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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
Published in Genome biology (13.08.2012)

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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
Published in Nature (London) (20.11.2014)

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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
Published in Science (American Association for the Advancement of Science) (24.12.2010)

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Comparative analysis of metazoan chromatin organization

by Ho, Joshua W. K., Jung, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng'en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A., Bowman, Sarah K., Chen, Q. Brent, Chen, Ron A.-J., Day, Daniel S., Dong, Yan, Dose, Andrea C., Duan, Xikun, Epstein, Charles B., Ercan, Sevinc, Feingold, Elise A., Ferrari, Francesco, Garrigues, Jacob M., Gehlenborg, Nils, Good, Peter J., Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M., Jeffers, Tess E., Kharchenko, Peter V., Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V., Kumar, Nischay, Langley, Sasha A., Larschan, Erica N., Latorre, Isabel, Libbrecht, Maxwell W., Lin, Xueqiu, Park, Richard, Pazin, Michael J., Pham, Hoang N., Plachetka, Annette, Qin, Bo, Schwartz, Yuri B., Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M., Xue, Huiling, Kingston, Robert E., Kim, Ju Han, Bernstein, Bradley E., Dernburg, Abby F., Pirrotta, Vincenzo, Kuroda, Mitzi I., Noble, William S., Tullius, Thomas D., Kellis, Manolis, MacAlpine, David M., Strome, Susan, Elgin, Sarah C. R., Liu, Xiaole Shirley, Lieb, Jason D., Ahringer, Julie, Karpen, Gary H., Park, Peter J.
Published in Nature (London) (28.08.2014)

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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
Published in Science (American Association for the Advancement of Science) (24.12.2010)

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Comparative analysis of the transcriptome across distant species

by Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R., Waterston, Robert
Published in Nature (London) (28.08.2014)

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Generation and Initial Analysis of More Than 15,000 Full-Length Human and Mouse cDNA Sequences

by Strausberg, Robert L, Feingold, Elise A, Grouse, Lynette H, Derge, Jeffery G, Klausner, Richard D, Collins, Francis S, Wagner, Lukas, Shenmen, Carolyn M, Schuler, Gregory D, Altschul, Stephen F, Zeeberg, Barry, Buetow, Kenneth H, Schaefer, Carl F, Bhat, Narayan K, Hopkins, Ralph F, Jordan, Heather, Moore, Troy, Max, Steve I, Wang, Jun, Hsieh, Florence, Diatchenko, Luda, Marusina, Kate, Farmer, Andrew A, Rubin, Gerald M, Hong, Ling, Stapleton, Mark, Soares, M Bento, Bonaldo, Maria F, Casavant, Tom L, Scheetz, Todd E, Brownstein, Michael J, Usdin, Ted B, Toshiyuki, Shiraki, Carninci, Piero, Prange, Christa, Raha, Sam S, Loquellano, Naomi A, Peters, Garrick J, Abramson, Rick D, Mullahy, Sara J, Bosak, Stephanie A, McEwan, Paul J, McKernan, Kevin J, Malek, Joel A, Gunaratne, Preethi H, Richards, Stephen, Worley, Kim C, Hale, Sarah, Garcia, Angela M, Gay, Laura J, Hulyk, Stephen W, Villalon, Debbie K, Muzny, Donna M, Sodergren, Erica J, Lu, Xiuhua, Gibbs, Richard A, Fahey, Jessica, Helton, Erin, Ketteman, Mark, Madan, Anuradha, Rodrigues, Stephanie, Sanchez, Amy, Whiting, Michelle, Madan, Anup, Young, Alice C, Shevchenko, Yuriy, Bouffard, Gerard G, Blakesley, Robert W, Touchman, Jeffrey W, Green, Eric D, Dickson, Mark C, Rodriguez, Alex C, Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M, Butterfield, Yaron S N, Krzywinski, Martin I, Skalska, Ursula, Smailus, Duane E, Schnerch, Angelique, Schein, Jacqueline E, Jones, Steven J M, Marra, Marco A
Published in Proceedings of the National Academy of Sciences - PNAS (24.12.2002)

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The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

by Gerhard, Daniela S, Wagner, Lukas, Feingold, Elise A, Shenmen, Carolyn M, Grouse, Lynette H, Schuler, Greg, Klein, Steven L, Old, Susan, Rasooly, Rebekah, Good, Peter, Guyer, Mark, Peck, Allison M, Derge, Jeffery G, Lipman, David, Collins, Francis S, Jang, Wonhee, Sherry, Steven, Feolo, Mike, Misquitta, Leonie, Lee, Eduardo, Rotmistrovsky, Kirill, Greenhut, Susan F, Schaefer, Carl F, Buetow, Kenneth, Bonner, Tom I, Haussler, David, Kent, Jim, Kiekhaus, Mark, Furey, Terry, Brent, Michael, Prange, Christa, Schreiber, Kirsten, Shapiro, Nicole, Bhat, Narayan K, Hopkins, Ralph F, Hsie, Florence, Driscoll, Tom, Soares, M Bento, Casavant, Tom L, Scheetz, Todd E, Brown-stein, Michael J, Usdin, Ted B, Toshiyuki, Shiraki, Carninci, Piero, Piao, Yulan, Dudekula, Dawood B, Ko, Minoru S H, Kawakami, Koichi, Suzuki, Yutaka, Sugano, Sumio, Gruber, C E, Smith, M R, Simmons, Blake, Moore, Troy, Waterman, Richard, Johnson, Stephen L, Ruan, Yijun, Wei, Chia Lin, Mathavan, S, Gunaratne, Preethi H, Wu, Jiaqian, Garcia, Angela M, Hulyk, Stephen W, Fuh, Edwin, Yuan, Ye, Sneed, Anna, Kowis, Carla, Hodgson, Anne, Muzny, Donna M, McPherson, John, Gibbs, Richard A, Fahey, Jessica, Helton, Erin, Ketteman, Mark, Madan, Anuradha, Rodrigues, Stephanie, Sanchez, Amy, Whiting, Michelle, Madari, Anup, Young, Alice C, Wetherby, Keith D, Granite, Steven J, Kwong, Peggy N, Brinkley, Charles P, Pearson, Russell L, Bouffard, Gerard G, Blakesly, Robert W, Green, Eric D, Dickson, Mark C, Rodriguez, Alex C, Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M, Butterfield, Yaron S N, Griffith, Malachi, Griffith, Obi L, Krzywinski, Martin I, Liao, Nancy, Morin, Ryan, Morrin, Ryan
Published in Genome research (01.10.2004)

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The completion of the Mammalian Gene Collection (MGC)

by Temple, Gary, Gerhard, Daniela S, Rasooly, Rebekah, Feingold, Elise A, Good, Peter J, Robinson, Cristen, Mandich, Allison, Derge, Jeffrey G, Lewis, Jeanne, Shoaf, Debonny, Collins, Francis S, Jang, Wonhee, Wagner, Lukas, Shenmen, Carolyn M, Misquitta, Leonie, Schaefer, Carl F, Buetow, Kenneth H, Bonner, Tom I, Yankie, Linda, Ward, Ming, Phan, Lon, Astashyn, Alex, Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maidak, Bonnie L, Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Riddick, Lillian, Webb, David, Weber, Janet, Wu, Wendy, Pruitt, Kim D, Maglott, Donna, Siepel, Adam, Brejova, Brona, Diekhans, Mark, Harte, Rachel, Baertsch, Robert, Kent, Jim, Haussler, David, Brent, Michael, Langton, Laura, Comstock, Charles L G, Stevens, Michael, Wei, Chaochun, van Baren, Marijke J, Salehi-Ashtiani, Kourosh, Murray, Ryan R, Ghamsari, Lila, Mello, Elizabeth, Lin, Chenwei, Pennacchio, Christa, Schreiber, Kirsten, Shapiro, Nicole, Marsh, Amber, Pardes, Elizabeth, Moore, Troy, Lebeau, Anita, Muratet, Mike, Simmons, Blake, Kloske, David, Sieja, Stephanie, Hudson, James, Sethupathy, Praveen, Brownstein, Michael, Bhat, Narayan, Lazar, Joseph, Jacob, Howard, Gruber, Chris E, Smith, Mark R, McPherson, John, Garcia, Angela M, Gunaratne, Preethi H, Wu, Jiaqian, Muzny, Donna, Gibbs, Richard A, Young, Alice C, Bouffard, Gerard G, Blakesley, Robert W, Mullikin, Jim, Green, Eric D, Dickson, Mark C, Rodriguez, Alex C, Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M, Hirst, Martin, Zeng, Thomas, Tse, Kane, Moksa, Michelle, Deng, Merinda, Ma, Kevin, Mah, Diana, Pang, Johnson, Taylor, Greg, Chuah, Eric, Deng, Athena
Published in Genome research (01.12.2009)

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