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Perspectives on ENCODE SCIE SCOPUS

Title: Perspectives on ENCODE

Authors: Abascal, Federico; Acosta, Reyes; Addleman, Nicholas J.; Adrian, Jessika; Afzal, Veena; Aken, Bronwen; Ai, Rizi; Akiyama, Jennifer A.; Jammal, Omar Al; Amrhein, Henry; Anderson, Stacie M.; Andrews, Gregory R.; Antoshechkin, Igor; Ardlie, Kristin G.; Armstrong, Joel; Astley, Matthew; Banerjee, Budhaditya; Barkal, Amira A.; Barnes, If H. A.; Barozzi, Iros; Barrell, Daniel; Barson, Gemma; Bates, Daniel; Baymuradov, Ulugbek K.; Bazile, Cassandra; Beer, Michael A.; Beik, Samantha; Bender, M. A.; Bennett, Ruth; Bouvrette, Louis Philip Benoit; Bernstein, Bradley E.; Berry, Andrew; Bhaskar, Anand; Bignell, Alexandra; Blue, Steven M.; Bodine, David M.; Boix, Carles; Boley, Nathan; Borrman, Tyler; Borsari, Beatrice; Boyle, Alan P.; Brandsmeier, Laurel A.; Breschi, Alessandra; Bresnick, Emery H.; Brooks, Jason A.; Buckley, Michael; Burge, Christopher B.; Byron, Rachel; Cahill, Eileen; Cai, Lingling; Cao, Lulu; Carty, Mark; Castanon, Rosa G.; Castillo, Andres; Chaib, Hassan; Chan, Esther T.; Chee, Daniel R.; Chee, Sora; Chen, Hao; Chen, Huaming; Chen, Jia-Yu; Chen, Songjie; Cherry, J. Michael; Chhetri, Surya B.; Choudhary, Jyoti S.; Chrast, Jacqueline; Chung, Dongjun; Clarke, Declan; Cody, Neal A. L.; Coppola, Candice J.; Coursen, Julie; D’Ippolito, Anthony M.; Dalton, Stephen; Danyko, Cassidy; Davidson, Claire; Davila-Velderrain, Jose; Davis, Carrie A.; Dekker, Job; Deran, Alden; DeSalvo, Gilberto; Despacio-Reyes, Gloria; Dewey, Colin N.; Dickel, Diane E.; Diegel, Morgan; Diekhans, Mark; Dileep, Vishnu; Ding, Bo; Djebali, Sarah; Dobin, Alexander; Dominguez, Daniel; Donaldson, Sarah; Drenkow, Jorg; Dreszer, Timothy R.; Drier, Yotam; Duff, Michael O.; Dunn, Douglass; Eastman, Catharine; Ecker, Joseph R.; Edwards, Matthew D.; El-Ali, Nicole; Elhajjajy, Shaimae I.; Elkins, Keri; Emili, Andrew; Epstein, Charles B.; Evans, Rachel C.; Ezkurdia, Iakes; Fan, Kaili; Farnham, Peggy J.; Farrell, Nina; Feingold, Elise A.; Ferreira, Anne-Maud; Fisher-Aylor, Katherine; Fitzgerald, Stephen; Flicek, Paul; Foo, Chuan Sheng; Fortier, Kevin; Frankish, Adam; Freese, Peter; Fu, Shaliu; Fu, Xiang-Dong; Fu, Yu; Fukuda-Yuzawa, Yoko; Fulciniti, Mariateresa; Funnell, Alister P. W.; Gabdank, Idan; Galeev, Timur; Gao, Mingshi; Giron, Carlos Garcia; Garvin, Tyler H.; Gelboin-Burkhart, Chelsea Anne; Georgolopoulos, Grigorios; Gerstein, Mark B.; Giardine, Belinda M.; Gifford, David K.; Gilbert, David M.; Gilchrist, Daniel A.; Gillespie, Shawn; Gingeras, Thomas R.; Gong, Peng; Gonzalez, Alvaro; Gonzalez, Jose M.; Good, Peter; Goren, Alon; Gorkin, David U.; Graveley, Brenton R.; Gray, Michael; Greenblatt, Jack F.; Griffiths, Ed; Groudine, Mark T.; Grubert, Fabian; Gu, Mengting; Guigó, Roderic; Guo, Hongbo; Guo, Yu; Guo, Yuchun; Gursoy, Gamze; Gutierrez-Arcelus, Maria; Halow, Jessica; Hardison, Ross C.; Hardy, Matthew; Hariharan, Manoj; Harmanci, Arif; Harrington, Anne; Harrow, Jennifer L.; Hashimoto, Tatsunori B.; Hasz, Richard D.; Hatan, Meital; Haugen, Eric; Hayes, James E.; He, Peng; He, Yupeng; Heidari, Nastaran; Hendrickson, David; Heuston, Elisabeth F.; Hilton, Jason A.; Hitz, Benjamin C.; Hochman, Abigail; Holgren, Cory; Hou, Lei; Hou, Shuyu; Hsiao, Yun-Hua E.; Hsu, Shanna; Huang, Hui; Hubbard, Tim J.; Huey, Jack; Hughes, Timothy R.; Hunt, Toby; Ibarrientos, Sean; Issner, Robbyn; Iwata, Mineo; Izuogu, Osagie; Jaakkola, Tommi; Jameel, Nader; Jansen, Camden; Jiang, Lixia; Jiang, Peng; Johnson, Audra; Johnson, Rory; Jungreis, Irwin; Kadaba, Madhura; Kasowski, Maya; Kasparian, Mary; Kato, Momoe; Kaul, Rajinder; Kawli, Trupti; Kay, Michael; Keen, Judith C.; Keles, Sunduz; Keller, Cheryl A.; Kelley, David; Kellis, Manolis; Kheradpour, Pouya; Kim, Daniel Sunwook; Kirilusha, Anthony; Klein, Robert J.; Knoechel, Birgit; Kuan, Samantha; Kulik, Michael J.; Kumar, Sushant; Kundaje, Anshul; Kutyavin, Tanya; Lagarde, Julien; Lajoie, Bryan R.; Lambert, Nicole J.; Lazar, John; Lee, Ah Young; Lee, Donghoon; Lee, Elizabeth; Lee, Jin Wook; Lee, Kristen; Leslie, Christina S.; Levy, Shawn; Li, Bin; Li, Hairi; Li, Nan; Li, Shantao; Li, Xiangrui; Li, Yang I.; Li, Ying; Li, Yining; Li, Yue; Lian, Jin; Libbrecht, Maxwell W.; Lin, Shin; Lin, Yiing; Liu, Dianbo; Liu, Jason; Liu, Peng; Liu, Tingting; Liu, X. Shirley; Liu, Yan; Liu, Yaping; Long, Maria; Lou, Shaoke; Loveland, Jane; Lu, Aiping; Lu, Yuheng; Lécuyer, Eric; Ma, Lijia; Mackiewicz, Mark; Mannion, Brandon J.; Mannstadt, Michael; Manthravadi, Deepa; Marinov, Georgi K.; Martin, Fergal J.; Mattei, Eugenio; McCue, Kenneth; McEown, Megan; McVicker, Graham; Meadows, Sarah K.; Meissner, Alex; Mendenhall, Eric M.; Messer, Christopher L.; Meuleman, Wouter; Meyer, Clifford; Miller, Steve; Milton, Matthew G.; Mishra, Tejaswini; Moore, Dianna E.; Moore, Helen M.; Moore, Jill E.; Moore, Samuel H.; Moran, Jennifer; Mortazavi, Ali; Mudge, Jonathan M.; Munshi, Nikhil; Murad, Rabi; Myers, Richard M.; Nandakumar, Vivek; Nandi, Preetha; Narasimha, Anil M.; Narayanan, Aditi K.; Naughton, Hannah; Navarro, Fabio C. P.; Navas, Patrick; Nazarovs, Jurijs; Nelson, Jemma; Neph, Shane; Neri, Fidencio Jun; Nery, Joseph R.; Nesmith, Amy R.; Newberry, J. Scott; Newberry, Kimberly M.; Ngo, Vu; Nguyen, Rosy; Nguyen, Thai B.; Nguyen, Tung; Nishida, Andrew; Noble, William S.; Novak, Catherine S.; Novoa, Eva Maria; Nuñez, Briana; O’Donnell, Charles W.; Olson, Sara; Onate, Kathrina C.; Otterman, Ericka; Ozadam, Hakan; Pagan, Michael; Palden, Tsultrim; Pan, Xinghua; Park, Yongjin; Partridge, E. Christopher; Paten, Benedict; Pauli-Behn, Florencia; Pazin, Michael J.; Pei, Baikang; Pennacchio, Len A.; Perez, Alexander R.; Perry, Emily H.; Pervouchine, Dmitri D.; Phalke, Nishigandha N.; Pham, Quan; Phanstiel, Doug H.; Plajzer-Frick, Ingrid; Pratt, Gabriel A.; Pratt, Henry E.; Preissl, Sebastian; Pritchard, Jonathan K.; Pritykin, Yuri; Purcaro, Michael J.; Qin, Qian; Quinones-Valdez, Giovanni; Rabano, Ines; Radovani, Ernest; Raj, Anil; Rajagopal, Nisha; Ram, Oren; Ramirez, Lucia; Ramirez, Ricardo N.; Rausch, Dylan; Raychaudhuri, Soumya; Raymond, Joseph; Razavi, Rozita; Reddy, Timothy E.; Reimonn, Thomas M.; Ren, Bing; Reymond, Alexandre; Reynolds, Alex; Rhie, Suhn K.; Rinn, John; Rivera, Miguel; Rivera-Mulia, Juan Carlos; Roberts, Brian; Rodriguez, Jose Manuel; Rozowsky, Joel; Ryan, Russell; Rynes, Eric; Salins, Denis N.; Sandstrom, Richard; Sasaki, Takayo; Sathe, Shashank; Savic, Daniel; Scavelli, Alexandra; Scheiman, Jonathan; Schlaffner, Christoph; Schloss, Jeffery A.; Schmitges, Frank W.; See, Lei Hoon; Sethi, Anurag; Setty, Manu; Shafer, Anthony; Shan, Shuo; Sharon, Eilon; Shen, Quan; Shen, Yin; Sherwood, Richard I.; Shi, Minyi; Shin, Sunyoung; Shoresh, Noam; Siebenthall, Kyle; Sisu, Cristina; Slifer, Teri; Sloan, Cricket A.; Smith, Anna; Snetkova, Valentina; Snyder, Michael P.; Spacek, Damek V.; Srinivasan, Sharanya; Srivas, Rohith; Stamatoyannopoulos, George; Stamatoyannopoulos, John A.; Stanton, Rebecca; Steffan, Dave; Stehling-Sun, Sandra; Strattan, J. Seth; Su, Amanda; Sundararaman, Balaji; Suner, Marie-Marthe; Syed, Tahin; Szynkarek, Matt; Tanaka, Forrest Y.; Tenen, Danielle; Teng, Mingxiang; Thomas, Jeffrey A.; Toffey, Dave; Tress, Michael L.; Trout, Diane E.; Trynka, Gosia; Tsuji, Junko; Upchurch, Sean A.; Ursu, Oana; Uszczynska-Ratajczak, Barbara; Uziel, Mia C.; Valencia, Alfonso; Biber, Benjamin Van; van der Velde, Arjan G.; Van Nostrand, Eric L.; Vaydylevich, Yekaterina; Vazquez, Jesus; Victorsen, Alec; Vielmetter, Jost; Vierstra, Jeff; Visel, Axel; Vlasova, Anna; Vockley, Christopher M.; Volpi, Simona; Vong, Shinny; Wang, Hao; Wang, Mengchi; Wang, Qin; Wang, Ruth; Wang, Tao; Wang, Wei; Wang, Xiaofeng; Wang, Yanli; Watson, Nathaniel K.; Wei, Xintao; Wei, Zhijie; Weisser, Hendrik; Weissman, Sherman M.; Welch, Rene; Welikson, Robert E.; Weng, Zhiping; Westra, Harm-Jan; Whitaker, John W.; White, Collin; White, Kevin P.; Wildberg, Andre; Williams, Brian A.; Wine, David; Witt, Heather N.; Wold, Barbara; Wolf, Maxim; Wright, James; Xiao, Rui; Xiao, Xinshu; Xu, Jie; Xu, Jinrui; Yan, Koon-Kiu; Yan, Yongqi; Yang, Hongbo; Yang, Xinqiong; Yang, Yi-Wen; Yardımcı, Galip Gürkan; Yee, Brian A.; Yeo, Gene W.; Young, Taylor; Yu, Tianxiong; Yue, Feng; Zaleski, Chris; Zang, Chongzhi; Zeng, Haoyang; Zeng, Weihua; Zerbino, Daniel R.; Zhai, Jie; Zhan, Lijun; Zhan, Ye; Zhang, Bo; Zhang, Jialing; Zhang, Jing; Zhang, Kai; Zhang, Lijun; Zhang, Peng; Zhang, Qi; Zhang, Xiao-Ou; Zhang, Yanxiao; Zhang, Zhizhuo; Zhao, Yuan; Zheng, Ye; Zhong, Guoqing; Zhou, Xiao-Qiao; Zhu, Yun; Zimmerman, Jared; Snyder, Michael P.; Gingeras, Thomas R.; Moore, Jill E.; Weng, Zhiping; Gerstein, Mark B.; Ren, Bing; Hardison, Ross C.; Stamatoyannopoulos, John A.; Graveley, Brenton R.; Feingold, Elise A.; Pazin, Michael J.; Pagan, Michael; Gilchrist, Daniel A.; Hitz, Benjamin C.; Cherry, J. Michael; Bernstein, Bradley E.; Mendenhall, Eric M.; Zerbino, Daniel R.; Frankish, Adam; Flicek, Paul; Myers, Richard M.

Date Issued: 2020-07

Publisher: Nature Publishing Group

Abstract: The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.