Computational analysis of core promoters in the Drosophila genome
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* Corresponding author: Uwe Ohler ohler@mit.edu
Genome Biology 2002, 3:research0087-0087.12 doi:10.1186/gb-2002-3-12-research0087
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Proceedings
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The genomic features that affect the lengths of 5’ untranslated regions in multicellular eukaryotes Chun-Hsi Chen, Hsuan-Yu Lin, Chia-Lin Pan, Feng-Chi Chen BMC Bioinformatics 2011, 12(Suppl 9):S3 (5 October 2011) |
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Research article
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 Molecular Biology 2011, 12:32 (1 August 2011) |
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Research article
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 (27 June 2011) |
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Review
TBP-related factors: a paradigm of diversity in transcription initiation Waseem Akhtar, Gert Jan C Veenstra Cell & Bioscience 2011, 1:23 (27 June 2011) |
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Research
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 Biology 2011, 12:R43 (11 May 2011) A map of the dynamically changing chromatin landscape throughout Drosophila development.
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Research
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler Genome Biology 2009, 10:R73 (9 July 2009) A map of transcription start sites across the |
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Research article
Mara E Pitulescu, Martin Teichmann, Lingfei Luo, Michael Kessel BMC Biochemistry 2009, 10:16 (10 June 2009) A novel transcriptional regulator, isoform 2 of the TATA-binding protein-like factor-interacting protein (TIPT2), binds to the cell cycle regulatory protein geminin, and together they cooperate with chromatin associated factors and the basal transcription machinery to activate transcription synergistically.
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Research article
Qianqian Zhu, Marc S Halfon BMC Genomics 2009, 10:9 (7 January 2009) |
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Method
Kevin Brick, Junichi Watanabe, Elisabetta Pizzi Genome Biology 2008, 9:R178 (18 December 2008) A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties. |
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Research article
Evolution of the holozoan ribosome biogenesis regulon Seth J Brown, Michael D Cole, Albert J Erives BMC Genomics 2008, 9:442 (24 September 2008) |
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Research article
Evolutionary origin of regulatory regions of retrogenes in Drosophila Yongsheng Bai, Claudio Casola, Esther Betrán BMC Genomics 2008, 9:241 (22 May 2008) |
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Research article
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 (25 February 2008) |
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Method
Determining promoter location based on DNA structure first-principles calculations J Ramon Goñi, Alberto Pérez, David Torrents, Modesto Orozco Genome Biology 2007, 8:R263 (11 December 2007) A new method is presented which predicts promoter regions based on atomistic molecular dynamics simulations of small oligonucleotides, without requiring information on sequence conservation or features. |
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Research article
MetaProm: a neural network based meta-predictor for alternative human promoter prediction Junwen Wang, Lyle H Ungar, Hung Tseng, Sridhar Hannenhalli BMC Genomics 2007, 8:374 (17 October 2007) |
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Review
Computational analyses of eukaryotic promoters Michael Q Zhang BMC Bioinformatics 2007, 8(Suppl 6):S3 (27 September 2007) |
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Research article
Michelle K Smith, Barbara T Wakimoto BMC Developmental Biology 2007, 7:21 (26 March 2007) |
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Research article
Identification of plant promoter constituents by analysis of local distribution of short sequences Yoshiharu Y Yamamoto, Hiroyuki Ichida, Minami Matsui, Junichi Obokata, Tetsuya Sakurai, Masakazu Satou, Motoaki Seki, Kazuo Shinozaki, Tomoko Abe BMC Genomics 2007, 8:67 (8 March 2007) |
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Research article
Kenneth W Berendzen, Kurt Stüber, Klaus Harter, Dierk Wanke BMC Bioinformatics 2006, 7:522 (30 November 2006) |
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Review
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment Vladimir B Bajic, Michael R Brent, Randall H Brown, Adam Frankish, Jennifer Harrow, Uwe Ohler, Victor V Solovyev, Sin Tan Genome Biology 2006, 7(Suppl 1):S3 (7 August 2006) |
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Research
Comparative genomics of Drosophila and human core promoters Peter C FitzGerald, David Sturgill, Andrey Shyakhtenko, Brian Oliver, Charles Vinson Genome Biology 2006, 7:R53 (7 July 2006) Comparison of DNA sequence distributions in |
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Research article
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs Victor X Jin, Gregory AC Singer, Francisco J Agosto-Pérez, Sandya Liyanarachchi, Ramana V Davuluri BMC Bioinformatics 2006, 7:114 (7 March 2006) |
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Research article
Comprehensive analysis of the base composition around the transcription start site in Metazoa Stein Aerts, Gert Thijs, Michal Dabrowski, Yves Moreau, Bart De Moor BMC Genomics 2004, 5:34 (1 June 2004) The local base composition (GC content) varies significantly around the transcription start sites of annotated genes in several metazoan genomes, but the degree of the variation differs among animal classes.
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Research
Prediction of Saccharomyces cerevisiae replication origins Adam M Breier, Sourav Chatterji, Nicholas R Cozzarelli Genome Biology 2004, 5:R22 (4 March 2004) This study presents the first algorithm, Oriscan, to predict eukaryotic replication origins and examines the structure of the origins and evolutionary conservation of origin sequences at the nucleotide level in several |
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Minireview
Haiqiong Montalta-He, Heinrich Reichert Genome Biology 2003, 4:205 (28 January 2003) The establishment of a database of gene-expression patterns derived from systematic highthroughput |
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Research
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis Genome Biology 2002, 3:research0083-0083.22 (31 December 2002) This article is part of a collection on Release 3 of the... The recent completion of the |
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Software
Apollo: a sequence annotation editor SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002) This article is part of a collection on Release 3 of the... Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the |
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Software
An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) This article is part of a collection on Release 3 of the... In the course of annotating the |