Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer by Lowdon, Rebecca F, Wang, Ting

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Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm by Zhang, Bo, Zhou, Yan, Lin, Nan, Lowdon, Rebecca F, Hong, Chibo, Nagarajan, Raman P, Cheng, Jeffrey B, Li, Daofeng, Stevens, Michael, Lee, Hyung Joo, Xing, Xiaoyun, Zhou, Jia, Sundaram, Vasavi, Elliott, Ginell, Gu, Junchen, Shi, Taoping, Gascard, Philippe, Sigaroudinia, Mahvash, Tlsty, Thea D, Kadlecek, Theresa, Weiss, Arthur, O'Geen, Henriette, Farnham, Peggy J, Maire, Cécile L, Ligon, Keith L, Madden, Pamela A F, Tam, Angela, Moore, Richard, Hirst, Martin, Marra, Marco A, Zhang, Baoxue, Costello, Joseph F, Wang, Ting

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Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation by Zhou, Jia, Sears, Renee L, Xing, Xiaoyun, Zhang, Bo, Li, Daofeng, Rockweiler, Nicole B, Jang, Hyo Sik, Choudhary, Mayank N K, Lee, Hyung Joo, Lowdon, Rebecca F, Arand, Jason, Tabers, Brianne, Gu, C Charles, Cicero, Theodore J, Wang, Ting

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Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish by Jang, Hyo Sik, Chen, Yujie, Ge, Jiaxin, Wilkening, Alicia N, Hou, Yiran, Lee, Hyung Joo, Choi, You Rim, Lowdon, Rebecca F, Xing, Xiaoyun, Li, Daofeng, Kaufman, Charles K, Johnson, Stephen L, Wang, Ting

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Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser by Zhou, Xin, Li, Daofeng, Zhang, Bo, Lowdon, Rebecca F, Rockweiler, Nicole B, Sears, Renee L, Madden, Pamela A F, Smirnov, Ivan, Costello, Joseph F, Wang, Ting

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Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers by Zhang, Bo, Xing, XiaoYun, Li, Jing, Lowdon, Rebecca F, Zhou, Yan, Lin, Nan, Zhang, Baoxue, Sundaram, Vasavi, Chiappinelli, Katherine B, Hagemann, Ian S, Mutch, David G, Goodfellow, Paul J, Wang, Ting

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Evolution of Epigenetic Regulation in Vertebrate Genomes by Lowdon, Rebecca F, Jang, Hyo Sik, Wang, Ting

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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types by Lowdon, Rebecca F., Zhang, Bo, Bilenky, Misha, Mauro, Thea, Li, Daofeng, Gascard, Philippe, Sigaroudinia, Mahvash, Farnham, Peggy J., Bastian, Boris C., Tlsty, Thea D., Marra, Marco A., Hirst, Martin, Costello, Joseph F., Wang, Ting, Cheng, Jeffrey B.

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A comparative encyclopedia of DNA elements in the mouse genome by Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Kaul, Rajinder, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Antoshechkin, Igor, See, Lei-Hoon, Zaleski, Chris, Dobin, Alex, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Boyle, Alan P., Euskirchen, Ghia, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Wilken, Matthew S., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Dunn, Douglas, Humbert, Richard, De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Orkin, Stuart H., Levasseur, Dana, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Zhong, Sheng, Good, Peter J., Adams, Leslie B., Zhou, Xiao-Qiao, Pazin, Michael J., Feingold, Elise A., Wold, Barbara, Taylor, James, Mortazavi, Ali, Weissman, Sherman M., Stamatoyannopoulos, John A., Snyder, Michael P., Guigo, Roderic, Gingeras, Thomas R., Beer, Michael A., Ren, Bing

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An encyclopedia of mouse DNA elements (Mouse ENCODE) by Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, Adams, Leslie B

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Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease by Zhang, Bo, Kim, M. Yvonne, Elliot, GiNell, Zhou, Yan, Zhao, Guangfeng, Li, Daofeng, Lowdon, Rebecca F., Gormley, Matthew, Kapidzic, Mirhan, Robinson, Joshua F., McMaster, Michael T., Hong, Chibo, Mazor, Tali, Hamilton, Emily, Sears, Renee L., Pehrsson, Erica C., Marra, Marco A., Jones, Steven J.M., Bilenky, Misha, Hirst, Martin, Wang, Ting, Costello, Joseph F., Fisher, Susan J.

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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project by Gerstein, Mark B, Lu, Zhi John, Van Nostrand, Eric L, Cheng, Chao, Liu, Tao, Yip, Kevin Y, Robilotto, Rebecca, Rechtsteiner, Andreas, Ikegami, Kohta, Alves, Pedro, Chateigner, Aurelien, Morris, Mitzi, Feng, Xin, Leng, Jing, Vielle, Anne, Niu, Wei, Rhrissorrakrai, Kahn, Alexander, Roger P, Barber, Galt, Brdlik, Cathleen M, Brennan, Jennifer, Brouillet, Jeremy Jean, Carr, Adrian, Cheung, Ming-Sin, Clawson, Hiram, Contrino, Sergio, Dannenberg, Luke O, Dernburg, Abby F, Dosé, Andréa C, Egelhofer, Thea, Euskirchen, Ghia, Ewing, Brent, Gassmann, Reto, Good, Peter J, Green, Phil, Gullier, Francois, Gutwein, Michelle, Habegger, Lukas, Henikoff, Jorja G, Henz, Stefan R, Hinrichs, Angie, Hyman, Tony, Iniguez, A. Leo, Janette, Judith, Jensen, Morten, Kato, Masaomi, Kent, W. James, Kephart, Ellen, Khurana, Ekta, Kim, John K, Lai, Eric C, Latorre, Isabel, Lewis, Suzanna, Lloyd, Paul, Lochovsky, Lucas, Lubling, Yaniv, Lyne, Rachel, MacCoss, Michael, Mackowiak, Sebastian D, Mangone, Marco, McKay, Sheldon, Mecenas, Desirea, Merrihew, Gennifer, Miller, David M. III, Muroyama, Andrew, Murray, John I, Ooi, Siew-Loon, Pham, Hoang, Phippen, Taryn, Rajewsky, Nikolaus, Rätsch, Gunnar, Rosenbaum, Heidi, Ruzanov, Peter, Sboner, Andrea, Scheid, Paul, Shou, Chong, Slack, Frank J, Slightam, Cindie, Spencer, William C, Stinson, E.O, Vafeados, Dionne, Voronina, Ksenia, Wang, Guilin, Washington, Nicole L, Whittle, Christina M, Wu, Beijing, Yan, Koon-Kiu, Zeller, Georg, Zhong, Mei, Zhou, Xingliang, Strome, Susan, Gunsalus, Kristin C, Micklem, Gos, Liu, X. Shirley, Kim, Stuart K, Henikoff, Steven, Piano, Fabio, Snyder, Michael, Stein, Lincoln, Waterston, Robert H

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methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser by Zhou, Xin, Li, Daofeng, Lowdon, Rebecca F, Costello, Joseph F, Wang, Ting

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Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos by Lee, Hyung Joo, Lowdon, Rebecca F., Maricque, Brett, Zhang, Bo, Stevens, Michael, Li, Daofeng, Johnson, Stephen L., Wang, Ting

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Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos by Lee, Hyung Joo, Lowdon, Rebecca F., Maricque, Brett, Zhang, Bo, Stevens, Michael, Li, Daofeng, Johnson, Stephen L., Wang, Ting

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An integrated encyclopedia of DNA elements in the human genome by Kundaje, Anshul, Collins, Patrick J, Davis, Carrie A, Khatun, Jainab, Lajoie, Bryan R, Landt, Stephen G, Safi, Alexias, Altshuler, Robert C, Cheng, Chao, Greven, Melissa, Hoffman, Michael M, Lassmann, Timo, Thurman, Robert E, Wu, Weisheng, Xi, Hualin S, Zhuang, Jiali, Gunter, Chris, Dekker, Job, Elnitski, Laura, Giddings, Morgan C, Margulies, Elliott H, Stamatoyannopoulos, John A, Wold, Barbara, Kuiper, Heather C, Dobin, Alex, Tanzer, Andrea, Xue, Chenghai, Zaleski, Chris, Roder, Maik, Baer, Michael T, Bell, Kimberly, Gordon, Assaf, Howald, Cedric, Johnson, Rory, Kingswood, Colin, Li, Guoliang, Luo, Oscar J, Robyr, Daniel, Ruan, Xiaoan, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Wang, Huaien, Hayashizaki, Yoshihide, Hannon, Gregory J, Malladi, Venkat S, Dreszer, Timothy R, Showers, Kimberly A, London, Darin, Zhang, Zhancheng, Keefe, Damian, Zheng, Meizhen, Vielmetter, Jost, Jain, Preti, Pusey, Barbara, Meadows, Sarah K, Absher, Devin M, Pennachio, Len A, Abyzov, Alexej, Barrell, Daniel, Bignell, Alexandra, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Hunt, Toby, Jungreis, Irwin, Loveland, Jane, Manthravadi, Deepa, Pei, Baikang, Snow, Catherine, Zhang, Zhengdong, Alexander, Roger P, Balasubramanian, Suganthi, Bettinger, Keith, Cayting, Philip, Habegger, Lukas, Lamarre-Vincent, Nathan, Lindahl-Allen, Marianne, Monahan, Hannah, Patacsil, Dorrelyn, Struhl, Kevin, Ma, Lijia, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Bates, Daniel L, Canfield, Theresa K, Boatman, Lisa, Neph, Shane J, Roach, Vaughn, Sanchez, Minerva E, Shafer, Anthony O, Vernot, Benjamin, Weaver, Molly A, Akey, Joshua M, Bender, Michael, Navas, Patrick, Hussami, Nadine, Schaub, Marc A

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Characterization of neurotransmitter phenotypes in the developing Xenopus retina by Lowdon, Rebecca F., Saha, Margaret S.

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Integrative analysis of 111 reference human epigenomes by 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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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE by Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V, Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L, Landolin, Jane M, Bristow, Christopher A, Ma, Lijia, Lin, Michael F, Washietl, Stefan, Arshinoff, Bradley I, Ay, Ferhat, Meyer, Patrick E, Robine, Nicolas, Washington, Nicole L, Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D, Candeias, Rogerio, Carlson, Joseph W, Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y, Will, Sebastian, Alekseyenko, Artyom A, Artieri, Carlo, Booth, Benjamin W, Brooks, Angela N, Dai, Qi, Davis, Carrie A, Duff, Michael O, Feng, Xin, Gorchakov, Andrey A, Gu, Tingting, Henikoff, Jorja G, Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K, Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K, Riddle, Nicole C, Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E, Schwartz, Yuri B, Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H, Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E, Brent, Michael R, Cherbas, Lucy, Elgin, Sarah C.R, Gingeras, Thomas R, Grossman, Robert, Hoskins, Roger A, Kaufman, Thomas C, Kent, William, Kuroda, Mitzi I, Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W, Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R, Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J, Celniker, Susan E, Henikoff, Steven, Karpen, Gary H, Lai, Eric C, MacAlpine, David M, Stein, Lincoln D, White, Kevin P, Kellis, Manolis

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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms [version 1; peer review: 1 approved, 3 approv... by Walker, Kimberly, Kalra, Divya, Lowdon, Rebecca, Chen, Guangyi, Molik, David, Soto, Daniela C., Dabbaghie, Fawaz, Khleifat, Ahmad Al, Mahmoud, Medhat, Paulin, Luis F, Raza, Muhammad Sohail, Pfeifer, Susanne P., Agustinho, Daniel Paiva, Aliyev, Elbay, Avdeyev, Pavel, Barrozo, Enrico R., Behera, Sairam, Billingsley, Kimberley, Chong, Li Chuin, Choubey, Deepak, De Coster, Wouter, Fu, Yilei, Gener, Alejandro R., Hefferon, Timothy, Henke, David Morgan, Höps, Wolfram, Illarionova, Anastasia, Jochum, Michael D., Jose, Maria, Kesharwani, Rupesh K., Kolora, Sree Rohit Raj, Kubica, Jędrzej, Lakra, Priya, Lattimer, Damaris, Liew, Chia-Sin, Lo, Bai-Wei, Lo, Chunhsuan, Lötter, Anneri, Majidian, Sina, Mendem, Suresh Kumar, Mondal, Rajarshi, Ohmiya, Hiroko, Parvin, Nasrin, Peralta, Carolina, Poon, Chi-Lam, Prabhakaran, Ramanandan, Saitou, Marie, Sammi, Aditi, Sanio, Philippe, Sapoval, Nicolae, Syed, Najeeb, Treangen, Todd, Wang, Gaojianyong, Xu, Tiancheng, Yang, Jianzhi, Zhang, Shangzhe, Zhou, Weiyu, Sedlazeck, Fritz J, Busby, Ben

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