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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

Is Cited by the Following 23 Articles in this Archive:

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
Ignacio Maeso, Manuel Irimia, Juan J. Tena, Esther González-Pérez, David Tran, Vydianathan Ravi, Byrappa Venkatesh, Sonsoles Campuzano, José Luis Gómez-Skarmeta, Jordi Garcia-Fernàndez
Genome Res. 2012 April; 22(4): 642–655. doi: 10.1101/gr.132233.111
PMCID:
PMC3317147
Free in PMC on 2012/10/01
Transphyletic conservation of developmental regulatory state in animal evolution
José Luis Royo, Ignacio Maeso, Manuel Irimia, Feng Gao, Isabelle S. Peter, Carla S. Lopes, Salvatore D'Aniello, Fernando Casares, Eric H. Davidson, Jordi Garcia-Fernández, José Luis Gómez-Skarmeta
Proc Natl Acad Sci U S A. 2011 August 23; 108(34): 14186–14191. Published online 2011 August 15. doi: 10.1073/pnas.1109037108
PMCID:
PMC3161536
Abstract Full Text PDF–1.0M Supplementary Material
Evolution of Gene Regulatory Networks that Control Embryonic Development of the Body Plan
Isabelle S. Peter, Eric H. Davidson
Cell. Author manuscript; available in PMC 2012 March 18.
Published in final edited form as: Cell. 2011 March 18; 144(6): 970–985. doi: 10.1016/j.cell.2011.02.017
PMCID:
PMC3076009
Abstract Full Text PDF–529K
Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position
Michael Lang, Yavor Hadzhiev, Nicol Siegel, Chris T Amemiya, Carolina Parada, Uwe Strähle, May-Britt Becker, Ferenc Müller, Axel Meyer
EvoDevo. 2010; 1: 11. Published online 2010 November 3. doi: 10.1186/2041-9139-1-11
PMCID:
PMC2992049
Abstract Full Text PDF–5.3M Supplementary Material
Two Lamprey Hedgehog Genes Share Non-Coding Regulatory Sequences and Expression Patterns with Gnathostome Hedgehogs
Shungo Kano, Jin-Hua Xiao, Joana Osório, Marc Ekker, Yavor Hadzhiev, Ferenc Müller, Didier Casane, Ghislaine Magdelenat, Sylvie Rétaux
PLoS One. 2010; 5(10): e13332. Published online 2010 October 13. doi: 10.1371/journal.pone.0013332
PMCID:
PMC2954159
Abstract Full Text PDF–11M Supplementary Material
Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
Marcin von Grotthuss, Michael Ashburner, José M. Ranz
Genome Res. 2010 August; 20(8): 1084–1096. doi: 10.1101/gr.103713.109
PMCID:
PMC2909571
Abstract Full Text PDF–805K
Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae
Michael Lang, Elvira Juan
Nucleic Acids Res. 2010 October; 38(19): 6404–6417. Published online 2010 June 11. doi: 10.1093/nar/gkq504
PMCID:
PMC2965233
Abstract Full Text PDF–984K Supplementary Material
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons
Xianjun Dong, Pavla Navratilova, David Fredman, Øyvind Drivenes, Thomas S. Becker, Boris Lenhard
Nucleic Acids Res. 2010 March; 38(4): 1071–1085. Published online 2010 March. doi: 10.1093/nar/gkp1124
PMCID:
PMC2831330
Abstract Full Text PDF–6.5M Supplementary Material
Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates
Gayle K. McEwen, Debbie K. Goode, Hugo J. Parker, Adam Woolfe, Heather Callaway, Greg Elgar
PLoS Genet. 2009 December; 5(12): e1000762. Published online 2009 December 11. doi: 10.1371/journal.pgen.1000762
PMCID:
PMC2781166
Abstract Full Text PDF–1.6M Supplementary Material
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
Paulo P. Amaral, Christine Neyt, Simon J. Wilkins, Marjan E. Askarian-Amiri, Susan M. Sunkin, Andrew C. Perkins, John S. Mattick
RNA. 2009 November; 15(11): 2013–2027. doi: 10.1261/rna.1705309
PMCID:
PMC2764477
Abstract Full Text PDF–1.0M
CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses
Helge G. Roider, Boris Lenhard, Aditi Kanhere, Stefan A. Haas, Martin Vingron
Nucleic Acids Res. 2009 October; 37(19): 6305–6315. Published online 2009 October. doi: 10.1093/nar/gkp682
PMCID:
PMC2770660
Abstract Full Text PDF–8.3M Supplementary Material
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif
Amar Drawid, Nupur Gupta, Vijayalakshmi H Nagaraj, Céline Gélinas, Anirvan M Sengupta
BMC Bioinformatics. 2009; 10: 208. Published online 2009 July 7. doi: 10.1186/1471-2105-10-208
PMCID:
PMC2718928
Abstract Full Text PDF–943K Supplementary Material
In search of a unifying theory of complex brain evolution
Leah Krubitzer
Ann N Y Acad Sci. Author manuscript; available in PMC 2010 March 1.
Published in final edited form as: Ann N Y Acad Sci. 2009 March; 1156: 44–67. doi: 10.1111/j.1749-6632.2009.04421.x
PMCID:
PMC2666944
Full Text PDF–1.7M
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites
Baochen Shi, Xiangqian Guo, Tao Wu, Sitong Sheng, Jie Wang, Geir Skogerbø, Xiaopeng Zhu, Runsheng Chen
BMC Genomics. 2009; 10: 92. Published online 2009 February 25. doi: 10.1186/1471-2164-10-92
PMCID:
PMC2651899
Abstract Full Text PDF–616K Supplementary Material
Genic regions of a large salamander genome contain long introns and novel genes
Jeramiah J Smith, Srikrishna Putta, Wei Zhu, Gerald M Pao, Inder M Verma, Tony Hunter, Susan V Bryant, David M Gardiner, Timothy T Harkins, S Randal Voss
BMC Genomics. 2009; 10: 19. Published online 2009 January 13. doi: 10.1186/1471-2164-10-19
PMCID:
PMC2633012
Abstract Full Text PDF–1.3M Supplementary Material
Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries
Charleston W. K. Chiang, Adnan Derti, Daniel Schwartz, Michael F. Chou, Joel N. Hirschhorn, C.-ting Wu
Genetics. 2008 December; 180(4): 2277–2293. doi: 10.1534/genetics.108.096537
PMCID:
PMC2600958
Abstract Full Text PDF–1.2M
Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus
Larry J Dishaw, M Gail Mueller, Natasha Gwatney, John P Cannon, Robert N Haire, Ronda T Litman, Chris T Amemiya, Tatsuya Ota, Lee Rowen, Gustavo Glusman, Gary W Litman
BMC Genet. 2008; 9: 78. Published online 2008 December 1. doi: 10.1186/1471-2156-9-78
PMCID:
PMC2632668
Abstract Full Text PDF–1.0M Supplementary Material
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
Pär G Engström, David Fredman, Boris Lenhard
Genome Biol. 2008; 9(2): R34. Published online 2008 February 15. doi: 10.1186/gb-2008-9-2-r34
PMCID:
PMC2374709
Abstract Full Text PDF–5.1M Supplementary Material
The animal in the genome: comparative genomics and evolution
Richard R Copley
Philos Trans R Soc Lond B Biol Sci. 2008 April 27; 363(1496): 1453–1461. Published online 2008 January 11. doi: 10.1098/rstb.2007.2235
PMCID:
PMC2614226
Abstract Full Text PDF–734K
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
Pär G. Engström, Shannan J. Ho Sui, Øyvind Drivenes, Thomas S. Becker, Boris Lenhard
Genome Res. 2007 December; 17(12): 1898–1908. doi: 10.1101/gr.6669607
PMCID:
PMC2099597
Abstract Full Text PDF–1.0M
Association of the Matrix Attachment Region Recognition Signature with coding regions in Caenorhabditis elegans
Alasdair Anthony, Mark Blaxter
BMC Genomics. 2007; 8: 418. Published online 2007 November 15. doi: 10.1186/1471-2164-8-418
PMCID:
PMC2234258
Abstract Full Text PDF–848K Supplementary Material
Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time
Dorota Retelska, Emmanuel Beaudoing, Cédric Notredame, C Victor Jongeneel, Philipp Bucher
BMC Genomics. 2007; 8: 398. Published online 2007 October 31. doi: 10.1186/1471-2164-8-398
PMCID:
PMC2211324
Abstract Full Text PDF–1008K Supplementary Material
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
Adam Woolfe, Greg Elgar
Genome Biol. 2007; 8(4): R53. Published online 2007 April 11. doi: 10.1186/gb-2007-8-4-r53
PMCID:
PMC1896008
Abstract Full Text PDF–1.9M Supplementary Material
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