Zebrafish as a model for systems biology

References

• Aanes , H. , Winata , C. L. , Ling , C. H. , Chen , J. P. , Srinivasan , K. G. , Lee , S. G. , … and Aanes , S. 2011 . Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition . Genome Research , 21 : 1328 – 1338 .
   PubMed Web of Science ®Google Scholar
• Abramsson , A. , Westman-Brinkmalm , A. , Pannee , J. , Gustavsson , M. , Otter , M. V. , Blennow , K. , … and Zetterberg , H. 2010 . Proteomics profiling of single organs from individual adult zebrafish . Zebrafish , 7 : 161 – 168 .
   PubMed Web of Science ®Google Scholar
• Akagi , J. , Khoshmanesh , K. , Evans , B. , Hall , C.J. , Crosier , K. E. , Cooper , J. M. , … and Wlodkowic , D. 2012 . Miniaturized embryo array for automated trapping, immobilization and microperfusion of zebrafish embryos . PLoS One , 7 : e36630
   PubMed Web of Science ®Google Scholar
• Ali , S. , Champagne , D. L. , Alia , A. and Richardson , M. K. 2011 . Large-scale analysis of acute ethanol exposure in zebrafish development: A critical time window and resilience . PLoS One , 6 : e20037
   PubMedGoogle Scholar
• Amali , A. , Rekha , R. , Lin , C. , Wang , W. L. , Gong , H. Y. , Her , G. M. and Wu , J. L. 2006 . Thioacetamide induced liver damage in zebrafish embryo as a disease model for steatohepatitis . Journal of Biomedical Science , 13 : 225 – 232 .
   PubMed Web of Science ®Google Scholar
• Amsterdam , A. and Hopkins , N. 2006 . Mutagenesis strategies in zebrafish for identifying genes involved in development and disease . Trends in Genetics , 22 : 473 – 478 .
   PubMed Web of Science ®Google Scholar
• Barbazuk , W. B. , Korf , I. , Kadavi , C. , Heyen , J. , Tate , S. , Wun , E. , … and Johnson , S. L. 2000 . The syntenic relationship of the zebrafish and human genomes . Genome Research , 10 : 1351 – 1358 .
   PubMed Web of Science ®Google Scholar
• Biales , A. D. , Bencic , D. C. , Villeneuve , D. L. , Ankley , G. T. and Lattier , D. L. 2011 . Proteomic analysis of zebrafish brain tissue following exposure to the pesticide prochloraz . Aquatic Toxicology , 105 : 618 – 628 .
   PubMed Web of Science ®Google Scholar
• Bian , Y. H. , Xu , C. , Li , J. , Xu , J. , Zhang , H. and Du , S. 2011 . Development of a transgenic zebrafish model expressing GFP in the notochord, somite and liver directed by the hfe2 gene promoter . Transgenic Research , 20 : 787 – 798 .
   PubMed Web of Science ®Google Scholar
• Brownlie , A. , Donovan , A. , Pratt , S. J. , Paw , B. H. , Oates , A. C. , Brugnara , C. , … and Zon , L. I. 1998 . Positional cloning of the zebrafish sauternes gene: A model for congenital sideroblastic anaemia . Nature Genetics , 20 : 244 – 250 .
   PubMed Web of Science ®Google Scholar
• Bruggeman , F. J. and Westerhoff , H. V. 2007 . The nature of systems biology . Trends in Microbiology , 15 : 45 – 50 .
   PubMed Web of Science ®Google Scholar
• Chandrasekar , G. , Arner , A. , Kitambi , S. S. , Dahlman-Wright , K. and Lendahl , M. A. 2011 . Developmental toxicity of the environmental pollutant 4-nonylphenol in zebrafish . Neurotoxicology and Teratology , 33 : 752 – 764 .
   PubMed Web of Science ®Google Scholar
• Chaudhry , H. W. , Dashoush , N. H. , Tang , H. , Zhang , L. , Wang , X. , Wu , E. X. and Wolgemuth , D. J. 2004 . Cyclin A2 mediates cardiomyocyte mitosis in the postmitotic myocardium . Journal of Biological Chemistry , 279 : 35858 – 35866 .
   PubMed Web of Science ®Google Scholar
• Chen , C.-F. , Chu , C.-Y. , Chen , T. H. , Lee , S. J. , Shen , C. N. and Hsiao , C.-D. 2011 . Establishment of a transgenic zebrafish line for superficial skin ablation and functional validation of apoptosis modulators in vivo . PLoS One , 6 : e20654
   PubMed Web of Science ®Google Scholar
• Cox , B. , Kotlyar , M. , Evangelou , A. I. , Ignatchenko , V. , Ignatchenko , A. , Whiteley , K. , … and Kislinger , T. 2009 . Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology . Molecular System Biology , 5 : 279
   PubMed Web of Science ®Google Scholar
• Creton , R. 2009 . Automated analysis of behavior in zebrafish larvae . Behavioural Brain Research , 203 : 127 – 136 .
   PubMed Web of Science ®Google Scholar
• De Castro , M. R. , Lima , J. V. , Salomao De Freitas , D. P. , De Souza Valente , R. , Dummer , N. S. , De Aguiar , R. B. , … and Barros , D. M. 2009 . Behavioral and neurotoxic effects of arsenic exposure in zebrafish (Danio rerio, Teleostei: Cyprinidae) . Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology , 150 : 337 – 342 .
   PubMed Web of Science ®Google Scholar
• Deo , R. C. and MacRae , C. A. 2010 . The zebrafish: Scalable in vivo modeling for systems biology . Wiley Interdisciplinary Reviews: Systems Biology and Medicine , 3 : 335 – 346 .
   PubMed Web of Science ®Google Scholar
• Detrich, H. W., III, & Kevin, F. S. (2008). Fluorescent proteins in zebrafish cell and developmental biology. In F. S. Kevin (Ed.), Methods in Cell Biology (pp. 219–241). Oxford: Academic Press.
   Google Scholar
• Ding , Y. J. and Chen , Y. H. 2012 . Developmental nephrotoxicity of aristolochic acid in a zebrafish model . Toxicology and Applied Pharmacology , 261 : 59 – 65 .
   PubMed Web of Science ®Google Scholar
• Dodd , A. , Curtis , P. M. , Williams , L. C. and Love , D. R. 2000 . Zebrafish: Bridging the gap between development and disease . Human Molecular Genetics , 9 : 2443 – 2449 .
   PubMed Web of Science ®Google Scholar
• Drummond , I. A. , Majumdar , A. , Hentschel , H. , Elger , M. , Solnica-Krezel , L. , Schier , A.F. , … and Fishman , M. C. 1998 . Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function . Development , 125 : 4655 – 4667 .
   PubMed Web of Science ®Google Scholar
• Dunn , W. B. , Bailey , N. J. C. and Johnson , H. E. 2005 . Measuring the metabolome: Current analytical technologies . Analyst , 130 : 606 – 625 .
   PubMed Web of Science ®Google Scholar
• Fewell , A. M. and Roddick , J. G. 1993 . Interactive antifungal activity of the glycoalkaloids α-solanine and α-chaconine . Phytochemistry , 33 : 323 – 328 .
   Web of Science ®Google Scholar
• Fisher , S. , Jagadeeswaran , P. and Halpern , M. E. 2003 . Radiographic analysis of zebrafish skeletal defects . Developmental Biology , 264 : 64 – 76 .
   PubMed Web of Science ®Google Scholar
• Forst , C. V. 2006 . Host-pathogen systems biology . Drug Discovery Today , 11 : 220 – 227 .
   PubMed Web of Science ®Google Scholar
• Garrity , D. M. , Childs , S. and Fishman , M. C. 2002 . The heartstrings mutation in zebrafish causes heart/fin Tbx5 deficiency syndrome . Development , 129 : 4635 – 4645 .
   PubMed Web of Science ®Google Scholar
• Gerhard, D. S., Wagner, L., Feingold, E. A., Shenmen, C. M., Grouse, L. H., Schuler, G., … Malek, J.; MGC Project Team. (2004). The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Research, 14, 2121–2127.
   Google Scholar
• Gilchrist , A. , Au , C. E. , Hiding , J. , Bell , A. W. , Fernandez-Rodriguez , J. , Lesimple , S. , … and Bergeron , J. J. M. 2006 . Quantitative proteomics analysis of the secretory pathway . Cell , 127 : 1265 – 1281 .
   PubMed Web of Science ®Google Scholar
• Goldsmith , J. R. and Jobin , C. 2012 . Think small: Zebrafish as a model system of human pathology . Journal of Biomedicine and Biotechnology , 2012 : 12
   Google Scholar
• Gong , Z. , Ju , B. , Wang , X. , He , J. , Wan , H. , Sudha , P. M. and Yan , T. 2002 . Green fluorescent protein expression in germ-line transmitted transgenic zebrafish under a stratified epithelial promoter from Keratin8 . Developmental Dynamics , 223 : 204 – 215 .
   PubMed Web of Science ®Google Scholar
• Gstaiger , M. and Aebersold , R. 2009 . Applying mass spectrometry-based proteomics to genetics, genomics and network biology . Natue Reviews. Genetics , 10 : 617 – 627 .
   PubMed Web of Science ®Google Scholar
• Guerrera , I. and Kleiner , O. 2005 . Application of mass spectrometry in proteomics . Bioscience Reports , 25 : 71 – 93 .
   PubMed Web of Science ®Google Scholar
• Gygi , S. P. , Corthals , G. L. , Zhang , Y. , Rochon , Y. and Aebersold , R. 2000 . Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology . Proceedings of the National Academy of Sciences of the United States of America , 97 : 9390 – 9395 .
   PubMed Web of Science ®Google Scholar
• Han , X. , Aslanian , A. and Yates , J. R. III . 2008 . Mass spectrometry for proteomics . Current Opinion in Chemical Biology , 12 : 483 – 490 .
   PubMed Web of Science ®Google Scholar
• Hanai , J. I. , Cao , P. , Tanksale , P. , Imamura , S. , Koshimizu , E. , Zhao , J. , … and Lecker , S. H. 2007 . The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity . Journal of Clinical Investigation , 117 : 3940 – 3951 .
   PubMed Web of Science ®Google Scholar
• Harbers , M. and Carninci , P. 2005 . Tag-based approaches for transcriptome research and genome annotation . Nature Methods , 2 : 495 – 502 .
   PubMed Web of Science ®Google Scholar
• Hayashi , S. , Akiyama , S. , Tamaru , Y. , Takeda , Y. , Fujiwara , T. , Inoue , K. , … and Fukusaki , E. 2009 . A novel application of metabolomics in vertebrate development . Biochemical and Biophysical Research Communications , 386 : 268 – 272 .
   PubMed Web of Science ®Google Scholar
• Herbert , B. R. , Harry , J. L. , Packer , N. H. , Gooley , A. A. , Pedersen , S. K. and Williams , K. L. 2001 . What place for polyacrylamide in proteomics? . Trends in Biotechnology , 19 : S3 – S9 .
   PubMed Web of Science ®Google Scholar
• Higashijima , S. I. , Okamoto , H. , Ueno , N. , Hotta , Y. and Eguchi , G. 1997 . High-frequency generation of transgenic zebrafish which reliably express gfp in whole muscles or the whole body by using promoters of zebrafish origin . Developmental Biology , 192 : 289 – 299 .
   PubMed Web of Science ®Google Scholar
• Higgs , R. E. , Knierman , M. D. , Gelfanova , V. , Butler , J. P. and Hale , J. E. 2005 . Comprehensive label-free method for the relative quantification of proteins from biological samples . Journal of Proteome Research , 4 : 1442 – 1450 .
   PubMed Web of Science ®Google Scholar
• Hill , A. J. , Teraoka , H. , Heideman , W. and Peterson , R. E. 2005 . Zebrafish as a model vertebrate for investigating chemical toxicity . Toxicological Sciences , 86 : 6 – 19 .
   PubMed Web of Science ®Google Scholar
• Huang , Q. Y. , Huang , L. and Huang , H. Q. 2010 . Proteomic analysis of methyl parathion-responsive proteins in zebrafish (Danio rerio) brain . Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology , 153 : 67 – 74 .
   PubMed Web of Science ®Google Scholar
• Ideker , T. , Galitski , T. and Hood , L. 2001 . A new approach to decoding life: Systems biology . Annual Review of Genomics and Human Genetics , 2 : 343 – 372 .
   PubMed Web of Science ®Google Scholar
• Ingolia , N. T. , Brar , G. A. , Rouskin , S. , McGeachy , A. M. and Weissman , J. S. 2012 . The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments . Nature Protocol , 7 : 1534 – 1550 .
   PubMed Web of Science ®Google Scholar
• Issaq , H. J. , Chan , K. C. , Janini , G. M. , Conrads , T. P. and Veenstra , T. D. 2005 . Multidimensional separation of peptides for effective proteomic analysis . Journal of Chromatography B , 817 : 35 – 47 .
   PubMed Web of Science ®Google Scholar
• Jang , Z. H. , Chung , H. C. , Ahn , Y. G. , Kwon , Y. K. , Kim , J. S. , Ryu , J. H. , … and Hwang , G. S. 2012 . Metabolic profiling of an alcoholic fatty liver in zebrafish (Danio rerio) . Molecular BioSystems , 8 : 2001 – 2009 .
   PubMedGoogle Scholar
• Jung , S. H. , Kim , S. , Chung , A. Y. , Kim , H. T. , So , J. H. , Ryu , J. , … and Kim , C. H. 2009 . Visualization of myelination in GFP-transgenic zebrafish . Developmental Dynamics , 239 : 592 – 597 .
   Web of Science ®Google Scholar
• Katagiri , F. 2003 . Attacking complex problems with the power of systems biology . Plant Physiology , 132 : 417 – 419 .
   PubMed Web of Science ®Google Scholar
• Kishi , S. , Bayliss , P. E. , Uchiyama , J. J. , Koshimizu , E. , Qi , J. , Nanjappa , P. , … and Roberts , T. M. 2008 . The identification of zebrafish mutants showing alterations in senescence-associated biomarkers . PLoS Genetics , 4 : e1000152
   PubMed Web of Science ®Google Scholar
• Kitano , H. 2007 . “ Scientific challanges in system biology ” . In Introduction to system biology , Edited by: Choi , S. 3 – 11 . Totowa , NJ : Humana Press .
   Google Scholar
• Knapik , E. W. 2000 . ENU mutagenesis in zebrafish from genes to complex diseases . Mammalian Genome , 11 : 511 – 519 .
   PubMed Web of Science ®Google Scholar
• Kohl , P. , Crampin , E. J. , Quinn , T. A. and Noble , D. 2010 . Systems biology: An approach . Clinical Pharmacology and Therapeutics , 88 : 25 – 33 .
   PubMed Web of Science ®Google Scholar
• Kültz , D. , Fiol , D. , Valkova , N. , Gomez-Jimenez , S. , Chan , S. Y. and Lee , J. 2007 . Functional genomics and proteomics of the cellular osmotic stress response in ‘non-model’ organisms . Journal of Experimental Biology , 210 : 1593 – 1601 .
   PubMed Web of Science ®Google Scholar
• Langenau , D. M. , Traver , D. , Ferrando , A. A. , Kutok , J. L. , Aster , J. C. , Kanki , J. P. , … and Look , A. T. 2003 . Myc-induced T cell leukemia in transgenic zebrafish . Science , 299 : 887 – 890 .
   PubMed Web of Science ®Google Scholar
• Langheinrich , U. , Vacun , G. and Wagner , T. 2003 . Zebrafish embryos express an orthologue of HERG and are sensitive toward a range of QT-prolonging drugs inducing severe arrhythmia . Toxicology and Applied Pharmacology , 193 : 370 – 382 .
   PubMed Web of Science ®Google Scholar
• Lieschke , G. J. and Currie , P. D. 2007 . Animal models of human disease: Zebrafish swim into view . Nature Review Genetics , 8 : 353 – 367 .
   PubMed Web of Science ®Google Scholar
• Liu , S. and Leach , S. D. 2011 . Zebrafish models for cancer . Annual Review of Pathology: Mechanisms of Disease , 6 : 71 – 93 .
   PubMed Web of Science ®Google Scholar
• Liu , X. S. 2007 . Getting started in tiling microarray analysis . PLoS Computational Biology , 3 : e183
   PubMed Web of Science ®Google Scholar
• Lucitt , M. B. , Price , T. S. , Pizarro , A. , Wu , W. , Yocum , A. K. , Seiler , C. , … and Grosser , T. 2008 . Analysis of the zebrafish proteome during embryonic development . Molecular & Cellular Proteomics , 7 : 981 – 994 .
   PubMed Web of Science ®Google Scholar
• Madsen , E. C. , Morcos , P. A. , Mendelsohn , B. A. and Gitlin , J. D. 2008 . In vivo correction of a Menkes disease model using antisense oligonucleotides . Proceedings of the National Academy of Sciences of the United States of America , 105 : 3909 – 3914 .
   PubMed Web of Science ®Google Scholar
• Malone , M. H. and Robichaud , R. C. 1962 . Hippocratic screening for pure or crude drug materials . Lloydia , 25 : 320 – 332 .
   Google Scholar
• Mathias , J. R. , Perrin , B. J. , Liu , T. X. , Kanki , J. , Look , A. T. and Huttenlocher , A. 2006 . Resolution of inflammation by retrograde chemotaxis of neutrophils in transgenic zebrafish . Journal of Leukocyte Biology , 80 : 1281 – 1288 .
   PubMed Web of Science ®Google Scholar
• McCarty , L. S. and Mackay , D. 1993 . Enhancing ecotoxicological modeling and assessment. Body residues and modes of toxic action . Environmental Science & Technology , 27 : 1718 – 1728 .
   Web of Science ®Google Scholar
• Milan , D. J. , Peterson , T. A. , Ruskin , J. N. , Peterson , R. T. and MacRae , C. A. 2003 . Drugs that induce repolarization abnormalities cause bradycardia in zebrafish . Circulation , 107 : 1355 – 1358 .
   PubMed Web of Science ®Google Scholar
• Mitulović , G. and Mechtler , K. 2006 . HPLC techniques for proteomics analysis-a short overview of latest developments . Briefings in Functional Genomics & Proteomics , 5 : 249 – 260 .
   PubMedGoogle Scholar
• Moco , S. , Vervoort , J. , Bino , R. J. , De Vos , R. C. H. and Bino , R. 2007 . Metabolomics technologies and metabolite identification . TrAC Trends in Analytical Chemistry , 26 : 855 – 866 .
   Web of Science ®Google Scholar
• Moens , C. B. , Donn , T. M. , Wolf-Saxon , E. R. and Ma , T. P. 2008 . Reverse genetics in zebrafish by TILLING . Briefings in Functional Genomics & Proteomics , 7 : 454 – 459 .
   PubMedGoogle Scholar
• Monetti , M. , Nagaraj , N. , Sharma , K. and Mann , M. 2011 . Large-scale phosphosite quantification in tissues by a spike-in SILAC method . Nature Methods , 8 : 655 – 658 .
   PubMed Web of Science ®Google Scholar
• Monteoliva , L. and Albar , J. P. 2004 . Differential proteomics: An overview of gel and non-gel based approaches . Briefings in Functional Genomics & Proteomics , 3 : 220 – 239 .
   PubMedGoogle Scholar
• Munkittrick , K. R. and McCarty , L. S. 1995 . An integrated approach to aquatic ecosystem health: Top-down, bottom-up or middle-out? . Journal of Aquatic Ecosystem Stress and Recovery , 4 : 77 – 90 .
   Google Scholar
• Muto , A. , Orger , M. B. , Wehman , A. M. , Smear , M. C. , Kay , J. N. , Page-Mccaw , P. S. , … and Baier , H. 2005 . Forward genetic analysis of visual behavior in zebrafish . PLoS Genetics , 1 : e66
   PubMed Web of Science ®Google Scholar
• Nibbe , R. K. , Koyutürk , M. and Chance , M. R. 2010 . An integrative omics approach to identify functional sub-networks in human colorectal cancer . PLoS Computational Biology , 6 : e1000639
   PubMed Web of Science ®Google Scholar
• Ong , E. S. , Chor , C. F. , Zou , L. and Ong , C. N. 2009 . A multi-analytical approach for metabolomic profiling of zebrafish (Danio rerio) livers . Molecular BioSystems , 5 : 288 – 298 .
   PubMed Web of Science ®Google Scholar
• Ong , S. E. , Blagoev , B. , Kratchmarova , I. , Kristensen , D. B. , Steen , H. , Pandey , A. and Mann , M. 2002 . Stable isotope labeling by amino acids in cell culture, silac, as a simple and accurate approach to expression proteomics . Molecular & Cellular Proteomics , 1 : 376 – 386 .
   PubMed Web of Science ®Google Scholar
• Papan , C. and Chen , L. 2009 . Metabolic fingerprinting reveals developmental regulation of metabolites during early zebrafish embryogenesis . OMICS: A Journal of Integrative Biology , 13 : 397 – 405 .
   PubMed Web of Science ®Google Scholar
• Paquet , D. , Bhat , R. , Sydow , A. , Mandelkow , E.-M. , Berg , S. , Hellberg , S. , … and Haass , C. 2009 . A zebrafish model of tauopathy allows in vivo imaging of neuronal cell death and drug evaluation . Journal of Clinical Investigation , 119 : 1382 – 1395 .
   PubMed Web of Science ®Google Scholar
• Paquet , D. , Schmid , B. and Haass , C. 2010 . Transgenic zebrafish as a novel animal model to study tauopathies and other neurodegenerative disorders in vivo . Neurodegenerative Diseases , 7 : 99 – 102 .
   PubMed Web of Science ®Google Scholar
• Parng , C. , Roy , N. M. , Ton , C. , Lin , Y. and McGrath , P. 2007 . Neurotoxicity assessment using zebrafish . Journal of Pharmacological and Toxicological Methods , 55 : 103 – 112 .
   PubMedGoogle Scholar
• Parng , C. , Seng , W. L. , Semino , C. and McGrath , P. 2002 . Zebrafish: A preclinical model for drug screening . Assay and Drug Development Technologies , 1 : 41 – 48 .
   PubMed Web of Science ®Google Scholar
• Parsons , M. J. , Pollard , S. M. , Saude , L. , Feldman , B. , Coutinho , P. , Hirst , E. M. A. and Stemple , D. L. 2002 . Zebrafish mutants identify an essential role for laminins in notochord formation . Development , 129 : 3137 – 3146 .
   PubMed Web of Science ®Google Scholar
• Petrie , H. L. , Hohn , C. and Hanson , L. 2009 . Characterization of rag1 mutant zebrafish leukocytes . BMC Immunology , 10 : 1 – 8 .
   PubMed Web of Science ®Google Scholar
• Peng , H. C. , Wang , Y. H. , Wen , C. C. , Wang , W. H. , Cheng , C. C. and Chen , Y. H. 2010 . Nephrotoxicity assessments of acetaminophen during zebrafish embryogenesis . Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology , 151 : 480 – 486 .
   PubMed Web of Science ®Google Scholar
• Ponnudurai , R. P. , Basak , T. , Ahmad , S. , Bhardwaj , G. , Chauhan , R. K. , Singh , R. A. , … and Sengupta , S. 2012 . Proteomic analysis of zebrafish (Danio rerio) embryos exposed to cyclosporine A . Journal of Proteomics , 75 : 1004 – 1017 .
   PubMed Web of Science ®Google Scholar
• Postlethwait , J. H. , Woods , I. G. , Ngo-Hazelett , P. , Yan , Y. L. , Kelly , P. D. , Chu , F. , … and Talbot , W. S. 2000 . Zebrafish comparative genomics and the origins of vertebrate chromosomes . Genome Research , 10 : 1890 – 1902 .
   PubMed Web of Science ®Google Scholar
• Reinders , J. , Zahedi , R. P. , Pfanner , N. , Meisinger , C. and Sickmann , A. 2006 . Toward the complete yeast mitochondrial proteome: Multidimensional separation techniques for mitochondrial proteomics . Journal of Proteome Research , 5 : 1543 – 1554 .
   PubMed Web of Science ®Google Scholar
• Ross , P. L. , Huang , Y. N. , Marchese , J. N. , Williamson , B. , Parker , K. , Hattan , S. , … and Pappin , D. J. 2004 . Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents . Molecular and Cellular Proteomics , 3 : 1154 – 1169 .
   PubMed Web of Science ®Google Scholar
• Sager , J. , Bai , Q. and Burton , E. 2010 . Transgenic zebrafish models of neurodegenerative diseases . Brain Structure and Function , 214 : 285 – 302 .
   PubMed Web of Science ®Google Scholar
• Schwend , T. and Ahlgren , S. 2009 . Zebrafish con/disp1 reveals multiple spatiotemporal requirements for Hedgehog-signaling in craniofacial development . BMC Developmental Biology , 9 : 59
   PubMed Web of Science ®Google Scholar
• Shepard , J. L. , Amatruda , J. F. , Finkelstein , D. , Ziai , J. , Finley , K. R. , Stern , H. M. , … and Zon , L. I. 2007 . A mutation in separase causes genome instability and increased susceptibility to epithelial cancer . Genes & Development , 21 : 55 – 59 .
   PubMed Web of Science ®Google Scholar
• Shiraki , T. , Kondo , S. , Katayama , S. , Waki , K. , Kasukawa , T. , Kawaji , H. , … and Hayashizaki , Y. 2003 . Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage . Proceedings of the National Academy of Sciences of the United States of America , 100 : 15776 – 15781 .
   PubMed Web of Science ®Google Scholar
• Shulaev , V. 2006 . Metabolomics technology and bioinformatics . Briefings in Bioinformatics , 7 : 128 – 139 .
   PubMed Web of Science ®Google Scholar
• Sleep , E. , Boué , S. , Jopling , C. , Raya , M. , Raya , Á. and Belmonte , J. C. I. 2010 . Transcriptomics approach to investigate zebrafish heart regeneration . Journal of Cardiovascular Medicine , 11 : 369 – 380 .
   PubMed Web of Science ®Google Scholar
• Soanes , K. H. , Achenbach , J. C. , Burton , I. W. , Hui , J. P. M. , Penny , S. L. and Karakach , T. K. 2011 . Molecular characterization of zebrafish embryogenesis via dna microarrays and multiplatform time course metabolomics studies . Jounal of Proteome Research , 10 : 5102 – 5117 .
   PubMed Web of Science ®Google Scholar
• Spitsbergen , J. M. and Kent , M. L. 2003 . The state of the art of the zebrafish model for toxicology and toxicologic pathology research advantages and current limitations . Toxicologic pathology , 31 : 62 – 87 .
   PubMedGoogle Scholar
• Stehr , C. M. , Linbo , T. L. , Incardona , J. P. and Scholz , N. L. 2006 . The developmental neurotoxicity of fipronil: Notochord degeneration and locomotor defects in zebrafish embryos and larvae . Toxicological Sciences , 92 : 270 – 278 .
   PubMed Web of Science ®Google Scholar
• Streisinger , G. , Walker , C. , Dower , N. , Knauber , D. and Singer , F. 1981 . Production of clones of homozygous diploid zebra fish (Brachydanio rerio) . Nature , 291 : 293 – 296 .
   PubMed Web of Science ®Google Scholar
• Sukardi , H. , Ung , C. Y. , Gong , Z. Y. and Lam , S. H. 2010 . Incorporating zebrafish omics into chemical biology and toxicology . Zebrafish , 7 : 41 – 52 .
   PubMed Web of Science ®Google Scholar
• Sun , X. J. , Xu , P. F. , Zhou , T. , Hu , M. , Fu , C. T. , Zhang , Y. , … and Chen , Z. 2008 . Genome-wide survey and developmental expression mapping of zebrafish set domain-containing genes . PLoS One , 3 : e1499
   PubMed Web of Science ®Google Scholar
• Taesotikul , T. , Panthong , A. , Kanjanapothi , D. , Verpoorte , R. and Scheffer , J. J. C. 1989 . Hippocratic screening of ethanolic extracts from two Tabernaemontana species . Journal of Ethnopharmacology , 27 : 99 – 106 .
   PubMed Web of Science ®Google Scholar
• Tay , T. L. , Lin , Q. , Seow , T. K. , Tan , K. H. , Hew , C. L. and Gong , Z. 2006 . Proteomic analysis of protein profiles during early development of the zebrafish, Danio rerio . Proteomics , 6 : 3176 – 3188 .
   PubMed Web of Science ®Google Scholar
• Thisse , C. and Thisse , B. 2008 . High-resolution in situ hybridization to whole-mount zebrafish embryos . Nature Protocols , 3 : 59 – 69 .
   PubMed Web of Science ®Google Scholar
• Ton , C. and Parng , C. 2005 . The use of zebrafish for assessing ototoxic and otoprotective agents . Hearing Research , 208 : 79 – 88 .
   PubMed Web of Science ®Google Scholar
• Tong , S. K. , Mouriec , K. , Kuo , M. W. , Pellegrini , E. , Gueguen , M.-M. , Brion , F. , … and Chung , B. C. 2009 . A cyp19a1b-gfp (aromatase B) transgenic zebrafish line that expresses GFP in radial glial cells . Genesis , 47 : 67 – 73 .
   PubMed Web of Science ®Google Scholar
• Trede , N. S. , Ota , T. , Kawasaki , H. , Paw , B. H. , Katz , T. , Demarest , B. , … and Zon , L. I. 2008 . Zebrafish mutants with disrupted early T-cell and thymus development identified in early pressure screen . Developmental Dynamics , 237 : 2575 – 2584 .
   PubMed Web of Science ®Google Scholar
• Ung , C. , Lam , S. , Hlaing , M. , Winata , C. , Korzh , S. , Mathavan , S. and Gong , Z. 2010 . Mercury-induced hepatotoxicity in zebrafish: In vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation . BMC Genomics , 11 : 212
   PubMed Web of Science ®Google Scholar
• Verpoorte , R. , Choi , Y. H. , Mustafa , N. and Kim , H. K. 2008 . Metabolomics: Back to basics . Phytochemistry Reviews , 7 : 525 – 537 .
   Google Scholar
• Vesterlund , L. , Jiao , H. , Unneberg , P. , Hovatta , O. and Kere , J. 2011 . The zebrafish transcriptome during early development . BMC Developmental Biology , 11 : 30
   PubMed Web of Science ®Google Scholar
• Wang , W. , Liu , X. , Gelinas , D. , Ciruna , B. and Sun , Y. 2007 . A fully automated robotic system for microinjection of zebrafish embryos . PLoS One , 2 : e862
   PubMed Web of Science ®Google Scholar
• Wang , Z. , Gerstein , M. and Snyder , M. 2009 . RNA-Seq: A revolutionary tool for transcriptomics . Nature Review Genetics , 10 : 57 – 63 .
   PubMed Web of Science ®Google Scholar
• Wang , D. , Jao , L.-E. , Zheng , N. , Dolan , K. , Ivey , J. , Zonies , S. , … and Burgess , S. M. 2007 . Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions . Proceedings of the National Academy of Sciences of the United States of America , 104 : 12428 – 12433 .
   PubMed Web of Science ®Google Scholar
• Wang , M. , You , J. , Bemis , K. G. , Tegeler , T. J. and Brown , D. P. G. 2008 . Label-free mass spectrometry-based protein quantification technologies in proteomic analysis . Briefings in Functional Genomics & Proteomics , 7 : 329 – 339 .
   PubMedGoogle Scholar
• Way , J. C. and Silver , P. A. 2007 . Systems engineering without an engineer: Why we need systems biology . Complexity , 13 : 22 – 29 .
   Web of Science ®Google Scholar
• Wielhouwer , E. M. , Ali , S. , Al-Afandi , A. , Blom , M. T. , Olde Riekerink , M. B. , Poelma , C. , … and Richardson , M. K. 2011 . Zebrafish embryo development in a microfluidic flow-through system . Lab on a Chip , 11 : 1815 – 1824 .
   PubMed Web of Science ®Google Scholar
• Wishart , D. S. 2008 . Applications of metabolomics in drug discovery and development . Drugs in R & D , 9 : 307 – 322 .
   Google Scholar
• Wu , W. W. , Wang , G. , Baek , S. J. and Shen , R.-F. 2006 . Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D Gel- or LC-MALDI TOF/TOF . Journal of Proteome Research , 5 : 651 – 658 .
   PubMed Web of Science ®Google Scholar
• Xi , Y. , Ryan , J. , Noble , S. , Yu , M. , Yilbas , A. E. and Ekker , M. 2010 . Impaired dopaminergic neuron development and locomotor function in zebrafish with loss of pink1 function . European Journal of Neuroscience , 31 : 623 – 633 .
   PubMed Web of Science ®Google Scholar
• Zhang , Y. , Wang , C. , Huang , L. , Chen , R. , Chen , Y. and Zuo , Z. 2012 . Low-level pyrene exposure causes cardiac toxicity in zebrafish (Danio rerio) embryos . Aquatic Toxicology , 114–115 : 119 – 124 .
   PubMed Web of Science ®Google Scholar
• Zhao , S. , Xie , P. , Li , G. , Jun , C. , Cai , Y. , Xiong , Q. and Zhao , Y. 2012 . The proteomic study on cellular responses of the testes of zebrafish (Danio rerio) exposed to microcystin-RR . Proteomics , 12 : 300 – 312 .
   PubMed Web of Science ®Google Scholar
• Zheng , W. , Wang , Z. , Collins , J. E. , Andrews , R. M. , Stemple , D. and Gong , Z. 2011 . Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung . PLoS One , 6 : e24019
   PubMed Web of Science ®Google Scholar
• Zhuo , H.-Q. , Huang , L. , Huang , H.-Q. and Cai , Z. 2012 . Effects of chronic tramadol exposure on the zebrafish brain: A proteomic study . Journal of Proteomics , 75 : 3351 – 3364 .
   PubMed Web of Science ®Google Scholar