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Results: 1 to 20 of 120

1.

Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D.

Methods Mol Biol. 2009;541:1-22. doi: 10.1007/978-1-59745-243-4_1. Review.

PMID:
19381547
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Promoter analysis: gene regulatory motif identification with A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Spouge JL, Landsman D.

Methods Mol Biol. 2009;537:263-76. doi: 10.1007/978-1-59745-251-9_13.

PMID:
19378149
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Sample scale-free gene regulatory network using gene ontology.

Chen G, Larsen P, Almasri E, Dai Y.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5523-6.

PMID:
17946312
[PubMed - indexed for MEDLINE]
4.

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements.

Tharakaraman K, Mariño-Ramírez L, Sheetlin S, Landsman D, Spouge JL.

Bioinformatics. 2005 Jun;21 Suppl 1:i440-8.

PMID:
15961489
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

PMID:
19426448
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Transcriptional networks: reverse-engineering gene regulation on a global scale.

Chua G, Robinson MD, Morris Q, Hughes TR.

Curr Opin Microbiol. 2004 Dec;7(6):638-46. Review.

PMID:
15556037
[PubMed - indexed for MEDLINE]
7.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

PMID:
18950538
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M.

Genome Res. 2001 Jul;11(7):1175-86.

PMID:
11435399
[PubMed - indexed for MEDLINE]
Free Article
9.

Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast: "in silico" and "wet-lab" approaches.

Mira NP, Teixeira MC, Sá-Correia I.

Methods Mol Biol. 2012;809:27-48. doi: 10.1007/978-1-61779-376-9_2.

PMID:
22113266
[PubMed - indexed for MEDLINE]
10.
11.

Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast.

Ye C, Galbraith SJ, Liao JC, Eskin E.

PLoS Comput Biol. 2009 Mar;5(3):e1000311. doi: 10.1371/journal.pcbi.1000311. Epub 2009 Mar 20.

PMID:
19300475
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.

Haverty PM, Hansen U, Weng Z.

Nucleic Acids Res. 2004 Jan 2;32(1):179-88. Print 2004.

PMID:
14704355
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18257930
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach.

Siddharthan R.

J Biosci. 2007 Aug;32(5):863-70. Review.

PMID:
17914228
[PubMed - indexed for MEDLINE]
Free Article
15.

An improved Gibbs sampling method for motif discovery via sequence weighting.

Chen X, Jiang T.

Comput Syst Bioinformatics Conf. 2006:239-47.

PMID:
17369642
[PubMed - indexed for MEDLINE]
Free Article
16.

Construction of gene networks with hybrid approach from expression profile and gene ontology.

Jing L, Ng MK, Liu Y.

IEEE Trans Inf Technol Biomed. 2010 Jan;14(1):107-18. doi: 10.1109/TITB.2009.2033056. Epub 2009 Sep 29.

PMID:
19789116
[PubMed - indexed for MEDLINE]
17.

A copula method for modeling directional dependence of genes.

Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.

BMC Bioinformatics. 2008 May 1;9:225. doi: 10.1186/1471-2105-9-225.

PMID:
18447957
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A universal framework for regulatory element discovery across all genomes and data types.

Elemento O, Slonim N, Tavazoie S.

Mol Cell. 2007 Oct 26;28(2):337-50.

PMID:
17964271
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A multistep bioinformatic approach detects putative regulatory elements in gene promoters.

Bortoluzzi S, Coppe A, Bisognin A, Pizzi C, Danieli GA.

BMC Bioinformatics. 2005 May 18;6:121.

PMID:
15904489
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identifying regulatory networks by combinatorial analysis of promoter elements.

Pilpel Y, Sudarsanam P, Church GM.

Nat Genet. 2001 Oct;29(2):153-9.

PMID:
11547334
[PubMed - indexed for MEDLINE]

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