Gene-specific patterns of expression variation across organs and species

by Breschi, Alessandra, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D, Dobin, Alex, Davis, Carrie A, Gingeras, Thomas R, Guigó, Roderic
Published in Genome Biology

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

by 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
Published in Nature communications

Landscape of transcription in human cells

by DJEBALI, Sarah, DAVIS, Carrie A, CHENGHAI XUE, MARINOV, Georgi K, KHATUN, Jainab, WILLIAMS, Brian A, ZALESKI, Chris, ROZOWSKY, Joel, RÖDER, Maik, KOKOCINSKI, Felix, ABDELHAMID, Rehab F, ALIOTO, Tyler, MERKEL, Angelika, ANTOSHECHKIN, Igor, BAER, Michael T, BAR, Nadav S, BATUT, Philippe, BELL, Kimberly, BELL, Ian, CHAKRABORTTY, Sudipto, XIAN CHEN, CHRAST, Jacqueline, CURADO, Joao, DOBIN, Alex, DERRIEN, Thomas, DRENKOW, Jorg, DUMAIS, Erica, DUMAIS, Jacqueline, DUTTAGUPTA, Radha, FALCONNET, Emilie, FASTUCA, Meagan, FEJES-TOTH, Kata, FERREIRA, Pedro, FOISSAC, Sylvain, LASSMANN, Timo, FULLWOOD, Melissa J, HUI GAO, GONZALEZ, David, GORDON, Assaf, GUNAWARDENA, Harsha, HOWALD, Cedric, JHA, Sonali, JOHNSON, Rory, KAPRANOV, Philipp, KING, Brandon, MORTAZAVI, Ali, KINGSWOOD, Colin, LUO, Oscar J, PARK, Eddie, PERSAUD, Kimberly, PREALL, Jonathan B, RIBECA, Paolo, RISK, Brian, ROBYR, Daniel, SAMMETH, Michael, SCHAFFER, Lorian, TANZER, Andrea, LAGARDE, Julien, WEI LIN, SCHLESINGER, Felix
Published in Nature (London)

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)

Principles of regulatory information conservation between mouse and human

by Cheng, Yong, Ma, Zhihai, Kim, Bong-Hyun, Wu, Weisheng, Cayting, Philip, Boyle, Alan P, Sundaram, Vasavi, Xing, Xiaoyun, Dogan, Nergiz, Li, Jingjing, Euskirchen, Ghia, Lin, Shin, Lin, Yiing, Visel, Axel, Kawli, Trupti, Yang, Xinqiong, Patacsil, Dorrelyn, Keller, Cheryl A, Giardine, Belinda, Kundaje, Anshul, Wang, Ting, Pennacchio, Len A, Weng, Zhiping, Hardison, Ross C, Snyder, Michael P
Published in Nature (London)

The developmental transcriptome of Drosophila melanogaster

by Graveley, Brenton R, Celniker, Susan E, 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
Published in Nature (London)

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

Dynamics of microRNA expression during mouse prenatal development

by 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
Published in Genome research

Evidence for transcript networks composed of chimeric RNAs in human cells

by 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
Published in PloS one

The molecular basis of the cellular taxonomy of the human body

by Breschi, Alessandra, Davis, Carrie, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D., Vlasova, Anna, Dobin, Alex, Zaleski, Chris, Drenkow, Jorg, Danyko, Cassidy, Scavelli, Alexandra, Munoz, Manuel, Garrido, Diego, Reverter, Ferran, Gingeras, Thomas R., Guigo, Roderic
Published in Human genomics

Evidence for transcript networks composed of chimeric RNAs in human cells

by Djebali, Sarah, Lagarde, Julien, Lacroix, Vincent, Foissac, Sylvain, Ribeca, Paolo, Martin, David, Guigó Serra, Roderic, Gingeras, Thomas R
Published in PloS one

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

by Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E., Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C., Buchanan, Alex, van Baren, Marijke J., Spangler, Ryan, Rollins, M. Rick, Spellman, Paul T., Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A., Caloian, Cristian, Watson, John D., Uhrig, Sebastian, Haas, Brian J., Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, Zhang, Hongjiu, Wang, Yifan, Guan, Yuanfang, Nguyen, Cu, Sugai, Christopher, Jha, Alokkumar, Li, Jing Woei, Dobin, Alexander, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C., Stuart, Joshua M., Ellrott, Kyle
Published in Cell systems

Abstract 1572: FZD6 and RYK, non-canonical Wnt receptors in pancreatic cancer progression

by Stevens, Payton D., Sall, Emily, Zhong, Alex, Hostetter, Galen, Madaj, Zachary, Thalappillil, Jennifer, Dobin, Alexander, Park, Youngkyu, Tuveson, David A., Williams, Bart O.
Published in Cancer research (Chicago, Ill.)