Gorodkin J - Search Results

1

Multiple structural alignment and clustering of RNA sequences.

Torarinsson E, Havgaard JH, Gorodkin J. Torarinsson E, et al. Among authors: gorodkin j. Bioinformatics. 2007 Apr 15;23(8):926-32. doi: 10.1093/bioinformatics/btm049. Epub 2007 Feb 25. Bioinformatics. 2007. PMID: 17324941

2

CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.

Geissler AS, Fehler AO, Poulsen LD, González-Tortuero E, Kallehauge TB, Alkan F, Anthon C, Seemann SE, Rasmussen MD, Breüner A, Hjort C, Vinther J, Gorodkin J. Geissler AS, et al. Among authors: gorodkin j. J Ind Microbiol Biotechnol. 2023 Feb 17;50(1):kuac028. doi: 10.1093/jimb/kuac028. J Ind Microbiol Biotechnol. 2023. PMID: 36564025 Free PMC article.

3

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

Gorodkin J, Heyer LJ, Stormo GD. Gorodkin J, et al. Proc Int Conf Intell Syst Mol Biol. 1997;5:120-3. Proc Int Conf Intell Syst Mol Biol. 1997. PMID: 9322025

4

MatrixPlot: visualizing sequence constraints.

Gorodkin J, Staerfeldt HH, Lund O, Brunak S. Gorodkin J, et al. Bioinformatics. 1999 Sep;15(9):769-70. doi: 10.1093/bioinformatics/15.9.769. Bioinformatics. 1999. PMID: 10498780

5

Discovering common stem-loop motifs in unaligned RNA sequences.

Gorodkin J, Stricklin SL, Stormo GD. Gorodkin J, et al. Nucleic Acids Res. 2001 May 15;29(10):2135-44. doi: 10.1093/nar/29.10.2135. Nucleic Acids Res. 2001. PMID: 11353083 Free PMC article.

6

Semi-automated update and cleanup of structural RNA alignment databases.

Gorodkin J, Zwieb C, Knudsen B. Gorodkin J, et al. Bioinformatics. 2001 Jul;17(7):642-5. doi: 10.1093/bioinformatics/17.7.642. Bioinformatics. 2001. PMID: 11448882

7

A mini-greedy algorithm for faster structural RNA stem-loop search.

Gorodkin J, Lyngso RB, Stormo GD. Gorodkin J, et al. Genome Inform. 2001;12:184-93. Genome Inform. 2001. PMID: 11791237

8

Evolutionary rate variation and RNA secondary structure prediction.

Knudsen B, Andersen ES, Damgaard C, Kjems J, Gorodkin J. Knudsen B, et al. Among authors: gorodkin j. Comput Biol Chem. 2004 Jul;28(3):219-26. doi: 10.1016/j.compbiolchem.2004.04.001. Comput Biol Chem. 2004. PMID: 15261152

9

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.

Havgaard JH, Lyngsø RB, Stormo GD, Gorodkin J. Havgaard JH, et al. Among authors: gorodkin j. Bioinformatics. 2005 May 1;21(9):1815-24. doi: 10.1093/bioinformatics/bti279. Epub 2005 Jan 18. Bioinformatics. 2005. PMID: 15657094

10

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Havgaard JH, Lyngsø RB, Gorodkin J. Havgaard JH, et al. Among authors: gorodkin j. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3. doi: 10.1093/nar/gki473. Nucleic Acids Res. 2005. PMID: 15980555 Free PMC article.

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