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De novo discovery of structured ncRNA motifs in genomic sequences.
Ruzzo WL, Gorodkin J. Ruzzo WL, et al. Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15. Methods Mol Biol. 2014. PMID: 24639166 Review.
Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM.
Havgaard J, Kaur S, Gorodkin J. Havgaard J, et al. Curr Protoc Bioinformatics. 2012 Sep;Chapter 12:Unit12.11. doi: 10.1002/0471250953.bi1211s39. Curr Protoc Bioinformatics. 2012. PMID: 22948726
Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J. Sabarinathan R, et al. PLoS One. 2014 Jan 8;9(1):e82699. doi: 10.1371/journal.pone.0082699. eCollection 2014. PLoS One. 2014. PMID: 24416147 Free PMC article.
Comparative RNA Genomics.
Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Backofen R, et al. Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14. Methods Mol Biol. 2018. PMID: 29277874
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: gorodkin j. BMC Genomics. 2018 Dec 11;19(1):899. doi: 10.1186/s12864-018-5234-4. BMC Genomics. 2018. PMID: 30537930 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. Bioinformatics. 2017 Jul 15;33(14):2089-2096. doi: 10.1093/bioinformatics/btx114. Bioinformatics. 2017. PMID: 28334186 Free PMC article.
CONTACT: or SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: or SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioin …
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.
Concepts and introduction to RNA bioinformatics.
Gorodkin J, Hofacker IL, Ruzzo WL. Gorodkin J, et al. Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1. Methods Mol Biol. 2014. PMID: 24639152 Review.
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