ArticleJournal of anatomy2010
The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain.
Article in Journal of anatomy, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Spatial transcriptomics reveal developmental dynamics of the human cerebral cortex and striatum.Science China. Life sciences · 2026Article
- Midgut protrusion, rotation, and retraction induced by temporal alteration in differential growth.Biomechanics and modeling in mechanobiology · 2025Article
- Gpr101 expression during early stages of murine development.Gene expression patterns : GEP · 2025Article
- Unraveling microglial spatial organization in the developing human brain with DeepCellMap, a deep learning approach coupled with spatial statistics.Nature communications · 2025Article
- 3D atlas of the human fetal chondrocranium in the middle trimester.Scientific data · 2024Article
- Species Choice and Model Use: Reviving Research on Human Development.Journal of the history of biology · 2024Article
- Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models.BMC medical informatics and decision making · 2023Article
- Reconstituting human somitogenesis in vitro.Nature · 2023Article
- Exploring Visualisation for Embryology Education: A Twenty-First-Century Perspective.Advances in experimental medicine and biology · 2022Article
- External surface anatomy of the postfolding human embryo: Computer-aided, three-dimensional reconstruction of printable digital specimens.Journal of anatomy · 2021Article
- Species-specific pace of development is associated with differences in protein stability.Science (New York, N.Y.) · 2020Article
- Gene expression across mammalian organ development.Nature · 2019Article
- Recessive gene disruptions in autism spectrum disorder.Nature genetics · 2019Article
- Self-organized developmental patterning and differentiation in cerebral organoids.The EMBO journal · 2017Article
- Regulation of cerebral cortical neurogenesis by the Pax6 transcription factor.Frontiers in cellular neuroscience · 2015Article
- My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.Journal of biomedical semantics · 2015Article
- Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.BMC systems biology · 2014Article
- Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells.Cell stem cell · 2013Article
- Article
- Web tools for large-scale 3D biological images and atlases.BMC bioinformatics · 2012Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
We are developing a three-dimensional (3D) atlas of the human embryonic brain using anatomical landmarks and gene expression data to define major subdivisions through 12 stages of development [Carnegie Stages (CS) 12-23; approximately 26-56 days post conception (dpc)]. Virtual 3D anatomical models are generated from intact specimens using optical projection tomography (OPT). Using MAPAINT software, selected gene expression data, gathered using standard methods of in situ hybridization and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie stage. In these models, anatomical domains, defined on the basis of morphological landmarks and comparative knowledge of expression patterns in vertebrates, are linked to a developmental neuroanatomic ontology. Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g. PAX6, GAD65 and OLIG2) are being used to confirm and/or refine the human anatomical domain boundaries. We have also developed interpolation software that digitally generates a full domain from partial data. Currently, the 3D models and a preliminary set of anatomical domains and ontology are available on the atlas pages along with gene expression data from approximately 100 genes in the HUDSEN Human Spatial Gene Expression Database (http://www.hudsen.org). The aim is that full 3D data will be generated from expression data used to define a more detailed set of anatomical domains linked to a more advanced anatomy ontology and all of these will be available online, contributing to the long-term goal of the atlas, which is to help maximize the effective use and dissemination of data wherever it is generated.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.