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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: gorodkin j. Algorithms Mol Biol. 2010 May 21;5:22. doi: 10.1186/1748-7188-5-22. Algorithms Mol Biol. 2010. PMID: 20492641 Free PMC article.
Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM.
Havgaard J, Kaur S, Gorodkin J. Havgaard J, et al. Among authors: gorodkin j. Curr Protoc Bioinformatics. 2012 Sep;Chapter 12:Unit12.11. doi: 10.1002/0471250953.bi1211s39. Curr Protoc Bioinformatics. 2012. PMID: 22948726
RILogo: visualizing RNA-RNA interactions.
Menzel P, Seemann SE, Gorodkin J. Menzel P, et al. Among authors: gorodkin j. Bioinformatics. 2012 Oct 1;28(19):2523-6. doi: 10.1093/bioinformatics/bts461. Epub 2012 Jul 23. Bioinformatics. 2012. PMID: 22826541
Semiautomated improvement of RNA alignments.
Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J. Andersen ES, et al. Among authors: gorodkin j. RNA. 2007 Nov;13(11):1850-9. doi: 10.1261/rna.215407. Epub 2007 Sep 5. RNA. 2007. PMID: 17804647 Free PMC article.
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. Among authors: gorodkin j. PLoS One. 2014 Jan 8;9(1):e82699. doi: 10.1371/journal.pone.0082699. eCollection 2014. PLoS One. 2014. PMID: 24416147 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: gorodkin j. Genes (Basel). 2018 Dec 4;9(12):604. doi: 10.3390/genes9120604. Genes (Basel). 2018. PMID: 30518121 Free PMC article.
Comparative RNA Genomics.
Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Backofen R, et al. Among authors: gorodkin j. Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14. Methods Mol Biol. 2018. PMID: 29277874
Special Issue: Computational Analysis of RNA Structure and Function.
Gorodkin J. Gorodkin J. Genes (Basel). 2019 Jan 16;10(1):55. doi: 10.3390/genes10010055. Genes (Basel). 2019. PMID: 30654585 Free PMC article.
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J. Alkan F, et al. Among authors: gorodkin j. Nucleic Acids Res. 2017 May 5;45(8):e60. doi: 10.1093/nar/gkw1325. Nucleic Acids Res. 2017. PMID: 28108657 Free PMC article.
RAIN: RNA-protein Association and Interaction Networks.
Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J. Junge A, et al. Among authors: gorodkin j. Database (Oxford). 2017 Jan 10;2017:baw167. doi: 10.1093/database/baw167. Print 2017. Database (Oxford). 2017. PMID: 28077569 Free PMC article.
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