scholarly journals The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

2016 ◽  
Vol 45 (D1) ◽  
pp. D758-D768 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Anne Eagle ◽  
David Fashena ◽  
Ken Frazer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Disease ◽  
Model Organism ◽  
Disease Models ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals ZFIN, The zebrafish model organism database: Updates and new directions

genesis ◽  
2015 ◽  
Vol 53 (8) ◽  
pp. 498-509 ◽  
Author(s):  
Leyla Ruzicka ◽  
Yvonne M. Bradford ◽  
Ken Frazer ◽  
Douglas G. Howe ◽  
Holly Paddock ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model ◽  
Database Updates ◽  
New Directions

scholarly journals ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

2012 ◽  
Vol 41 (D1) ◽  
pp. D854-D860 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Tom Conlin ◽  
Anne E. Eagle ◽  
David Fashena ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals First person – Gideon Hughes

2020 ◽  
Vol 13 (10) ◽  
pp. dmm047415
Keyword(s):  
Machine Learning ◽  
Tissue Regeneration ◽  
Model Organism ◽  
Early Career ◽  
Disease Models ◽  
First Person ◽  
Zebrafish Model ◽  
Early Career Researchers ◽  
The University ◽  
Selection Of

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Gideon Hughes is first author on ‘Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease’, published in DMM. Gideon conducted the research described in this article while a PhD student in Betsy Pownall's lab at the University of York, York, UK. He is now a postdoc in the lab of Henry Roehl at the University of Sheffield, Sheffield, UK, using the zebrafish as a model organism to study human disease and tissue regeneration, combining his research with his interest in computer science.

scholarly journals ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

2019 ◽  
Author(s):  
Justine Dardaillon ◽  
Delphine Dauga ◽  
Paul Simion ◽  
Emmanuel Faure ◽  
Takeshi A Onuma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Model Organism ◽  
Gene Expression Profiles ◽  
Sister Group ◽  
Model Organism Database ◽  
Oikopleura Dioica ◽  
Genetic Features ◽  
Taxonomic Range ◽  
Or Gene

Abstract ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

scholarly journals Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

2019 ◽  
Author(s):  
Joshua D Fortriede ◽  
Troy J Pells ◽  
Stanley Chu ◽  
Praneet Chaturvedi ◽  
DongZhuo Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Model Organism ◽  
Gene Expression Omnibus ◽  
The Body ◽  
Data Mapping ◽  
Model Organism Database ◽  
Ncbi Gene Expression Omnibus ◽  
Network Analyses ◽  
Deep Integration ◽  
Next Generation Sequencing Ngs

Abstract Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated ‘gene expression as a phenotype’ and gene regulatory network analyses.

scholarly journals ZFIN: enhancements and updates to the zebrafish model organism database

2010 ◽  
Vol 39 (Database) ◽  
pp. D822-D829 ◽  
Author(s):  
Y. Bradford ◽  
T. Conlin ◽  
N. Dunn ◽  
D. Fashena ◽  
K. Frazer ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes

2007 ◽  
Vol 36 (Database) ◽  
pp. D768-D772 ◽  
Author(s):  
J. Sprague ◽  
L. Bayraktaroglu ◽  
Y. Bradford ◽  
T. Conlin ◽  
N. Dunn ◽  
...  
Keyword(s):  
Model Organism ◽  
Information Network ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals Design, Implementation and Maintenance of a Model Organism Database forArabidopsis thaliana

2004 ◽  
Vol 5 (4) ◽  
pp. 362-369 ◽  
Author(s):  
Danforth Weems ◽  
Neil Miller ◽  
Margarita Garcia-Hernandez ◽  
Eva Huala ◽  
Seung Y. Rhee
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Metabolic Pathways ◽  
Model Organism ◽  
Information Resource ◽  
Model Organism Database ◽  
Software Developers ◽  
Web Based ◽  
Model Plant ◽  
Community Information

TheArabidopsisInformation Resource (TAIR) is a web-based community database for the model plantArabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.

Sign in / Sign up

Export Citation Format

Share Document