Is it time to change the reference genome? by Ballouz, Sara, Dobin, Alexander, Gillis, Jesse A

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Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods by Haas, Brian J, Dobin, Alexander, Li, Bo, Stransky, Nicolas, Pochet, Nathalie, Regev, Aviv

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STAR: ultrafast universal RNA-seq aligner by Dobin, Alexander, Davis, Carrie A, Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R

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Comparison of the transcriptional landscapes between human and mouse tissues by 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.

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High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression by Batut, Philippe, Dobin, Alexander, Plessy, Charles, Carninci, Piero, Gingeras, Thomas R

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Genome-wide antisense transcription drives mRNA processing in bacteria by Lasa, Iñigo, Toledo-Arana, Alejandro, Dobin, Alexander, Villanueva, Maite, de los Mozos, Igor Ruiz, Vergara-Irigaray, Marta, Segura, Víctor, Fagegaltier, Delphine, Penadés, José R, Valle, Jaione, Solano, Cristina, Gingeras, Thomas R

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The transcriptional diversity of 25 Drosophila cell lines by 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

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Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud by Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Marco, Cristina F, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth D, Jackson, David P, Martienssen, Robert A, McCombie, William R, Micklos, David A, Schatz, Michael C, Ware, Doreen H, Gingeras, Thomas R

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Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses by Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander

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Expanded encyclopaedias of DNA elements in the human and mouse genomes by Moore, Jill E., Purcaro, Michael J., Pratt, Henry E., Epstein, Charles B., Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A., Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L., Freese, Peter, Gorkin, David U., Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A., Mortazavi, Ali, Keller, Cheryl A., Zhang, Xiao-Ou, Elhajjajy, Shaimae I., Huey, Jack, Dickel, Diane E., Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B., Zhang, Jialing, Victorsen, Alec, White, Kevin P., Visel, Axel, Yeo, Gene W., Burge, Christopher B., Lécuyer, Eric, Gilbert, David M., Dekker, Job, Rinn, John, Mendenhall, Eric M., Ecker, Joseph R., Kellis, Manolis, Klein, Robert J., Noble, William S., Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J., Cherry, J. Michael, Myers, Richard M., Ren, Bing, Graveley, Brenton R., Gerstein, Mark B., Pennacchio, Len A., Snyder, Michael P., Bernstein, Bradley E., Wold, Barbara, Hardison, Ross C., Gingeras, Thomas R., Stamatoyannopoulos, John A., Weng, Zhiping

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Comparative cellular analysis of motor cortex in human, marmoset and mouse by Bakken, Trygve E., Jorstad, Nikolas L., Hu, Qiwen, Lake, Blue B., Tian, Wei, Kalmbach, Brian E., Crow, Megan, Hodge, Rebecca D., Krienen, Fenna M., Sorensen, Staci A., Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D., Aldridge, Andrew I., Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Daigle, Tanya L., Dalley, Rachel, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T., Herb, Brian R., Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Liu, Christine S., Lucero, Jacinta D., Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A., Moussa, Marmar, Nery, Joseph R., Nicovich, Philip R., Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K., Owen, Scott, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M., Rimorin, Christine, Rivkin, Angeline, Romanow, William J., Sedeño-Cortés, Adriana E., Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A., Behrens, M. Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R., Höllt, Thomas, Horwitz, Gregory D., Keene, C. Dirk, Kharchenko, Peter V., Lelieveldt, Boudewijn P., Luo, Chongyuan, Mukamel, Eran A., Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H., Smith, Kimberly, Spain, William J., White, Owen R., Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z., McCarroll, Steven A., Ting, Jonathan T., Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R., Linnarsson, Sten, Lein, Ed S.

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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

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Comparative transcriptomics reveals human-specific cortical features by Jorstad, Nikolas L, Song, Janet H T, Exposito-Alonso, David, Suresh, Hamsini, Castro-Pacheco, Nathan, Krienen, Fenna M, Yanny, Anna Marie, Close, Jennie, Gelfand, Emily, Long, Brian, Seeman, Stephanie C, Travaglini, Kyle J, Basu, Soumyadeep, Beaudin, Marc, Bertagnolli, Darren, Crow, Megan, Ding, Song-Lin, Eggermont, Jeroen, Glandon, Alexandra, Goldy, Jeff, Kiick, Katelyn, Kroes, Thomas, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Siletti, Kimberly, Somasundaram, Saroja, Tieu, Michael, Torkelson, Amy, Feng, Guoping, Hopkins, William D, Höllt, Thomas, Keene, C Dirk, Linnarsson, Sten, McCarroll, Steven A, Lelieveldt, Boudewijn P, Sherwood, Chet C, Smith, Kimberly, Walsh, Christopher A, Dobin, Alexander, Gillis, Jesse, Lein, Ed S, Hodge, Rebecca D, Bakken, Trygve E

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Perspectives on ENCODE by Snyder, Michael P., Gingeras, Thomas R., Moore, Jill E., Weng, Zhiping, Gerstein, Mark B., Ren, Bing, Hardison, Ross C., Stamatoyannopoulos, John A., Graveley, Brenton R., Feingold, Elise A., Pazin, Michael J., Pagan, Michael, Gilchrist, Daniel A., Hitz, Benjamin C., Cherry, J. Michael, Bernstein, Bradley E., Mendenhall, Eric M., Zerbino, Daniel R., Frankish, Adam, Flicek, Paul, Myers, Richard M.

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A benchmark for RNA-seq quantification pipelines by 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

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The fractured landscape of RNA-seq alignment: the default in our STARs by Ballouz, Sara, Dobin, Alexander, Gingeras, Thomas R, Gillis, Jesse

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A Simple Model for Transition Width and Cluster Size in Perpendicular Recording by Richter, H.J., Dobin, A.Y.

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The long noncoding RNA ROCKI regulates inflammatory gene expression by Zhang, Qiong, Chao, Ti‐Chun, Patil, Veena S, Qin, Yue, Tiwari, Shashi Kant, Chiou, Joshua, Dobin, Alexander, Tsai, Chih‐Ming, Li, Zhonghan, Dang, Jason, Gupta, Shagun, Urdahl, Kevin, Nizet, Victor, Gingeras, Thomas R, Gaulton, Kyle J, Rana, Tariq M

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Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets by Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David L.

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A user's guide to the encyclopedia of DNA elements (ENCODE) by Consortium, The ENCODEProject

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