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International Journal for Multiscale Computational Engineering
IF: 1.016 5-Year IF: 1.194 SJR: 0.452 SNIP: 0.68 CiteScore™: 1.18

ISSN Print: 1543-1649
ISSN Online: 1940-4352

International Journal for Multiscale Computational Engineering

DOI: 10.1615/IntJMultCompEng.v8.i4.20
pages 369-378

Mathematical and Biological Scientists Assess the State of the Art in RNA Science at an IMA Workshop, RNA in Biology, Bioengineering, and Biotechnology

Tamar Schlick
New York University


Highlights of the IMA workshop RNA in Biology, Bioengineering, and Biotechnology are summarized, including recent developments in RNA secondary structure prediction and RNA design, innovative mathematical constructs for RNA structure, bioinformatics advances in RNA structure analysis and prediction, and experimental progress in RNA folding and imaging.


  1. Baird, N., Westof, E., Qin, H., Pan, T., and Sosnick, T., Structures of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. DOI: 10.1016/j.jmb.2005.07.010

  2. Bindewald, E., Hayes, R., Yingling, Y., Kasprzak, W., and Shapiro, B., RNAJunction: A database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. DOI: 10.1093/nar/gkm842

  3. Brion, P. andWestof, E., Hierarchy and dynamics of RNA folding. DOI: 10.1146/annurev.biophys.26.1.113

  4. Chworos, A., Severcan, I., Koyfman, A.,Weinkam, P., Oroudjev, E., Hansma, H., and Jaeger, L., Building programmable jigsaw puzzles with RNA. DOI: 10.1126/science.1104686

  5. Dirks, R., Lin, M., Winfree, E., and Pierce, N., Paradigms for computational nucleic acid design. DOI: 10.1093/nar/gkh291

  6. Dror, O., Nussinov, R., and Wolfson, H., The ARTS web server for aligning RNA tertiary structures. DOI: 10.1093/nar/gkl312

  7. Hamelryck, T., Kent, J., and Krogh, A., Sampling realistic protein conformations using local structural bias. DOI: 10.1371/journal.pcbi.0020131

  8. Heitsch, C., Condon, A., and Hoos, H., From RNA Secondary Structure to Coding Theory: A Combinatorial Approach.

  9. Hyeon, C. and Thirumalai, D., Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. DOI: 10.1021/ja0771641

  10. Ikawa, Y., Tsuda, K., Matsumura, S., and Inoue, T., De Novo synthesis and development of an RNA enzyme. DOI: 10.1073/pnas.0405886101

  11. Jaeger, L. and Chworos, A., The architectonics of programmable RNA and DNA nanostructures. DOI: 10.1016/

  12. Kim, N., Gan, H., and Schlick, T., Computational proposal of structured RNA pools for in vitro selection of RNAs.

  13. Kim, N., Shin, J., Elmetwaly, S., Gan, H., and Schlick, T., RAGPOOLS: RNA-as-graph-pools-A web server for assisting the design of structured RNA pools for in vitro selection. DOI: 10.1093/bioinformatics/btm439

  14. Kim, N., Izzo, J. A., Elmetwely, S., Gan, H. H., and Schlick, T., Computational generation and screening of RNA motifs in large nucleotide sequence pools. DOI: 10.1093/nar/gkq282

  15. Koculi, E., Hyeon, C., Thirumalai, D., and Woodson, S., Charge density of divalent metal cations determines RNA stability. DOI: 10.1021/ja068027r

  16. Laing, C. and Schlick, T., Computational approaches to 3D modeling of RNA. DOI: 10.1088/0953-8984/22/28/283101

  17. Lareau, L., Inada, M., Green, R., Wengrod, J., and Brenner, S., Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. DOI: 10.1038/nature05676

  18. Leontis, N., Altman, R., Berman, H., Brenner, S., Brown, J., Engelke, D., Harvey, S., Holbrook, S., Jossinet, F.,Lewis, S., Major, F., Mathews, D., Richardson, J., Williamson, J., and Westof, E., The RNA ontology consortium: An open invitation to the rna community. DOI: 10.1261/rna.2343206

  19. Lescoute, A. andWestof, E., The interaction networks of structured RNAs. DOI: 10.1093/nar/gkl963

  20. Mathews, D., Sabina, J., Zuker, M., and Turner, D., Expanded Sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. DOI: 10.1006/jmbi.1999.2700

  21. Mathews, D. and Turner, D., Dynalign: An algorithm for Finding the secondary structure common to two RNA sequences. DOI: 10.1006/jmbi.2001.5351

  22. Muckstein, U., Tafer, H., Hackermuller, J., Bernhart, S., Stadler, P., and Hofacker, I., Thermodynamics of RNARNA binding. DOI: 10.1093/bioinformatics/btl024

  23. Ndifon, W. and Nkwanta, A., An RNA foldability metric; Implications for the design of rapidly foldable RNA sequences. DOI: 10.1016/j.bpc.2005.11.012

  24. Parisien, M. and Major, F., The MC-fold and MC-sym pipeline infers RNA structure from sequence data. DOI: 10.1038/nature06684.

  25. Pedersen, J., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E., Kent, J., Miller, W., and Haussler, D., Identification and classification of conserved RNA secondary structures in the human genome. DOI: 10.1371/journal.pcbi.0020033

  26. Reeder, J., Reeder, J., and Giegerich, R., Locomotif: From graphical motif description to RNA motif search. DOI: 10.1093/bioinformatics/btm179

  27. Rong, Y. and Luse, K., Examples of knots with the same polynomials. DOI: 10.1142/S0218216506004725

  28. Saito, H. and Inoue, T., RNA and RNP as newmolecular parts in synthetic biology. DOI: 10.1016/j.jbiotec.2007.07.952

  29. Sarver, M., Zirbel, C., Stombaugh, J., Mokdad, A., and Leontis, N., FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. DOI: 10.1007/s00285-007-0110-x

  30. St-Onge, K., Thinault, P., Hamel, S., and Major, F., Modeling RNA tertiary structure motifs by graph grammers. DOI: 10.1093/nar/gkm069

  31. Vernizzi, G., Orland, H., and Zee, A., Enumeration of RNA structures by matrix models. DOI: 10.1103/PhysRevLett.94.168103

  32. Wilson, T., McLeod, A., and Lilley, D., A guanine nucleobase important for catalysis by the VS ribozyme. DOI: 10.1038/sj.emboj.7601698

  33. Wong, T., Sosnick, T., and Pan, T., Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. DOI: 10.3410/f.1098109.554093

  34. Xin, Y., Laing, C., Leontis, N., and Schlick, T., Annotation of tertiary interactions in RNA structures reveals variations and correlations. DOI: 10.1261/rna.1249208

  35. Yin, P., Choi, H., Calvert, C., and Pierce, N., Programming biomolecular self-assembly pathways. DOI: 10.1038/nature06451

  36. Yingling, Y. and Shapiro, B., Computational design of an RNA hexagonal nanoring and an RNA nanotube. DOI: 10.1021/nl070984r

  37. Zhu, H., Yuan, Q., Casselman, A., Emery-Le, M., Emery, P., and Reppert, S. M., Cryptochromes define a novel circadian clock mechanism in monarch butterflies that may underlie sun compass navigation. DOI: 10.1371/journal.pbio.0060004

  38. Zuker, M., Mfold web server for nucleic acid folding and hybridization prediction. DOI: 10.1093/nar/gkg595

  39. Zuker, M. and Stiegler, P., Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. DOI: 10.1093/nar/9.1.133

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