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Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage
Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller, Elia Stupka
Genome Biol. 2006; 7(7): R56. Published online 2006 July 19. doi: 10.1186/gb-2006-7-7-r56
PMCID:
PMC1779573
Abstract Full Text PDF–1.0M Supplementary Material
 Is Cited by the Following 14 Articles in this Archive:
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
Andrew L. Hufton, Susanne Mathia, Helene Braun, Udo Georgi, Hans Lehrach, Martin Vingron, Albert J. Poustka, Georgia Panopoulou
Genome Res. 2009 November; 19(11): 2036–2051. doi: 10.1101/gr.093237.109
PMCID:
PMC2775584
Abstract Full Text PDF–1.5M
Conservation of core gene expression in vertebrate tissues
Esther T Chan, Gerald T Quon, Gordon Chua, Tomas Babak, Miles Trochesset, Ralph A Zirngibl, Jane Aubin, Michael JH Ratcliffe, Andrew Wilde, Michael Brudno, Quaid D Morris, Timothy R Hughes
J Biol. 2009; 8(3): 33. Published online 2009 April 16. doi: 10.1186/jbiol130
PMCID:
PMC2689434
Abstract Full Text PDF–1.8M Supplementary Material
Identification of direct T-box target genes in the developing zebrafish mesoderm
Aaron T. Garnett, Tina M. Han, Michael J. Gilchrist, James C. Smith, Michael B. Eisen, Fiona C. Wardle, Sharon L. Amacher
Development. 2009 March 1; 136(5): 749–760. Published online 2009 January 21. doi: 10.1242/dev.024703
PMCID:
PMC2685943
Abstract Full Text Supplementary Material
Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend
David M McGaughey, Zachary E Stine, Jimmy L Huynh, Ryan M Vinton, Andrew S McCallion
BMC Genomics. 2009; 10: 8. Published online 2009 January 7. doi: 10.1186/1471-2164-10-8
PMCID:
PMC2630312
Abstract Full Text PDF–1.5M Supplementary Material
Dispensability of mammalian DNA
Cory McLean, Gill Bejerano
Genome Res. 2008 November; 18(11): 1743–1751. doi: 10.1101/gr.080184.108
PMCID:
PMC2577864
Abstract Full Text PDF–656K
Evolution of the mammalian transcription factor binding repertoire via transposable elements
Guillaume Bourque, Bernard Leong, Vinsensius B. Vega, Xi Chen, Yen Ling Lee, Kandhadayar G. Srinivasan, Joon-Lin Chew, Yijun Ruan, Chia-Lin Wei, Huck Hui Ng, Edison T. Liu
Genome Res. 2008 November; 18(11): 1752–1762. doi: 10.1101/gr.080663.108
PMCID:
PMC2577865
Abstract Full Text PDF–911K
Uncovering cis Regulatory Codes Using Synthetic Promoter Shuffling
Ali Kinkhabwala, Călin C. Guet
PLoS ONE. 2008; 3(4): e2030. Published online 2008 April 30. doi: 10.1371/journal.pone.0002030
PMCID:
PMC2321153
Abstract Full Text PDF–664K
TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
Alison P Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh
BMC Genomics. 2007; 8: 441. Published online 2007 November 29. doi: 10.1186/1471-2164-8-441
PMCID:
PMC2148067
Abstract Full Text PDF–627K Supplementary Material
Identification and Analysis of a Conserved Tcfap2a Intronic Enhancer Element Required for Expression in Facial and Limb Bud Mesenchyme
Weiguo Feng, Jian Huang, Jian Zhang, Trevor Williams
Mol Cell Biol. 2008 January; 28(1): 315–325. Published online 2007 November 5. doi: 10.1128/MCB.01168-07
PMCID:
PMC2223317
Abstract Full Text PDF–688K Supplementary Material
CONDOR: a database resource of developmentally associated conserved non-coding elements
Adam Woolfe, Debbie K Goode, Julie Cooke, Heather Callaway, Sarah Smith, Phil Snell, Gayle K McEwen, Greg Elgar
BMC Dev Biol. 2007; 7: 100. Published online 2007 August 30. doi: 10.1186/1471-213X-7-100
PMCID:
PMC2020477
Abstract Full Text PDF–1.0M
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction
Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Strähle, Ferenc Müller
Genome Biol. 2007; 8(6): R106. Published online 2007 June 8. doi: 10.1186/gb-2007-8-6-r106
PMCID:
PMC2394741
Abstract Full Text PDF–814K Supplementary Material
Multiple non-collinear TF-map alignments of promoter regions
Enrique Blanco, Roderic Guigó, Xavier Messeguer
BMC Bioinformatics. 2007; 8: 138. Published online 2007 April 24. doi: 10.1186/1471-2105-8-138
PMCID:
PMC1878506
Abstract Full Text PDF–574K
Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers
Amir Ali Abbasi, Zissis Paparidis, Sajid Malik, Debbie K. Goode, Heather Callaway, Greg Elgar, Karl-Heinz Grzeschik
PLoS ONE. 2007; 2(4): e366. Published online 2007 April 11. doi: 10.1371/journal.pone.0000366
PMCID:
PMC1838922
Abstract Full Text PDF–597K
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar
Genome Biol. 2007; 8(2): R15. Published online 2007 February 2. doi: 10.1186/gb-2007-8-2-r15
PMCID:
PMC1852409
Abstract Full Text PDF–411K Supplementary Material
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