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Items: 1 to 20 of 130


RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.

Wenzel A, Akbasli E, Gorodkin J.

Bioinformatics. 2012 Nov 1;28(21):2738-46. doi: 10.1093/bioinformatics/bts519. Epub 2012 Aug 24.


TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Harmanci AO, Sharma G, Mathews DH.

BMC Bioinformatics. 2011 Apr 20;12:108. doi: 10.1186/1471-2105-12-108.


PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.

Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J.

Bioinformatics. 2011 Jan 15;27(2):211-9. doi: 10.1093/bioinformatics/btq634. Epub 2010 Nov 18.


RNAplex: a fast tool for RNA-RNA interaction search.

Tafer H, Hofacker IL.

Bioinformatics. 2008 Nov 15;24(22):2657-63. doi: 10.1093/bioinformatics/btn193. Epub 2008 Apr 23.


Fast accessibility-based prediction of RNA-RNA interactions.

Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL.

Bioinformatics. 2011 Jul 15;27(14):1934-40. doi: 10.1093/bioinformatics/btr281. Epub 2011 May 18.


sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.

Ying X, Cao Y, Wu J, Liu Q, Cha L, Li W.

PLoS One. 2011;6(7):e22705. doi: 10.1371/journal.pone.0022705. Epub 2011 Jul 22.


Fast and effective prediction of microRNA/target duplexes.

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R.

RNA. 2004 Oct;10(10):1507-17.


Dynamic programming algorithms for RNA structure prediction with binding sites.

Poolsap U, Kato Y, Akutsu T.

Pac Symp Biocomput. 2010:98-107.


RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.

Kato Y, Sato K, Hamada M, Watanabe Y, Asai K, Akutsu T.

Bioinformatics. 2010 Sep 15;26(18):i460-6. doi: 10.1093/bioinformatics/btq372.


deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J.

Bioinformatics. 2012 Jan 1;28(1):17-24. doi: 10.1093/bioinformatics/btr598. Epub 2011 Nov 3.


MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

Lindgreen S, Gardner PP, Krogh A.

Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.


Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

Kiryu H, Kin T, Asai K.

Bioinformatics. 2007 Feb 15;23(4):434-41. Epub 2006 Dec 20.


STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.

Dalli D, Wilm A, Mainz I, Steger G.

Bioinformatics. 2006 Jul 1;22(13):1593-9. Epub 2006 Apr 13.


MiRTif: a support vector machine-based microRNA target interaction filter.

Yang Y, Wang YP, Li KB.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S4. doi: 10.1186/1471-2105-9-S12-S4.


Computational analysis of microRNA targets in Caenorhabditis elegans.

Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M.

Gene. 2006 Jan 3;365:2-10. Epub 2005 Dec 13.


Prediction of Ras-effector interactions using position energy matrices.

Kiel C, Serrano L.

Bioinformatics. 2007 Sep 1;23(17):2226-30. Epub 2007 Jun 28.


Analysis of energy-based algorithms for RNA secondary structure prediction.

Hajiaghayi M, Condon A, Hoos HH.

BMC Bioinformatics. 2012 Feb 1;13:22. doi: 10.1186/1471-2105-13-22.


IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.

Busch A, Richter AS, Backofen R.

Bioinformatics. 2008 Dec 15;24(24):2849-56. doi: 10.1093/bioinformatics/btn544. Epub 2008 Oct 21.


TargetRNA: a tool for predicting targets of small RNA action in bacteria.

Tjaden B.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W109-13. doi: 10.1093/nar/gkn264. Epub 2008 May 13.

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