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Computational analysis of core promoters in the Drosophila genome
Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin
Genome Biol. 2002; 3(12): research0087.1–87.12. Published online 2002 December 20. doi: 10.1186/gb-2002-3-12-research0087
PMCID:
PMC151189
Abstract Full Text PDF–182K Supplementary Material
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 Is Cited by the Following 54 Articles in this Archive:
Functional characterization of the sciarid BhC4-1 core promoter in transgenic Drosophila
Adriana C Garcia, Daniel LG Gitaí, Fernanda C Humann, Maria L Paçó-Larson, Nadia Monesi
BMC Mol Biol. 2011; 12: 32. Published online 2011 August 1. doi: 10.1186/1471-2199-12-32
PMCID:
PMC3160885
Abstract Full Text PDF–3.2M Supplementary Material
TBP-related factors: a paradigm of diversity in transcription initiation
Waseem Akhtar, Gert Jan C Veenstra
Cell Biosci. 2011; 1: 23. Published online 2011 June 27. doi: 10.1186/2045-3701-1-23
PMCID:
PMC3142196
Abstract Full Text PDF–2.6M
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters
Bastiaan JH Jansen, Iziah E Sama, Dagmar Eleveld-Trancikova, Maaike A van Hout-Kuijer, Joop H Jansen, Martijn A Huynen, Gosse J Adema
BMC Genomics. 2011; 12: 330. Published online 2011 June 27. doi: 10.1186/1471-2164-12-330
PMCID:
PMC3146452
Abstract Full Text PDF–994K Supplementary Material
An ANN-GA model based promoter prediction in Arabidopsis thaliana using tilling microarray data
Hrishikesh Mishra, Nitya Singh, Krishna Misra, Tapobrata Lahiri
Bioinformation. 2011; 6(6): 240–243. Published online 2011 June 6.
PMCID:
PMC3159145
Abstract Full Text PDF–196K Supplementary Material
Abnormal Dosage Compensation of Reporter Genes Driven by the Drosophila Glass Multiple Reporter (GMR) Enhancer-Promoter
Corey Laverty, Fang Li, Esther J. Belikoff, Maxwell J. Scott
PLoS One. 2011; 6(5): e20455. Published online 2011 May 31. doi: 10.1371/journal.pone.0020455
PMCID:
PMC3105068
Abstract Full Text PDF–3.4M Supplementary Material
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos
Genome Biol. 2011; 12(5): R43. Published online 2011 May 11. doi: 10.1186/gb-2011-12-5-r43
PMCID:
PMC3219966
Abstract Full Text PDF–1.5M Supplementary Material
Core promoter T-blocks correlate with gene expression levels in C. elegans
Vladislav Grishkevich, Tamar Hashimshony, Itai Yanai
Genome Res. 2011 May; 21(5): 707–717. doi: 10.1101/gr.113381.110
PMCID:
PMC3083087
Abstract Full Text PDF–1.3M
Novel Core Promoter Elements and a Cognate Transcription Factor in the Divergent Unicellular Eukaryote Trichomonas vaginalis
Alias J. Smith, Lorissa Chudnovsky, Augusto Simoes-Barbosa, Maria G. Delgadillo-Correa, Zophonias O. Jonsson, James A. Wohlschlegel, Patricia J. Johnson
Mol Cell Biol. 2011 April; 31(7): 1444–1458. doi: 10.1128/MCB.00745-10
PMCID:
PMC3135286
Abstract Full Text PDF–2.8M
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
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
The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery
Trevor J. Parry, Joshua W.M. Theisen, Jer-Yuan Hsu, Yuan-Liang Wang, David L. Corcoran, Moriah Eustice, Uwe Ohler, James T. Kadonaga
Genes Dev. 2010 September 15; 24(18): 2013–2018. doi: 10.1101/gad.1951110
PMCID:
PMC2939363
Abstract Full Text PDF–441K
Genome-Wide Distribution of Transposed Dissociation Elements in Maize
Erik Vollbrecht, Jon Duvick, Justin P. Schares, Kevin R. Ahern, Prasit Deewatthanawong, Ling Xu, Liza J. Conrad, Kazuhiro Kikuchi, Tammy A. Kubinec, Bradford D. Hall, Rebecca Weeks, Erica Unger-Wallace, Michael Muszynski, Volker P. Brendel, Thomas P. Brutnell
Plant Cell. 2010 June; 22(6): 1667–1685. Published online 2010 June 25. doi: 10.1105/tpc.109.073452
PMCID:
PMC2910982
Abstract Full Text PDF–1.6M
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
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
Characterization of sINR, a strict version of the Initiator core promoter element
Ganit Yarden, Rofa Elfakess, Kfir Gazit, Rivka Dikstein
Nucleic Acids Res. 2009 July; 37(13): 4234–4246. Published online 2009 July. doi: 10.1093/nar/gkp315
PMCID:
PMC2715227
Abstract Full Text PDF–2.7M Supplementary Material
TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation
Mara E Pitulescu, Martin Teichmann, Lingfei Luo, Michael Kessel
BMC Biochem. 2009; 10: 16. Published online 2009 June 10. doi: 10.1186/1471-2091-10-16
PMCID:
PMC2702275
Abstract Full Text PDF–2.7M Supplementary Material
Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements
Ramakrishnan Anish, Mohammad B. Hossain, Raymond H. Jacobson, Shinako Takada
PLoS ONE. 2009; 4(4): e5103. Published online 2009 April 1. doi: 10.1371/journal.pone.0005103
PMCID:
PMC2659449
Abstract Full Text PDF–2.3M 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
Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum
Kevin Brick, Junichi Watanabe, Elisabetta Pizzi
Genome Biol. 2008; 9(12): R178. Published online 2008 December 18. doi: 10.1186/gb-2008-9-12-r178
PMCID:
PMC2646282
Abstract Full Text PDF–783K 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
Evolution of the holozoan ribosome biogenesis regulon
Seth J Brown, Michael D Cole, Albert J Erives
BMC Genomics. 2008; 9: 442. Published online 2008 September 24. doi: 10.1186/1471-2164-9-442
PMCID:
PMC2570694
Abstract Full Text PDF–1.0M Supplementary Material
Evolutionary origin of regulatory regions of retrogenes in Drosophila
Yongsheng Bai, Claudio Casola, Esther Betrán
BMC Genomics. 2008; 9: 241. Published online 2008 May 22. doi: 10.1186/1471-2164-9-241
PMCID:
PMC2413143
Abstract Full Text PDF–319K Supplementary Material
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
Links between core promoter and basic gene features influence gene expression
Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, Rivka Dikstein
BMC Genomics. 2008; 9: 92. Published online 2008 February 25. doi: 10.1186/1471-2164-9-92
PMCID:
PMC2279122
Abstract Full Text PDF–302K Supplementary Material
The LysR-Type Transcriptional Regulator LeuO Controls Expression of Several Genes in Salmonella enterica Serovar Typhi
I. Hernández-Lucas, A. L. Gallego-Hernández, S. Encarnación, M. Fernández-Mora, A. G. Martínez-Batallar, H. Salgado, R. Oropeza, E. Calva
J Bacteriol. 2008 March; 190(5): 1658–1670. Published online 2007 December 21. doi: 10.1128/JB.01649-07
PMCID:
PMC2258680
Abstract Full Text PDF–1.0M Supplementary Material
Determining promoter location based on DNA structure first-principles calculations
J Ramon Goñi, Alberto Pérez, David Torrents, Modesto Orozco
Genome Biol. 2007; 8(12): R263. Published online 2007 December 11. doi: 10.1186/gb-2007-8-12-r263
PMCID:
PMC2246265
Abstract Full Text PDF–360K Supplementary Material
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