Strategies for measuring evolutionary conservation of RNA secondary structures

Autor: Hofacker Ivo L, Bernhart Stephan H, Gruber Andreas R, Washietl Stefan

Publikováno v: BMC Bioinformatics, Vol 9, Iss 1, p 122 (2008)

Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolut

Externí odkaz: https://doaj.org/article/18134ca5ec7f4f298f2e1a0e42d5ba80

Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses

Autor: Washietl Stefan, Eisenhaber Frank

Publikováno v: BMC Bioinformatics, Vol 4, Iss 1, p 55 (2003)

Abstract Background The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. Since adenoviruses hav

Externí odkaz: https://doaj.org/article/fb42f65ad571403e9f841004c0d39acc

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Autor: The modeENCODE Consortium, 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

Publikováno v: Science, 2010 Dec . 330(6012), 1787-1797.

Externí odkaz: https://www.jstor.org/stable/40986582

RNAs Everywhere: genome‐wide annotation of structured RNAs

Autor: Backofen, Rolf, Bernhart, Stephan H., Flamm, Christoph, Fried, Claudia, Fritzsch, Guido, Hackermüller, Jörg, Hertel, Jana, Hofacker, Ivo L., Missal, Kristin, Mosig, Axel, Prohaska, Sonja J., Rose, Dominic, Stadler, Peter F., Tanzer, Andrea, Washietl, Stefan, Will, Sebastian

Starting with the discovery of microRNAs and the advent of genome‐wide transcriptomics, non‐protein‐coding transcripts have moved from a fringe topic to a central field research in molecular biology. In this contribution we review the state of

Externí odkaz: https://ul.qucosa.de/id/qucosa%3A32161
https://ul.qucosa.de/api/qucosa%3A32161/attachment/ATT-0/

Evolutionary patterns of non-coding RNAs

Autor: Bompfünewerer, Athanasius F., Flamm, Christoph, Fried, Claudia, Fritzsch, Guido, Hofacker, Ivo L., Lehmann, Jörg, Missal, Kristin, Mosig, Axel, Müller, Bettina, Prohaska, Sonja J., Stadler, Bärbel M. R., Stadler, Peter F., Tanzer, Andrea, Washietl, Stefan, Witwer, Christina

A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and

Externí odkaz: https://ul.qucosa.de/id/qucosa%3A32169
https://ul.qucosa.de/api/qucosa%3A32169/attachment/ATT-0/