Comparative RNA Genomics.

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[80]  Rolf Backofen,et al.  Accessibility and conservation , 2012, RNA biology.

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[82]  Sebastian Will,et al.  Structure-based whole-genome realignment reveals many novel noncoding RNAs , 2012, RECOMB.

[83]  Peter F. Stadler,et al.  Hidden treasures in unspliced EST data , 2012, Theory in Biosciences.

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[116]  Peter F. Stadler,et al.  RNAz 2.0: Improved Noncoding RNA Detection , 2010, Pacific Symposium on Biocomputing.

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[128]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

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[131]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[132]  Peter F. Stadler,et al.  Non-coding RNA annotation of the genome of Trichoplax adhaerens , 2009, Nucleic acids research.

[133]  D. Mathews,et al.  Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.

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[138]  Sebastian Will,et al.  RNAalifold: improved consensus structure prediction for RNA alignments , 2008, BMC Bioinformatics.

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[143]  Pontus Larsson,et al.  De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring. , 2008, Genome research.

[144]  Tanja Gesell,et al.  Dinucleotide controlled null models for comparative RNA gene prediction , 2008, BMC Bioinformatics.

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[148]  Sonja J. Prohaska,et al.  Evolutionary patterns of non-coding RNAs , 2005, Theory in Biosciences.

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[150]  Stephan H. Bernhart,et al.  Strategies for measuring evolutionary conservation of RNA secondary structures , 2008, BMC Bioinformatics.

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[152]  Walter L. Ruzzo,et al.  How accurately is ncRNA aligned within whole-genome multiple alignments? , 2007, BMC Bioinformatics.

[153]  Jan Gorodkin,et al.  Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix , 2007, PLoS Comput. Biol..

[154]  Shane J. Neph,et al.  Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline , 2007, Nucleic acids research.

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[156]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

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