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ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen
Genome Biol. 2008; 9(4): R66. Published online 2008 April 7. doi: 10.1186/gb-2008-9-4-r66
PMCID:
PMC2643937
Abstract Full Text PDF–817K
 Is Cited by the Following 11 Articles in this Archive:
Computational Identification of Transcriptional Regulators in Human Endotoxemia
Tung T. Nguyen, Panagiota T. Foteinou, Steven E. Calvano, Stephen F. Lowry, Ioannis P. Androulakis
PLoS One. 2011; 6(5): e18889. Published online 2011 May 27. doi: 10.1371/journal.pone.0018889
PMCID:
PMC3103499
Abstract Full Text PDF–1.1M Supplementary Material
Selective Genomic Targeting by FRA-2/FOSL2 Transcription Factor: REGULATION OF THE Rgs4 GENE IS MEDIATED BY A VARIANT ACTIVATOR PROTEIN 1 (AP-1) PROMOTER SEQUENCE/CREB-BINDING PROTEIN (CBP) MECHANISM
Jeff S. Davies, David C. Klein, David A. Carter
J Biol Chem. 2011 April 29; 286(17): 15227–15239. Published online 2011 March 2. doi: 10.1074/jbc.M110.201996
PMCID:
PMC3083148
Abstract Full Text Supplementary Material
Assessing Computational Methods of Cis-Regulatory Module Prediction
Jing Su, Sarah A. Teichmann, Thomas A. Down
PLoS Comput Biol. 2010 December; 6(12): e1001020. Published online 2010 December 2. doi: 10.1371/journal.pcbi.1001020
PMCID:
PMC2996316
Abstract Full Text PDF–1.1M Supplementary Material
Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, Andreas Zell
PLoS One. 2010; 5(11): e13876. Published online 2010 November 30. doi: 10.1371/journal.pone.0013876
PMCID:
PMC2994704
Abstract Full Text PDF–1.3M Supplementary Material
Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification
Stein Aerts, Xiao-Jiang Quan, Annelies Claeys, Marina Naval Sanchez, Phillip Tate, Jiekun Yan, Bassem A. Hassan
PLoS Biol. 2010 July; 8(7): e1000435. Published online 2010 July 27. doi: 10.1371/journal.pbio.1000435
PMCID:
PMC2910651
Abstract Full Text PDF–1.5M Supplementary Material
Genome-wide prediction of transcription factor binding sites using an integrated model
Kyoung-Jae Won, Bing Ren, Wei Wang
Genome Biol. 2010; 11(1): R7. Published online 2010 January 22. doi: 10.1186/gb-2010-11-1-r7
PMCID:
PMC2847719
Abstract Full Text PDF–2.4M Supplementary Material
Modeling tissue-specific structural patterns in human and mouse promoters
Alexis Vandenbon, Kenta Nakai
Nucleic Acids Res. 2010 January; 38(1): 17–25. Published online 2010 January. doi: 10.1093/nar/gkp866
PMCID:
PMC2800225
Abstract Full Text PDF–1.5M Supplementary Material
Systems Biology of Embryogenesis
Lucas B. Edelman, Sriram Chandrasekaran, Nathan D. Price
Reprod Fertil Dev. Author manuscript; available in PMC 2010 August 13.
Published in final edited form as: Reprod Fertil Dev. 2010; 22(1): 98–105. doi: 10.1071/RD09215
PMCID:
PMC2921326
Abstract Full Text PDF–735K
Identifying regulatory elements in eukaryotic genomes
Leelavati Narlikar, Ivan Ovcharenko
Brief Funct Genomic Proteomic. 2009 July; 8(4): 215–230. Published online 2009 June 4. doi: 10.1093/bfgp/elp014
PMCID:
PMC2764519
Abstract Full Text PDF–177K
Night/Day Changes in Pineal Expression of >600 Genes: CENTRAL ROLE OF ADRENERGIC/cAMP SIGNALING
Michael J. Bailey, Steven L. Coon, David A. Carter, Ann Humphries, Jong-so Kim, Qiong Shi, Pascaline Gaildrat, Fabrice Morin, Surajit Ganguly, John B. Hogenesch, Joan L. Weller, Martin F. Rath, Morten Møller, Ruben Baler, David Sugden, Zoila G. Rangel, Peter J. Munson, David C. Klein
J Biol Chem. 2009 March 20; 284(12): 7606–7622. doi: 10.1074/jbc.M808394200
PMCID:
PMC2658055
Abstract Full Text Supplementary Material
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal
BMC Bioinformatics. 2009; 10(Suppl 1): S30. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S30
PMCID:
PMC2648767
Abstract Full Text PDF–832K Supplementary Material
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