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Items: 1 to 20 of 111

1.

Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets.

Prykhozhij SV, Marsico A, Meijsing SH.

Zebrafish. 2013 Sep;10(3):303-15. doi: 10.1089/zeb.2012.0865.

2.

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

Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M.

Nucleic Acids Res. 2003 Jan 1;31(1):241-3.

3.

Identification of estrogen target genes during zebrafish embryonic development through transcriptomic analysis.

Hao R, Bondesson M, Singh AV, Riu A, McCollum CW, Knudsen TB, Gorelick DA, Gustafsson JÅ.

PLoS One. 2013 Nov 6;8(11):e79020. doi: 10.1371/journal.pone.0079020.

4.

4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53.

5.

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

Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D768-72.

6.

A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts.

Ouyang M, Garnett AT, Han TM, Hama K, Lee A, Deng Y, Lee N, Liu HY, Amacher SL, Farber SA, Ho SY.

Gene Expr Patterns. 2008 Feb;8(3):171-80.

7.

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.

Van Slyke CE, Bradford YM, Westerfield M, Haendel MA.

J Biomed Semantics. 2014 Feb 25;5(1):12. doi: 10.1186/2041-1480-5-12.

8.

ZFIN: enhancements and updates to the Zebrafish Model Organism Database.

Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Howe DG, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Bauer Schaper H, Schaper K, Shao X, Singer A, Sprague J, Sprunger B, Van Slyke C, Westerfield M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D822-9. doi: 10.1093/nar/gkq1077.

9.

Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database.

Belmamoune M, Verbeek FJ.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-92.

PMID:
20134060
10.

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

Ruzicka L, Bradford YM, Frazer K, Howe DG, Paddock H, Ramachandran S, Singer A, Toro S, Van Slyke CE, Eagle AE, Fashena D, Kalita P, Knight J, Mani P, Martin R, Moxon SA, Pich C, Schaper K, Shao X, Westerfield M.

Genesis. 2015 Aug;53(8):498-509. doi: 10.1002/dvg.22868.

11.

A graphical systems model and tissue-specific functional gene sets to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis.

Villeneuve DL, Garcia-Reyero N, Martinović-Weigelt D, Li Z, Watanabe KH, Orlando EF, Lalone CA, Edwards SW, Burgoon LD, Denslow ND, Perkins EJ, Ankley GT.

Mutat Res. 2012 Aug 15;746(2):151-62. doi: 10.1016/j.mrgentox.2011.12.016.

PMID:
22227403
12.
13.

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

Howe DG, Bradford YM, Eagle A, Fashena D, Frazer K, Kalita P, Mani P, Martin R, Moxon ST, Paddock H, Pich C, Ramachandran S, Ruzicka L, Schaper K, Shao X, Singer A, Toro S, Van Slyke C, Westerfield M.

Nucleic Acids Res. 2016 Nov 28. pii: gkw1116. [Epub ahead of print]

14.

Pentachlorophenol exposure causes Warburg-like effects in zebrafish embryos at gastrulation stage.

Xu T, Zhao J, Hu P, Dong Z, Li J, Zhang H, Yin D, Zhao Q.

Toxicol Appl Pharmacol. 2014 Jun 1;277(2):183-91. doi: 10.1016/j.taap.2014.03.004.

PMID:
24642059
15.

Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.

Yang L, Zou M, Fu B, He S.

BMC Genomics. 2013 Jan 31;14:65. doi: 10.1186/1471-2164-14-65.

16.

Glucocorticoids alter craniofacial development and increase expression and activity of matrix metalloproteinases in developing zebrafish (Danio rerio).

Hillegass JM, Villano CM, Cooper KR, White LA.

Toxicol Sci. 2008 Apr;102(2):413-24. doi: 10.1093/toxsci/kfn010.

17.

Tissue enrichment analysis for C. elegans genomics.

Angeles-Albores D, N Lee RY, Chan J, Sternberg PW.

BMC Bioinformatics. 2016 Sep 13;17(1):366. doi: 10.1186/s12859-016-1229-9.

18.

Exploring zebrafish genomic, functional and phenotypic data using ZFIN.

Ramachandran S, Ruef B, Pich C, Sprague J.

Curr Protoc Bioinformatics. 2010 Sep;Chapter 1:Unit 1.18. doi: 10.1002/0471250953.bi0118s31.

19.

Global gene expression analysis using a zebrafish oligonucleotide microarray platform.

Peterson SM, Freeman JL.

J Vis Exp. 2009 Aug 10;(30). pii: 1471. doi: 10.3791/1471.

20.

Mining gene expression data by interpreting principal components.

Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE.

BMC Bioinformatics. 2006 Apr 7;7:194.

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