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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: richter as. Algorithms Mol Biol. 2010 May 21;5:22. doi: 10.1186/1748-7188-5-22. Algorithms Mol Biol. 2010. PMID: 20492641 Free PMC article.
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J. Seemann SE, et al. Among authors: richter as. Bioinformatics. 2011 Jan 15;27(2):211-9. doi: 10.1093/bioinformatics/btq634. Epub 2010 Nov 18. Bioinformatics. 2011. PMID: 21088024 Free PMC article.
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?
Richter AS, Backofen R. Richter AS, et al. RNA Biol. 2012 Jul;9(7):954-65. doi: 10.4161/rna.20294. Epub 2012 Jul 1. RNA Biol. 2012. PMID: 22767260 Free PMC article.
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.
Wright PR, Georg J, Mann M, Sorescu DA, Richter AS, Lott S, Kleinkauf R, Hess WR, Backofen R. Wright PR, et al. Among authors: richter as. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W119-23. doi: 10.1093/nar/gku359. Epub 2014 May 16. Nucleic Acids Res. 2014. PMID: 24838564 Free PMC article.
Bioinformatics of prokaryotic RNAs.
Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF. Backofen R, et al. Among authors: richter as. RNA Biol. 2014;11(5):470-83. doi: 10.4161/rna.28647. Epub 2014 Apr 2. RNA Biol. 2014. PMID: 24755880 Free PMC article. Review.
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
Busch A, Richter AS, Backofen R. Busch A, et al. Among authors: richter as. Bioinformatics. 2008 Dec 15;24(24):2849-56. doi: 10.1093/bioinformatics/btn544. Epub 2008 Oct 21. Bioinformatics. 2008. PMID: 18940824 Free PMC article.
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1.
Richter AS, Schleberger C, Backofen R, Steglich C. Richter AS, et al. Bioinformatics. 2010 Jan 1;26(1):1-5. doi: 10.1093/bioinformatics/btp609. Epub 2009 Oct 22. Bioinformatics. 2010. PMID: 19850757 Free PMC article.
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA.
Smith C, Heyne S, Richter AS, Will S, Backofen R. Smith C, et al. Among authors: richter as. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W373-7. doi: 10.1093/nar/gkq316. Epub 2010 May 5. Nucleic Acids Res. 2010. PMID: 20444875 Free PMC article.
Comparative genomics boosts target prediction for bacterial small RNAs.
Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J. Wright PR, et al. Among authors: richter as. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96. doi: 10.1073/pnas.1303248110. Epub 2013 Aug 26. Proc Natl Acad Sci U S A. 2013. PMID: 23980183 Free PMC article.
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R. Raden M, et al. Among authors: richter as. Nucleic Acids Res. 2018 Jul 2;46(W1):W25-W29. doi: 10.1093/nar/gky329. Nucleic Acids Res. 2018. PMID: 29788132 Free PMC article.
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