Gene-specific patterns of expression variation across organs and species

por Breschi, Alessandra, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D., Dobin, Alex, Davis, Carrie A., Gingeras, Thomas R., Guigó, Roderic
Publicado 2016

Dynamics of microRNA expression during mouse prenatal development

por Rahmanian, Sorena, Murad, Rabi, Breschi, Alessandra, Zeng, Weihua, Mackiewicz, Mark, Williams, Brian, Davis, Carrie A., Roberts, Brian, Meadows, Sarah, Moore, Dianna, Trout, Diane, Zaleski, Chris, Dobin, Alex, Sei, Lei-Hoon, Drenkow, Jorg, Scavelli, Alex, Gingeras, Thomas R., Wold, Barbara J., Myers, Richard M., Guigó, Roderic, Mortazavi, Ali
Publicado 2019

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

por Pervouchine, Dmitri D., Djebali, Sarah, Breschi, Alessandra, Davis, Carrie A., Barja, Pablo Prieto, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael A., Notredame, Cedric, Guigó, Roderic, Gingeras, Thomas R.
Publicado 2015

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

por Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M., Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Martin, David, Murray, Ryan R., Yang, Xinping, Ghamsari, Lila, Lin, Chenwei, Bell, Ian, Dumais, Erica, Drenkow, Jorg, Tress, Michael L., Gelpí, Josep Lluís, Orozco, Modesto, Valencia, Alfonso, van Berkum, Nynke L., Lajoie, Bryan R., Vidal, Marc, Stamatoyannopoulos, John, Batut, Philippe, Dobin, Alex, Harrow, Jennifer, Hubbard, Tim, Dekker, Job, Frankish, Adam, Salehi-Ashtiani, Kourosh, Reymond, Alexandre, Antonarakis, Stylianos E., Guigó, Roderic, Gingeras, Thomas R.
Publicado 2012

The Developmental Transcriptome of Drosophila melanogaster

por Graveley, Brenton R., Brooks, Angela N., Carlson, Joseph W., Duff, Michael O., Landolin, Jane M., Yang, Li, Artieri, Carlo G., van Baren, Marijke J., Boley, Nathan, Booth, Benjamin W., Brown, James B., Cherbas, Lucy, Davis, Carrie A., Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H., Mattiuzzo, Nicolas R., Miller, David, Sturgill, David, Tuch, Brian B., Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E., Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E., Wan, Kenneth H., Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J., Brenner, Steven E., Brent, Michael R., Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Oliver, Brian, Celniker, Susan E.
Publicado 2010

The ENCODE Uniform Analysis Pipelines

por Hitz, Benjamin C., Jin-Wook, Lee, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, Kent, W. James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael
Publicado 2023

The ENCODE Uniform Analysis Pipelines

por Hitz, Benjamin C., Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, Kent, W. James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael
Publicado 2023

Landscape of transcription in human cells

por Djebali, Sarah, Davis, Carrie A., Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali M., Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K., Khatun, Jainab, Williams, Brian A., Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Bar, Nadav S., Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J., Park, Eddie, Persaud, Kimberly, Preall, Jonathan B., Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory, Giddings, Morgan C., Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R.
Publicado 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE)

por 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, Lajoie1, 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
Publicado 2012

Comparative Analysis of the Transcriptome across Distant Species

por 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
Publicado 2014

A comparative encyclopedia of DNA elements in the mouse genome

por Yue, Feng, Cheng, Yong, Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Thurman, Robert E., Kaul, Rajinder, Rynes, Eric, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Amrhein, Henry, Fisher-Aylor, Katherine, Antoshechkin, Igor, DeSalvo, Gilberto, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Zaleski, Chris, Dobin, Alex, Prieto, Pablo, Lagarde, Julien, Bussotti, Giovanni, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Byron, Rachel, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Kellis, Manolis, Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Jain, Deepti, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Kawli, Trupti, Boyle, Alan P., Euskirchen, Ghia, Kundaje, Anshul, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Erickson, Drew T., Kirkup, Vanessa M., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Lacerda de Sousa, Beatriz, Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, James Kent, W., Ramalho Santos, Miguel, Herrero, Javier, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Haugen, Eric, Dunn, Douglas, Reynolds, Alex P., Neph, Shane, Humbert, Richard, Scott Hansen, R., De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Eichler, Evan E., Orkin, Stuart H., Levasseur, Dana, Papayannopoulou, Thalia, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Blobel, Gerd A., Cao, Xiaoyi, Zhong, Sheng, Wang, Ting, Good, Peter J., Lowdon, Rebecca F., 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., Gilbert, David M., Hardison, Ross C., Beer, Michael A., Ren, Bing
Publicado 2014