DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts von Roulois, David, Loo Yau, Helen, Singhania, Rajat, Wang, Yadong, Danesh, Arnavaz, Shen, Shu Yi, Han, Han, Liang, Gangning, Jones, Peter A., Pugh, Trevor J., O’Brien, Catherine, De Carvalho, Daniel D.

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Biological roles of RNA m7G modification and its implications in cancer von Zhang, Xin, Zhu, Wen-Yan, Shen, Shu-Yi, Shen, Jia-Hao, Chen, Xiao-Dong

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Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet von Viner, Coby, Ishak, Charles A, Johnson, James, Walker, Nicolas J, Shi, Hui, Sjöberg-Herrera, Marcela K, Shen, Shu Yi, Lardo, Santana M, Adams, David J, Ferguson-Smith, Anne C, De Carvalho, Daniel D, Hainer, Sarah J, Bailey, Timothy L, Hoffman, Michael M

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Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA von Shen, Shu Yi, Burgener, Justin M., Bratman, Scott V., De Carvalho, Daniel D.

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Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes von Nassiri, Farshad, Chakravarthy, Ankur, Feng, Shengrui, Shen, Shu Yi, Nejad, Romina, Zuccato, Jeffrey A., Voisin, Mathew R., Patil, Vikas, Horbinski, Craig, Aldape, Kenneth, Zadeh, Gelareh, De Carvalho, Daniel D.

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Cerebrospinal fluid methylome-based liquid biopsies for accurate malignant brain neoplasm classification von Zuccato, Jeffrey A, Patil, Vikas, Mansouri, Sheila, Voisin, Mathew, Chakravarthy, Ankur, Shen, Shu Yi, Nassiri, Farshad, Mikolajewicz, Nicholas, Trifoi, Mara, Skakodub, Anna, Zacharia, Brad, Glantz, Michael, De Carvalho, Daniel D, Mansouri, Alireza, Zadeh, Gelareh

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Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma von Burgener, Justin M, Zou, Jinfeng, Zhao, Zhen, Zheng, Yangqiao, Shen, Shu Yi, Huang, Shao Hui, Keshavarzi, Sareh, Xu, Wei, Liu, Fei-Fei, Liu, Geoffrey, Waldron, John N, Weinreb, Ilan, Spreafico, Anna, Siu, Lillian L, de Almeida, John R, Goldstein, David P, Hoffman, Michael M, De Carvalho, Daniel D, Bratman, Scott V

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The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors von Chen, Sujun, Petricca, Jessica, Ye, Wenbin, Guan, Jiansheng, Zeng, Yong, Cheng, Nicholas, Gong, Linsey, Shen, Shu Yi, Hua, Junjie T., Crumbaker, Megan, Fraser, Michael, Liu, Stanley, Bratman, Scott V., van der Kwast, Theodorus, Pugh, Trevor, Joshua, Anthony M., De Carvalho, Daniel D., Chi, Kim N., Awadalla, Philip, Ji, Guoli, Feng, Felix, Wyatt, Alexander W., He, Housheng Hansen

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The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population von Medina, Tiago S, Murison, Alex, Smith, Michelle, Kinker, Gabriela S, Chakravarthy, Ankur, Vitiello, Glauco A F, Turpin, Williams, Shen, Shu Yi, Yau, Helen L, Sarmento, Olga F, Faubion, William, Lupien, Mathieu, Silverberg, Mark S, Arrowsmith, Cheryl H, De Carvalho, Daniel D

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An open-label, phase II multicohort study of an oral hypomethylating agent CC-486 and durvalumab in advanced solid tumors von Taylor, Kirsty, Loo Yau, Helen, Chakravarthy, Ankur, Wang, Ben, Shen, Shu Yi, Ettayebi, Ilias, Ishak, Charles A, Bedard, Philippe L, Abdul Razak, Albiruni, R Hansen, Aaron, Spreafico, Anna, Cescon, Dave, Butler, Marcus O, Oza, Amit M, Lheureux, Stephanie, Stjepanovic, Neda, Van As, Brendan, Boross-Harmer, Sarah, Wang, Lisa, Pugh, Trevor J, Ohashi, Pamela S, Siu, Lillian L, De Carvalho, Daniel D

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Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment von Peter, Madonna R, Bilenky, Misha, Isserlin, Ruth, Bader, Gary D, Shen, Shu Yi, De Carvalho, Daniel D, Hansen, Aaron R, Hu, Pingzhao, Fleshner, Neil E, Joshua, Anthony M, Hirst, Martin, Bapat, Bharati

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Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls von Wilson, Samantha L., Shen, Shu Yi, Harmon, Lauren, Burgener, Justin M., Triche, Tim, Bratman, Scott V., De Carvalho, Daniel D., Hoffman, Michael M.

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Seasonal variation of bacterial endophytes in urban trees von Shen, Shu Yi, Fulthorpe, Roberta

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Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes von Nuzzo, Pier Vitale, Berchuck, Jacob E., Korthauer, Keegan, Spisak, Sandor, Nassar, Amin H., Abou Alaiwi, Sarah, Chakravarthy, Ankur, Shen, Shu Yi, Bakouny, Ziad, Boccardo, Francesco, Steinharter, John, Bouchard, Gabrielle, Curran, Catherine R., Pan, Wenting, Baca, Sylvan C., Seo, Ji-Heui, Lee, Gwo-Shu Mary, Michaelson, M. Dror, Chang, Steven L., Waikar, Sushrut S., Sonpavde, Guru, Irizarry, Rafael A., Pomerantz, Mark, De Carvalho, Daniel D., Choueiri, Toni K., Freedman, Matthew L.

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Sensitive tumour detection and classification using plasma cell-free DNA methylomes von Shen, Shu Yi, Singhania, Rajat, Fehringer, Gordon, Chakravarthy, Ankur, Roehrl, Michael H. A., Chadwick, Dianne, Zuzarte, Philip C., Borgida, Ayelet, Wang, Ting Ting, Li, Tiantian, Kis, Olena, Zhao, Zhen, Spreafico, Anna, Medina, Tiago da Silva, Wang, Yadon, Roulois, David, Ettayebi, Ilias, Chen, Zhuo, Chow, Signy, Murphy, Tracy, Arruda, Andrea, O’Kane, Grainne M., Liu, Jessica, Mansour, Mark, McPherson, John D., O’Brien, Catherine, Leighl, Natasha, Bedard, Philippe L., Fleshner, Neil, Liu, Geoffrey, Minden, Mark D., Gallinger, Steven, Goldenberg, Anna, Pugh, Trevor J., Hoffman, Michael M., Bratman, Scott V., Hung, Rayjean J., De Carvalho, Daniel D.

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Epigenomic Prognosis: Predicting fetal growth restriction beyond ultrasound markers von Smith, Keaton W., Yuen, Natalie, Shen, Shu Yi, Girard, Sylvie, Cheng, Nicholas, Awadalla, Philip, Triche, Tim, Bratman, Scott V., De Carvalho, Daniel D., Hoffman, Michael, Wilson, Samantha

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A new method to absolutely quantify and enrich for circulating placenta DNA from maternal blood, using DNA methylation von Wilson, Samantha L., Shen, Shu Yi, Girard, Sylvie, De Carvalho, Daneil D., Hoffman, Michael M.

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Bacterial Endophytes Isolated from Plants in Natural Oil Seep Soils with Chronic Hydrocarbon Contamination von Lumactud, Rhea, Shen, Shu Yi, Lau, Mimas, Fulthorpe, Roberta

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DNA hypomethylating agents increase activation and cytolytic activity of CD8+ T cells von Loo Yau, Helen, Bell, Emma, Ettayebi, Ilias, de Almeida, Felipe Campos, Boukhaled, Giselle M., Shen, Shu Yi, Allard, David, Morancho, Beatriz, Marhon, Sajid A., Ishak, Charles A., Gonzaga, Isabela M., da Silva Medina, Tiago, Singhania, Rajat, Chakravarthy, Ankur, Chen, Raymond, Mehdipour, Parinaz, Pommey, Sandra, Klein, Christian, Amarante-Mendes, Gustavo P., Roulois, David, Arribas, Joaquín, Stagg, John, Brooks, David G., De Carvalho, Daniel D.

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Second trimester cell-free placental DNA methylation profiles in preterm birth subtypes von Wilson, Samantha L., Shen, Shu Yi, Yuen, Natalie, Agopian, Mary, Girard, Sylvie, Triche, Tim, De Carvalho, Daniel, Bratman, Scott, Hoffman, Michael M.

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