Citations
We're now using an web-based database to store and maintain references. If you are interested in helping us maintain and add to the reference list (all done on-line) please contact us. We also have the ability to tag references (perhaps with topics), and we may implement this feature for public display in the future.
List
View page 1 2- Cannone, J. J., M. N. Subramanian, J. R. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, L. V. Madabusi, N. Lin, N. Muller, Z. Pande, N. Shang, N. Yu, and R. R. Gutell. 2002. The comparative RNA web (CRW) site. BMC Bioinformatics 3:1-31.
- Eddy, S. R., and R. Durbin. 1994. RNA sequence analysis using covariance models. Nucleic Acids Research 22:2079-2088.
- Gesell, T., and A. von Haeseler. 2006. In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics 22:716-722.
- Gillespie, J. J. 2004. Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules. Molecular Phylogenetics and Evolution 2004:936-943.
- Gillespie, J. J., J. B. Munro, J. Heraty, M. J. Yoder, A. K. Owen, and A. E. Carmichael. 2005. A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea). Molecular Biology and Evolution 22:1593-1608.
- Gillespie, J. J., J. J. Cannone, R. R. Gutell, and A. I. Cognato. 2004. A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 from Rootworms and Related Leaf Beetles (Coleoptera: Chrysomelidae; Galerucinae). Insect Molecular Biology 2004:495-518.
- Giribet, G. 2001. Exploring the behavior of POY, a program for direct optimization of molecular data. Cladistics: the international journal of the Willi Hennig Society 17:S60-S70.
- Gowri-Shankar, V., and M. Rattray. 2006. On the correlation between compoistion and site-specific evolutionary rate: Implications for phylogenetic inference. Molecular Biology and Evolution 23:352-364.
- Griffiths-Jones, S., A. Bateman, T. A. Marshall, A. Khanna, and S. R. Eddy. 2003. Rfam: an RNA family database. Nucleic Acids Research 31:439-441.
- Hein, J., and B. Knudsen. 2003. Pfold: RNA secondary structure prediction using stochastic context-free grammars prediction using stochastic context-free grammars. Nucleic Acids Research 31:3423-3428.
- Hofacker, I. L., S. H. F. Bernhart, and P. F. Stadler. 2004. Alignment of RNA base pairing probability matrices. Bioinformatics 20:2222-2227.
- Honeycutt, R., and D. P. Mindell. 1990. Ribosomal RNA in Vertebrates: Evolution and Phylogenetic Application. Annual Review of Ecology and Systematics 21:541-566.
- Hudelot, C., V. Gowri-Shankar, H. Jow, M. Rattray, and P. G. Higgs. 2003. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Molecular Phylogenetics and Evolution 28:252.
- Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4:314-330.
- Knight, R., A. Birmingham, and M. Yarus. 2004. BayesFold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA 10:1323-1336.
- Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49:628-651.
- Nebel, M. E. 2004. Investigation of the Bernoulli model for RNA secondary structures. Bulletin of Mathematical Biology 66:925-964.
- Perriquet, O., H. Touzet, and M. Dauchet. 2003. Finding the common homologous structure shared by two homologous RNAs. Bioinformatics 19:108-116.
- Posada, D., and K. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
- Rivas, E., and S. R. Eddy. 2000. Secondary structure alone is generally not statistically significant for the detection fo noncoding RNAs. Bioinformatics 16:563-605.