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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. Algorithms Mol Biol. 2010 May 21;5:22. doi: 10.1186/1748-7188-5-22. Algorithms Mol Biol. 2010. PMID: 20492641 Free PMC article.
Associating transcription factors and conserved RNA structures with gene regulation in the human brain.
Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J. Hecker N, et al. Among authors: seemann se. Sci Rep. 2017 Jul 18;7(1):5776. doi: 10.1038/s41598-017-06200-4. Sci Rep. 2017. PMID: 28720872 Free PMC article.
The identification and functional annotation of RNA structures conserved in vertebrates.
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J. Seemann SE, et al. Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9. Genome Res. 2017. PMID: 28487280 Free PMC article.
DotAligner: identification and clustering of RNA structure motifs.
Smith MA, Seemann SE, Quek XC, Mattick JS. Smith MA, et al. Among authors: seemann se. Genome Biol. 2017 Dec 28;18(1):244. doi: 10.1186/s13059-017-1371-3. Genome Biol. 2017. PMID: 29284541 Free PMC article.
Identification and characterization of novel conserved RNA structures in Drosophila.
Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J. Kirsch R, et al. Among authors: seemann se. BMC Genomics. 2018 Dec 11;19(1):899. doi: 10.1186/s12864-018-5234-4. BMC Genomics. 2018. PMID: 30537930 Free PMC article.
Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures.
Sabarinathan R, Anthon C, Gorodkin J, Seemann SE. Sabarinathan R, et al. Among authors: seemann se. Genes (Basel). 2018 Dec 4;9(12):604. doi: 10.3390/genes9120604. Genes (Basel). 2018. PMID: 30518121 Free PMC article.
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R. Miladi M, et al. Among authors: seemann se. Bioinformatics. 2017 Jul 15;33(14):2089-2096. doi: 10.1093/bioinformatics/btx114. Bioinformatics. 2017. PMID: 28334186 Free PMC article.
Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.
Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J. Sükösd Z, et al. Among authors: seemann se. Nucleic Acids Res. 2015 Dec 2;43(21):10168-79. doi: 10.1093/nar/gkv1039. Epub 2015 Oct 17. Nucleic Acids Res. 2015. PMID: 26476446 Free PMC article.
Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J. Hecker N, et al. Among authors: seemann se. Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. doi: 10.1093/nar/gkv813. Epub 2015 Aug 17. Nucleic Acids Res. 2015. PMID: 26283181 Free PMC article.
Structured RNAs and synteny regions in the pig genome.
Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J. Anthon C, et al. Among authors: seemann se. BMC Genomics. 2014 Jun 10;15(1):459. doi: 10.1186/1471-2164-15-459. BMC Genomics. 2014. PMID: 24917120 Free PMC article.
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