The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb von Cotney, Justin, Leng, Jing, Yin, Jun, Reilly, Steven K., DeMare, Laura E., Emera, Deena, Ayoub, Albert E., Rakic, Pasko, Noonan, James P.

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Massively parallel approaches for characterizing noncoding functional variation in human evolution von Rong, Stephen, Root, Elise, Reilly, Steven K

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay von Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.

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Evolutionary changes in promoter and enhancer activity during human corticogenesis von Reilly, Steven K., Yin, Jun, Ayoub, Albert E., Emera, Deena, Leng, Jing, Cotney, Justin, Sarro, Richard, Rakic, Pasko, Noonan, James P.

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The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment von Cotney, Justin, Muhle, Rebecca A., Sanders, Stephan J., Liu, Li, Willsey, A. Jeremy, Niu, Wei, Liu, Wenzhong, Klei, Lambertus, Lei, Jing, Yin, Jun, Reilly, Steven K., Tebbenkamp, Andrew T., Bichsel, Candace, Pletikos, Mihovil, Sestan, Nenad, Roeder, Kathryn, State, Matthew W., Devlin, Bernie, Noonan, James P.

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Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism von Willsey, A. Jeremy, Sanders, Stephan J., Li, Mingfeng, Dong, Shan, Tebbenkamp, Andrew T., Muhle, Rebecca A., Reilly, Steven K., Lin, Leon, Fertuzinhos, Sofia, Miller, Jeremy A., Murtha, Michael T., Bichsel, Candace, Niu, Wei, Cotney, Justin, Ercan-Sencicek, A. Gulhan, Gockley, Jake, Gupta, Abha R., Han, Wenqi, He, Xin, Hoffman, Ellen J., Klei, Lambertus, Lei, Jing, Liu, Wenzhong, Liu, Li, Lu, Cong, Xu, Xuming, Zhu, Ying, Mane, Shrikant M., Lein, Ed S., Wei, Liping, Noonan, James P., Roeder, Kathryn, Devlin, Bernie, Sestan, Nenad, State, Matthew W.

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Origin and evolution of developmental enhancers in the mammalian neocortex von Emera, Deena, Yin, Jun, Reilly, Steven K., Gockley, Jake, Noonan, James P.

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Massively parallel discovery of human-specific substitutions that alter enhancer activity von Uebbing, Severin, Gockley, Jake, Reilly, Steven K., Kocher, Acadia A., Geller, Evan, Gandotra, Neeru, Scharfe, Curt, Cotney, Justin, Noonan, James P.

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Evolution of Gene Regulation in Humans von Reilly, Steven K, Noonan, James P

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Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation von Khetan, Shubham, Kales, Susan, Kursawe, Romy, Jillette, Alexandria, Ulirsch, Jacob C., Reilly, Steven K., Ucar, Duygu, Tewhey, Ryan, Stitzel, Michael L.

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The genomic landscape of cohesin-associated chromatin interactions von DeMare, Laura E, Leng, Jing, Cotney, Justin, Reilly, Steven K, Yin, Jun, Sarro, Richard, Noonan, James P

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Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells von Jagoda, Evelyn, Xue, James R, Reilly, Steven K, Dannemann, Michael, Racimo, Fernando, Huerta-Sanchez, Emilia, Sankararaman, Sriram, Kelso, Janet, Pagani, Luca, Sabeti, Pardis C, Capellini, Terence D

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Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH von Reilly, Steven K., Gosai, Sager J., Gutierrez, Alan, Mackay-Smith, Ava, Ulirsch, Jacob C., Kanai, Masahiro, Mouri, Kousuke, Berenzy, Daniel, Kales, Susan, Butler, Gina M., Gladden-Young, Adrianne, Bhuiyan, Redwan M., Stitzel, Michael L., Finucane, Hilary K., Sabeti, Pardis C., Tewhey, Ryan

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Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features von Ray, John P., de Boer, Carl G., Fulco, Charles P., Lareau, Caleb A., Kanai, Masahiro, Ulirsch, Jacob C., Tewhey, Ryan, Ludwig, Leif S., Reilly, Steven K., Bergman, Drew T., Engreitz, Jesse M., Issner, Robbyn, Finucane, Hilary K., Lander, Eric S., Regev, Aviv, Hacohen, Nir

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Machine-guided design of cell-type-targeting cis-regulatory elements von Gosai, Sager J., Castro, Rodrigo I., Fuentes, Natalia, Butts, John C., Mouri, Kousuke, Alasoadura, Michael, Kales, Susan, Nguyen, Thanh Thanh L., Noche, Ramil R., Rao, Arya S., Joy, Mary T., Sabeti, Pardis C., Reilly, Steven K., Tewhey, Ryan

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Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb von Cotney, Justin, Leng, Jing, Oh, Sunghee, DeMare, Laura E, Reilly, Steven K, Gerstein, Mark B, Noonan, James P

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay von Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.

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Multicenter integrated analysis of noncoding CRISPRi screens von Yao, David, Tycko, Josh, Oh, Jin Woo, Bounds, Lexi R., Gosai, Sager J., Lataniotis, Lazaros, Mackay-Smith, Ava, Doughty, Benjamin R., Gabdank, Idan, Schmidt, Henri, Guerrero-Altamirano, Tania, Siklenka, Keith, Guo, Katherine, White, Alexander D., Youngworth, Ingrid, Andreeva, Kalina, Ren, Xingjie, Barrera, Alejandro, Luo, Yunhai, Yardımcı, Galip Gürkan, Tewhey, Ryan, Kundaje, Anshul, Greenleaf, William J., Sabeti, Pardis C., Leslie, Christina, Pritykin, Yuri, Moore, Jill E., Beer, Michael A., Gersbach, Charles A., Reddy, Timothy E., Shen, Yin, Engreitz, Jesse M., Bassik, Michael C., Reilly, Steven K.

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Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolution von Griesemer, Dustin, Xue, James R., Reilly, Steven K., Ulirsch, Jacob C., Kukreja, Kalki, Davis, Joe R., Kanai, Masahiro, Yang, David K., Butts, John C., Guney, Mehmet H., Luban, Jeremy, Montgomery, Stephen B., Finucane, Hilary K., Novina, Carl D., Tewhey, Ryan, Sabeti, Pardis C.

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The Cell-Permeable Derivative of the Immunoregulatory Metabolite Itaconate, 4-Octyl Itaconate, Is Anti-Fibrotic in Systemic Sclerosis von Henderson, John, Dayalan Naidu, Sharadha, Dinkova-Kostova, Albena T., Przyborski, Stefan, Stratton, Richard, O′Reilly, Steven

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