{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T22:06:24Z","timestamp":1784153184468,"version":"3.55.0"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,3,9]],"date-time":"2011-03-09T00:00:00Z","timestamp":1299628800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms Mol Biol"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1748-7188-6-3","type":"journal-article","created":{"date-parts":[[2011,3,9]],"date-time":"2011-03-09T10:20:39Z","timestamp":1299666039000},"source":"Crossref","is-referenced-by-count":57,"title":["RNA Accessibility in cubic time"],"prefix":"10.1186","volume":"6","author":[{"given":"Stephan H","family":"Bernhart","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ullrike","family":"M\u00fcckstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo L","family":"Hofacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,3,9]]},"reference":[{"issue":"10","key":"116_CR1","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/ng2135","volume":"39","author":"M Kertesz","year":"2007","unstructured":"Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nat Genet. 2007, 39 (10): 1278-84. 10.1038\/ng2135","journal-title":"Nat Genet"},{"issue":"5","key":"116_CR2","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/nbt1404","volume":"26","author":"H Tafer","year":"2008","unstructured":"Tafer H, Ameres S, Obernosterer G, Gebeshuber C, Schroeder R, Martinez J, Hofacker I: The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol. 2008, 26 (5): 578-83. 10.1038\/nbt1404","journal-title":"Nat Biotechnol"},{"issue":"4","key":"116_CR3","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1016\/0022-2836(92)90462-S","volume":"224","author":"P Wikstr\u00f6m","year":"1992","unstructured":"Wikstr\u00f6m P, Lind L, Berg D, Bj\u00f6rk G: Importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Escherichia coli. J Mol Biol. 1992, 224 (4): 949-66.","journal-title":"J Mol Biol"},{"key":"116_CR4","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.gene.2004.11.043","volume":"345","author":"J Hackerm\u00fcller","year":"2005","unstructured":"Hackerm\u00fcller J, Meisner N, Auer M, Jaritz M, Stadler P: The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene. 2005, 345: 3-12.","journal-title":"Gene"},{"issue":"10","key":"116_CR5","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1093\/bioinformatics\/btl024","volume":"22","author":"U M\u00fcckstein","year":"2006","unstructured":"M\u00fcckstein U, Tafer H, Hackerm\u00fcller J, Bernhart S, Stadler P, Hofacker I: Thermodynamics of RNA-RNA binding. Bioinformatics. 2006, 22 (10): 1177-82.","journal-title":"Bioinformatics"},{"key":"116_CR6","first-page":"114","volume-title":"Bioinformatics Research and Development, Volume 13 of Communications in Computer and Information Science","author":"U M\u00fcckstein","year":"2008","unstructured":"M\u00fcckstein U, Tafer H, Bernhart SH, Hernandez-Rosales M, Vogel J, Stadler PF, Hofacker IL: Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. Bioinformatics Research and Development, Volume 13 of Communications in Computer and Information Science. Edited by: Elloumi M, K\u00fcng J, Linial M, Murphy R, Schneider K, Toma C. 2008, 114-127. Springer,"},{"issue":"24","key":"116_CR7","doi-asserted-by":"publisher","first-page":"2849","DOI":"10.1093\/bioinformatics\/btn544","volume":"24","author":"A Busch","year":"2008","unstructured":"Busch A, Richter A, Backofen R: IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics. 2008, 24 (24): 2849-56. 10.1093\/bioinformatics\/btn544","journal-title":"Bioinformatics"},{"issue":"10","key":"116_CR8","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/ng2135","volume":"39","author":"M Kertesz","year":"2007","unstructured":"Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nat Genet. 2007, 39 (10): 1278-84. 10.1038\/ng2135","journal-title":"Nat Genet"},{"issue":"5","key":"116_CR9","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1093\/nar\/29.5.1034","volume":"29","author":"Y Ding","year":"2001","unstructured":"Ding Y, Lawrence CE: Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res. 2001, 29 (5): 1034-46. 10.1093\/nar\/29.5.1034","journal-title":"Nucleic Acids Res"},{"issue":"1-2","key":"116_CR10","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1007\/s00285-007-0107-5","volume":"56","author":"A Bompf\u00fcnewerer","year":"2008","unstructured":"Bompf\u00fcnewerer A, Backofen R, Bernhart S, Hertel J, Hofacker I, Stadler P, Will S: Variations on RNA folding and alignment: lessons from Benasque. J Math Biol. 2008, 56 (1-2): 129-44.","journal-title":"J Math Biol"},{"issue":"24","key":"116_CR11","doi-asserted-by":"publisher","first-page":"7280","DOI":"10.1093\/nar\/gkg938","volume":"31","author":"Y Ding","year":"2003","unstructured":"Ding Y, Lawrence C: A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 2003, 31 (24): 7280-301. 10.1093\/nar\/gkg938","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"116_CR12","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"IL Hofacker","year":"1994","unstructured":"Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P: Fast Folding and Comparison of RNA Secondary Structures. Monatsh Chemie. 1994, 125 (2): 167-188. 10.1007\/BF00818163","journal-title":"Monatsh Chemie"},{"key":"116_CR13","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"JS McCaskill","year":"1990","unstructured":"McCaskill JS: The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers. 1990, 29: 1105-1119. 10.1002\/bip.360290621","journal-title":"Biopolymers"},{"key":"116_CR14","first-page":"D280","volume-title":"Nucleic Acids Res","author":"DH Turner","year":"2010","unstructured":"Turner DH, Mathews DH: NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. 2010, D280-2. 38 Database,","edition":"38"},{"key":"116_CR15","volume-title":"Bioinformatics","author":"H Tafer","year":"2011","unstructured":"Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL: Fast Accessibility-Based Prediction of RNA-RNA Interactions. Bioinformatics. 2011, ,"},{"issue":"12","key":"116_CR16","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.1016\/j.chembiol.2004.11.018","volume":"11","author":"A Serganov","year":"2004","unstructured":"Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ: Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol. 2004, 11 (12): 1729-1741. \n                    http:\/\/www.hubmed.org\/display.cgi?uids=15610857\n                    \n                   10.1016\/j.chembiol.2004.11.018","journal-title":"Chem Biol"}],"container-title":["Algorithms for Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1748-7188-6-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1748-7188-6-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1748-7188-6-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T18:43:44Z","timestamp":1548096224000},"score":1,"resource":{"primary":{"URL":"https:\/\/almob.biomedcentral.com\/articles\/10.1186\/1748-7188-6-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,9]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["116"],"URL":"https:\/\/doi.org\/10.1186\/1748-7188-6-3","relation":{},"ISSN":["1748-7188"],"issn-type":[{"value":"1748-7188","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,3,9]]},"article-number":"3"}}