Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation
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
Published in BMC genomics (12.09.2017)
Published in BMC genomics (12.09.2017)
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Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
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Published in Genome Biology (04.10.2021)
Published in Genome Biology (04.10.2021)
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Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser
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
Published in Nature biotechnology (01.04.2015)
Published in Nature biotechnology (01.04.2015)
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Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
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
Published in Genome research (01.09.2013)
Published in Genome research (01.09.2013)
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Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers
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
Published in BMC genomics (06.10.2014)
Published in BMC genomics (06.10.2014)
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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types
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.
Published in Nature communications (25.11.2014)
Published in Nature communications (25.11.2014)
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A comparative encyclopedia of DNA elements in the mouse genome
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
Published in Nature (London) (20.11.2014)
Published in Nature (London) (20.11.2014)
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Exploring long-range genome interactions using the WashU Epigenome Browser
Zhou, Xin, Lowdon, Rebecca F, Li, Daofeng, Lawson, Heather A, Madden, Pamela A F, Costello, Joseph F, Wang, Ting
Published in Nature methods (01.05.2013)
Published in Nature methods (01.05.2013)
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An encyclopedia of mouse DNA elements (Mouse ENCODE)
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
Published in Genome biology (13.08.2012)
Published in Genome biology (13.08.2012)
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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
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
Published in Science (American Association for the Advancement of Science) (24.12.2010)
Published in Science (American Association for the Advancement of Science) (24.12.2010)
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Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease
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.
Published in Developmental cell (03.05.2021)
Published in Developmental cell (03.05.2021)
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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
Xie, Mingchao, Hong, Chibo, Zhang, Bo, Lowdon, Rebecca F, Xing, Xiaoyun, Li, Daofeng, Zhou, Xin, Lee, Hyung Joo, Maire, Cecile L, Ligon, Keith L, Gascard, Philippe, Sigaroudinia, Mahvash, Tlsty, Thea D, Kadlecek, Theresa, Weiss, Arthur, O'Geen, Henriette, Farnham, Peggy J, Madden, Pamela A F, Mungall, Andrew J, Tam, Angela, Kamoh, Baljit, Cho, Stephanie, Moore, Richard, Hirst, Martin, Marra, Marco A, Costello, Joseph F, Wang, Ting
Published in Nature genetics (01.07.2013)
Published in Nature genetics (01.07.2013)
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Exploring long-range genome interaction data using the WashU Epigenome Browser
Zhou, Xin, Lowdon, Rebecca F., Li, Daofeng, Lawson, Heather A, Madden, Pamela A.F., Costello, Joseph F., Wang, Ting
Published in Nature methods (01.05.2013)
Published in Nature methods (01.05.2013)
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