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Results: 19

1.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ.

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.

PMID:
19906703
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome.

Lichtenberg J, Yilmaz A, Welch JD, Kurz K, Liang X, Drews F, Ecker K, Lee SS, Geisler M, Grotewold E, Welch LR.

BMC Genomics. 2009 Oct 8;10:463. doi: 10.1186/1471-2164-10-463.

PMID:
19814816
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Word-based characterization of promoters involved in human DNA repair pathways.

Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S18. doi: 10.1186/1471-2164-10-S1-S18.

PMID:
19594877
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing.

Feng J, Naiman DQ, Cooper B.

Mol Biosyst. 2009 Dec;5(12):1679-87. doi: 10.1039/b903031j. Epub 2009 Apr 30.

PMID:
19452047
[PubMed - indexed for MEDLINE]
5.

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
6.
7.

Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.

Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D.

Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6605-10. Epub 2006 Apr 24.

PMID:
16636294
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar.

Wang G, Yu T, Zhang W.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W412-6.

PMID:
15980501
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Assessing computational tools for the discovery of transcription factor binding sites.

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z.

Nat Biotechnol. 2005 Jan;23(1):137-44.

PMID:
15637633
[PubMed - indexed for MEDLINE]
10.

The ENCODE (ENCyclopedia Of DNA Elements) Project.

ENCODE Project Consortium.

Science. 2004 Oct 22;306(5696):636-40.

PMID:
15499007
[PubMed - indexed for MEDLINE]
11.

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.

Pavesi G, Mereghetti P, Mauri G, Pesole G.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203.

PMID:
15215380
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation.

Sinha S, Tompa M.

Nucleic Acids Res. 2003 Jul 1;31(13):3586-8.

PMID:
12824371
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors.

Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E.

BMC Bioinformatics. 2003 Jun 23;4:25. Epub 2003 Jun 23.

PMID:
12820902
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Finding composite regulatory patterns in DNA sequences.

Eskin E, Pevzner PA.

Bioinformatics. 2002;18 Suppl 1:S354-63.

PMID:
12169566
[PubMed - indexed for MEDLINE]
Free Article
15.

REPuter: the manifold applications of repeat analysis on a genomic scale.

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R.

Nucleic Acids Res. 2001 Nov 15;29(22):4633-42.

PMID:
11713313
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Separating real motifs from their artifacts.

Blanchette M, Sinha S.

Bioinformatics. 2001;17 Suppl 1:S30-8.

PMID:
11472990
[PubMed - indexed for MEDLINE]
Free Article
17.

Efficient detection of unusual words.

Apostolico A, Bock ME, Lonardi S, Xu X.

J Comput Biol. 2000 Feb-Apr;7(1-2):71-94.

PMID:
10890389
[PubMed - indexed for MEDLINE]
18.

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.

Rigoutsos I, Floratos A.

Bioinformatics. 1998;14(1):55-67. Erratum in: Bioinformatics 1998;14(2):229.

PMID:
9520502
[PubMed - indexed for MEDLINE]
Free Article
19.

Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences.

Schbath S, Prum B, de Turckheim E.

J Comput Biol. 1995 Fall;2(3):417-37.

PMID:
8521272
[PubMed - indexed for MEDLINE]
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