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Items: 14

1.

The identification and functional annotation of RNA structures conserved in vertebrates.

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9.

2.

Genome browsers.

Torarinsson E.

Methods Mol Biol. 2011;703:53-65. doi: 10.1007/978-1-59745-248-9_5.

PMID:
21125483
3.

De novo prediction of structured RNAs from genomic sequences.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL.

Trends Biotechnol. 2010 Jan;28(1):9-19. doi: 10.1016/j.tibtech.2009.09.006. Epub 2009 Nov 26. Review.

4.

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

Anandam P, Torarinsson E, Ruzzo WL.

Bioinformatics. 2009 Mar 1;25(5):668-9. doi: 10.1093/bioinformatics/btp006. Epub 2009 Jan 9.

PMID:
19136551
5.

Structural profiles of human miRNA families from pairwise clustering.

Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J.

Bioinformatics. 2009 Feb 1;25(3):291-4. doi: 10.1093/bioinformatics/btn628. Epub 2008 Dec 4.

PMID:
19059941
6.

WAR: Webserver for aligning structural RNAs.

Torarinsson E, Lindgreen S.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W79-84. doi: 10.1093/nar/gkn275. Epub 2008 May 20.

7.

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.

Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.

8.

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

Havgaard JH, Torarinsson E, Gorodkin J.

PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20.

9.

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.

RNA. 2007 Nov;13(11):1850-9. Epub 2007 Sep 5.

10.

Multiple structural alignment and clustering of RNA sequences.

Torarinsson E, Havgaard JH, Gorodkin J.

Bioinformatics. 2007 Apr 15;23(8):926-32. Epub 2007 Feb 25.

PMID:
17324941
11.

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.

Genome Res. 2006 Jul;16(7):885-9. Epub 2006 Jun 2. Erratum in: Genome Res. 2006 Nov;16(11):1439.

12.

The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.

Chen L, Brügger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA.

J Bacteriol. 2005 Jul;187(14):4992-9.

13.

Divergent transcriptional and translational signals in Archaea.

Torarinsson E, Klenk HP, Garrett RA.

Environ Microbiol. 2005 Jan;7(1):47-54.

PMID:
15643935
14.

Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements.

Brügger K, Torarinsson E, Redder P, Chen L, Garrett RA.

Biochem Soc Trans. 2004 Apr;32(Pt 2):179-83. Review.

PMID:
15046567

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