Morphogen rules: design principles of gradient-mediated embryo patterning
The Drosophila blastoderm and the vertebrate neural tube are archetypal examples of
morphogen-patterned tissues that create precise spatial patterns of different cell types. In …
morphogen-patterned tissues that create precise spatial patterns of different cell types. In …
Fiji: an open-source platform for biological-image analysis
J Schindelin, I Arganda-Carreras, E Frise, V Kaynig… - Nature …, 2012 - nature.com
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image
analysis. Fiji uses modern software engineering practices to combine powerful software …
analysis. Fiji uses modern software engineering practices to combine powerful software …
The Drosophila embryo at single-cell transcriptome resolution
N Karaiskos, P Wahle, J Alles, A Boltengagen, S Ayoub… - Science, 2017 - science.org
By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express
distinct gene combinations. Here, we used single-cell sequencing of precisely staged …
distinct gene combinations. Here, we used single-cell sequencing of precisely staged …
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
BF Miller, D Bambah-Mukku, C Dulac… - Genome …, 2021 - genome.cshlp.org
Recent technological advances have enabled spatially resolved measurements of
expression profiles for hundreds to thousands of genes in fixed tissues at single-cell …
expression profiles for hundreds to thousands of genes in fixed tissues at single-cell …
Image Data Resource: a bioimage data integration and publication platform
E Williams, J Moore, SW Li, G Rustici, A Tarkowska… - Nature …, 2017 - nature.com
Access to primary research data is vital for the advancement of science. To extend the data
types supported by community repositories, we built a prototype Image Data Resource …
types supported by community repositories, we built a prototype Image Data Resource …
Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy
Live imaging of large biological specimens is fundamentally limited by the short optical
penetration depth of light microscopes. To maximize physical coverage, we developed the …
penetration depth of light microscopes. To maximize physical coverage, we developed the …
Genome-wide RNA tomography in the zebrafish embryo
Advancing our understanding of embryonic development is heavily dependent on
identification of novel pathways or regulators. Although genome-wide techniques such as …
identification of novel pathways or regulators. Although genome-wide techniques such as …
Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy
Recording light-microscopy images of large, nontransparent specimens, such as developing
multicellular organisms, is complicated by decreased contrast resulting from light scattering …
multicellular organisms, is complicated by decreased contrast resulting from light scattering …
The gap gene network
J Jaeger - Cellular and Molecular Life Sciences, 2011 - Springer
Gap genes are involved in segment determination during the early development of the fruit
fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize …
fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize …
Using networks to measure similarity between genes: association index selection
Biological networks can be used to functionally annotate genes on the basis of interaction-
profile similarities. Metrics known as association indices can be used to quantify interaction …
profile similarities. Metrics known as association indices can be used to quantify interaction …