Dinucleotide controlled null models for comparative RNA gene prediction by Gesell Tanja, Washietl Stefan

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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 by Washietl Stefan, Eisenhaber Frank

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Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals by Washietl, Stefan, Kellis, Manolis, Garber, Manuel

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Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo by Rouskin, Silvi, Zubradt, Meghan, Washietl, Stefan, Kellis, Manolis, Weissman, Jonathan S.

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Strategies for measuring evolutionary conservation of RNA secondary structures by Hofacker Ivo L, Bernhart Stephan H, Gruber Andreas R, Washietl Stefan

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RNA Folding with Soft Constraints: Reconciliation of Probing Data and Thermodynamic Secondary Structure Prediction by Mag Washietl, Stefan, Hofacker, Ivo L., Stadler, Peter F., Kellis, Manolis

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Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes by Lin, Michael F., Kheradpour, Pouya, Mag Washietl, Stefan, Parker, Brian J., Pedersen, Jakob S., Kellis, Manolis

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Computational analysis of noncoding RNAs by Washietl, Stefan, Will, Sebastian, Hendrix, David A., Goff, Loyal, Rinn, John L., Berger, Bonnie, Kellis, Manolis

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A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals by Mag Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Ward, Lucas D., Jungreis, Irwin, Rasmussen, Matthew D., Kellis, Manolis

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Computational RNomics of Drosophilids by Hertel Jana, Reiche Kristin, Washietl Stefan, Hackermüller Jörg, Rose Dominic, Findeiß Sven, Stadler Peter F, Prohaska Sonja J

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New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes by Kellis, Manolis, Parker, Brian J., Moltke, Ida, Roth, Adam, Washietl, Stefan, Wen, Jiayu, Breaker, Ronald, Pedersen, Jakob Skou

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Optimization of parameters for coverage of low molecular weight proteins by Muller, Stephan A., Kohajda, Tibor, Findeiß, Sven, Stadler, Peter F., Mag Washietl, Stefan, Kellis, Manolis, Bergen, Martin von, Kalkhof, Stefan

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An integrated encyclopedia of DNA elements in the human genome by Altshuler, Robert Charles, Ernst, Jason, Kellis, Manolis, Kheradpour, Pouya, Ward, Lucas D., Eaton, Matthew Lucas, Hendrix, David A., Jungreis, Irwin, Lin, Michael F., Washietl, Stefan

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE by Kheradpour, Pouya, Bristow, Christopher A., Mag Washietl, Stefan, Ay, Ferhat, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel Sima, Will, Sebastian, Berger, Bonnie, Kellis, Manolis, Roy, Sushmita, Ernst, Jason, Lin, Michael F., Meyer, Patrick E., Di Stefano, Luisa, Candeias, Rogerio, Nordman, Jared T., Orr-Weaver, Terry L.

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