Comparative transcriptomics in human and mouse von Breschi, Alessandra, Gingeras, Thomas R., Guigó, Roderic

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Implications of chimaeric non-co-linear transcripts von Gingeras, Thomas R

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

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Long non-coding RNAs: definitions, functions, challenges and recommendations von Mattick, John S., Amaral, Paulo P., Carninci, Piero, Carpenter, Susan, Chang, Howard Y., Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E., Fitzgerald, Katherine A., Gingeras, Thomas R., Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B., Lee, Jeannie T., Mendell, Joshua T., Mercer, Timothy R., Moore, Kathryn J., Nakagawa, Shinichi, Rinn, John L., Spector, David L., Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E., Wu, Mian

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Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function von Zhang, Xiao-Ou, Gingeras, Thomas R, Weng, Zhiping

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Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment von Nechooshtan, Gal, Yunusov, Dinar, Chang, Kenneth, Gingeras, Thomas R

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Origin of phenotypes: genes and transcripts von Gingeras, Thomas R

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Considerations when investigating lncRNA function in vivo von Bassett, Andrew R, Akhtar, Asifa, Barlow, Denise P, Bird, Adrian P, Brockdorff, Neil, Duboule, Denis, Ephrussi, Anne, Ferguson-Smith, Anne C, Gingeras, Thomas R, Haerty, Wilfried, Higgs, Douglas R, Miska, Eric A, Ponting, Chris P

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Genome-wide transcription and the implications for genomic organization von Gingeras, Thomas R, Kapranov, Philipp, Willingham, Aarron T

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Synthetic spike-in standards for RNA-seq experiments von Jiang, Lichun, Schlesinger, Felix, Davis, Carrie A, Zhang, Yu, Li, Renhua, Salit, Marc, Gingeras, Thomas R, Oliver, Brian

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Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain von Dachet, Fabien, Brown, James B., Valyi-Nagy, Tibor, Narayan, Kunwar D., Serafini, Anna, Boley, Nathan, Gingeras, Thomas R., Celniker, Susan E., Mohapatra, Gayatry, Loeb, Jeffrey A.

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Comparison of the transcriptional landscapes between human and mouse tissues von 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 von Batut, Philippe, Dobin, Alexander, Plessy, Charles, Carninci, Piero, Gingeras, Thomas R

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The reality of pervasive transcription von Clark, Michael B, Amaral, Paulo P, Schlesinger, Felix J, Dinger, Marcel E, Taft, Ryan J, Rinn, John L, Ponting, Chris P, Stadler, Peter F, Morris, Kevin V, Morillon, Antonin, Rozowsky, Joel S, Gerstein, Mark B, Wahlestedt, Claes, Hayashizaki, Yoshihide, Carninci, Piero, Gingeras, Thomas R, Mattick, John S

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RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription von Kapranov, Philipp, Cheng, Jill, Dike, Sujit, Nix, David A., Duttagupta, Radharani, Willingham, Aarron T., Stadler, Peter F., Hertel, Jana, Hackermüller, Jörg, Hofacker, Ivo L., Bell, Ian, Cheung, Evelyn, Drenkow, Jorg, Dumais, Erica, Patel, Sandeep, Helt, Gregg, Ganesh, Madhavan, Ghosh, Srinka, Piccolboni, Antonio, Sementchenko, Victor, Tammana, Hari, Gingeras, Thomas R.

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Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA von Chakrabortty, Sudipto K, Prakash, Ashwin, Nechooshtan, Gal, Hearn, Stephen, Gingeras, Thomas R

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Genome-wide antisense transcription drives mRNA processing in bacteria von 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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Mapping RNA‐seq Reads with STAR von Dobin, Alexander, Gingeras, Thomas R.

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A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster von Zhang, Xueqing, Lian, Zheng, Padden, Carolyn, Gerstein, Mark B., Rozowsky, Joel, Snyder, Michael, Gingeras, Thomas R., Kapranov, Philipp, Weissman, Sherman M., Newburger, Peter E.

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Gene-specific patterns of expression variation across organs and species von Breschi, Alessandra, Djebali, Sarah, Gillis, Jesse, Pervouchine, Dmitri D, Dobin, Alex, Davis, Carrie A, Gingeras, Thomas R, Guigó, Roderic

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