Literature DB >> 33170210

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

Douglas G Howe1, Sridhar Ramachandran1, Yvonne M Bradford1, David Fashena1, Sabrina Toro1, Anne Eagle1, Ken Frazer1, Patrick Kalita1, Prita Mani1, Ryan Martin1, Sierra Taylor Moxon1, Holly Paddock1, Christian Pich1, Leyla Ruzicka1, Kevin Schaper1, Xiang Shao1, Amy Singer1, Ceri E Van Slyke1, Monte Westerfield1.   

Abstract

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. 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.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2021        PMID: 33170210      PMCID: PMC7778988          DOI: 10.1093/nar/gkaa1010

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  10 in total

Review 1.  Cross-organism analysis using InterMine.

Authors:  Rachel Lyne; Julie Sullivan; Daniela Butano; Sergio Contrino; Joshua Heimbach; Fengyuan Hu; Alex Kalderimis; Mike Lyne; Richard N Smith; Radek Štěpán; Rama Balakrishnan; Gail Binkley; Todd Harris; Kalpana Karra; Sierra A T Moxon; Howie Motenko; Steven Neuhauser; Leyla Ruzicka; Mike Cherry; Joel Richardson; Lincoln Stein; Monte Westerfield; Elizabeth Worthey; Gos Micklem
Journal:  Genesis       Date:  2015-07-08       Impact factor: 2.487

2.  Using ZFIN: Data Types, Organization, and Retrieval.

Authors:  Ceri E Van Slyke; Yvonne M Bradford; Douglas G Howe; David S Fashena; Sridhar Ramachandran; Leyla Ruzicka
Journal:  Methods Mol Biol       Date:  2018

3.  Automated generation of gene summaries at the Alliance of Genome Resources.

Authors:  Ranjana Kishore; Valerio Arnaboldi; Ceri E Van Slyke; Juancarlos Chan; Robert S Nash; Jose M Urbano; Mary E Dolan; Stacia R Engel; Mary Shimoyama; Paul W Sternberg; The Alliance Of Genome Resources
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

4.  NCBI GEO: archive for functional genomics data sets--update.

Authors:  Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

5.  InterMine: extensive web services for modern biology.

Authors:  Alex Kalderimis; Rachel Lyne; Daniela Butano; Sergio Contrino; Mike Lyne; Joshua Heimbach; Fengyuan Hu; Richard Smith; Radek Stěpán; Julie Sullivan; Gos Micklem
Journal:  Nucleic Acids Res       Date:  2014-04-21       Impact factor: 16.971

6.  JBrowse: a dynamic web platform for genome visualization and analysis.

Authors:  Robert Buels; Eric Yao; Colin M Diesh; Richard D Hayes; Monica Munoz-Torres; Gregg Helt; David M Goodstein; Christine G Elsik; Suzanna E Lewis; Lincoln Stein; Ian H Holmes
Journal:  Genome Biol       Date:  2016-04-12       Impact factor: 13.583

7.  The Ensembl Variant Effect Predictor.

Authors:  William McLaren; Laurent Gil; Sarah E Hunt; Harpreet Singh Riat; Graham R S Ritchie; Anja Thormann; Paul Flicek; Fiona Cunningham
Journal:  Genome Biol       Date:  2016-06-06       Impact factor: 13.583

8.  The Gene Ontology Resource: 20 years and still GOing strong.

Authors: 
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

9.  Expression Atlas update: from tissues to single cells.

Authors:  Irene Papatheodorou; Pablo Moreno; Jonathan Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A Fonseca; Anja Füllgrabe; Matthew Green; Ni Huang; Laura Huerta; Haider Iqbal; Monica Jianu; Suhaib Mohammed; Lingyun Zhao; Andrew F Jarnuczak; Simon Jupp; John Marioni; Kerstin Meyer; Robert Petryszak; Cesar Augusto Prada Medina; Carlos Talavera-López; Sarah Teichmann; Juan Antonio Vizcaino; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

Review 10.  The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases.

Authors: 
Journal:  Genetics       Date:  2019-12       Impact factor: 4.562

  10 in total
  7 in total

1.  Knock-in tagging in zebrafish facilitated by insertion into non-coding regions.

Authors:  Daniel S Levic; Naoya Yamaguchi; Siyao Wang; Holger Knaut; Michel Bagnat
Journal:  Development       Date:  2021-10-04       Impact factor: 6.862

2.  Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord.

Authors:  Héctor Sánchez-Iranzo; Aliaksandr Halavatyi; Alba Diz-Muñoz
Journal:  Elife       Date:  2022-06-06       Impact factor: 8.713

3.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  The Human Disease Ontology 2022 update.

Authors:  Lynn M Schriml; James B Munro; Mike Schor; Dustin Olley; Carrie McCracken; Victor Felix; J Allen Baron; Rebecca Jackson; Susan M Bello; Cynthia Bearer; Richard Lichenstein; Katharine Bisordi; Nicole Campion Dialo; Michelle Giglio; Carol Greene
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

5.  Implementation of Zebrafish Ontologies for Toxicology Screening.

Authors:  Anne E Thessen; Skylar Marvel; J C Achenbach; Stephan Fischer; Melissa A Haendel; Kimberly Hayward; Nils Klüver; Sarah Könemann; Jessica Legradi; Pamela Lein; Connor Leong; J Erik Mylroie; Stephanie Padilla; Dante Perone; Antonio Planchart; Rafael Miñana Prieto; Arantza Muriana; Celia Quevedo; David Reif; Kristen Ryan; Evelyn Stinckens; Lisa Truong; Lucia Vergauwen; Colette Vom Berg; Mitch Wilbanks; Bianca Yaghoobi; Jon Hamm
Journal:  Front Toxicol       Date:  2022-03-11

6.  Zebrafish information network, the knowledgebase for Danio rerio research.

Authors:  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; Monte Westerfield
Journal:  Genetics       Date:  2022-04-04       Impact factor: 4.562

7.  CaveCrawler: an interactive analysis suite for cavefish bioinformatics.

Authors:  Annabel Perry; Suzanne E McGaugh; Alex C Keene; Heath Blackmon
Journal:  G3 (Bethesda)       Date:  2022-07-29       Impact factor: 3.542

  7 in total

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