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Items: 1 to 20 of 113

1.

Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources.

Doyle F, Zaleski C, George AD, Stenson EK, Ricciardi A, Tenenbaum SA.

Methods Mol Biol. 2008;419:39-52. doi: 10.1007/978-1-59745-033-1_3.

PMID:
18369974
2.

Discovering common stem-loop motifs in unaligned RNA sequences.

Gorodkin J, Stricklin SL, Stormo GD.

Nucleic Acids Res. 2001 May 15;29(10):2135-44.

3.

Web-based tools for studying RNA structure and function.

George AD, Tenenbaum SA.

Methods Mol Biol. 2011;703:67-86. doi: 10.1007/978-1-59745-248-9_6.

PMID:
21125484
4.

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences.

Pavesi G, Mauri G, Stefani M, Pesole G.

Nucleic Acids Res. 2004 Jun 15;32(10):3258-69.

5.

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D75-80. doi: 10.1093/nar/gkp902.

6.

Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.

Xu X, Ji Y, Stormo GD.

PLoS Comput Biol. 2009 Apr;5(4):e1000338. doi: 10.1371/journal.pcbi.1000338.

7.
8.

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.

Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70.

9.

Bioinformatics approaches for studying untranslated regions of mRNAs.

Bagga PS.

Methods Mol Biol. 2008;419:1-21. doi: 10.1007/978-1-59745-033-1_1.

PMID:
18369972
10.

Informatic resources for identifying and annotating structural RNA motifs.

George AD, Tenenbaum SA.

Mol Biotechnol. 2009 Feb;41(2):180-93. doi: 10.1007/s12033-008-9114-z. Review.

11.

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.

Huang HY, Chien CH, Jen KH, Huang HD.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34.

12.

3'-UTR SIRF: a database for identifying clusters of whort interspersed repeats in 3' untranslated regions.

Andken BB, Lim I, Benson G, Vincent JJ, Ferenc MT, Heinrich B, Jarzylo LA, Man HY, Deshler JO.

BMC Bioinformatics. 2007 Jul 30;8:274.

13.

Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes.

Rabani M, Kertesz M, Segal E.

Methods Mol Biol. 2011;714:467-79. doi: 10.1007/978-1-61779-005-8_28.

PMID:
21431758
14.

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.

Liseron-Monfils C, Lewis T, Ashlock D, McNicholas PD, Fauteux F, Strömvik M, Raizada MN.

BMC Plant Biol. 2013 Mar 15;13:42. doi: 10.1186/1471-2229-13-42.

15.

Classification and assessment tools for structural motif discovery algorithms.

Badr G, Al-Turaiki I, Mathkour H.

BMC Bioinformatics. 2013;14 Suppl 9:S4. doi: 10.1186/1471-2105-14-S9-S4.

16.

RNA motif discovery: a computational overview.

Achar A, Sætrom P.

Biol Direct. 2015 Oct 9;10:61. doi: 10.1186/s13062-015-0090-5. Review.

17.

cisRED: a database system for genome-scale computational discovery of regulatory elements.

Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73.

18.

IncMD: incremental trie-based structural motif discovery algorithm.

Badr G, Al-Turaiki I, Turcotte M, Mathkour H.

J Bioinform Comput Biol. 2014 Oct;12(5):1450027. doi: 10.1142/S0219720014500279.

PMID:
25362841
19.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

20.

PSSMTS: position specific scoring matrices on tree structures.

Sato K, Morita K, Sakakibara Y.

J Math Biol. 2008 Jan;56(1-2):201-14.

PMID:
17619192
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