Beyaz, Semir, Kumar, Pawan (May 2020) Interleukin-22 receptor signaling in Paneth cells is critical for their maturation and antimicrobial function. In: Annual Meeting of the American-Association-of-Immunologists - Immunology 2020, May 8-12, 2020, Honolulu, HI. (Unpublished)

Roper, Jatin, Tammela, Tuomas, Cetinbas, Naniye Malli, Akkad, Adam, Roghanian, Ali, Rickelt, Steffen, Almeqdadi, Mohammad, Wu, Katherine, Oberli, Matthias, Sanchez-Rivera, Francisco, Park, Yoona, Liang, Xu, Eng, George, Taylor, Martin S, Azimi, Roxana, Kedrin, Dmitriy, Neupane, Rachit, Beyaz, Semir, Sicinska, Ewa T, Suarez, Yvelisse, Yoo, James, Chen, Lillian, Zukerberg, Lawrence, Katajisto, Pekka, Deshpande, Vikram, Bass, Adam, Tsichlis, Philip N, Lees, Jacqueline, Langer, Robert, Hynes, Richard O, Chen, Jianzhu, Bhutkar, Arjun J, Jacks, Tyler, Yilmaz, Omer H (May 2018) In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis. In: AACR Special Conference on Advances in Modeling Cancer in Mice - Technology, Biology, and Beyond.

Beyaz, Semir (May 2016) UTX controls lineage-specific epigenetic program and development of iNKT cells. In: Annual Meeting of the American-Association-of-Immunologists (AAI).