Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome von Yu, Miao, Hon, Gary C., Szulwach, Keith E., Song, Chun-Xiao, Zhang, Liang, Kim, Audrey, Li, Xuekun, Dai, Qing, Shen, Yin, Park, Beomseok, Min, Jung-Hyun, Jin, Peng, Ren, Bing, He, Chuan

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Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells von Xie, Shiqi, Duan, Jialei, Li, Boxun, Zhou, Pei, Hon, Gary C.

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5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation von Hon, Gary C., Song, Chun-Xiao, Du, Tingting, Jin, Fulai, Selvaraj, Siddarth, Lee, Ah Young, Yen, Chia-an, Ye, Zhen, Mao, Shi-Qing, Wang, Bang-An, Kuan, Samantha, Edsall, Lee E., Zhao, Boxuan Simen, Xu, Guo-Liang, He, Chuan, Ren, Bing

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In Situ Capture of Chromatin Interactions by Biotinylated dCas9 von Liu, Xin, Zhang, Yuannyu, Chen, Yong, Li, Mushan, Zhou, Feng, Li, Kailong, Cao, Hui, Ni, Min, Liu, Yuxuan, Gu, Zhimin, Dickerson, Kathryn E., Xie, Shiqi, Hon, Gary C., Xuan, Zhenyu, Zhang, Michael Q., Shao, Zhen, Xu, Jian

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Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues von Hon, Gary C, Rajagopal, Nisha, Shen, Yin, McCleary, David F, Yue, Feng, Dang, My D, Ren, Bing

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Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice von Hepler, Chelsea, Shan, Bo, Zhang, Qianbin, Henry, Gervaise H, Shao, Mengle, Vishvanath, Lavanya, Ghaben, Alexandra L, Mobley, Angela B, Strand, Douglas, Hon, Gary C, Gupta, Rana K

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Frequent sgRNA-barcode recombination in single-cell perturbation assays von Xie, Shiqi, Cooley, Anne, Armendariz, Daniel, Zhou, Pei, Hon, Gary C

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EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling von Liu, Feng, Hon, Gary C., Villa, Genaro R., Turner, Kristen M., Ikegami, Shiro, Yang, Huijun, Ye, Zhen, Li, Bin, Kuan, Samantha, Lee, Ah Young, Zanca, Ciro, Wei, Bowen, Lucey, Greg, Jenkins, David, Zhang, Wei, Barr, Cathy L., Furnari, Frank B., Cloughesy, Timothy F., Yong, William H., Gahman, Timothy C., Shiau, Andrew K., Cavenee, Webster K., Ren, Bing, Mischel, Paul S.

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Identification and characterization of cellular heterogeneity within the developing renal interstitium von England, Alicia R, Chaney, Christopher P, Das, Amrita, Patel, Mohita, Malewska, Alicia, Armendariz, Daniel, Hon, Gary C, Strand, Douglas W, Drake, Keri A, Carroll, Thomas J

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A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra von Henry, Gervaise H., Malewska, Alicia, Joseph, Diya B., Malladi, Venkat S., Lee, Jeon, Torrealba, Jose, Mauck, Ryan J., Gahan, Jeffrey C., Raj, Ganesh V., Roehrborn, Claus G., Hon, Gary C., MacConmara, Malcolm P., Reese, Jeffrey C., Hutchinson, Ryan C., Vezina, Chad M., Strand, Douglas W.

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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer von Hon, Gary C, Hawkins, R David, Caballero, Otavia L, Lo, Christine, Lister, Ryan, Pelizzola, Mattia, Valsesia, Armand, Ye, Zhen, Kuan, Samantha, Edsall, Lee E, Camargo, Anamaria Aranha, Stevenson, Brian J, Ecker, Joseph R, Bafna, Vineet, Strausberg, Robert L, Simpson, Andrew J, Ren, Bing

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Computational identification of clonal cells in single-cell CRISPR screens von Wang, Yihan, Xie, Shiqi, Armendariz, Daniel, Hon, Gary C

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Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells von Hawkins, R. David, Hon, Gary C., Lee, Leonard K., Ngo, QueMinh, Lister, Ryan, Pelizzola, Mattia, Edsall, Lee E., Kuan, Samantha, Luu, Ying, Klugman, Sarit, Antosiewicz-Bourget, Jessica, Ye, Zhen, Espinoza, Celso, Agarwahl, Saurabh, Shen, Li, Ruotti, Victor, Wang, Wei, Stewart, Ron, Thomson, James A., Ecker, Joseph R., Ren, Bing

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Histone modifications at human enhancers reflect global cell-type-specific gene expression von Heintzman, Nathaniel D., Hon, Gary C., Hawkins, R. David, Kheradpour, Pouya, Stark, Alexander, Harp, Lindsey F., Ye, Zhen, Lee, Leonard K., Stuart, Rhona K., Ching, Christina W., Ching, Keith A., Antosiewicz-Bourget, Jessica E., Liu, Hui, Zhang, Xinmin, Green, Roland D., Lobanenkov, Victor V., Stewart, Ron, Thomson, James A., Crawford, Gregory E., Kellis, Manolis, Ren, Bing

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Breaking enhancers to gain insights into developmental defects von Armendariz, Daniel A, Sundarrajan, Anjana, Hon, Gary C

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SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples von Zhang, Ze, Luo, Danni, Zhong, Xue, Choi, Jin Huk, Ma, Yuanqing, Wang, Stacy, Mahrt, Elena, Guo, Wei, Stawiski, Eric W, Modrusan, Zora, Seshagiri, Somasekar, Kapur, Payal, Hon, Gary C, Brugarolas, James, Wang, Tao

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Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma von Klein, Jason C, Wang, Lei, Strand, Douglas, Lastufka, Chewlan, Hosler, Gregory A, Hon, Gary C

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Towards functional maps of non-coding variants in cancer von Wang, Yihan, Hon, Gary C

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Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules von Xie, Shiqi, Armendariz, Daniel, Zhou, Pei, Duan, Jialei, Hon, Gary C.

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Blastocyst-like structures generated from human pluripotent stem cells von Yu, Leqian, Wei, Yulei, Duan, Jialei, Schmitz, Daniel A., Sakurai, Masahiro, Wang, Lei, Wang, Kunhua, Zhao, Shuhua, Hon, Gary C., Wu, Jun

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