PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D von Toska, Eneda, Osmanbeyoglu, Hatice U., Castel, Pau, Chan, Carmen, Hendrickson, Ronald C., Elkabets, Moshe, Dickler, Maura N., Scaltriti, Maurizio, Leslie, Christina S., Armstrong, Scott A., Baselga, José

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An ATR and CHK1 kinase signaling mechanism that limits origin firing during unperturbed DNA replication von Moiseeva, Tatiana N., Yin, Yandong, Calderon, Michael J., Qian, Chenao, Schamus-Haynes, Sandra, Sugitani, Norie, Osmanbeyoglu, Hatice U., Rothenberg, Eli, Watkins, Simon C., Bakkenist, Christopher J.

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WEE1 kinase inhibitor AZD1775 induces CDK1 kinase-dependent origin firing in unperturbed G1- and S-phase cells von Moiseeva, Tatiana N., Qian, Chenao, Sugitani, Norie, Osmanbeyoglu, Hatice U., Bakkenist, Christopher J.

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Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers von Tao, Yifeng, Ma, Xiaojun, Palmer, Drake, Schwartz, Russell, Lu, Xinghua, Osmanbeyoglu, Hatice Ulku

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Targeting Aurora B kinase prevents and overcomes resistance to EGFR inhibitors in lung cancer by enhancing BIM- and PUMA-mediated apoptosis von Tanaka, Kosuke, Yu, Helena A., Yang, Shaoyuan, Han, Song, Selcuklu, S. Duygu, Kim, Kwanghee, Ramani, Shriram, Ganesan, Yogesh Tengarai, Moyer, Allison, Sinha, Sonali, Xie, Yuchen, Ishizawa, Kota, Osmanbeyoglu, Hatice U., Lyu, Yang, Roper, Nitin, Guha, Udayan, Rudin, Charles M., Kris, Mark G., Hsieh, James J., Cheng, Emily H.

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Pancancer modelling predicts the context-specific impact of somatic mutations on transcriptional programs von Osmanbeyoglu, Hatice U., Toska, Eneda, Chan, Carmen, Baselga, José, Leslie, Christina S.

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A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance von Feng, Yongqiang, van der Veeken, Joris, Shugay, Mikhail, Putintseva, Ekaterina V., Osmanbeyoglu, Hatice U., Dikiy, Stanislav, Hoyos, Beatrice E., Moltedo, Bruno, Hemmers, Saskia, Treuting, Piper, Leslie, Christina S., Chudakov, Dmitriy M., Rudensky, Alexander Y.

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Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas von Lee, Sanghoon, Osmanbeyoglu, Hatice Ulku

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Recurrent Human Papillomavirus-Related Head and Neck Cancer Undergoes Metabolic Reprogramming and Is Driven by Oxidative Phosphorylation von Vyas, Avani, Harbison, R. Alex, Faden, Daniel L., Kubik, Mark, Palmer, Drake, Zhang, Qing, Osmanbeyoglu, Hatice U., Kiselyov, Kirill, Mendez, Eduardo, Duvvuri, Umamaheswar

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Linking signaling pathways to transcriptional programs in breast cancer von Osmanbeyoglu, Hatice U, Pelossof, Raphael, Bromberg, Jacqueline F, Leslie, Christina S

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SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators von Ma, Xiaojun, Somasundaram, Ashwin, Qi, Zengbiao, Hartman, Douglas J, Singh, Harinder, Osmanbeyoglu, Hatice Ulku

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Vascular endothelial profilin-1 drives a protumorigenic tumor microenvironment and tumor progression in renal cancer von Gau, David, Daoud, Andrew, Allen, Abigail, Joy, Marion, Sagan, April, Lee, Sanghoon, Lucas, Peter C, Duensing, Stefan, Boone, David, Osmanbeyoglu, Hatice U, Roy, Partha

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Egfl6 promotes ovarian cancer progression by enhancing the immunosuppressive functions of tumor-associated myeloid cells von Hamze Sinno, Sarah, Imperatore, Joshua A, Bai, Shoumei, Gomes-Jourdan, Noémie, Mafarachisi, Nyasha, Coronnello, Claudia, Zhang, Linan, Jašarević, Eldin, Osmanbeyoglu, Hatice U, Buckanovich, Ronald J, Cascio, Sandra

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Genomic and transcriptomic analysis of cutaneous squamous cell carcinoma arising in immunocompetent and immunosuppressed patients von Bibee, Kristin P, Kulkarni, Aditi, Lee, Sanghoon, Ho, Johan, Osmanbeyoglu, Hatice Ulku, Ferris, Robert L, Zandberg, Dan P

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Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers von Osmanbeyoglu, Hatice U., Shimizu, Fumiko, Rynne-Vidal, Angela, Alonso-Curbelo, Direna, Chen, Hsuan-An, Wen, Hannah Y., Yeung, Tsz-Lun, Jelinic, Petar, Razavi, Pedram, Lowe, Scott W., Mok, Samuel C., Chiosis, Gabriela, Levine, Douglas A., Leslie, Christina S.

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N-gram analysis of 970 microbial organisms reveals presence of biological language models von Osmanbeyoglu, Hatice Ulku, Ganapathiraju, Madhavi K

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Ets transcription factor GABP controls T cell homeostasis and immunity von Luo, Chong T., Osmanbeyoglu, Hatice U., Do, Mytrang H., Bivona, Michael R., Toure, Ahmed, Kang, Davina, Xie, Yuchen, Leslie, Christina S., Li, Ming O.

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Cancer-associated MSC drive tumor immune exclusion and resistance to immunotherapy, which can be overcome by Hedgehog inhibition von Cascio, Sandra, Chandler, Chelsea, Zhang, Linan, Sinno, Sarah, Gao, Bingsi, Onkar, Sayali, Bruno, Tullia C., Vignali, Dario A. A., Mahdi, Haider, Osmanbeyoglu, Hatice U., Vlad, Anda M., Coffman, Lan G., Buckanovich, Ronald J.

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Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression von Sugitani, Norie, Vendetti, Frank P., Cipriano, Andrew J., Pandya, Pinakin, Deppas, Joshua J., Moiseeva, Tatiana N., Schamus-Haynes, Sandra, Wang, Yiyang, Palmer, Drake, Osmanbeyoglu, Hatice U., Bostwick, Anna, Snyder, Nathaniel W., Gong, Yi-Nan, Aird, Katherine M., Delgoffe, Greg M., Beumer, Jan H., Bakkenist, Christopher J.

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STGIC: A graph and image convolution-based method for spatial transcriptomic clustering von Zhang, Chen, Gao, Junhui, Chen, Hong-Yu, Kong, Lingxin, Cao, Guangshuo, Guo, Xiangyu, Liu, Wei, Ren, Bin, Wei, Dong-Qing

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