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The Zebrafish Information Network: the zebrafish model organism database

J. Sprague
2006 Nucleic Acids Research  
10 The Zebrafish Information Network (ZFIN; http://zfin. org) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data.  ...  ZFIN provides an integrated representation of mutants, genes, genetic markers, 15 mapping panels, publications and community resources such as meeting announcements and contact information.  ...  ACKNOWLEDGEMENTS 5 Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkj086 pmid:16381936 pmcid:PMC1347449 fatcat:hn2czv6dkbg2rjpedqetwwym5i

The Zebrafish Information Network (ZFIN): the zebrafish model organism database

J. Sprague
2003 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data.  ...  ACKNOWLEDGEMENT Funds for the development of the Zebrafish Information Network are provided by the NIH (RR/HD 12546).  ...  INTRODUCTION The zebrafish has emerged as a model organism important for the identification and characterization of genes and pathways involved in development, organ function, behavior and disease.  ... 
doi:10.1093/nar/gkg027 pmid:12519991 pmcid:PMC165474 fatcat:5yyclbuwuzc5vhny2ueudbgrge

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

J. Sprague, L. Bayraktaroglu, Y. Bradford, T. Conlin, N. Dunn, D. Fashena, K. Frazer, M. Haendel, D. G. Howe, J. Knight, P. Mani, S. A.T. Moxon (+10 others)
2007 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN, http:// zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data.  ...  ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations.  ...  ACKNOWLEDGEMENTS Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkm956 pmid:17991680 pmcid:PMC2238839 fatcat:3jookkeqbfbifhku6ymfqsns7q

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

Leyla Ruzicka, Yvonne M. Bradford, Ken Frazer, Douglas G. Howe, Holly Paddock, Sridhar Ramachandran, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Anne E. Eagle, David Fashena, Patrick Kalita (+8 others)
2015 Genesis  
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research.  ...  The use of zebrafish as a model for human disease is increasing.  ...  Acknowledgments Grant Support: This work was supported by the National Human Genome Research Institute (HG002659, and HG004834) of the National Institutes of Health.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

Zebrafish Information Network, the knowledgebase for Danio rerio research

Yvonne M Bradford, Ceri E Van Slyke, Leyla Ruzicka, Amy Singer, Anne Eagle, David Fashena, Douglas G Howe, Ken Frazer, Ryan Martin, Holly Paddock, Christian Pich, Sridhar Ramachandran (+1 others)
2022 Genetics  
The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for Danio rerio genetic and genomic data.  ...  Recently, ZFIN and six other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of  ...  Introduction The Zebrafish Information Network (ZFIN, zfin.org) is the knowledgebase for the model organism Danio rerio (zebrafish).  ... 
doi:10.1093/genetics/iyac016 pmid:35166825 pmcid:PMC8982015 fatcat:v737talhbvbqdn4edyablydogi

The Zebrafish Information Network: major gene page and home page updates

Douglas G Howe, Sridhar Ramachandran, Yvonne M Bradford, David Fashena, Sabrina Toro, Anne Eagle, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock (+7 others)
2020 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio).  ...  Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms  ...  INTRODUCTION The Zebrafish Information Network (ZFIN) (https://zfin. org/) is the central repository for zebrafish (Danio rerio) genetic and genomic data.  ... 
doi:10.1093/nar/gkaa1010 pmid:33170210 pmcid:PMC7778988 fatcat:sofsxiaecncnnkvkeh3y5nwem4

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

J. Sprague
2001 Nucleic Acids Research  
The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish  ...  The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org).  ...  ACKNOWLEDGEMENTS The development of the Zebrafish Information Network is generously supported by the W.M. Keck Foundation. Funds are also provided by the NIH (RR/HD12546).  ... 
doi:10.1093/nar/29.1.87 pmid:11125057 pmcid:PMC29808 fatcat:hfkuvvjsebazjig7zdqamrc2ii

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Leyla Ruzicka, Douglas G Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E Van Slyke, Yvonne M Bradford, Anne Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin (+7 others)
2018 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio).  ...  ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO).  ...  INTRODUCTION The Zebrafish Information Network (ZFIN) (https://zfin. org/) is the central repository for zebrafish (Danio rerio) genetic and genomic data.  ... 
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

Constructing a fish metabolic network model

Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer
2010 Genome Biology  
We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data.  ...  This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types.  ...  We also thank the anonymous reviewers for their valuable suggestions.  ... 
doi:10.1186/gb-2010-11-11-r115 pmid:21114829 pmcid:PMC3156954 fatcat:rvxgmlc6kbgqdieml25yo2aave

A midbody component homolog, too much information/prc1-like, is required for microtubule reorganization during both cytokinesis and axis induction in the early zebrafish embryo [article]

Sreelaja Nair, Elaine L Welch, Cara E Moravec, Ryan L Trevena, Francisco Pelegri
2021 bioRxiv   pre-print
We show that the zebrafish maternal-effect mutation too much information (tmi) corresponds to zebrafish prc1-like (prc1l), which encodes a member of the MAP65/Ase1/PRC1family of microtubule-associated  ...  division at the egg-to-embryo transition.  ...  Here we describe a zebrafish maternal-effect mutation too much information (tmi), originally identified as essential for cytokinesis in the early embryo.  ... 
doi:10.1101/2021.06.10.447958 fatcat:42vojvujdzhk5fkknvh5lrilhq

Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow

Rabiatul-Adawiah Zainal-Abidin, Nor Afiqah-Aleng, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein
2022 Life  
We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network.  ...  The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network.  ...  However, PPI information on aquaculture species remains limited except for a model organism of zebrafish, Danio rerio. Zebrafish have become an essential organism since 1960.  ... 
doi:10.3390/life12050650 pmid:35629318 pmcid:PMC9143887 fatcat:djnoah54gvgafg4bl2nepoxqhu

Gene transcription in the zebrafish embryo: regulators and networks

M. Ferg, O. Armant, L. Yang, T. Dickmeis, S. Rastegar, U. Strahle
2013 Briefings in Functional Genomics  
The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos  ...  We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as  ...  CONCLUSIONS AND PERSPECTIVES Over the last 20 years, zebrafish has become a valuable model organism to address questions of gene regulation and regulatory networks.  ... 
doi:10.1093/bfgp/elt044 pmid:24152666 fatcat:ycst5jltevdcde4uobdxgtaxei

EuFishBioMed (COST Action BM0804): A European Network to Promote the Use of Small Fishes in Biomedical Research

Uwe Strähle, Laure Bally-Cuif, Robert Kelsh, Dimitris Beis, Marina Mione, Pertti Panula, Antonio Figueras, Yoav Gothilf, Christian Brösamle, Robert Geisler, Gudrun Knedlitschek
2012 Zebrafish  
/zf-models/information/contact.html).  ...  The database of EuFishBioMed lists 353 principal investigators from 23 European countries as network members.  ... 
doi:10.1089/zeb.2012.0742 pmid:22537014 pmcid:PMC3371258 fatcat:355nricyljg6xfnzuzylhigzly

Evolutionary plasticity of segmentation clock networks

A. J. Krol, D. Roellig, M.-L. Dequeant, O. Tassy, E. Glynn, G. Hattem, A. Mushegian, A. C. Oates, O. Pourquie
2011 Development  
Comparison of the mouse, chicken and zebrafish PSM oscillatory transcriptomes revealed networks of 40 to 100 cyclic genes mostly involved in Notch, Wnt and FGF signaling pathways.  ...  networks. .  ...  To improve the chicken and zebrafish microarray annotation we developed a database, Manteia, which links the Affymetrix probesets to the corresponding NCBI and Ensembl gene models and merges the available  ... 
doi:10.1242/dev.063834 pmid:21652651 pmcid:PMC3109603 fatcat:ehbchak33rg5dnery6bvxwqkge

Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

Pasan C. Fernando, Paula M. Mabee, Erliang Zeng
2020 BMC Bioinformatics  
We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions.  ...  We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes.  ...  The semantic network construction scripts were implemented on the High-Performance Computing (HPC) clusters at the University of South Dakota and the University of Iowa (Argon Cluster).  ... 
doi:10.1186/s12859-020-03773-2 pmid:33028186 fatcat:fpjge7fzwbda3kupjf3norgvea
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