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The regulatory content of intergenic DNA shapes genome architecture
Craig E Nelson, Bradley M Hersh, Sean B Carroll
Genome Biol. 2004; 5(4): R25. Published online 2004 March 15.
PMCID:
PMC395784
Abstract Full Text PDF–357K Supplementary Material

Is Cited by the Following 27 Articles in this Archive:

LOESS correction for length variation in gene set-based genomic sequence analysis
Anton Aboukhalil, Martha L. Bulyk
Bioinformatics. 2012 June 1; 28(11): 1446–1454. Published online 2012 April 5. doi: 10.1093/bioinformatics/bts155
PMCID:
PMC3356840
Free in PMC on 2013/06/01
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
Regulatory divergence in Drosophila revealed by mRNA-seq
C. Joel McManus, Joseph D. Coolon, Michael O. Duff, Jodi Eipper-Mains, Brenton R. Graveley, Patricia J. Wittkopp
Genome Res. 2010 June; 20(6): 816–825. doi: 10.1101/gr.102491.109
PMCID:
PMC2877578
Abstract Full Text PDF–788K
Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode
Shai S Shen-Orr, Yitzhak Pilpel, Craig P Hunter
Genome Biol. 2010; 11(6): R58. Published online 2010 June 1. doi: 10.1186/gb-2010-11-6-r58
PMCID:
PMC2911106
Abstract Full Text PDF–894K Supplementary Material
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler
Genome Biol. 2009; 10(7): R73. Published online 2009 July 9. doi: 10.1186/gb-2009-10-7-r73
PMCID:
PMC2728527
Abstract Full Text PDF–1.6M Supplementary Material
Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?
Walter Salzburger, Dirk Steinke, Ingo Braasch, Axel Meyer
J Mol Evol. 2009 September; 69(3): 207–216. Published online 2009 July 1. doi: 10.1007/s00239-009-9251-4
PMCID:
PMC2746894
Abstract Full Text PDF–324K Supplementary Material
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares
Genome Biol. 2008; 9(12): R176. Published online 2008 December 16. doi: 10.1186/gb-2008-9-12-r176
PMCID:
PMC2646280
Abstract Full Text PDF–550K Supplementary Material
Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression
Juliette Colinas, Scott C. Schmidler, Gil Bohrer, Borislav Iordanov, Philip N. Benfey
PLoS ONE. 2008; 3(11): e3670. Published online 2008 November 7. doi: 10.1371/journal.pone.0003670
PMCID:
PMC2576458
Abstract Full Text PDF–925K Supplementary Material
The effects of protein interactions, gene essentiality and regulatory regions on expression variation
Linqi Zhou, Xiaotu Ma, Fengzhu Sun
BMC Syst Biol. 2008; 2: 54. Published online 2008 June 26. doi: 10.1186/1752-0509-2-54
PMCID:
PMC2474594
Abstract Full Text PDF–744K Supplementary Material
Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
Jason G Mezey, Sergey V Nuzhdin, Fangfei Ye, Corbin D Jones
BMC Evol Biol. 2008; 8: 2. Published online 2008 January 7. doi: 10.1186/1471-2148-8-2
PMCID:
PMC2266709
Abstract Full Text PDF–1.4M Supplementary Material
Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila melanogaster Euchromatin
Pierre Fontanillas, Daniel L Hartl, Max Reuter
PLoS Genet. 2007 November; 3(11): e210. Prepublished online 2007 October 9. Published online 2007 November 30. doi: 10.1371/journal.pgen.0030210
PMCID:
PMC2098804
Abstract Full Text PDF–397K Supplementary Material
Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain
Ivan Conte, Paola Bovolenta
Genome Biol. 2007; 8(7): R137. Published online 2007 July 6. doi: 10.1186/gb-2007-8-7-r137
PMCID:
PMC2323233
Abstract Full Text PDF–1.1M Supplementary Material
Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network
Vanessa Vermeirssen, M. Inmaculada Barrasa, César A. Hidalgo, Jenny Aurielle B. Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-László Barabási, Albertha J.M. Walhout
Genome Res. 2007 July; 17(7): 1061–1071. doi: 10.1101/gr.6148107
PMCID:
PMC1899117
Abstract Full Text PDF–909K
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
Genome Biol. 2007; 8(6): R101. Published online 2007 June 5. doi: 10.1186/gb-2007-8-6-r101
PMCID:
PMC2394749
Abstract Full Text PDF–1.1M Supplementary Material
Extensive Polycistronism and Antisense Transcription in the Mammalian Hox Clusters
Gaëll Mainguy, Jan Koster, Joost Woltering, Hans Jansen, Antony Durston
PLoS ONE. 2007; 2(4): e356. Published online 2007 April 4. doi: 10.1371/journal.pone.0000356
PMCID:
PMC1831499
Abstract Full Text PDF–228K
The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana
Dirk Walther, Roman Brunnemann, Joachim Selbig
PLoS Genet. 2007 February; 3(2): e11. Prepublished online 2006 December 7. Published online 2007 February 9. doi: 10.1371/journal.pgen.0030011
PMCID:
PMC1796623
Abstract Full Text PDF–499K Supplementary Material
Genomic Selective Constraints in Murid Noncoding DNA
Daniel J Gaffney, Peter D Keightley
PLoS Genet. 2006 November; 2(11): e204. Prepublished online 2006 October 18. Published online 2006 November 24. doi: 10.1371/journal.pgen.0020204
PMCID:
PMC1657059
Abstract Full Text PDF–400K Supplementary Material
Towards the identification of essential genes using targeted genome sequencing and comparative analysis
Adam M Gustafson, Evan S Snitkin, Stephen CJ Parker, Charles DeLisi, Simon Kasif
BMC Genomics. 2006; 7: 265. Published online 2006 October 19. doi: 10.1186/1471-2164-7-265
PMCID:
PMC1624830
Abstract Full Text PDF–432K Supplementary Material
Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence
Lindsay S. Shopland, Christopher R. Lynch, Kevin A. Peterson, Kathleen Thornton, Nick Kepper, Johann von Hase, Stefan Stein, Sarah Vincent, Kelly R. Molloy, Gregor Kreth, Christoph Cremer, Carol J. Bult, Timothy P. O'Brien
J Cell Biol. 2006 July 3; 174(1): 27–38. doi: 10.1083/jcb.200603083
PMCID:
PMC2064156
Abstract Full Text PDF–1.7M Supplementary Material
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
Daniel L. Halligan, Peter D. Keightley
Genome Res. 2006 July; 16(7): 875–884. doi: 10.1101/gr.5022906
PMCID:
PMC1484454
Abstract Full Text PDF–514K
Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells
Anthony A Philippakis, Brian W Busser, Stephen S Gisselbrecht, Fangxue Sherry He, Beatriz Estrada, Alan M Michelson, Martha L Bulyk
PLoS Comput Biol. 2006 May; 2(5): e53. Published online 2006 May 26. doi: 10.1371/journal.pcbi.0020053
PMCID:
PMC1464814
Abstract Full Text PDF–652K Supplementary Material
Transposon-free regions in mammalian genomes
Cas Simons, Michael Pheasant, Igor V. Makunin, John S. Mattick
Genome Res. 2006 February; 16(2): 164–172. doi: 10.1101/gr.4624306
PMCID:
PMC1361711
Abstract Full Text PDF–279K
Transcriptional noise and cellular heterogeneity in mammalian macrophages
S Ramsey, A Ozinsky, A Clark, K.D Smith, P de Atauri, V Thorsson, D Orrell, H Bolouri
Philos Trans R Soc Lond B Biol Sci. 2006 March 29; 361(1467): 495–506. Published online 2006 February 1. doi: 10.1098/rstb.2005.1808
PMCID:
PMC1609340
Abstract Full Text PDF–1.2M Supplementary Material
A high frequency of overlapping gene expression in compacted eukaryotic genomes
Bryony A. P. Williams, Claudio H. Slamovits, Nicola J. Patron, Naomi M. Fast, Patrick J. Keeling
Proc Natl Acad Sci U S A. 2005 August 2; 102(31): 10936–10941. Published online 2005 July 21. doi: 10.1073/pnas.0501321102
PMCID:
PMC1182411
Abstract Full Text PDF–384K Supplementary Material
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
Bárbara Negre, Sònia Casillas, Magali Suzanne, Ernesto Sánchez-Herrero, Michael Akam, Michael Nefedov, Antonio Barbadilla, Pieter de Jong, Alfredo Ruiz
Genome Res. 2005 May; 15(5): 692–700. doi: 10.1101/gr.3468605
PMCID:
PMC1088297
Abstract Full Text PDF–920K
Evolution and functional classification of vertebrate gene deserts
Ivan Ovcharenko, Gabriela G. Loots, Marcelo A. Nobrega, Ross C. Hardison, Webb Miller, Lisa Stubbs
Genome Res. 2005 January; 15(1): 137–145. doi: 10.1101/gr.3015505
PMCID:
PMC540279
Abstract Full Text PDF–372K
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul, Eric D Siggia
BMC Bioinformatics. 2004; 5: 129. Published online 2004 September 9. doi: 10.1186/1471-2105-5-129
PMCID:
PMC521067
Abstract Full Text PDF–412K Supplementary Material
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