Massively parallel approaches for characterizing noncoding functional variation in human evolution
Rong, Stephen, Root, Elise, Reilly, Steven K
Published in Current opinion in genetics & development (01.10.2024)
Published in Current opinion in genetics & development (01.10.2024)
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Journal Article
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
Cotney, Justin, Leng, Jing, Yin, Jun, Reilly, Steven K., DeMare, Laura E., Emera, Deena, Ayoub, Albert E., Rakic, Pasko, Noonan, James P.
Published in Cell (03.07.2013)
Published in Cell (03.07.2013)
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Journal Article
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
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.
Published in Cell (02.06.2016)
Published in Cell (02.06.2016)
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Journal Article
Evolutionary changes in promoter and enhancer activity during human corticogenesis
Reilly, Steven K., Yin, Jun, Ayoub, Albert E., Emera, Deena, Leng, Jing, Cotney, Justin, Sarro, Richard, Rakic, Pasko, Noonan, James P.
Published in Science (American Association for the Advancement of Science) (06.03.2015)
Published in Science (American Association for the Advancement of Science) (06.03.2015)
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Journal Article
Origin and evolution of developmental enhancers in the mammalian neocortex
Emera, Deena, Yin, Jun, Reilly, Steven K., Gockley, Jake, Noonan, James P.
Published in Proceedings of the National Academy of Sciences - PNAS (10.05.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (10.05.2016)
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Journal Article
Massively parallel discovery of human-specific substitutions that alter enhancer activity
Uebbing, Severin, Gockley, Jake, Reilly, Steven K., Kocher, Acadia A., Geller, Evan, Gandotra, Neeru, Scharfe, Curt, Cotney, Justin, Noonan, James P.
Published in Proceedings of the National Academy of Sciences - PNAS (12.01.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (12.01.2021)
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Journal Article
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
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.
Published in Nature communications (10.03.2015)
Published in Nature communications (10.03.2015)
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Journal Article
Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism
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.
Published in Cell (21.11.2013)
Published in Cell (21.11.2013)
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Journal Article
Evolution of Gene Regulation in Humans
Reilly, Steven K, Noonan, James P
Published in Annual review of genomics and human genetics (31.08.2016)
Published in Annual review of genomics and human genetics (31.08.2016)
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Journal Article
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
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
Published in Molecular biology and evolution (01.01.2022)
Published in Molecular biology and evolution (01.01.2022)
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Journal Article
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
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
Published in Nature genetics (01.08.2021)
Published in Nature genetics (01.08.2021)
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Journal Article
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Khetan, Shubham, Kales, Susan, Kursawe, Romy, Jillette, Alexandria, Ulirsch, Jacob C., Reilly, Steven K., Ucar, Duygu, Tewhey, Ryan, Stitzel, Michael L.
Published in Nature communications (02.09.2021)
Published in Nature communications (02.09.2021)
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Journal Article
The genomic landscape of cohesin-associated chromatin interactions
DeMare, Laura E, Leng, Jing, Cotney, Justin, Reilly, Steven K, Yin, Jun, Sarro, Richard, Noonan, James P
Published in Genome research (01.08.2013)
Published in Genome research (01.08.2013)
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Journal Article
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
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
Published in Nature communications (06.03.2020)
Published in Nature communications (06.03.2020)
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Journal Article
Machine-guided design of cell-type-targeting cis-regulatory elements
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
Published in Nature (London) (31.10.2024)
Published in Nature (London) (31.10.2024)
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Journal Article
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
Cotney, Justin, Leng, Jing, Oh, Sunghee, DeMare, Laura E, Reilly, Steven K, Gerstein, Mark B, Noonan, James P
Published in Genome research (01.06.2012)
Published in Genome research (01.06.2012)
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Journal Article
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
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.
Published in Cell (22.02.2018)
Published in Cell (22.02.2018)
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Journal Article
Multicenter integrated analysis of noncoding CRISPRi screens
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.
Published in Nature methods (01.04.2024)
Published in Nature methods (01.04.2024)
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Journal Article
Author Correction: Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
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
Published in Nature genetics (01.10.2021)
Published in Nature genetics (01.10.2021)
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Journal Article
The Cell-Permeable Derivative of the Immunoregulatory Metabolite Itaconate, 4-Octyl Itaconate, Is Anti-Fibrotic in Systemic Sclerosis
Henderson, John, Dayalan Naidu, Sharadha, Dinkova-Kostova, Albena T., Przyborski, Stefan, Stratton, Richard, O′Reilly, Steven
Published in Cells (Basel, Switzerland) (10.08.2021)
Published in Cells (Basel, Switzerland) (10.08.2021)
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