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Items: 1 to 20 of 116

1.

Seeder: discriminative seeding DNA motif discovery.

Fauteux F, Blanchette M, Strömvik MV.

Bioinformatics. 2008 Oct 15;24(20):2303-7. doi: 10.1093/bioinformatics/btn444. Epub 2008 Aug 21.

2.

Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.

3.

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.

4.

A survey of DNA motif finding algorithms.

Das MK, Dai HK.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S21. Review.

5.

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.

7.

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs.

Garcia-Alcalde F, Blanco A, Shepherd AJ.

BMC Bioinformatics. 2010 Nov 8;11:551. doi: 10.1186/1471-2105-11-551.

8.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

9.

A cluster refinement algorithm for motif discovery.

Li G, Chan TM, Leung KS, Lee KH.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):654-68. doi: 10.1109/TCBB.2009.25.

PMID:
21030733
10.

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.

Fauteux F, Strömvik MV.

BMC Plant Biol. 2009 Oct 20;9:126. doi: 10.1186/1471-2229-9-126.

12.

De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I.

PLoS Comput Biol. 2011 Feb 10;7(2):e1001070. doi: 10.1371/journal.pcbi.1001070. Erratum in: PLoS Comput Biol. 2011 Oct;7(10). doi: 10.1371/annotation/a0b541dc-472b-4076-a435-499ce9519335.

13.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70.

14.

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Klepper K, Drabløs F.

BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9.

15.

GAME: detecting cis-regulatory elements using a genetic algorithm.

Wei Z, Jensen ST.

Bioinformatics. 2006 Jul 1;22(13):1577-84. Epub 2006 Apr 21.

17.

Assessment of composite motif discovery methods.

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F.

BMC Bioinformatics. 2008 Feb 26;9:123. doi: 10.1186/1471-2105-9-123.

18.

A uniform projection method for motif discovery in DNA sequences.

Raphael B, Liu LT, Varghese G.

IEEE/ACM Trans Comput Biol Bioinform. 2004 Apr-Jun;1(2):91-4.

PMID:
17048384
19.

POWRS: position-sensitive motif discovery.

Davis IW, Benninger C, Benfey PN, Elich T.

PLoS One. 2012;7(7):e40373. doi: 10.1371/journal.pone.0040373. Epub 2012 Jul 5.

20.

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.

Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G.

Bioinformatics. 2009 Aug 15;25(16):2126-33. doi: 10.1093/bioinformatics/btp278. Epub 2009 Apr 23.

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