Gorodkin J - Search Results

1

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.

2

Alteration of microglial metabolism and inflammatory profile contributes to neurotoxicity in a hiPSC-derived microglia model of frontotemporal dementia 3.

Haukedal H, Syshøj Lorenzen S, Winther Westi E, Corsi GI, Gadekar VP, McQuade A, Davtyan H, Doncheva NT, Schmid B, Chandrasekaran A, Seemann SE, Cirera S, Blurton-Jones M, Meyer M, Gorodkin J, Aldana BI, Freude K. Haukedal H, et al. Among authors: gorodkin j. Brain Behav Immun. 2023 Oct;113:353-373. doi: 10.1016/j.bbi.2023.07.024. Epub 2023 Aug 3. Brain Behav Immun. 2023. PMID: 37543250 Free article.

3

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.

4

tmRDB (tmRNA database).

Knudsen B, Wower J, Zwieb C, Gorodkin J. Knudsen B, et al. Among authors: gorodkin j. Nucleic Acids Res. 2001 Jan 1;29(1):171-2. doi: 10.1093/nar/29.1.171. Nucleic Acids Res. 2001. PMID: 11125081 Free PMC article.

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

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

9

The tmRDB and SRPDB resources.

Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. Andersen ES, et al. Among authors: gorodkin j. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D163-8. doi: 10.1093/nar/gkj142. Nucleic Acids Res. 2006. PMID: 16381838 Free PMC article.

10

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.

Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J. Torarinsson E, et al. Among authors: gorodkin j. Genome Res. 2006 Jul;16(7):885-9. doi: 10.1101/gr.5226606. Epub 2006 Jun 2. Genome Res. 2006. PMID: 16751343 Free PMC article.

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