Gorodkin J - Search Results

1

Does rapid sequence divergence preclude RNA structure conservation in vertebrates?

Seemann SE, Mirza AH, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Workman CT, Pociot F, Tommerup N, Gorodkin J, Ruzzo WL. Seemann SE, et al. Among authors: gorodkin j. Nucleic Acids Res. 2022 Mar 21;50(5):2452-2463. doi: 10.1093/nar/gkac067. Nucleic Acids Res. 2022. PMID: 35188540 Free PMC article.

2

Finding the most significant common sequence and structure motifs in a set of RNA sequences.

Gorodkin J, Heyer LJ, Stormo GD. Gorodkin J, et al. Nucleic Acids Res. 1997 Sep 15;25(18):3724-32. doi: 10.1093/nar/25.18.3724. Nucleic Acids Res. 1997. PMID: 9278497 Free PMC article.

3

Detection of RNA structures in porcine EST data and related mammals.

Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J. Seemann SE, et al. Among authors: gorodkin j. BMC Genomics. 2007 Sep 10;8:316. doi: 10.1186/1471-2164-8-316. BMC Genomics. 2007. PMID: 17845718 Free PMC article.

4

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J. Torarinsson E, et al. Among authors: gorodkin j. Genome Res. 2008 Feb;18(2):242-51. doi: 10.1101/gr.6887408. Epub 2007 Dec 20. Genome Res. 2008. PMID: 18096747 Free PMC article.

5

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.

Seemann SE, Gorodkin J, Backofen R. Seemann SE, et al. Among authors: gorodkin j. 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.

6

Sequence assembly.

Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J. Scheibye-Alsing K, et al. Among authors: gorodkin j. Comput Biol Chem. 2009 Apr;33(2):121-36. doi: 10.1016/j.compbiolchem.2008.11.003. Epub 2008 Dec 6. Comput Biol Chem. 2009. PMID: 19152793 Review.

7

De novo prediction of structured RNAs from genomic sequences.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. Gorodkin J, et al. Trends Biotechnol. 2010 Jan;28(1):9-19. doi: 10.1016/j.tibtech.2009.09.006. Epub 2009 Nov 26. Trends Biotechnol. 2010. PMID: 19942311 Free PMC article. Review.

8

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.

9

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: gorodkin j. Bioinformatics. 2011 Jan 15;27(2):211-9. doi: 10.1093/bioinformatics/btq634. Epub 2010 Nov 18. Bioinformatics. 2011. PMID: 21088024 Free PMC article.

10

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.

Seemann SE, Menzel P, Backofen R, Gorodkin J. Seemann SE, et al. Among authors: gorodkin j. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W107-11. doi: 10.1093/nar/gkr248. Epub 2011 May 23. Nucleic Acids Res. 2011. PMID: 21609960 Free PMC article.

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