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Comparative genomics of Drosophila and human core promoters
Peter C FitzGerald, David Sturgill, Andrey Shyakhtenko, Brian Oliver, Charles Vinson
Genome Biol. 2006; 7(7): R53. Published online 2006 July 7. doi: 10.1186/gb-2006-7-7-r53
PMCID:
PMC1779564
Abstract Full Text PDF–2.0M
 Is Cited by the Following 26 Articles in this Archive:
Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila
Sergei S Ryazansky, Vladimir A Gvozdev, Eugene Berezikov
BMC Genomics. 2011; 12: 371. Published online 2011 July 19. doi: 10.1186/1471-2164-12-371
PMCID:
PMC3150300
Abstract Full Text PDF–1.6M Supplementary Material
Nucleotide composition-linked divergence of vertebrate core promoter architecture
Simon J. van Heeringen, Waseem Akhtar, Ulrike G. Jacobi, Robert C. Akkers, Yutaka Suzuki, Gert Jan C. Veenstra
Genome Res. 2011 March; 21(3): 410–421. doi: 10.1101/gr.111724.110
PMCID:
PMC3044855
Abstract Full Text PDF–1.6M
Control of Germline torso Expression by the BTB/POZ Domain Protein Pipsqueak Is Required for Embryonic Terminal Patterning in Drosophila
Marco Grillo, Marc Furriols, Jordi Casanova, Stefan Luschnig
Genetics. 2011 February; 187(2): 513–521. doi: 10.1534/genetics.110.121624
PMCID:
PMC3030493
Abstract Full Text PDF–2.4M
Genome-wide analysis of promoter architecture in Drosophila melanogaster
Roger A. Hoskins, Jane M. Landolin, James B. Brown, Jeremy E. Sandler, Hazuki Takahashi, Timo Lassmann, Charles Yu, Benjamin W. Booth, Dayu Zhang, Kenneth H. Wan, Li Yang, Nathan Boley, Justen Andrews, Thomas C. Kaufman, Brenton R. Graveley, Peter J. Bickel, Piero Carninci, Joseph W. Carlson, Susan E. Celniker
Genome Res. 2011 February; 21(2): 182–192. doi: 10.1101/gr.112466.110
PMCID:
PMC3032922
Abstract Full Text PDF–900K
Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level
Elizabeth A. Rach, Deborah R. Winter, Ashlee M. Benjamin, David L. Corcoran, Ting Ni, Jun Zhu, Uwe Ohler
PLoS Genet. 2011 January; 7(1): e1001274. Published online 2011 January 13. doi: 10.1371/journal.pgen.1001274
PMCID:
PMC3020932
Abstract Full Text PDF–3.1M 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
A paired-end sequencing strategy to map the complex landscape of transcription initiation
Ting Ni, David L Corcoran, Elizabeth A Rach, Shen Song, Eric P Spana, Yuan Gao, Uwe Ohler, Jun Zhu
Nat Methods. Author manuscript; available in PMC 2011 October 19.
Published in final edited form as: Nat Methods. 2010 July; 7(7): 521–527. Published online 2010 May 23. doi: 10.1038/nmeth.1464
PMCID:
PMC3197272
Abstract Full Text PDF–577K Supplementary Material
Turnover and lineage-specific broadening of the transcription start site in a testis-specific retrogene
Mehran Sorourian, Esther Betrán
Fly (Austin) Author manuscript; available in PMC 2010 April 17.
Published in final edited form as: Fly (Austin). 2010 January; 4(1): 3–11. Published online 2010 January 30.
PMCID:
PMC2855778
Abstract Full Text PDF–2.4M Supplementary Material
Promoting developmental transcription
Uwe Ohler, David A. Wassarman
Development. 2010 January 1; 137(1): 15–26. doi: 10.1242/dev.035493
PMCID:
PMC2796937
Abstract Full Text
Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery
Tamar Juven-Gershon, James T. Kadonaga
Dev Biol. Author manuscript; available in PMC 2010 March 15.
Published in final edited form as: Dev Biol. 2010 March 15; 339(2): 225–229. Published online 2009 August 13. doi: 10.1016/j.ydbio.2009.08.009
PMCID:
PMC2830304
Abstract Full Text PDF–1.0M
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
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
Ken Daigoro Yokoyama, Uwe Ohler, Gregory A. Wray
Nucleic Acids Res. 2009 July; 37(13): e92. Published online 2009 July. doi: 10.1093/nar/gkp423
PMCID:
PMC2715254
Abstract Full Text PDF–4.4M Supplementary Material
A transcription factor affinity-based code for mammalian transcription initiation
Molly Megraw, Fernando Pereira, Shane T. Jensen, Uwe Ohler, Artemis G. Hatzigeorgiou
Genome Res. 2009 April; 19(4): 644–656. doi: 10.1101/gr.085449.108
PMCID:
PMC2665783
Abstract Full Text PDF–1.1M
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster
Qianqian Zhu, Marc S Halfon
BMC Genomics. 2009; 10: 9. Published online 2009 January 7. doi: 10.1186/1471-2164-10-9
PMCID:
PMC2631479
Abstract Full Text PDF–1.7M Supplementary Material
Evolution of Drosophila ribosomal protein gene core promoters
Xiaotu Ma, Kangyu Zhang, Xiaoman Li
Gene. Author manuscript; available in PMC 2011 December 6.
Published in final edited form as: Gene. 2009 March 1; 432(1-2): 54–59. Published online 2008 November 7. doi: 10.1016/j.gene.2008.10.025
PMCID:
PMC3232064
Abstract Full Text PDF–1.2M
Quality of regulatory elements in Drosophila retrogenes
Yongsheng Bai, Claudio Casola, Esther Betrán
Genomics. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Genomics. 2009 January; 93(1): 83–89. Published online 2008 October 23. doi: 10.1016/j.ygeno.2008.09.006
PMCID:
PMC2753227
Abstract Full Text PDF–708K Supplementary Material
Caudal, a key developmental regulator, is a DPE-specific transcriptional factor
Tamar Juven-Gershon, Jer-Yuan Hsu, James T. Kadonaga
Genes Dev. 2008 October 15; 22(20): 2823–2830. doi: 10.1101/gad.1698108
PMCID:
PMC2569877
Abstract Full Text PDF–462K
The RNA Polymerase II Core Promoter – the Gateway to Transcription
Tamar Juven-Gershon, Jer-Yuan Hsu, Joshua W. M. Theisen, James T. Kadonaga
Curr Opin Cell Biol. Author manuscript; available in PMC 2008 November 24.
Published in final edited form as: Curr Opin Cell Biol. 2008 June; 20(3): 253–259. Published online 2008 April 22. doi: 10.1016/j.ceb.2008.03.003
PMCID:
PMC2586601
Abstract Full Text PDF–148K
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori, Kenta Nakai
BMC Genomics. 2008; 9: 112. Published online 2008 March 1. doi: 10.1186/1471-2164-9-112
PMCID:
PMC2292176
Abstract Full Text PDF–461K Supplementary Material
All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues
Julian M Rozenberg, Andrey Shlyakhtenko, Kimberly Glass, Vikas Rishi, Maxim V Myakishev, Peter C FitzGerald, Charles Vinson
BMC Genomics. 2008; 9: 67. Published online 2008 February 5. doi: 10.1186/1471-2164-9-67
PMCID:
PMC2267717
Abstract Full Text PDF–1.2M Supplementary Material
Generic eukaryotic core promoter prediction using structural features of DNA
Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre Rouzé, Yves Van de Peer
Genome Res. 2008 February; 18(2): 310–323. doi: 10.1101/gr.6991408
PMCID:
PMC2203629
Abstract Full Text PDF–1.0M
Constraint and turnover in sex-biased gene expression in the genus Drosophila
Yu Zhang, David Sturgill, Michael Parisi, Sudhir Kumar, Brian Oliver
Nature. Author manuscript; available in PMC 2008 May 14.
Published in final edited form as: Nature. 2007 November 8; 450(7167): 233–237. doi: 10.1038/nature06323
PMCID:
PMC2386141
Abstract Full Text PDF–1.5M Supplementary Material
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
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets
Buyong Ma, Yongping Pan, Jie Zheng, Arnold J. Levine, Ruth Nussinov
Nucleic Acids Res. 2007 May; 35(9): 2986–3001. Published online 2007 April 16. doi: 10.1093/nar/gkm192
PMCID:
PMC1888811
Abstract Full Text PDF–1.0M Supplementary Material
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
Thomas A Down, Casey M Bergman, Jing Su, Tim J. P Hubbard
PLoS Comput Biol. 2007 January; 3(1): e7. Prepublished online 2006 December 5. Published online 2007 January 19. doi: 10.1371/journal.pcbi.0030007
PMCID:
PMC1779301
Abstract Full Text PDF–1.3M Supplementary Material
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
Uwe Ohler
Nucleic Acids Res. 2006 November; 34(20): 5943–5950. Published online 2006 November 26. doi: 10.1093/nar/gkl608
PMCID:
PMC1635271
Abstract Full Text PDF–391K
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