Search Results - "Faryabi, B"

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability by Barlow, Jacqueline H., Faryabi, Robert B., Callén, Elsa, Wong, Nancy, Malhowski, Amy, Chen, Hua Tang, Gutierrez-Cruz, Gustavo, Sun, Hong-Wei, McKinnon, Peter, Wright, George, Casellas, Rafael, Robbiani, Davide F., Staudt, Louis, Fernandez-Capetillo, Oscar, Nussenzweig, André

“…DNA double-strand breaks (DSBs) in B lymphocytes arise stochastically during replication or as a result of targeted DNA damage by activation-induced cytidine…”
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BRCA1 Functions Independently of Homologous Recombination in DNA Interstrand Crosslink Repair by Bunting, Samuel F., Callén, Elsa, Kozak, Marina L., Kim, Jung Min, Wong, Nancy, López-Contreras, Andrés J., Ludwig, Thomas, Baer, Richard, Faryabi, Robert B., Malhowski, Amy, Chen, Hua-Tang, Fernandez-Capetillo, Oscar, D'Andrea, Alan, Nussenzweig, André

“…Brca1 is required for DNA repair by homologous recombination (HR) and normal embryonic development. Here we report that deletion of the DNA damage response…”
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ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells by Verma, Priyanka, Zhou, Yeqiao, Cao, Zhendong, Deraska, Peter V., Deb, Moniher, Arai, Eri, Li, Weihua, Shao, Yue, Puentes, Laura, Li, Yiwen, Patankar, Sonali, Mach, Robert H., Faryabi, Robert B., Shi, Junwei, Greenberg, Roger A.

“…The response to poly(ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair and the abundance of lesions that trap…”
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53BP1 Mediates Productive and Mutagenic DNA Repair through Distinct Phosphoprotein Interactions by Callen, Elsa, Di Virgilio, Michela, Kruhlak, Michael J., Nieto-Soler, Maria, Wong, Nancy, Chen, Hua-Tang, Faryabi, Robert B., Polato, Federica, Santos, Margarida, Starnes, Linda M., Wesemann, Duane R., Lee, Ji-Eun, Tubbs, Anthony, Sleckman, Barry P., Daniel, Jeremy A., Ge, Kai, Alt, Frederick W., Fernandez-Capetillo, Oscar, Nussenzweig, Michel C., Nussenzweig, André

“…The DNA damage response (DDR) protein 53BP1 protects DNA ends from excessive resection in G1, and thereby favors repair by nonhomologous end-joining (NHEJ) as…”
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Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance by Perlman, Brent S., Burget, Noah, Zhou, Yeqiao, Schwartz, Gregory W., Petrovic, Jelena, Modrusan, Zora, Faryabi, Robert B.

“…Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of…”
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AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics by Mongia, Aanchal, Zohora, Fatema Tuz, Burget, Noah G., Zhou, Yeqiao, Saunders, Diane C., Wang, Yue J., Brissova, Marcela, Powers, Alvin C., Kaestner, Klaus H., Vahedi, Golnaz, Naji, Ali, Schwartz, Gregory W., Faryabi, Robert B.

“…Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image…”
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TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes by Schwartz, Gregory W., Zhou, Yeqiao, Petrovic, Jelena, Pear, Warren S., Faryabi, Robert B.

“…Emerging single-cell epigenomic assays are used to investigate the heterogeneity of chromatin activity and its function. However, identifying cells with…”
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The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR+ CD8+ effector state, and its deletion improves checkpoint blockade by McClory, Susan E., Bardhan, Oishi, Rome, Kelly S., Giles, Josephine R., Baxter, Amy E., Xu, Lanwei, Gimotty, Phyllis A., Faryabi, Robert B., Wherry, E. John, Pear, Warren S., Jordan, Martha S.

“…CD8+ T cell exhaustion (TEX) impairs the ability of T cells to clear chronic infection or cancer. While TEX are hypofunctional, some TEX retain effector gene…”
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Differential Integration of Transcriptome and Proteome Identifies Pan-Cancer Prognostic Biomarkers by Schwartz, Gregory W, Petrovic, Jelena, Zhou, Yeqiao, Faryabi, Robert B

“…High-throughput analysis of the transcriptome and proteome individually are used to interrogate complex oncogenic processes in cancer. However, an outstanding…”
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A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas by Ryan, Russell J.H., Petrovic, Jelena, Rausch, Dylan M., Zhou, Yeqiao, Lareau, Caleb A., Kluk, Michael J., Christie, Amanda L., Lee, Winston Y., Tarjan, Daniel R., Guo, Bingqian, Donohue, Laura K.H., Gillespie, Shawn M., Nardi, Valentina, Hochberg, Ephraim P., Blacklow, Stephen C., Weinstock, David M., Faryabi, Robert B., Bernstein, Bradley E., Aster, Jon C., Pear, Warren S.

“…Gain-of-function Notch mutations are recurrent in mature small B cell lymphomas such as mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL), but…”
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The DNA Damage- and Transcription-Associated Protein Paxip1 Controls Thymocyte Development and Emigration by Callen, Elsa, Faryabi, Robert B., Luckey, Megan, Hao, Bingtao, Daniel, Jeremy A., Yang, Wenjing, Sun, Hong-Wei, Dressler, Greg, Peng, Weiqun, Chi, Hongbo, Ge, Kai, Krangel, Michael S., Park, Jung-Hyun, Nussenzweig, André

“…Histone 3 lysine 4 trimethylation (H3K4me3) is associated with promoters of active genes and found at hot spots for DNA recombination. Here we have shown that…”
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Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL by Stein, Sarah J, Mack, Ethan A, Rome, Kelly S, Pajcini, Kostandin V, Ohtani, Takuya, Xu, Lanwei, Li, Yunlei, Meijerink, Jules P P, Faryabi, Robert B, Pear, Warren S

“…Trib2 is highly expressed in human T cell acute lymphoblastic leukemia (T-ALL) and is a direct transcriptional target of the oncogenic drivers Notch and TAL1…”
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On approximate stochastic control in genetic regulatory networks by Faryabi, B, Datta, A, Dougherty, E R

“…The control of probabilistic Boolean networks as a model of genetic regulatory networks is formulated as an optimal stochastic control problem and has been…”
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Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy by Li, Jinyang, Byrne, Katelyn T., Yan, Fangxue, Yamazoe, Taiji, Chen, Zeyu, Baslan, Timour, Richman, Lee P., Lin, Jeffrey H., Sun, Yu H., Rech, Andrew J., Balli, David, Hay, Ceire A., Sela, Yogev, Merrell, Allyson J., Liudahl, Shannon M., Gordon, Naomi, Norgard, Robert J., Yuan, Salina, Yu, Sixiang, Chao, Timothy, Ye, Shuai, Eisinger-Mathason, T.S. Karin, Faryabi, Robert B., Tobias, John W., Lowe, Scott W., Coussens, Lisa M., Wherry, E. John, Vonderheide, Robert H., Stanger, Ben Z.

“…The biological and functional heterogeneity between tumors—both across and within cancer types—poses a challenge for immunotherapy. To understand the factors…”
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Spatial promoter-enhancer hubs in cancer: organization, regulation, and function by Zhao, Jingru, Faryabi, Robert B

“…Transcriptional dysregulation is a hallmark of cancer and can be driven by altered enhancer landscapes. Recent studies in genome organization have revealed…”
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Optimal Intervention Strategies for Cyclic Therapeutic Methods by Vahedi $^$, Golnaz, Faryabi, Babak, Chamberland, Jean-Francois, Datta, Aniruddha, Dougherty, Edward R.

“…External control of a genetic regulatory network is used for the purpose of avoiding undesirable states such as those associated with a disease. Certain types…”
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Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques by Petrovic, Jelena, Zhou, Yeqiao, Fasolino, Maria, Goldman, Naomi, Schwartz, Gregory W., Mumbach, Maxwell R., Nguyen, Son C., Rome, Kelly S., Sela, Yogev, Zapataro, Zachary, Blacklow, Stephen C., Kruhlak, Michael J., Shi, Junwei, Aster, Jon C., Joyce, Eric F., Little, Shawn C., Vahedi, Golnaz, Pear, Warren S., Faryabi, Robert B.

“…Chromatin loops enable transcription-factor-bound distal enhancers to interact with their target promoters to regulate transcriptional programs. Although…”
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EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells by Zhou, Yeqiao, Petrovic, Jelena, Zhao, Jingru, Zhang, Wu, Bigdeli, Ashkan, Zhang, Zhen, Berger, Shelley L., Pear, Warren S., Faryabi, Robert B.

“…Chromatin misfolding has been implicated in cancer pathogenesis; yet, its role in therapy resistance remains unclear. Here, we systematically integrated…”
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DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier by Santos, Margarida A., Faryabi, Robert B., Ergen, Aysegul V., Day, Amanda M., Malhowski, Amy, Canela, Andres, Onozawa, Masahiro, Lee, Ji-Eun, Callen, Elsa, Gutierrez-Martinez, Paula, Chen, Hua-Tang, Wong, Nancy, Finkel, Nadia, Deshpande, Aniruddha, Sharrow, Susan, Rossi, Derrick J., Ito, Keisuke, Ge, Kai, Aplan, Peter D., Armstrong, Scott A., Nussenzweig, André

“…Histone methyl-transferase MLL4 is required for stem-cell activity and an aggressive form of acute myeloid leukaemia harbouring the MLL–AF9 oncogene. Tumour…”
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TooManyCells identifies and visualizes relationships of single-cell clades by Schwartz, Gregory W., Zhou, Yeqiao, Petrovic, Jelena, Fasolino, Maria, Xu, Lanwei, Shaffer, Sydney M., Pear, Warren S., Vahedi, Golnaz, Faryabi, Robert B.

“…Identifying and visualizing transcriptionally similar cells is instrumental for accurate exploration of the cellular diversity revealed by single-cell…”
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