Not logged in A limited set of transcriptional programs define major cell types Breschi, Alessandra; Munoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A.; Garrido-Martin, Diego; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Reverter, Ferran; Snyder, Michael P.; Gingeras, Thomas R.; Guigo, Roderic Share Save
Dynamics of microRNA expression during mouse prenatal development 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.; Guigo, Roderic; Mortazavi, Ali Share Save
Prevention of data duplication for high throughput sequencing repositories Gabdank, Idan; Chan, Esther T.; Davidson, Jean M.; Hilton, Jason A.; Davis, Carrie A.; Baymuradov, Ulugbek K.; Narayanan, Aditi; Onate, Kathrina C.; Graham, Keenan; Miyasato, Stuart R.; Dreszer, Timothy R.; Strattan, J. Seth; Jolanki, Otto; Tanaka, Forrest Y.; Hitz, Benjamin C.; Sloan, Cricket A.; Cherry, J. Michael Share Save
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Perez-Lluch, Silvia; Abad, Amaya; Davis, Carrie; Gingeras, Thomas R.; Frankish, Adam; Harrow, Jennifer; Guigo, Roderic; Johnson, Rory Share Save
The Encyclopedia of DNA elements (ENCODE): data portal update Davis, Carrie A.; Hitz, Benjamin C.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Hilton, Jason A.; Jain, Kriti; Baymuradov, Ulugbek K.; Narayanan, Aditi K.; Onate, Kathrina C.; Graham, Keenan; Miyasato, Stuart R.; Dreszer, Timothy R.; Strattan, J. Seth; Jolanki, Otto; Tanaka, Forrest Y.; Cherry, J. Michael Share Save
A benchmark for RNA-seq quantification pipelines (vol 17, 74, 2016) Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. Share Save
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A benchmark for RNA-seq quantification pipelines (vol 17, 74, 2016) Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. Share Save
A benchmark for RNA-seq quantification pipelines Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. Share Save
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression 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; Guigo, Roderic; Gingeras, Thomas R. Share Save
Comparison of the transcriptional landscapes between human and mouse tissues Lin, Shin; Lin, Yiing; Nery, Joseph R.; Urich, Mark A.; Breschi, Alessandra; Davis, Carrie A.; Dobin, Alexander; Zaleski, Christopher; Beer, Michael A.; Chapman, William C.; Gingeras, Thomas R.; Ecker, Joseph R.; Snyder, Michael P. Share Save
Understanding transcriptional regulation by integrative analysis of transcription factor binding data Cheng, Chao; Alexander, Roger; Min, Renqiang; Leng, Jing; Yip, Kevin Y.; Rozowsky, Joel; Yan, Koon-Kiu; Dong, Xianjun; Djebali, Sarah; Ruan, Yijun; Davis, Carrie A.; Carninci, Piero; Lassman, Timo; Gingerasi, Thomas R.; Guigo, Roderic; Birney, Ewan; Weng, Zhiping; Snyder, Michael; Gerstein, Mark Share Save
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; Gonzalez, Jose M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigo, Roderic Share Save
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs Tilgner, Hagen; Knowles, David G.; Johnson, Rory; Davis, Carrie A.; Chakrabortty, Sudipto; Djebali, Sarah; Curado, Joao; Snyder, Michael; Gingeras, Thomas R.; Guigo, Roderic Share Save
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. Share Save
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The transcriptional diversity of 25 Drosophila cell lines Cherbas, Lucy; Willingham, Aarron; Zhang, Dayu; Yang, Li; Zou, Yi; Eads, Brian D.; Carlson, Joseph W.; Landolin, Jane M.; Kapranov, Philipp; Dumais, Jacqueline; Samsonova, Anastasia; Choi, Jeong-Hyeon; Roberts, Johnny; Davis, Carrie A.; Tang, Haixu; van Baren, Marijke J.; Ghosh, Srinka; Dobin, Alexander; Bell, Kim; Lin, Wei; Langton, Laura; Duff, Michael O.; Tenney, Aaron E.; Zaleski, Chris; Brent, Michael R.; Hoskins, Roger A.; Kaufman, Thomas C.; Andrews, Justen; Graveley, Brenton R.; Perrimon, Norbert; Celniker, Susan E.; Gingeras, Thomas R.; Cherbas, Peter Share Save
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan Plessy, Charles; Bertin, Nicolas; Takahashi, Hazuki; Simone, Roberto; Salimullah, Md; Lassmann, Timo; Vitezic, Morana; Severin, Jessica; Olivarius, Signe; Lazarevic, Dejan; Hornig, Nadine; Orlando, Valerio; Bell, Ian; Gao, Hui; Dumais, Jacqueline; Kapranov, Philipp; Wang, Huaien; Davis, Carrie A.; Gingeras, Thomas R.; Kawai, Jun; Daub, Carsten O.; Hayashizaki, Yoshihide; Gustincich, Stefano; Carninci, Piero Share Save
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