K. Byron, M.C.-Cervantes, J.T.L. Wang, W.C. Lin, and Y. Park
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 S.R. Eddy, Non-coding RNA genes and the modern RNAworld, Nature Reviews Genetics, 2, 2001, 919–929.
 G. Storz, An expanding universe of noncoding RNAs, Science,296, 2002, 1260–1263.
 J.S. Mattick & I. V. Makunin, Non-coding RNA, HumanMolecular Genetics, 15 Spec No 1, 2006, R17–R29.
 F.F. Costa, Non-coding RNAs: Lost in translation? Gene,386, 2007, 1–10.
 Y. Park & M.I. Kuroda, Epigenetic aspects of X-chromosomedosage compensation, Science, 293(5532), 2001, 1083–1085.
 Y. Park, R.L. Kelley, H. Oh, M.I. Kuroda, & V.H. Meller, Ex-tent of chromatin spreading determined by roX RNA recruit-ment of MSL proteins, Science, 298(5598), 2002, 1620–1623.
 S. Park, Y.I. Kang, J.G. Sypula, J. Choi, H. Oh, & Y. Park,An evolutionarily conserved domain of roX2 RNA is suﬃcientfor induction of H4-Lys16 acetylation on the Drosophila Xchromosome, Genetics, 177(3), 2007, 1429–1437.
 S. Park, M.I. Kuroda, & Y. Park, Regulation of histone H4Lys16 acetylation by predicted alternative secondary structuresin roX noncoding RNAs. Molecular and Cellular Biology,28(16), 2008, 4952–4962.
 A. Stark, et al., Discovery of functional elements in 12Drosophila genomes using evolutionary signatures. Nature,450, 2007, 219–232.
 A. Wang, W. Ruzzo, & M. Tompa, How accurately is ncRNAaligned within whole-genome multiple alignments? BMCBioinformatics, 8, 2007, 417.
 R. Durbin, S. Eddy, A. Krogh, & G. Mitchison, Biologicalsequence analysis: probabilistic models of proteins and Nucleicacids (Cambridge UK: Cambridge University Press 1998),277–297.
 E.P. Nawrocki, D.L. Kolbe, & S.R. Eddy, Infernal 1.0: Inferenceof RNA alignments, Bioinformatics, 25(10), 2009, 1335–1337.
 S. Griﬃths-Jones, A. Bateman, M. Marshall, A. Khanna, &S.R. Eddy, Rfam: An RNA family database, Nucleic AcidsResearch, 31, 2003, 439–441.
 S. Griﬃths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R.Eddy, & A. Bateman, Rfam: Annotating non-coding RNAs incomplete genomes, Nucleic Acids Research, 33, 2005, D121–D124.
 L.A. Kavanaugh & F.S. Dietrich, Non-coding RNA predictionand veriﬁcation in Saccharomyces cerevisiae, PLoS Genetcis5 (1), 2009, e1000321.
 J. Liu, J.T.L. Wang, J. Hu, & B. Tian, A method for aligningRNA secondary structures and its application to RNA motifdetection, BMC Bioinformatics 6, 2005, 89.
 I.L. Hofacker, Vienna RNA secondary structure server, NucleicAcids Research 31, 2003, 3429–3431.
 Y. Tabei, H. Kiryu, T. Kin, & K. Asai, A fast structuralmultiple alignment method for long RNA sequences, BMCBioinformatics, 9, 2008, 33.
 A.R. Gruber, R. Neubock, I.L. Hofacker, & S. Washietl, TheRNAz web server: Prediction of thermodynamically stableand evolutionarily conserved RNA structures, Nucleic AcidsResearch, 35, 2007, W335–W338.
 M. Khaladkar, J. Liu, D. Wen, J.T.L. Wang, & B. Tian,Mining small RNA structure elements in untranslated regionsof human and mouse mRNAs using structure-based alignment,BMC Genomics, 9, 2008, 189.
 M. Khaladkar, V. Patel, V. Bellofatto, J. Wilusz, & J.T.L.Wang, Detecting conserved secondary structures in RNAmolecules using constrained structural alignment, Computa-tional Biology and Chemistry, 32, 2008, 264–272.
 M. Khaladkar, V. Bellofatto, J.T.L. Wang, B. Tian, & B.A.Shapiro, RADAR: A web server for RNA data analysis andresearch, Nucleic Acids Research, 35, 2007, W300–W304.
 L. Peng, L.K. Ng, & S. See, YellowRiver: A ﬂexible highperformance cluster computing service for grid, ProceedingsEighth IEEE International Conference on High-PerformanceComputing in Asia-Paciﬁc Region, 2005, 553–558.
 A. Subramanian, M. Kaufmann, & B. Morgenstern, DIALIGN-TX: Greedy and progressive approaches for segment-basedmultiple sequence alignment, Algorithms for Molecular Biology,3, 2008, 6.
 C. Stuckenholz, V.H. Meller, & M.I. Kuroda, Functionalredundancy within roX1, a noncoding RNA involved in dosagecompensation in Drosophila melanogaster, Genetics, 164, 2003,1003–1014.
 E.K. Freyhult, J.P. Bollback, & P.P. Gardner, Exploringgenomic dark matter: A critical assessment of the performanceof homology search methods on noncoding RNA, GenomeResearch, 17(1), 2007, 117–125.
 Z. Yao, Z. Weinberg, & W.L. Ruzzo, CMﬁnder – A covariancemodel based RNA motif ﬁnding algorithm, Bioinformatics,22(4), 2006, 445–452.
 Z. Weinberg & W.L. Ruzzo, Sequence-based heuristics forfaster annotation of non-coding RNA families, Bioinformatics,22, 2006, 35–39.
 The FlyBase Consortium, FlyBase – The Drosophila database,Nucleic Acids Research, 22, 1994, 3456–3458.