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Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2002 | Pubmed ID: 11805330
Systematic determination of patterns of gene expression during Drosophila embryogenesis.
Genome biology , 2002 | Pubmed ID: 12537577
Computational identification of Drosophila microRNA genes.
Genome biology , 2003 | Pubmed ID: 12844358
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2005 | Pubmed ID: 16330759
Global analysis of patterns of gene expression during Drosophila embryogenesis.
Genome biology , 2007 | Pubmed ID: 17645804
Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
BMC neuroscience , 2007 | Pubmed ID: 17672901
Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.
Cell Oct, 2007 | Pubmed ID: 17923096
Mapping the gene expression universe.
Current opinion in genetics & development Dec, 2008 | Pubmed ID: 18809490
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome biology , 2008 | Pubmed ID: 19087263
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Bioinformatics (Oxford, England) Jun, 2009 | Pubmed ID: 19346324
CATMAID: collaborative annotation toolkit for massive amounts of image data.
Bioinformatics (Oxford, England) Aug, 2009 | Pubmed ID: 19376822
A toolkit for high-throughput, cross-species gene engineering in Drosophila.
Nature methods Jun, 2009 | Pubmed ID: 19465918
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Genome biology , 2009 | Pubmed ID: 19589141
In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura.
PloS one , 2010 | Pubmed ID: 20126626
Visualization of image data from cells to organisms.
Nature methods Mar, 2010 | Pubmed ID: 20195255
Mapping the complexity of transcription control in higher eukaryotes.
Genome biology , 2010 | Pubmed ID: 20441601
Software for bead-based registration of selective plane illumination microscopy data.
Nature methods Jun, 2010 | Pubmed ID: 20508634
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.
Bioinformatics (Oxford, England) Jun, 2010 | Pubmed ID: 20529937
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Bioinformatics (Oxford, England) Sep, 2010 | Pubmed ID: 20624780
Meeting report: first light sheet based fluorescence microscopy workshop.
Biotechnology journal Aug, 2010 | Pubmed ID: 20652906
An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.
PLoS biology , 2010 | Pubmed ID: 20957184
Gene expression divergence recapitulates the developmental hourglass model.
Nature Dec, 2010 | Pubmed ID: 21150996
linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.
Bioinformatics (Oxford, England) Jul, 2011 | Pubmed ID: 21596792
Restoration of uneven illumination in light sheet microscopy images.
Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada Aug, 2011 | Pubmed ID: 21682937
Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 22065453
Recombination-mediated genetic engineering of large genomic DNA transgenes.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 22065454
Abundant occurrence of basal radial glia in the subventricular zone of embryonic neocortex of a lissencephalic primate, the common marmoset Callithrix jacchus.
Cerebral cortex (New York, N.Y. : 1991) Feb, 2012 | Pubmed ID: 22114084
The evolution of early animal embryos: conservation or divergence?
Trends in ecology & evolution Jul, 2012 | Pubmed ID: 22520868
Elastic volume reconstruction from series of ultra-thin microscopy sections.
Nature methods Jul, 2012 | Pubmed ID: 22688414
TrakEM2 software for neural circuit reconstruction.
PloS one , 2012 | Pubmed ID: 22723842
Current challenges in open-source bioimage informatics.
Nature methods Jul, 2012 | Pubmed ID: 22743770
Fiji: an open-source platform for biological-image analysis.
Nature methods Jul, 2012 | Pubmed ID: 22743772
Biological imaging software tools.
Nature methods Jul, 2012 | Pubmed ID: 22743775
ImgLib2--generic image processing in Java.
Bioinformatics (Oxford, England) Nov, 2012 | Pubmed ID: 22962343
An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis.
PLoS genetics , 2012 | Pubmed ID: 23300473
OpenSPIM: an open-access light-sheet microscopy platform.
Nature methods Jul, 2013 | Pubmed ID: 23749304
The earliest transcribed zygotic genes are short, newly evolved, and different across species.
Cell reports Jan, 2014 | Pubmed ID: 24440719
Going "open" with mesoscopy: a new dimension on multi-view imaging.
Protoplasma Mar, 2014 | Pubmed ID: 24442669
Bioimage Informatics in the context of Drosophila research.
Methods (San Diego, Calif.) Jun, 2014 | Pubmed ID: 24732429
Efficient Bayesian-based multiview deconvolution.
Nature methods Jun, 2014 | Pubmed ID: 24747812
Open-source solutions for SPIMage processing.
Methods in cell biology , 2014 | Pubmed ID: 24974045
Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences.
BioEssays : news and reviews in molecular, cellular and developmental biology Feb, 2015 | Pubmed ID: 25400101
An adaptive threshold in mammalian neocortical evolution.
PLoS biology Nov, 2014 | Pubmed ID: 25405475
Guide to light-sheet microscopy for adventurous biologists.
Nature methods Jan, 2015 | Pubmed ID: 25549268
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.
eLife , 2015 | Pubmed ID: 25838129
Endogenously tagged rab proteins: a resource to study membrane trafficking in Drosophila.
Developmental cell May, 2015 | Pubmed ID: 25942626
BigDataViewer: visualization and processing for large image data sets.
Nature methods Jun, 2015 | Pubmed ID: 26020499
Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy.
Mechanisms of development Nov, 2015 | Pubmed ID: 26428533
An automated workflow for parallel processing of large multiview SPIM recordings.
Bioinformatics (Oxford, England) Dec, 2015 | Pubmed ID: 26628585
A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.
Developmental biology Mar, 2016 | Pubmed ID: 26851213
A genome-wide resource for the analysis of protein localisation in Drosophila.
eLife , 2016 | Pubmed ID: 26896675
Comment on "Cortical folding scales universally with surface area and thickness, not number of neurons".
Science (New York, N.Y.) Feb, 2016 | Pubmed ID: 26912886
Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch.
Development (Cambridge, England) Jan, 2019 | Pubmed ID: 30642837
Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.
Nature Apr, 2019 | Pubmed ID: 30918398
Publisher Correction: Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.
Nature Apr, 2019 | Pubmed ID: 30971828