Aanes H, Collas P, Aleström P (2014) Transcriptome dynamics and diversity in the early zebrafish embryo. Brief Funct Genom. https://doi.org/10.1093/bfgp/elt049
Adams VR, Leggas M (2007) Sunitinib malate for the treatment of metastatic renal cell carcinoma and gastrointestinal stromal tumors. Clin Ther 29(7):1338–1353. https://doi.org/10.1016/j.clinthera.2007.07.022
Article CAS PubMed Google Scholar
Ankley GT, Edwards SW (2018) The adverse outcome pathway: a multifaceted framework supporting 21st century toxicology. Curr Opin Toxicol 9:1–7. https://doi.org/10.1016/j.cotox.2018.03.004
Article PubMed PubMed Central Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM (2000) Gene ontology: tool for the unification of biology. Gene Ontol Consort Nature Genet 25(1):25–29. https://doi.org/10.1038/75556
Bar-Joseph Z, Gitter A, Simon I (2012) Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet 13(8):552–564. https://doi.org/10.1038/nrg3244
Article CAS PubMed Google Scholar
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry J, Michael; Sherlock, Gavin, (2004) GO::termfinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics (Oxford, England) 20(18):3710–3715. https://doi.org/10.1093/bioinformatics/bth456
Article CAS PubMed Google Scholar
Bradford YM, van Slyke CE, Ruzicka L, Singer A, Eagle A, Fashena D (2022) Zebrafish information network, the knowledgebase for Danio rerio research. Genetics. https://doi.org/10.1093/genetics/iyac016
Article PubMed PubMed Central Google Scholar
Brox S, Seiwert B, Küster E, Reemtsma T (2016) Toxicokinetics of polar chemicals in zebrafish embryo (Danio rerio): influence of physicochemical properties and of biological processes. Environ Sci Technol 50(18):10264–10272. https://doi.org/10.1021/acs.est.6b04325
Article CAS PubMed Google Scholar
Carmeliet P, Jain RK (2000) Angiogenesis in cancer and other diseases. Nature 407(6801):249–257. https://doi.org/10.1038/35025220
Article CAS PubMed Google Scholar
Carney EW, Scialli AR, Watson RE, DeSesso JM (2004) Mechanisms regulating toxicant disposition to the embryo during early pregnancy: an interspecies comparison. Birth Defect Res Embryo Today Rev 72(4):345–360. https://doi.org/10.1002/bdrc.20027
Cha Y, Ryun; Weinstein, Brant M. (2007) Visualization and experimental analysis of blood vessel formation using transgenic zebrafish. Birth Defect Res Embryo Today Rev. https://doi.org/10.1002/bdrc.20103
Challa A, Kumar; Chatti, Kiranam, (2013) Conservation and early expression of zebrafish tyrosine kinases support the utility of zebrafish as a model for tyrosine kinase biology. Zebrafish 10(3):264–274. https://doi.org/10.1089/zeb.2012.0781
Article CAS PubMed PubMed Central Google Scholar
D’Amato RJ, Loughnan MS, Flynn E, Folkman J (1994) Thalidomide is an inhibitor of angiogenesis. Proc Natl Acad Sci USA 91(9):4082–4085. https://doi.org/10.1073/pnas.91.9.4082
Article CAS PubMed PubMed Central Google Scholar
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO (2021) Twelve years of SAMtools and BCFtools. GigaScience. https://doi.org/10.1093/gigascience/giab008
Article PubMed PubMed Central Google Scholar
Dhillon SS, Torell F, Donten M, Lundstedt-Enkel K, Bennett K, Rännar S et al (2019) Metabolic profiling of zebrafish embryo development from blastula period to early larval stages. PLoS ONE. https://doi.org/10.1371/journal.pone.0213661
Article PubMed PubMed Central Google Scholar
Durinck S, Moreau Y, Kasprzyk A, Davis S, Moor B, de; Brazma, Alvis; Huber, Wolfgang, (2005) BioMart and bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (Oxford, England) 21(16):3439–3440. https://doi.org/10.1093/bioinformatics/bti525
Article CAS PubMed Google Scholar
Edwards PA, Kast HR, Anisfeld AM (2002) BAREing it all: the adoption of LXR and FXR and their roles in lipid homeostasis. J Lipid Res 43(1):2–12. https://doi.org/10.1016/S0022-2275(20)30180-2
Article CAS PubMed Google Scholar
Esteves F, Rueff J, Kranendonk M (2021) The central role of cytochrome P450 in xenobiotic metabolism-a brief review on a fascinating enzyme family. J Xenobio 11(3):94–114. https://doi.org/10.3390/jox11030007
Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England) 32(19):3047–3048. https://doi.org/10.1093/bioinformatics/btw354
Article CAS PubMed Google Scholar
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P et al (2018) The reactome pathway knowledgebase. Nucleic Acids Res 46(D1):D649–D655. https://doi.org/10.1093/nar/gkx1132
Article CAS PubMed Google Scholar
Galaxy T, platform for accessible, reproducible and collaborative biomedical analyses, (2022) update (2022). Nucl Acid Res 50(W1):W345–W351
Gloss BS, Signal B, Cheetham SW, Gruhl F, Kaczorowski DC, Perkins AC, Dinger ME (2017) High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci. Sci Rep 7(1):6731. https://doi.org/10.1038/s41598-017-06110-5
Article CAS PubMed PubMed Central Google Scholar
Gotink KJ, Verheul HMW (2010) Anti-angiogenic tyrosine kinase inhibitors: what is their mechanism of action? Angiogenesis 13(1):1–14. https://doi.org/10.1007/s10456-009-9160-6
Article CAS PubMed Google Scholar
Hartmann J, Thomas; Haap, Michael; Kopp, Hans-Georg; Lipp, Hans-Peter, (2009) Tyrosine kinase inhibitors - a review on pharmacology, metabolism and side effects. Curr Drug Metab 10(5):470–481. https://doi.org/10.2174/138920009788897975
Article CAS PubMed Google Scholar
Hastie T, Tibshirani R (1986) Generalized additive models. Statist Sci. https://doi.org/10.1214/ss/1177013604
Heinonen M, Guipaud O, Milliat F, Buard V, Micheau B, Tarlet G et al (2015) Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction. Bioinformatics (Oxford, England) 31(5):728–735. https://doi.org/10.1093/bioinformatics/btu699
Article CAS PubMed Google Scholar
Houk BE, Bello CL, Kang D, Amantea M (2009) A population pharmacokinetic meta-analysis of sunitinib malate (SU11248) and its primary metabolite (SU12662) in healthy volunteers and oncology patients. Clin Cancer Res Official J Am Ass 15(7):2497–2506. https://doi.org/10.1158/1078-0432.CCR-08-1893
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496(7446):498–503. https://doi.org/10.1038/nature12111
Article CAS PubMed PubMed Central Google Scholar
International Organization for Standardization (1996) Water quality — Determination of the acute lethal toxicity of substances to a freshwater fish [Brachydanio rerio Hamilton-Buchanan (Teleostei, Cyprinidae)] - Part 3: Flow-through method. Geneva: ISO; 1996. ISO Standard No. 7346–3:1996
Irie N, Kuratani S (2011) Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat Commun. https://doi.org/10.1038/ncomms1248
Isogai S, Horiguchi M, Weinstein BM (2001) The vascular anatomy of the developing zebrafish: an atlas of embryonic and early larval development. Dev Biol 230(2):278–301.
Comments (0)