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Items: 1 to 20 of 188

1.

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62.

2.

Decoding cis-regulatory DNAs in the Drosophila genome.

Markstein M, Levine M.

Curr Opin Genet Dev. 2002 Oct;12(5):601-6. Review.

PMID:
12200166
3.

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs.

Starr MO, Ho MC, Gunther EJ, Tu YK, Shur AS, Goetz SE, Borok MJ, Kang V, Drewell RA.

Dev Biol. 2011 Nov 15;359(2):290-302. doi: 10.1016/j.ydbio.2011.07.028.

4.
5.

CREME: Cis-Regulatory Module Explorer for the human genome.

Sharan R, Ben-Hur A, Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W253-6.

6.

Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel.

Matyash A, Chung HR, J├Ąckle H.

J Biol Chem. 2004 Jul 16;279(29):30689-96.

7.
8.

Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex.

Akbari OS, Bousum A, Bae E, Drewell RA.

Dev Biol. 2006 May 15;293(2):294-304. Review.

9.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

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

PMID:
16362910
10.

Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.

GuhaThakurta D, Xie T, Anand M, Edwards SW, Li G, Wang SS, Schadt EE.

BMC Genomics. 2006 Sep 15;7:235.

11.
12.

Computational identification of Ftz/Ftz-F1 downstream target genes.

Bowler T, Kosman D, Licht JD, Pick L.

Dev Biol. 2006 Nov 1;299(1):78-90.

14.

Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms.

Andrioli LP, Vasisht V, Theodosopoulou E, Oberstein A, Small S.

Development. 2002 Nov;129(21):4931-40.

15.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J.

Nat Protoc. 2008;3(10):1578-88. doi: 10.1038/nprot.2008.97.

PMID:
18802439
16.

Transcription control of a gene for Drosophila transcription factor, DREF by DRE and cis-elements conserved between Drosophila melanogaster and virilis.

Kwon E, Seto H, Hirose F, Ohshima N, Takahashi Y, Nishida Y, Yamaguchi M.

Gene. 2003 May 8;309(2):101-16.

PMID:
12758126
17.

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.

Xie D, Cai J, Chia NY, Ng HH, Zhong S.

Genome Res. 2008 Aug;18(8):1325-35. doi: 10.1101/gr.072769.107.

18.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

19.

Computational detection of cis -regulatory modules.

Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B.

Bioinformatics. 2003 Oct;19 Suppl 2:ii5-14.

20.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299.

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