Candidate silencer elements for the human and mouse genomes von Doni Jayavelu, Naresh, Jajodia, Ajay, Mishra, Arpit, Hawkins, R. David

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Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy von Bengtsson, Niclas E., Hall, John K., Odom, Guy L., Phelps, Michael P., Andrus, Colin R., Hawkins, R. David, Hauschka, Stephen D., Chamberlain, Joel R., Chamberlain, Jeffrey S.

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Integrative analysis of 111 reference human epigenomes von Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Bilenky, Misha, Yen, Angela, Heravi-Moussavi, Alireza, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ziller, Michael J., Amin, Viren, Whitaker, John W., Schultz, Matthew D., Ward, Lucas D., Sarkar, Abhishek, Quon, Gerald, Sandstrom, Richard S., Eaton, Matthew L., Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Coarfa, Cristian, Harris, R. Alan, Shoresh, Noam, Epstein, Charles B., Gjoneska, Elizabeta, Leung, Danny, Xie, Wei, Hawkins, R. David, Lister, Ryan, Hong, Chibo, Gascard, Philippe, Mungall, Andrew J., Moore, Richard, Chuah, Eric, Tam, Angela, Canfield, Theresa K., Hansen, R. Scott, Kaul, Rajinder, Sabo, Peter J., Bansal, Mukul S., Carles, Annaick, Dixon, Jesse R., Farh, Kai-How, Feizi, Soheil, Karlic, Rosa, Kim, Ah-Ram, Kulkarni, Ashwinikumar, Li, Daofeng, Lowdon, Rebecca, Elliott, GiNell, Mercer, Tim R., Neph, Shane J., Onuchic, Vitor, Polak, Paz, Rajagopal, Nisha, Ray, Pradipta, Sallari, Richard C., Siebenthall, Kyle T., Sinnott-Armstrong, Nicholas A., Stevens, Michael, Thurman, Robert E., Wu, Jie, Zhang, Bo, Zhou, Xin, Beaudet, Arthur E., Boyer, Laurie A., De Jager, Philip L., Farnham, Peggy J., Fisher, Susan J., Haussler, David, Jones, Steven J. M., Li, Wei, Marra, Marco A., McManus, Michael T., Sunyaev, Shamil, Thomson, James A., Tlsty, Thea D., Tsai, Li-Huei, Wang, Wei, Waterland, Robert A., Zhang, Michael Q., Chadwick, Lisa H., Bernstein, Bradley E., Costello, Joseph F., Ecker, Joseph R., Hirst, Martin, Meissner, Alexander, Milosavljevic, Aleksandar, Ren, Bing, Stamatoyannopoulos, John A., Wang, Ting, Kellis, Manolis

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Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells von Xie, Wei, Schultz, Matthew D., Lister, Ryan, Hou, Zhonggang, Rajagopal, Nisha, Ray, Pradipta, Whitaker, John W., Tian, Shulan, Hawkins, R. David, Leung, Danny, Yang, Hongbo, Wang, Tao, Lee, Ah Young, Swanson, Scott A., Zhang, Jiuchun, Zhu, Yun, Kim, Audrey, Nery, Joseph R., Urich, Mark A., Kuan, Samantha, Yen, Chia-an, Klugman, Sarit, Yu, Pengzhi, Suknuntha, Kran, Propson, Nicholas E., Chen, Huaming, Edsall, Lee E., Wagner, Ulrich, Li, Yan, Ye, Zhen, Kulkarni, Ashwinikumar, Xuan, Zhenyu, Chung, Wen-Yu, Chi, Neil C., Antosiewicz-Bourget, Jessica E., Slukvin, Igor, Stewart, Ron, Zhang, Michael Q., Wang, Wei, Thomson, James A., Ecker, Joseph R., Ren, Bing

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Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells von Lister, Ryan, Pelizzola, Mattia, Kida, Yasuyuki S., Hawkins, R. David, Nery, Joseph R., Hon, Gary, Antosiewicz-Bourget, Jessica, O’Malley, Ronan, Castanon, Rosa, Klugman, Sarit, Downes, Michael, Yu, Ruth, Stewart, Ron, Ren, Bing, Thomson, James A., Evans, Ronald M., Ecker, Joseph R.

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The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition von Sperber, Henrik, Mathieu, Julie, Wang, Yuliang, Ferreccio, Amy, Hesson, Jennifer, Xu, Zhuojin, Fischer, Karin A., Devi, Arikketh, Detraux, Damien, Gu, Haiwei, Battle, Stephanie L., Showalter, Megan, Valensisi, Cristina, Bielas, Jason H., Ericson, Nolan G., Margaretha, Lilyana, Robitaille, Aaron M., Margineantu, Daciana, Fiehn, Oliver, Hockenbery, David, Blau, C. Anthony, Raftery, Daniel, Margolin, Adam A., Hawkins, R. David, Moon, Randall T., Ware, Carol B., Ruohola-Baker, Hannele

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Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential von Kyttälä, Aija, Moraghebi, Roksana, Valensisi, Cristina, Kettunen, Johannes, Andrus, Colin, Pasumarthy, Kalyan Kumar, Nakanishi, Mahito, Nishimura, Ken, Ohtaka, Manami, Weltner, Jere, Van Handel, Ben, Parkkonen, Olavi, Sinisalo, Juha, Jalanko, Anu, Hawkins, R. David, Woods, Niels-Bjarne, Otonkoski, Timo, Trokovic, Ras

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Three-dimensional genome architecture and emerging technologies: looping in disease von Mishra, Arpit, Hawkins, R David

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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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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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Derivation of naïve human embryonic stem cells von Ware, Carol B., Nelson, Angelique M., Mecham, Brigham, Hesson, Jennifer, Zhou, Wenyu, Jonlin, Erica C., Jimenez-Caliani, Antonio J., Deng, Xinxian, Cavanaugh, Christopher, Cook, Savannah, Tesar, Paul J., Okada, Jeffrey, Margaretha, Lilyana, Sperber, Henrik, Choi, Michael, Balu, C. Anthony, Treuting, Piper M., Hawkins, R. David, Cirulli, Vincenzo, Ruohola-Baker, Hannele

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Histone modifications at human enhancers reflect global cell-type-specific gene expression von Ren, Bing, 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

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Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation von Rummukainen, Petri, Tarkkonen, Kati, Dudakovic, Amel, Al-Majidi, Rana, Nieminen-Pihala, Vappu, Valensisi, Cristina, Hawkins, R David, van Wijnen, Andre J, Kiviranta, Riku

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Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation von Yu, Bo, Doni Jayavelu, Naresh, Battle, Stephanie L, Mar, Jessica C, Schimmel, Timothy, Cohen, Jacques, Hawkins, R David

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Global Chromatin State Analysis Reveals Lineage-Specific Enhancers during the Initiation of Human T helper 1 and T helper 2 Cell Polarization von Hawkins, R. David, Larjo, Antti, Tripathi, Subhash K., Wagner, Ulrich, Luu, Ying, Lönnberg, Tapio, Raghav, Sunil K., Lee, Leonard K., Lund, Riikka, Ren, Bing, Lähdesmäki, Harri, Lahesmaa, Riitta

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome von Ren, Bing, Heintzman, Nathaniel D, Stuart, Rhona K, Hon, Gary, Fu, Yutao, Ching, Christina W, Hawkins, R David, Barrera, Leah O, Van Calcar, Sara, Qu, Chunxu, Ching, Keith A, Wang, Wei, Weng, Zhiping, Green, Roland D, Crawford, Gregory E

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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications von Costello, Joseph F, Harris, R Alan, Wang, Ting, Coarfa, Cristian, Nagarajan, Raman P, Hong, Chibo, Downey, Sara L, Johnson, Brett E, Fouse, Shaun D, Delaney, Allen, Zhao, Yongjun, Olshen, Adam, Ballinger, Tracy, Zhou, Xin, Forsberg, Kevin J, Gu, Junchen, Echipare, Lorigail, O'Geen, Henriette, Lister, Ryan, Pelizzola, Mattia, Xi, Yuanxin, Epstein, Charles B, Bernstein, Bradley E, Hawkins, R David, Ren, Bing, Chung, Wen-Yu, Gu, Hongcang, Bock, Christoph, Gnirke, Andreas, Zhang, Michael Q, Haussler, David, Ecker, Joseph R, Li, Wei, Farnham, Peggy J, Waterland, Robert A, Meissner, Alexander, Marra, Marco A, Hirst, Martin, Milosavljevic, Aleksandar

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Methods for Identifying Higher-Order Chromatin Structure von Sajan, Samin A, Hawkins, R. David

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Identification of functional enhancer variants associated with type I diabetes in CD4+ T cells von Mishra, Arpit, Jajodia, Ajay, Weston, Eryn, Jayavelu, Naresh Doni, Garcia, Mariana, Hossack, Daniel, Hawkins, R David

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An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation von Saarimäki-Vire, Jonna, Balboa, Diego, Russell, Mark A., Saarikettu, Juha, Kinnunen, Matias, Keskitalo, Salla, Malhi, Amrinder, Valensisi, Cristina, Andrus, Colin, Eurola, Solja, Grym, Heli, Ustinov, Jarkko, Wartiovaara, Kirmo, Hawkins, R. David, Silvennoinen, Olli, Varjosalo, Markku, Morgan, Noel G., Otonkoski, Timo

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