The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Fast and reliable prediction of noncoding RNAs
Open accessAbstract
We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small number of aligned sequences and is suitable for large-scale genomic screens. It consists of two basic components: ( i ) a measure for RNA secondary structure conservation based on computing a consensus secondary structure, and ( ii ) a measure for thermodynamic stability, which, in the spirit of a z score, is normalized with respect to both sequence length and base composition but can be calculated without sampling from shuffled sequences. Functional RNA secondary structures can be identified in multiple sequence alignments with high sensitivity and high specificity. We demonstrate that this approach is not only much more accurate than previous methods but also significantly faster. The method is implemented in the program rnaz , which can be downloaded from www.tbi.univie.ac.at/~wash/RNAz . We screened all alignments of length n ≥ 50 in the Comparative Regulatory Genomics database, which compiles conserved noncoding elements in upstream regions of orthologous genes from human, mouse, rat, Fugu , and zebrafish. We recovered all of the known noncoding RNAs and cis-acting elements with high significance and found compelling evidence for many other conserved RNA secondary structures not described so far to our knowledge.
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LIBSVM: A library for support vector machines
Chang, C.-C., & Lin, C.-J. (2011) · ACM Transactions on Intelligent Systems and Technology · doi:10.1145/1961189.1961199 · Cited by 40,918
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
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Ultraconserved Elements in the Human Genome
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004) · Science · doi:10.1126/science.1098119 · Cited by 1,732
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Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
Cited by
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098
Self-citationThe ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
A high-resolution map of human evolutionary constraint using 29 mammals
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108
Chen, X. H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., Heinemeyer, I., Morgenstern, B., Voss, B., Hess, W. R., Reva, O., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1325 · Cited by 873
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Will, S., Reiche, K., Hofacker, I. L., Stadler, P. F., & Backofen, R. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030065 · Cited by 499
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Metadata
- Authors
- Washietl, S., Hofacker, I. L., & Stadler, P. F.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-01-21
- Volume
- 102
- Issue
- 7
- Pages
- 2454-2459
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2140302584
- Cited by
- 665
- References
- 6
- FWCI
- 23.28
- Type
- journal article
- Language
- en
- Open access
- green
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