Genome Biology

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Systematic determination of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker and Gerald M Rubin*

Genome Biology 2002, 3:research0088-0088.14 doi:10.1186/gb-2002-3-12-research0088

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BioMed Central: 27 citations

Review   Open Access

TBP-related factors: a paradigm of diversity in transcription initiation

Waseem Akhtar, Gert Jan C Veenstra Cell & Bioscience 2011, 1:23 (27 June 2011)

Research   Open Access Highly Accessed

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.

Research article   Open Access

Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis

Alejandro Zúñiga, Christian Hödar, Patricia Hanna, Freddy Ibáñez, Pablo Moreno, Rodrigo Pulgar, Luis Pastenes, Mauricio González, Verónica Cambiazo BMC Biology 2009, 7:61 (22 September 2009)

Many previously uncharacterized genes uncovered by a subtractive hybridization analysis of early Drosophila development are spatiotemporally regulated during embryogenesis, including genes encoding a set of secreted and transmembrane proteins.

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Deciphering the genetic code of morphogenesis using functional genomics

Athea Vichas, Jennifer A Zallen Journal of Biology 2009, 8:76 (22 September 2009)

Vichas and Zallen review the routes from genome-wide data-sets to functional characterization, in the light of a temporal and spatial screen published in BMC Biology which identifies 55 previously unknown genes expressed during Drosophila gastrulation.

Research   Open Access Highly Accessed

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009)

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.

Research   Open Access Highly Accessed

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)

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

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)

Research   Open Access Highly Accessed

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 Biology 2008, 9:R176 (16 December 2008)

Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.

Database   Open Access

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L Finley BMC Genomics 2008, 9:461 (7 October 2008)

Research article   Open Access Highly Accessed

Identification of genes influencing dendrite morphogenesis in developing peripheral sensory and central motor neurons

Yimiao Ou, Barbara Chwalla, Matthias Landgraf, Donald J van Meyel Neural Development 2008, 3:16 (10 July 2008)

Method   Open Access Highly Accessed

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

Andra Ivan, Marc S Halfon, Saurabh Sinha Genome Biology 2008, 9:R22 (28 January 2008)

Prediction of cis-regulatory modules ab initio, without any input of relevant motifs, is achieved with two novel methods.

Proceedings   Open Access

Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering

Manjunatha Jagalur, Chris Pal, Erik Learned-Miller, R Thomas Zoeller, David Kulp BMC Bioinformatics 2007, 8(Suppl 10):S5 (21 December 2007)

Proceedings   Open Access

Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data

Ivan G Costa, Roland Krause, Lennart Opitz, Alexander Schliep BMC Bioinformatics 2007, 8(Suppl 10):S3 (21 December 2007)

Research article   Open Access Highly Accessed

Sex-specific DoublesexM expression in subsets of Drosophila somatic gonad cells

Leonie U Hempel, Brian Oliver BMC Developmental Biology 2007, 7:113 (12 October 2007)

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Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach

Tiago R Magalhães, Jessica Palmer, Pavel Tomancak, Katherine S Pollard BMC Neuroscience 2007, 8:59 (31 July 2007)

Research   Open Access Highly Accessed

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, Gerald M Rubin Genome Biology 2007, 8:R145 (23 July 2007)

Embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome were documented, of which 40% show tissue-restricted expression.

Research   Open Access

Automatic image analysis for gene expression patterns of fly embryos

Hanchuan Peng, Fuhui Long, Jie Zhou, Garmay Leung, Michael B Eisen, Eugene W Myers BMC Cell Biology 2007, 8(Suppl 1):S7 (10 July 2007)

Research article   Open Access

The non-dosage compensated Lsp1α gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes

Vikki M Weake, Maxwell J Scott BMC Molecular Biology 2007, 8:35 (19 May 2007)

Research   Open Access

The exceptional stem cell system of Macrostomum lignano: Screening for gene expression and studying cell proliferation by hydroxyurea treatment and irradiation

Daniela Pfister, Katrien De Mulder, Isabelle Philipp, Georg Kuales, Martina Hrouda, Paul Eichberger, Gaetan Borgonie, Volker Hartenstein, Peter Ladurner Frontiers in Zoology 2007, 4:9 (9 March 2007)

Research article   Open Access

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome

Mikhail Lipatov, Kapa Lenkov, Dmitri A Petrov, Casey M Bergman BMC Biology 2005, 3:24 (12 November 2005)

Less than 1% of Drosophila transcripts contain 'chimeric' transposable elements, whereas a large proportion of mammalian genomes are known to be derived from TEs; population genetics implies that most fly gene-TE chimeras are deleterious, but a few may contribute to novel gene sequences.

Methodology   Open Access

A streamlined method for systematic, high resolution in situ analysis of mRNA distribution in plants

Sinéad Drea, Julia Corsar, Brian Crawford, Peter Shaw, Liam Dolan, John H Doonan Plant Methods 2005, 1:8 (6 October 2005)

Research article   Open Access

Genes involved in Drosophila glutamate receptor expression and localization

Faith LW Liebl, David E Featherstone BMC Neuroscience 2005, 6:44 (28 June 2005)

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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker Genome Biology 2004, 5:R61 (20 August 2004)

27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed that conservation of binding-site clusters accurately discriminates functional regions from non-functional ones.

Research   Open Access Highly Accessed

The regulatory content of intergenic DNA shapes genome architecture

Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004)

The relationship between regulatory complexity and gene spacing was examined in Caenorhabditis elegans and Drosophila melanogaster. Intergenic distance, and hence genome architecture, is shaped by regulatory information contained in noncoding DNA.

Research   Open Access Highly Accessed

An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome

M Hild, B Beckmann, SA Haas, B Koch, V Solovyev, C Busold, K Fellenberg, M Boutros, M Vingron, F Sauer, JD Hoheisel, R Paro Genome Biology 2003, 5:R3 (22 December 2003)

A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly.

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Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis

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 in situ hybridization studies on whole-mount Drosophila embryos vastly increases the breadth and depth that can be reached by developmental genetics.