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Published in Journal of adolescent health (01.04.2022)
Published in Journal of adolescent health (01.04.2022)
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STAR: ultrafast universal RNA-seq aligner
Dobin, Alexander, Davis, Carrie A, Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R
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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
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling
Weissmueller, Susann, Manchado, Eusebio, Saborowski, Michael, Morris, 4th, John P, Wagenblast, Elvin, Davis, Carrie A, Moon, Sung-Hwan, Pfister, Neil T, Tschaharganeh, Darjus F, Kitzing, Thomas, Aust, Daniela, Markert, Elke K, Wu, Jianmin, Grimmond, Sean M, Pilarsky, Christian, Prives, Carol, Biankin, Andrew V, Lowe, Scott W
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High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Carbonell, Silvia, Pérez-Lluch, Sílvia, Abad, Amaya, Davis, Carrie, Gingeras, Thomas R, Frankish, Adam, Harrow, Jennifer, Guigo, Roderic, Johnson, Rory
Published in Nature genetics (01.12.2017)
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Synthetic spike-in standards for RNA-seq experiments
Jiang, Lichun, Schlesinger, Felix, Davis, Carrie A, Zhang, Yu, Li, Renhua, Salit, Marc, Gingeras, Thomas R, Oliver, Brian
Published in Genome research (01.09.2011)
Published in Genome research (01.09.2011)
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Accurate identification of human Alu and non-Alu RNA editing sites
Ramaswami, Gokul, Lin, Wei, Piskol, Robert, Tan, Meng How, Davis, Carrie, Li, Jin Billy
Published in Nature methods (01.06.2012)
Published in Nature methods (01.06.2012)
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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.
Published in Proceedings of the National Academy of Sciences - PNAS (02.12.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (02.12.2014)
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Diversity and dynamics of the Drosophila transcriptome
Brown, James B., Boley, Nathan, Eisman, Robert, May, Gemma E., Stoiber, Marcus H., Duff, Michael O., Booth, Ben W., Wen, Jiayu, Park, Soo, Suzuki, Ana Maria, Wan, Kenneth H., Yu, Charles, Zhang, Dayu, Carlson, Joseph W., Cherbas, Lucy, Eads, Brian D., Miller, David, Mockaitis, Keithanne, Roberts, Johnny, Davis, Carrie A., Frise, Erwin, Hammonds, Ann S., Olson, Sara, Shenker, Sol, Sturgill, David, Samsonova, Anastasia A., Weiszmann, Richard, Robinson, Garret, Hernandez, Juan, Andrews, Justen, Bickel, Peter J., Carninci, Piero, Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Lai, Eric C., Oliver, Brian, Perrimon, Norbert, Graveley, Brenton R., Celniker, Susan E.
Published in Nature (London) (28.08.2014)
Published in Nature (London) (28.08.2014)
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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, Guigó, Roderic
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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A limited set of transcriptional programs define major cell types
Breschi, Alessandra, Muñoz-Aguirre, Manuel, Wucher, Valentin, Davis, Carrie A, Garrido-Martín, 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, Guigó, Roderic
Published in Genome research (01.07.2020)
Published in Genome research (01.07.2020)
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Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
Tilgner, Hagen, Knowles, David G, Johnson, Rory, Davis, Carrie A, Chakrabortty, Sudipto, Djebali, Sarah, Curado, João, Snyder, Michael, Gingeras, Thomas R, Guigó, Roderic
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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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
Published in Genome Biology (23.04.2016)
Published in Genome Biology (23.04.2016)
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Gene-specific patterns of expression variation across organs and species
Breschi, Alessandra, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D, Dobin, Alex, Davis, Carrie A, Gingeras, Thomas R, Guigó, Roderic
Published in Genome Biology (08.07.2016)
Published in Genome Biology (08.07.2016)
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Systematic evaluation of spliced alignment programs for RNA-seq data
Engström, Pär G, Steijger, Tamara, Sipos, Botond, Grant, Gregory R, Kahles, André, Rätsch, Gunnar, Goldman, Nick, Hubbard, Tim J, Harrow, Jennifer, Guigó, Roderic, Bertone, Paul
Published in Nature methods (01.12.2013)
Published in Nature methods (01.12.2013)
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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, Gingeras, Thomas R, Guigó, Roderic, Birney, Ewan, Weng, Zhiping, Snyder, Michael, Gerstein, Mark
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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The developmental transcriptome of Drosophila melanogaster
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Published in Nature (London) (24.03.2011)
Published in Nature (London) (24.03.2011)
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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster
Oliver, Brian, Lieb, Jason D, Disteche, Christine M, Deng, Xinxian, Hiatt, Joseph B, Nguyen, Di Kim, Ercan, Sevinc, Sturgill, David, Hillier, LaDeana W, Schlesinger, Felix, Davis, Carrie A, Reinke, Valerie J, Gingeras, Thomas R, Shendure, Jay, Waterston, Robert H
Published in Nature genetics (01.12.2011)
Published in Nature genetics (01.12.2011)
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