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215 results
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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.
Seemann SE, Richter AS, Gorodkin J, Backofen R. Seemann SE, et al. Among authors: backofen r. Algorithms Mol Biol. 2010 May 21;5:22. doi: 10.1186/1748-7188-5-22. Algorithms Mol Biol. 2010. PMID: 20492641 Free PMC article.
INFO-RNA--a fast approach to inverse RNA folding.
Busch A, Backofen R. Busch A, et al. Among authors: backofen r. Bioinformatics. 2006 Aug 1;22(15):1823-31. doi: 10.1093/bioinformatics/btl194. Epub 2006 May 18. Bioinformatics. 2006. PMID: 16709587
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
Hiller M, Pudimat R, Busch A, Backofen R. Hiller M, et al. Among authors: backofen r. Nucleic Acids Res. 2006;34(17):e117. doi: 10.1093/nar/gkl544. Epub 2006 Sep 20. Nucleic Acids Res. 2006. PMID: 16987907 Free PMC article.
RNAs everywhere: genome-wide annotation of structured RNAs.
Athanasius F Bompfünewerer Consortium, Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, Washietl S, Will S. Athanasius F Bompfünewerer Consortium, et al. Among authors: backofen r. J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25. doi: 10.1002/jez.b.21130. J Exp Zool B Mol Dev Evol. 2007. PMID: 17171697 Review.
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Will S, et al. Among authors: backofen r. PLoS Comput Biol. 2007 Apr 13;3(4):e65. doi: 10.1371/journal.pcbi.0030065. Epub 2007 Feb 22. PLoS Comput Biol. 2007. PMID: 17432929 Free PMC article.
INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.
Busch A, Backofen R. Busch A, et al. Among authors: backofen r. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W310-3. doi: 10.1093/nar/gkm218. Epub 2007 Apr 22. Nucleic Acids Res. 2007. PMID: 17452349 Free PMC article.
Locality and gaps in RNA comparison.
Backofen R, Chen S, Hermelin D, Landau GM, Roytberg MA, Weimann O, Zhang K. Backofen R, et al. J Comput Biol. 2007 Oct;14(8):1074-87. doi: 10.1089/cmb.2007.0062. J Comput Biol. 2007. PMID: 17985988
Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA.
Siebert S, Backofen R. Siebert S, et al. Among authors: backofen r. Methods Mol Biol. 2007;395:489-502. doi: 10.1007/978-1-59745-514-5_31. Methods Mol Biol. 2007. PMID: 17993694
Pre-mRNA secondary structures influence exon recognition.
Hiller M, Zhang Z, Backofen R, Stamm S. Hiller M, et al. Among authors: backofen r. PLoS Genet. 2007 Nov;3(11):e204. doi: 10.1371/journal.pgen.0030204. PLoS Genet. 2007. PMID: 18020710 Free PMC article.
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.
Seemann SE, Gorodkin J, Backofen R. Seemann SE, et al. Among authors: backofen r. Nucleic Acids Res. 2008 Nov;36(20):6355-62. doi: 10.1093/nar/gkn544. Epub 2008 Oct 4. Nucleic Acids Res. 2008. PMID: 18836192 Free PMC article.
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