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Results: 1 to 20 of 93

1.

Identification of degenerate motifs using position restricted selection and hybrid ranking combination.

Peng CH, Hsu JT, Chung YS, Lin YJ, Chow WY, Hsu DF, Tang CY.

Nucleic Acids Res. 2006;34(22):6379-91. Epub 2006 Nov 27.

PMID:
17130169
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Bounded search for de novo identification of degenerate cis-regulatory elements.

Carlson JM, Chakravarty A, Khetani RS, Gross RH.

BMC Bioinformatics. 2006 May 15;7:254.

PMID:
16700920
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
17953763
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
[PubMed - indexed for MEDLINE]
5.

Limitations and potentials of current motif discovery algorithms.

Hu J, Li B, Kihara D.

Nucleic Acids Res. 2005 Sep 2;33(15):4899-913. Print 2005.

PMID:
16284194
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
18302777
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID:
12101404
[PubMed - indexed for MEDLINE]
8.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

PMID:
16477324
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The limits of de novo DNA motif discovery.

Simcha D, Price ND, Geman D.

PLoS One. 2012;7(11):e47836. doi: 10.1371/journal.pone.0047836. Epub 2012 Nov 7.

PMID:
23144830
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

SCOPE: a web server for practical de novo motif discovery.

Carlson JM, Chakravarty A, DeZiel CE, Gross RH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W259-64. Epub 2007 May 7.

PMID:
17485471
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A transdimensional Bayesian model for pattern recognition in DNA sequences.

Li SM, Wakefield J, Self S.

Biostatistics. 2008 Oct;9(4):668-85. doi: 10.1093/biostatistics/kxm058. Epub 2008 Mar 18.

PMID:
18349034
[PubMed - indexed for MEDLINE]
Free Article
12.

A survey of DNA motif finding algorithms.

Das MK, Dai HK.

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

PMID:
18047721
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
17893078
[PubMed - indexed for MEDLINE]
Free Article
14.

Position specific variation in the rate of evolution in transcription factor binding sites.

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB.

BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28.

PMID:
12946282
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.

PMID:
17559676
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9. Epub 2003 Mar 10.

PMID:
12627170
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
23323883
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

Martyanov V, Gross RH.

J Vis Exp. 2011 May 31;(51). pii: 2703. doi: 10.3791/2703.

PMID:
21673638
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
18718942
[PubMed - indexed for MEDLINE]
Free PMC Article

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