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Literature DB >> 15044242

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.

Stein Aerts¹, Peter Van Loo, Yves Moreau, Bart De Moor.

Abstract

SUMMARY: The implementation of a genetic algorithm is described that provides a fast method of searching for the optimal combination of transcription factor binding sites in a set of regulatory sequences. AVAILABILITY: The algorithm can be used transparently as a web service from within the Toucan software. Toucan can be accessed at http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php. A standalone version of the software is available upon request.

Entities: Chemical

Mesh：

Year: 2004 PMID： 15044242 DOI： 10.1093/bioinformatics/bth179

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

13 in total

1. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.

Authors: Mathieu Blanchette; Alain R Bataille; Xiaoyu Chen; Christian Poitras; Josée Laganière; Céline Lefèbvre; Geneviève Deblois; Vincent Giguère; Vincent Ferretti; Dominique Bergeron; Benoit Coulombe; François Robert
Journal: Genome Res Date: 2006-04-10 Impact factor: 9.043

2. Recent computational approaches to understand gene regulation: mining gene regulation in silico.

Authors: I Abnizova; T Subhankulova; Wr Gilks
Journal: Curr Genomics Date: 2007-04 Impact factor: 2.236

3. Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.

Authors: Jason Gertz; Linda Riles; Peter Turnbaugh; Su-Wen Ho; Barak A Cohen
Journal: Genome Res Date: 2005-08 Impact factor: 9.043

4. ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.

Authors: Hong Sun; Tijl De Bie; Valerie Storms; Qiang Fu; Thomas Dhollander; Karen Lemmens; Annemieke Verstuyf; Bart De Moor; Kathleen Marchal
Journal: BMC Bioinformatics Date: 2009-01-30 Impact factor: 3.169

5. Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.

Authors: Hong Sun; Tias Guns; Ana Carolina Fierro; Lieven Thorrez; Siegfried Nijssen; Kathleen Marchal
Journal: Nucleic Acids Res Date: 2012-03-15 Impact factor: 16.971

10. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Authors: Peter Van Loo; Stein Aerts; Bernard Thienpont; Bart De Moor; Yves Moreau; Peter Marynen
Journal: Genome Biol Date: 2008-04-07 Impact factor: 13.583

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.

1. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.

2. Recent computational approaches to understand gene regulation: mining gene regulation in silico.

3. Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.

4. ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.

5. Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.

6. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

7. PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

8. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics.

9. A survey of motif discovery methods in an integrated framework.

10. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?