ArticleNucleic acids research2022
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Sea urchin eggs contain a plastid-derived structure that contributes to their development.PLoS biology · 2026Article
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design.Plant communications · 2026Review
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Skeletogenic Expression of Integrin Alpha, Talin and Npnt Genes and Npnt Role in Sea Urchin Skeletogenesis.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2026Article
- Gene expression and enzyme activity analysis of carbohydrate digestion in Strongylocentrotus purpuratus larvae.The Journal of experimental biology · 2025Article
- Evolutionary History of Bilaterian FoxP Genes: Complex Ancestral Functions and Evolutionary Changes Spanning 2R-WGD in the Vertebrate Lineage.Molecular biology and evolution · 2025Article
- Horizontal Transfer of msp130 Genes and the Evolution of Metazoan Biocalcification.Genome biology and evolution · 2025Article
- Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.Genome biology and evolution · 2025Article
- A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.Integrative organismal biology (Oxford, England) · 2025Article
- Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes.Nature ecology & evolution · 2024Article
- Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin Lytechinus pictus.Development (Cambridge, England) · 2024Article
- Localization and origins of juvenile skeletogenic cells in the sea urchin Lytechinuspictus.Developmental biology · 2024Article
- Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories.Nature ecology & evolution · 2024Article
- A feather star is born: embryonic development and nervous system organization in the crinoidOpen biology · 2024Article
- Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution.PLoS biology · 2024Article
- Article
- Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchinbioRxiv : the preprint server for biology · 2024Article
- Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems.PLoS biology · 2024Article
- ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis.eLife · 2024Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.
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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.