Havgaard JH - Search Results

1

Structural profiles of human miRNA families from pairwise clustering.

Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J. Kaczkowski B, et al. Among authors: havgaard jh. Bioinformatics. 2009 Feb 1;25(3):291-4. doi: 10.1093/bioinformatics/btn628. Epub 2008 Dec 4. Bioinformatics. 2009. PMID: 19059941

2

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

Havgaard JH, Lyngsø RB, Gorodkin J. Havgaard JH, et al. 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.

3

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: havgaard jh. 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.

4

Multiple structural alignment and clustering of RNA sequences.

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

5

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

Havgaard JH, Torarinsson E, Gorodkin J. Havgaard JH, et al. PLoS Comput Biol. 2007 Oct;3(10):1896-908. doi: 10.1371/journal.pcbi.0030193. Epub 2007 Aug 20. PLoS Comput Biol. 2007. PMID: 17937495 Free PMC article.

6

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.

Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J. Sundfeld D, et al. Among authors: havgaard jh. Bioinformatics. 2016 Apr 15;32(8):1238-40. doi: 10.1093/bioinformatics/btv748. Epub 2015 Dec 24. Bioinformatics. 2016. PMID: 26704597 Free PMC article.

7

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. Bioinformatics. 2005 May 1;21(9):1815-24. doi: 10.1093/bioinformatics/bti279. Epub 2005 Jan 18. Bioinformatics. 2005. PMID: 15657094

8

RNA structural alignments, part I: Sankoff-based approaches for structural alignments.

Havgaard JH, Gorodkin J. Havgaard JH, et al. Methods Mol Biol. 2014;1097:275-90. doi: 10.1007/978-1-62703-709-9_13. Methods Mol Biol. 2014. PMID: 24639164

9

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. Among authors: havgaard jh. Bioinformatics. 2017 Jul 15;33(14):2089-2096. doi: 10.1093/bioinformatics/btx114. Bioinformatics. 2017. PMID: 28334186 Free PMC article.

10

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 12:12.11.1-12.11.15. doi: 10.1002/0471250953.bi1211s39. Curr Protoc Bioinformatics. 2012. PMID: 22948726

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