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MYC phase separation selectively modulates the transcriptome ( may , 10.1038/s41594-024-01322-6, 2024) Yang, Junjiao; Chung, Chan-, I; Koach, Jessica; Liu, Hongjiang; Navalkar, Ambuja; He, Hao; Ma, Zhimin; Zhao, Qian; Yang, Xiaoyu; He, Liang; Mittag, Tanja; Shen, Yin; Weiss, William A.; Shu, Xiaokun Share Save
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Pardo-Palacios, Francisco J.; Wang, Dingjie; Reese, Fairlie; Diekhans, Mark; Carbonell-Sala, Silvia; Williams, Brian; Loveland, Jane E.; De Maria, Maite; Adams, Matthew S.; Balderrama-Gutierrez, Gabriela; Behera, Amit K.; Gonzalez Martinez, Jose M.; Hunt, Toby; Lagarde, Julien; Liang, Cindy E.; Li, Haoran; Meade, Marcus Jerryd; Moraga Amador, David A.; Prjibelski, Andrey D.; Birol, Inanc; Bostan, Hamed; Brooks, Ashley M.; Celik, Muhammed Hasan; Chen, Ying; Du, Mei R. M.; Felton, Colette; Goeke, Jonathan; Hafezqorani, Saber; Herwig, Ralf; Kawaji, Hideya; Lee, Joseph; Li, Jian-Liang; Lienhard, Matthias; Mikheenko, Alla; Mulligan, Dennis; Nip, Ka Ming; Pertea, Mihaela; Ritchie, Matthew E.; Sim, Andre D.; Tang, Alison D.; Wan, Yuk Kei; Wang, Changqing; Wong, Brandon Y.; Yang, Chen; Barnes, If; Berry, Andrew E.; Capella-Gutierrez, Salvador; Cousineau, Alyssa; Dhillon, Namrita; Fernandez-Gonzalez, Jose M.; Ferrandez-Peral, Luis; Garcia-Reyero, Natalia; Goetz, Stefan; Hernandez-Ferrer, Carles; Kondratova, Liudmyla; Liu, Tianyuan; Martinez-Martin, Alessandra; Menor, Carlos; Mestre-Tomas, Jorge; Mudge, Jonathan M.; Panayotova, Nedka G.; Paniagua, Alejandro; Repchevsky, Dmitry; Ren, Xingjie; Rouchka, Eric; Saint-John, Brandon; Sapena, Enrique; Sheynkman, Leon; Smith, Melissa Laird; Suner, Marie-Marthe; Takahashi, Hazuki; Youngworth, Ingrid A.; Carninci, Piero; Denslow, Nancy D.; Guigo, Roderic; Hunter, Margaret E.; Maehr, Rene; Shen, Yin; Tilgner, Hagen U.; Wold, Barbara J.; Vollmers, Christopher; Frankish, Adam; Au, Kin Fai; Sheynkman, Gloria M.; Mortazavi, Ali; Conesa, Ana; Brooks, Angela N. Share Save
MYC phase separation selectively modulates the transcriptome Yang, Junjiao; Chung, Chan-, I; Koach, Jessica; Liu, Hongjiang; Navalkar, Ambuja; He, Hao; Ma, Zhimin; Zhao, Qian; Yang, Xiaoyu; He, Liang; Mittag, Tanja; Shen, Yin; Weiss, William A.; Shu, Xiaokun Share Save
A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex Liang, Xiaoyi G.; Hoang, Kendy; Meyerink, Brandon L.; Pratiksha, Kc; Paraiso, Kitt; Wang, Li; Jones, Ian R.; Zhang, Yue; Katzman, Sol; Finn, Thomas S.; Tsyporin, Jeremiah; Qu, Fangyuan; Chen, Zhaoxu; Visel, Axel; Kriegstein, Arnold; Shen, Yin; Pilaz, Louis - Jan; Chen, Bin Share Save
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; Yardimci, Galip Gurkan; 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. Share Save
Phase separation of YAP-MAML2 differentially regulates the transcriptome Chung, Chan-, I; Yang, Junjiao; Yang, Xiaoyu; Liu, Hongjiang; Ma, Zhimin; Szulzewsky, Frank; Holland, Eric C.; Shen, Yin; Shu, Xiaokun Share Save
High-throughput PRIME-editing screens identify functional DNA variants in the human genome Ren, Xingjie; Yang, Han; Nierenberg, Jovia L.; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin Share Save
Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells Wu, David; Poddar, Aunoy; Ninou, Elpiniki; Hwang, Elizabeth; Cole, Mitchel A.; Liu, S. John; Horlbeck, Max A.; Chen, Jin; Replogle, Joseph M.; Carosso, Giovanni A.; Eng, Nicolas W. L.; Chang, Jonghoon; Shen, Yin; Weissman, Jonathan S.; Lim, Daniel A. Share Save
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Coordinated Transcriptional and Catabolic Programs Support Iron-Dependent Adaptation to RAS-MAPK Pathway Inhibition in Pancreatic Cancer Ravichandran, Mirunalini; Hu, Jingjie; Cai, Charles; Ward, Nathan P.; Venida, Anthony; Foakes, Callum; Kuljanin, Miljan; Yang, Annan; Hennessey, Connor J.; Yang, Yang; Desousa, Brandon R.; Rademaker, Gilles; Staes, Annelot A. L.; Cakir, Zeynep; Jain, Isha H.; Aguirre, Andrew J.; Mancias, Joseph D.; Shen, Yin; DeNicola, Gina M.; Perera, Rushika M. Share Save
The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression Yang, Han; Ting, Xia; Geng, Yue-Hang; Xie, Yuntao; Nierenberg, Jovia L.; Huo, Yan-Fei; Zhou, Yan-Ting; Huang, Yang; Yu, Yu-Qing; Yu, Xin-Yao; Li, Xiao-Fei; Ziv, Elad; Zhang, Hongquan; Fang, Wei-Gang; Shen, Yin; Tian, Xin-Xia Share Save
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data Rowland, Bryce; Huh, Ruth; Hou, Zoey; Crowley, Cheynna; Wen, Jia; Shen, Yin; Hu, Ming; Giusti-Rodriguez, Paola; Sullivan, Patrick F.; Li, Yun Share Save
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath Ren, Xingjie; Wang, Mengchi; Li, Bingkun; Jamieson, Kirsty; Zheng, Lina; Jones, Ian R.; Li, Bin; Takagi, Maya Asami; Lee, Jerry; Maliskova, Lenka; Tam, Tsz Wai; Yu, Miao; Hu, Rong; Lee, Lindsay; Abnousi, Armen; Li, Gang; Li, Yun; Hu, Ming; Ren, Bing; Wang, Wei; Shen, Yin Share Save
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia Ushiki, Aki; Zhang, Yichi; Xiong, Chenling; Zhao, Jingjing; Georgakopoulos-Soares, Ilias; Kane, Lauren; Jamieson, Kirsty; Bamshad, Michael J.; Nickerson, Deborah A.; Shen, Yin; Lettice, Laura A.; Silveira-Lucas, Elizabeth Lemos; Petit, Florence; Ahituv, Nadav Share Save
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