Publications

Publications

1. Nasalean, L., Stombaugh, J., Zirbel, C.L. and Leontis, N.B. (In Press), Non-Protein Coding RNAs. Springer Berlin Heidelberg

2. Brown, J.W., Birmingham, A., Griffiths, P.E., Jossinet, F., Kachouri-Lafond, R., Knight, R., Lang, B.F., Leontis, N., Steger, G., Stombaugh, J., Westhof, E. The RNA structure alignment ontology. (2009) RNA.Sep;15(9):1623-31.Abstract

3. Xin, Y., Laing, C., Leontis, N.B. and Schlick, T. (2008) Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA (New York, N.Y, 14, 2465-2477. Abstract

4. Vicens, Q., Paukstelis, P.J., Westhof, E., Lambowitz, A.M. and Cech, T.R. (2008) Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA (New York, N.Y, 14, 2013-2029. Abstract

5. Smit, S., Rother, K., Heringa, J. and Knight, R. (2008) From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. RNA (New York, N.Y, 14, 410-416. Abstract

6. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. Journal of mathematical biology, 56, 215-252. Abstract

7. Richardson, J.S., Schneider, B., Murray, L.W., Kapral, G.J., Immormino, R.M., Headd, J.J., Richardson, D.C., Ham, D., Hershkovits, E., Williams, L.D. et al. (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (New York, N.Y, 14, 465-481. Abstract

8. Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55. Abstract

9. Mitra, S., Shcherbakova, I.V., Altman, R.B., Brenowitz, M. and Laederach, A. (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic acids research, 36, e63. Abstract

10. Laederach, A., Das, R., Vicens, Q., Pearlman, S.M., Brenowitz, M., Herschlag, D. and Altman, R.B. (2008) Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature protocols, 3, 1395-1401. Abstract

11. St-Onge, K., Thibault, P., Hamel, S. and Major, F. (2007) Modeling RNA tertiary structure motifs by graph-grammars. Nucleic acids research, 35, 1726-1736. Abstract

12. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology, 25, 1251-1255. Abstract

13. Lisi, V. and Major, F. (2007) A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA (New York, N.Y, 13, 1537-1545. Abstract

14. Laederach, A., Chan, J.M., Schwartzman, A., Willgohs, E. and Altman, R.B. (2007) Coplanar and coaxial orientations of RNA bases and helices. RNA (New York, N.Y, 13, 643-650. Abstract

15. Laederach, A. (2007) Informatics challenges in structured RNA. Briefings in bioinformatics, 8, 294-303. Abstract

16. Kim, N., Shin, J.S., Elmetwaly, S., Gan, H.H. and Schlick, T. (2007) RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics (Oxford, England), 23, 2959-2960. Abstract

17. Kim, N., Gan, H.H. and Schlick, T. (2007) A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA (New York, N.Y, 13, 478-492. Abstract

18. Jossinet, F., Ludwig, T.E. and Westhof, E. (2007) RNA structure: bioinformatic analysis. Current opinion in microbiology, 10, 279-285. Abstract

19. Hammann, C. and Westhof, E. (2007) Searching genomes for ribozymes and riboswitches. Genome biology, 8, 210. Abstract

20. Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall, W.B., 3rd, Snoeyink, J., Richardson, J.S. et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic acids research, 35, W375-383. Abstract

21. Marck, C., Kachouri-Lafond, R., Lafontaine, I., Westhof, E., Dujon, B. and Grosjean, H. (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic acids research, 34, 1816-1835. Abstract

22. Leontis, N.B., Altman, R.B., Berman, H.M., Brenner, S.E., Brown, J.W., Engelke, D.R., Harvey, S.C., Holbrook, S.R., Jossinet, F., Lewis, S.E. et al. (2006) The RNA Ontology Consortium: an open invitation to the RNA community. RNA (New York, N.Y, 12, 533-541. Abstract