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Global analysis of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak†, Benjamin P Berman†, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker* and Gerald M Rubin

Genome Biology 2007, 8:R145 doi:10.1186/gb-2007-8-7-r145

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A comparative gene expression database for invertebrates

Mattias Ormestad, Mark Q Martindale, Eric Röttinger EvoDevo 2011, 2:17 (24 August 2011)

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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)

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A map of the dynamically changing chromatin landscape throughout Drosophila development.

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Mapping the complexity of transcription control in higher eukaryotes

Pavel Tomancak, Uwe Ohler Genome Biology 2010, 11:115 (30 April 2010)

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Recent large analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009)

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Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.

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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 Biology 2009, 10:R73 (9 July 2009)

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A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.

Methodology article   Open Access

Biases in Drosophila melanogaster protein trap screens

Jelena Aleksic, Ranko Lazic, Ilka Müller, Steven R Russell, Boris Adryan BMC Genomics 2009, 10:249 (28 May 2009)

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The zinc finger protein Zn72D and DEAD box helicase Belle interact and control maleless mRNA and protein levels

Kathleen A Worringer, Feixia Chu, Barbara Panning BMC Molecular Biology 2009, 10:33 (22 April 2009)

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Methodology article   Open Access

A bag-of-words approach for Drosophila gene expression pattern annotation

Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye BMC Bioinformatics 2009, 10:119 (21 April 2009)

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