ArticleNucleic acids research2013
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 65 citations in OpenAlex.
- Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles.Molecular biology and evolution · 2025Article
- Tracing Homopolymers in Oikopleura dioica's Mitogenome.Genome biology and evolution · 2024Article
- Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.Genome biology and evolution · 2024Article
- Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions.Biochemical Society transactions · 2022Article
- Metazoans and Intrinsic Apoptosis: An Evolutionary Analysis of the Bcl-2 Family.International journal of molecular sciences · 2022Article
- The Genome of the "Sea Vomit"Life (Basel, Switzerland) · 2021Article
- Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos.Frontiers in cell and developmental biology · 2021Article
- Massive Gene Loss and Function Shuffling in Appendicularians Stretch the Boundaries of Chordate Wnt Family Evolution.Frontiers in cell and developmental biology · 2021Article
- Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer.Genes · 2020Article
- A chordate species lackingProceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms.Molecular biology and evolution · 2020Article
- Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR.BMC genomics · 2019Article
- Article
- Widespread use of the "ascidian" mitochondrial genetic code in tunicates.F1000Research · 2019Article
- Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica.BMC developmental biology · 2018Article
- Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.BMC genomics · 2018Article
- Diatom bloom-derived biotoxins cause aberrant development and gene expression in the appendicularian chordateCommunications biology · 2018Article
- Modified whole-mount in situ hybridisation and immunohistochemistry protocols without removal of the vitelline membrane in the appendicularian Oikopleura dioica.Development genes and evolution · 2017Article
- Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi.BMC genomics · 2017Article
- DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO (http://www.geneontology.org/) and InterPro (http://www.ebi.ac.uk/interpro/) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide downloadable gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.
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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.