{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T12:47:03Z","timestamp":1771073223721,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,11,18]],"date-time":"2015-11-18T00:00:00Z","timestamp":1447804800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"name":"Baden-W\u00fcrttemberg Ministry of Science, Research and Arts","award":["MWK Grant 7533-7-11.6.1"],"award-info":[{"award-number":["MWK Grant 7533-7-11.6.1"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0815-6","type":"journal-article","created":{"date-parts":[[2015,11,18]],"date-time":"2015-11-18T11:46:37Z","timestamp":1447847197000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["antaRNA \u2013 Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization"],"prefix":"10.1186","volume":"16","author":[{"given":"Robert","family":"Kleinkauf","sequence":"first","affiliation":[]},{"given":"Torsten","family":"Houwaart","sequence":"additional","affiliation":[]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Mann","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,11,18]]},"reference":[{"issue":"6287","key":"815_CR1","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1038\/346818a0","volume":"346","author":"AD Ellington","year":"1990","unstructured":"Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990; 346(6287):818\u201322. doi: 10.1038\/346818a0 .","journal-title":"Nature"},{"issue":"4968","key":"815_CR2","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1126\/science.2200121","volume":"249","author":"C Tuerk","year":"1990","unstructured":"Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990; 249(4968):505\u201315.","journal-title":"Science"},{"issue":"7","key":"815_CR3","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/nrd3141","volume":"9","author":"AD Keefe","year":"2010","unstructured":"Keefe AD, Pai S, Ellington A. Aptamers as therapeutics. Nat Rev Drug Discov. 2010; 9(7):537\u201350. doi: 10.1038\/nrd3141 .","journal-title":"Nat Rev Drug Discov"},{"issue":"4","key":"815_CR4","doi-asserted-by":"publisher","first-page":"668","DOI":"10.3390\/ijms9040668","volume":"9","author":"KT Guo","year":"2008","unstructured":"Guo KT, Ziemer G, Paul A, Wendel HP. CELL-SELEX: novel perspectives of aptamer-based therapeutics. Int J Mol Sci. 2008; 9(4):668. doi: 10.3390\/ijms9040668 .","journal-title":"Int J Mol Sci"},{"issue":"12","key":"815_CR5","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.4155\/tde.13.118","volume":"4","author":"JP Dassie","year":"2013","unstructured":"Dassie JP, Giangrande PH. Current progress on aptamer-targeted oligonucleotide therapeutics. Ther Deliv. 2013; 4(12):1527\u201346.","journal-title":"Ther Deliv"},{"issue":"5","key":"815_CR6","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1016\/j.biomaterials.2011.10.062","volume":"33","author":"N Chen","year":"2012","unstructured":"Chen N, Zhang Z, Soontornworajit B, Zhou J, Wang Y. Cell adhesion on an artificial extracellular matrix using aptamer-functionalized PEG hydrogels. Biomaterials. 2012; 33(5):1353\u201362. doi: 10.1016\/j.biomaterials.2011.10.062 .","journal-title":"Biomaterials"},{"issue":"3","key":"815_CR7","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.tig.2014.01.003","volume":"30","author":"RM Terns","year":"2014","unstructured":"Terns RM, Terns MP. CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet. 2014; 30(3):111\u20138. doi: 10.1016\/j.tig.2014.01.003 .","journal-title":"Trends Genet"},{"issue":"7530","key":"815_CR8","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/nature13769","volume":"516","author":"MR O\u0106onnell","year":"2014","unstructured":"O\u0106onnell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR\/Cas9. Nature. 2014; 516(7530):263\u20136. doi: 10.1038\/nature13769 .","journal-title":"Nature"},{"issue":"15","key":"815_CR9","doi-asserted-by":"publisher","first-page":"3312","DOI":"10.1093\/bioinformatics\/bti507","volume":"21","author":"A Busch","year":"2005","unstructured":"Busch A, Will S, Backofen R. SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinformatics. 2005; 21(15):3312\u20133.","journal-title":"Bioinformatics"},{"issue":"02","key":"815_CR10","doi-asserted-by":"publisher","first-page":"1350001","DOI":"10.1142\/S0219720013500017","volume":"11","author":"JA Garcia-Martin","year":"2013","unstructured":"Garcia-Martin JA, Clote P, Dotu I. RNAiFold: a constraint programming algorithm for RNA inverse folding and molecular design. J Bioinform Comput Biol. 2013; 11(02):1350001. doi: 10.1142\/S0219720013500017 , PMID: 23600819.","journal-title":"J Bioinform Comput Biol"},{"key":"815_CR11","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. Monatshefte Chemie. 1994; 125:167\u201388.","journal-title":"Monatshefte Chemie"},{"issue":"Web Server issu","key":"815_CR12","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1093\/nar\/gkm218","volume":"35","author":"A Busch","year":"2007","unstructured":"Busch A, Backofen R. INFO-RNA\u2013a server for fast inverse RNA folding satisfying sequence constraints. Nucleic Acids Res. 2007; 35(Web Server issue):310\u20133. doi: 10.1093\/nar\/gkm218 .","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"815_CR13","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1186\/1471-2105-13-260","volume":"13","author":"R Lyngso","year":"2012","unstructured":"Lyngso R, Anderson J, Sizikova E, Badugu A, Hyland T, Hein J. Frnakenstein: multiple target inverse RNA folding. BMC Bioinf. 2012; 13(1):260. doi: 10.1186\/1471-2105-13-260 .","journal-title":"BMC Bioinf"},{"issue":"9","key":"815_CR14","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.1093\/bioinformatics\/btu001","volume":"30","author":"ET Ali","year":"2014","unstructured":"Ali ET, Mohammad G, Morteza MN. Evolutionary solution for the RNA design problem. Bioinformatics. 2014; 30(9):1250\u20138. doi: 10.1093\/bioinformatics\/btu001 .","journal-title":"Bioinformatics"},{"issue":"3","key":"815_CR15","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1002\/jcc.21633","volume":"32","author":"JN Zadeh","year":"2011","unstructured":"Zadeh JN, Wolfe BR, Pierce NA. Nucleic acid sequence design via efficient ensemble defect optimization. J Comb Chem. 2011; 32(3):439\u201352. doi: 10.1002\/jcc.21633 .","journal-title":"J Comb Chem"},{"issue":"22","key":"815_CR16","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btt494","volume":"29","author":"L Weinbrand","year":"2013","unstructured":"Weinbrand L, Avihoo A, Barash D. RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. Bioinformatics. 2013; 29(22):2938\u201340. doi: 10.1093\/bioinformatics\/btt494 .","journal-title":"Bioinformatics"},{"issue":"11","key":"815_CR17","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1007\/PL00000795","volume":"58","author":"P Fechter","year":"2001","unstructured":"Fechter P, Rudinger-Thirion J, Florentz C, Giege R. Novel features in the tRNA-like world of plant viral RNAs. Cell Mol Life Sci CMLS. 2001; 58(11):1547\u201361. doi: 10.1007\/PL00000795 .","journal-title":"Cell Mol Life Sci CMLS"},{"issue":"6","key":"815_CR18","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1016\/j.tibs.2008.04.007","volume":"33","author":"J Kieft","year":"2008","unstructured":"Kieft J. Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci. 2008; 33(6):274\u201383. doi: 10.1016\/j.tibs.2008.04.007 .","journal-title":"Trends Biochem Sci"},{"issue":"5","key":"815_CR19","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/j.molcel.2005.01.017","volume":"17","author":"C Theimer","year":"2006","unstructured":"Theimer C, Blois C, Feigon J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell. 2006; 17(5):671\u201382. doi: 10.1016\/j.molcel.2005.01.017 .","journal-title":"Mol Cell"},{"issue":"D1","key":"815_CR20","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1093\/nar\/gku1063","volume":"43","author":"EP Nawrocki","year":"2015","unstructured":"Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 2015; 43(D1):130\u20137. doi: 10.1093\/nar\/gku1063 .","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"815_CR21","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/1748-7188-5-27","volume":"5","author":"J Gao","year":"2010","unstructured":"Gao J, Li L, Reidys C. Inverse folding of RNA pseudoknot structures. Algorithm Mol B. 2010; 5(1):27. doi: 10.1186\/1748-7188-5-27 .","journal-title":"Algorithm Mol B"},{"key":"815_CR22","doi-asserted-by":"publisher","first-page":"36","DOI":"10.3389\/fgene.2012.00036","volume":"3","author":"A Taneda","year":"2012","unstructured":"Taneda A. Multi-objective genetic algorithm for pseudoknotted RNA sequence design. Front Genet. 2012; 3:36. doi: 10.3389\/fgene.2012.00036 .","journal-title":"Front Genet"},{"issue":"13","key":"815_CR23","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1093\/bioinformatics\/btr215","volume":"27","author":"K Sato","year":"2011","unstructured":"Sato K, Kato Y, Hamada M, Akutsu T, Asai K. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics. 2011; 27(13):85\u201393. doi: 10.1093\/bioinformatics\/btr215 .","journal-title":"Bioinformatics"},{"issue":"10","key":"815_CR24","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1261\/rna.7284905","volume":"11","author":"J Ren","year":"2005","unstructured":"Ren J, Rastegari B, Condon A, Hoos H. Hotknots: heuristic prediction of RNA secondary structures including pseudoknots. RNA. 2005; 11(10):1494\u20131504. doi: 10.1261\/rna.7284905 .","journal-title":"RNA"},{"issue":"6166","key":"815_CR25","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1126\/science.1246981","volume":"343","author":"T Wang","year":"2014","unstructured":"Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014; 343(6166):80\u20134. doi: 10.1126\/science.1246981 .","journal-title":"Science"},{"issue":"7","key":"815_CR26","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1038\/nbt986","volume":"22","author":"FJ Isaacs","year":"2004","unstructured":"Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol. 2004; 22(7):841\u20137. doi: 10.1038\/nbt986 .","journal-title":"Nat Biotechnol"},{"issue":"5","key":"815_CR27","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1038\/nbt1208","volume":"24","author":"FJ Isaacs","year":"2006","unstructured":"Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nat Biotechnol. 2006; 24(5):545\u20134. doi: 10.1038\/nbt1208 .","journal-title":"Nat Biotechnol"},{"issue":"19","key":"815_CR28","doi-asserted-by":"publisher","first-page":"3114","DOI":"10.1093\/bioinformatics\/btv319","volume":"31","author":"R Kleinkauf","year":"2015","unstructured":"Kleinkauf R, Mann M, Backofen R. antaRNA \u2013 ant colony based RNA sequence design. Bioinformatics. 2015; 31(19):3114\u20133121. doi: 10.1093\/bioinformatics\/btv319 .","journal-title":"Bioinformatics"},{"issue":"3","key":"815_CR29","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1093\/bioinformatics\/btu649","volume":"31","author":"S Janssen","year":"2014","unstructured":"Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics. 2014; 31(3):423\u2013425. doi: 10.1093\/bioinformatics\/btu649 .","journal-title":"Bioinformatics"},{"key":"815_CR30","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1093\/nar\/gkq316","volume":"38 Suppl","author":"C Smith","year":"2010","unstructured":"Smith C, Heyne S, Richter AS, Will S, Backofen R. Freiburg RNA tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Res. 2010; 38 Suppl:373\u20137. doi: 10.1093\/nar\/gkq316 .","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"815_CR31","doi-asserted-by":"publisher","first-page":"3377","DOI":"10.1093\/bioinformatics\/btv372","volume":"31","author":"P Kerpedjiev","year":"2015","unstructured":"Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015; 31(20):3377\u20133379. doi: 10.1093\/bioinformatics\/btv372 .","journal-title":"Bioinformatics"},{"key":"815_CR32","unstructured":"Gr\u00fcning B, Smith C, Houwaart T, Soranzo N, Rasche E. Galaxy Tools - a collection of bioinformatics and cheminformatics tools for the Galaxy environment. https:\/\/github.com\/bgruening\/galaxytools . Accessed 14 Nov 2015."},{"key":"815_CR33","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/1290.001.0001","volume-title":"Ant Colony Optimization","author":"M Dorigo","year":"2004","unstructured":"Dorigo M, St\u00fctzle T. Ant Colony Optimization. Scituate, MA, USA: Bradford Company; 2004."},{"issue":"4","key":"815_CR34","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1109\/MCI.2006.329691","volume":"1","author":"M Dorigo","year":"2006","unstructured":"Dorigo M, Birattari M, St\u00fctzle T. Ant colony optimization \u2013 artificial ants as a computational intelligence technique. IEEE Comput Intell Mag. 2006; 1(4):28\u201339.","journal-title":"IEEE Comput Intell Mag"},{"key":"815_CR35","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","volume":"6","author":"R Lorenz","year":"2011","unstructured":"Lorenz R, Bernhart SH, H\u00f6ner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA package 2.0. Algorithms Mol Biol. 2011; 6:26. doi: 10.1186\/1748-7188-6-26 .","journal-title":"Algorithms Mol Biol"},{"issue":"6","key":"815_CR36","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1371\/journal.pbio.0030213","volume":"3","author":"DW Staple","year":"2005","unstructured":"Staple DW, Butcher SE. Pseudoknots: RNA structures with diverse functions. PLoS Biol. 2005; 3(6):213. doi: 10.1371\/journal.pbio.0030213 .","journal-title":"PLoS Biol"},{"issue":"1","key":"815_CR37","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/nar\/9.1.133","volume":"9","author":"M Zuker","year":"1981","unstructured":"Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9(1):133\u201348.","journal-title":"Nucleic Acids Res"},{"key":"815_CR38","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/nar\/gkn806","volume":"37","author":"M Taufer","year":"2009","unstructured":"Taufer M, Licon A, Araiza R, Mireles D, van Batenburg FHD, Gultyaev AP, et al. PseudoBase ++: an extension of pseudobase for easy searching, formatting and visualization of pseudoknots. Nucleic Acid Res. 2009; 37:127\u201335.","journal-title":"Nucleic Acid Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0815-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0815-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0815-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T17:14:08Z","timestamp":1567358048000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0815-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,18]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["815"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0815-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,11,18]]},"article-number":"389"}}