Research
General Information
ZIRC
ZFIN ID: ZDB-LAB-991005-53
Zebrafish International Resource Center (ZIRC)
PI/Director: Varga, Zoltan M.
Westerfield, Monte
Co-PI: Kent, Michael
Contact Person: Quinn, Erin
Email: zirc@zebrafish.org
URL: http://zebrafish.org/
Address: 5274 University of Oregon Eugene, OR 97403-5274 USA
Phone: (541) 346-6028 x10
Fax:
Line Designation: rc


GENOMIC FEATURES ORIGINATING FROM THIS LAB

STATEMENT OF RESEARCH INTERESTS
The Zebrafish International Resource Center provides a central repository for wild-type and mutant strains of zebrafish (Danio rerio) and for materials and information about zebrafish research. Materials and zebrafish strains are collected from and distributed to the research community.

Obtain stocks, cDNAs, ESTs or other materials on-line form
Submit stocks using our on-line form
Pathology services on-line form
Husbandry services on-line form

Standards and procedures for maintaining healthy strains of zebrafish are being developed and a manual for prevention, diagnosis, and treatment of diseases affecting zebrafish is being prepared.



LAB MEMBERS
Murray, Katy MD/Veterinarian Hwang-Shum, Jen-Jen Research Staff Nasiadka, Andrzej Research Staff
Bauer, Justin Fish Facility Staff Carmichael, Carrie Fish Facility Staff Clark, Renee Fish Facility Staff
Lains, David Fish Facility Staff Loucks, Evyn Fish Facility Staff Marston, Dagmara Fish Facility Staff
Matthews, Jennifer Fish Facility Staff Smith, Calvin Fish Facility Staff Williams, Evan Fish Facility Staff
Hennesy, Gordon Technical Staff Holland, Ron Technical Staff Freeman, April Administrative Staff
Quinn, Erin Administrative Staff


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS
Sullivan, J., Karra, K., Moxon, S.A.T., Vallejos, A., Motenko, H., Wong, J.D., Aleksic, J., Balakrishnan, R., Binkley, G., Harris, T., Hitz, B., Jayaraman, P., Lyne, R., Neuhauser, S., Pich, C., Smith, R.N., Trinh, Q., Cherry, J.M., Richardson, J., Stein, L., Twigger, S., Westerfield, M., Worthey, E., and Micklem, G. (2013) InterMOD: integrated data and tools for the unification of model organism research Sci. Rep..
Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G.J., White, S., Chow, W., Kilian, B., Quintais, L.T., Guerra-Assunção, J.A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.H., Eyre, T., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S.F., Laird, G.K., Lloyd, D., Kenyon, E., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J., Sims, S., McLay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Eliott, D., Threadgold, G., Harden, G., Ware, D., Mortimer, B., Kerry, G., Heath, P., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C., Wood, J., Clark, S., Pelan, S., Griffiths, G., Smith, M., Glithero, R., Howden, P., Barker, N., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., McGuire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol, S., Barker, G., Whitehead, S., Kay, M., Brown, J., Murnane, C., Gray, E., Humphries, M., Sycamore, N., Barker, D., Saunders, D., Wallis, J., Babbage, A., Hammond, S., Mashreghi-Mohammadi, M., Barr, L., Martin, S., Wray, P., Ellington, A., Matthews, N., Ellwood, M., Woodmansey, R., Clark, G., Cooper, J., Tromans, A., Grafham, D., Skuce, C., Pandian, R., Andrews, R., Harrison, E., Kimberley, A., Garnett, J., Fosker, N., Hall, R., Garner, P., Kelly, D., Bird, C., Palmer, S., Gehring, I., Berger, A., Dooley, C.M., Ersan-Ürün, Z., Eser, C., Geiger, H., Geisler, M., Karotki, L., Kirn, A., Konantz, J., Konantz, M., Oberländer, M., Rudolph-Geiger, S., Teucke, M., Osoegawa, K., Zhu, B., Rapp, A., Widaa, S., Langford, C., Yang, F., Carter, N.P., Harrow, J., Ning, Z., Herrero, J., Searle, S.M., Enright, A., Geisler, R., Plasterk, R.H., Lee, C., Westerfield, M., de Jong, P.J., Zon, L.I., Postlethwait, J.H., Nüsslein-Volhard, C., Hubbard, T.J., Crollius, H.R., Rogers, J., and Stemple, D.L. (2013) The zebrafish reference genome sequence and its relationship to the human genome Nature496:498-503.
Paquette, C.E., Kent, M.L., Buchner, C., Tanguay, R.L., Guillemin, K., Mason, T.J., and Peterson, T.S. (2013) A Retrospective Study of the Prevalence and Classification of Intestinal Neoplasia in Zebrafish (Danio rerio) Zebrafish.
Doelken, S.C., Köhler, S., Mungall, C.J., Gkoutos, G.V., Ruef, B.J., Smith, C., Smedley, D., Bauer, S., Klopocki, E., Schofield, P.N., Westerfield, M., Robinson, P.N., and Lewis, S.E. (2013) Phenotypic overlap in the contribution of individual genes to CNV pathogenicity Dis. Model. Mech.6(2):358-372.
Neal, J.T., Peterson, T.S., Kent, M.L., and Guillemin, K. (2013) H. pylori Virulence Factor CagA Increases Intestinal Cell Proliferation by Wnt Pathway Activation in a Transgenic Zebrafish Model Dis. Model. Mech..
Peterson, T.S., Heidel, J.R., Murray, K.N., Sanders, J.L., Anderson, W.I., and Kent, M.L. (2013) Malignant Dysembryoplastic Neuroepithelial Tumour in a Zebrafish (Danio rerio) J. Comp. Pathol.148(2-3):220-224.
Howe, D.G., Bradford, Y.M., Conlin, T., Eagle, A.E., Fashena, D., Frazer, K., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics Nucleic Acids Res.41(D1):D854-860.
Dahdul, W.M., Balhoff, J.P., Blackburn, D.C., Diehl, A.D., Haendel, M.A., Hall, B.K., Lapp, H., Lundberg, J.G., Mungall, C.J., Ringwald, M., Segerdell, E., Van Slyke, C.E., Vickaryous, M.K., Westerfield, M., and Mabee, P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system PLoS One7(12):e51070.
Corvi, M.M., Stanley, K.A., Peterson, T.S., Kent, M.L., Feist, S.W., La Du, J.K., Volz, D.C., Hosmer, A.J., and Tanguay, R.L. (2012) Investigating the Impact of Chronic Atrazine Exposure on Sexual Development in Zebrafish Birth Defects Res. B Dev. Reprod. Toxicol.95(4):276-288.
Mabee, B.P., Balhoff, J.P., Dahdul, W.M., Lapp, H., Midford, P.E., Vision, T.J., and Westerfield, M. (2012) 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton J. Appl. Ichthyol.28(3):300-305.
Gao, J., Zhang, C., Yang, B., Sun, L., Zhang, C., Westerfield, M., and Peng, G. (2012) Dcc Regulates Asymmetric Outgrowth of Forebrain Neurons in Zebrafish PLoS One7(5):e36516.
Loucks, E., and Ahlgren, S. (2012) Assessing teratogenic changes in a zebrafish model of fetal alcohol exposure J. Vis. Exp.61:3704.
Kent, M.L., and Varga, Z. (2012) Introduction: use of zebrafish in research and importance of health and husbandry ILAR J.53(2):89-94.
Kent, M.L., Harper, C., and Wolf, J.C. (2012) Documented and potential research impacts of subclinical diseases in zebrafish ILAR J.53(2):126-134.
Matthews, M., and Varga, Z.M. (2012) Anesthesia and euthanasia in zebrafish ILAR J.53(2):192-204.
Nasiadka, A., and Clark, M.D. (2012) Zebrafish breeding in the laboratory environment ILAR J.53(2):161-168.
Sanders, J.L., Watral, V., and Kent, M.L. (2012) Microsporidiosis in zebrafish research facilities ILAR J.53(2):106-113.
Cali, A., Kent, M., Sanders, J., Pau, C., and Takvorian, P.M. (2011) Development, Ultrastructural Pathology, and Taxonomic Revision of the Microsporidial Genus, Pseudoloma and Its Type Species Pseudoloma neurophilia, in Skeletal Muscle and Nervous Tissue of Experimentally Infected Zebrafish Danio rerio J. Eukaryot. Microbiol.59(1):40-8.
Sanders, J.L., and Kent, M.L. (2011) Development of a sensitive assay for the detection of Pseudoloma neurophilia in laboratory populations of the zebrafish Danio rerio Dis. Aquat. Organ.96(2):145-156.
Phillips, J.B., Blanco-Sanchez, B., Lentz, J.J., Tallafuss, A., Khanobdee, K., Sampath, S., Jacobs, Z.G., Han, P.F., Mishra, M., Williams, D.S., Keats, B.J., Washbourne, P., and Westerfield, M. (2011) Harmonin (Ush1c) is required in zebrafish Muller glial cells for photoreceptor synaptic development and function Dis. Model. Mech.4(6):786-800.
Lawrence, C., Ennis, D.G., Harper, C., Kent, M.L., Murray, K., and Sanders, G.E. (2011) The challenges of implementing pathogen control strategies for fishes used in biomedical research Comp. Biochem. Physiol. C Toxicol. Pharmacol.155(1):160-6.
Varga, Z.M., and Tiersch, T.R. (2011) Workshop and panel discussion: High-throughput cryopreservation of germplasm as an exchange currency for genetic resources Comp. Biochem. Physiol. C Toxicol. Pharmacol..
Kent, M.L., Buchner, C., Watral, V.G., Sanders, J.L., Ladu, J., Peterson, T.S., and Tanguay, R.L. (2011) Development and maintenance of a specific pathogen-free (SPF) zebrafish research facility for Pseudoloma neurophilia Dis. Aquat. Organ.95(1):73-79.
Schwend, T., Loucks, E.J., Snyder, D., and Ahlgren, S.C. (2011) Requirement of Npc1 and availability of cholesterol for early embryonic cell movements in Zebrafish J. Lipid Res.52(7):1328-44.
Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Bauer Schaper, H., Schaper, K., Shao, X., Singer, A., Sprague, J., Sprunger, B., Van Slyke, C., and Westerfield, M. (2011) ZFIN: enhancements and updates to the zebrafish model organism database Nucleic Acids Res.39(suppl 1):D822-D829.
Howe, D.G., Frazer, K., Fashena, D., Ruzicka, L., Bradford, Y., Ramachandran, S., Ruef, B.J., Van Slyke, C., Singer, A., and Westerfield, M. (2011) Data extraction, transformation, and dissemination through ZFIN Methods Cell Biol.104:311-325.
Murray, K.N., Bauer, J., Tallen, A., Matthews, J.L., Westerfield, M., and Varga, Z.M. (2011) Characterization and management of asymptomatic mycobacterium infections at the zebrafish international resource center J. Am. Assoc. Lab. Anim. Sci.50(5):675-679.
Murray, K.N., Dreska, M., Nasiadka, A., Rinne, M., Matthews, J.L., Carmichael, C., Bauer, J., Varga, Z.M., and Westerfield, M. (2011) Transmission, Diagnosis, and Recommendations for Control of Pseudoloma neurophilia Infections in Laboratory Zebrafish (Danio rerio) Facilities Comp. Med.61(4):322-329.
Varga, Z.M. (2011) Aquaculture and husbandry at the zebrafish international resource center Methods Cell Biol.104:453-478.
Delaurier, A., Eames, B.F., Blanco-Sánchez, B., Peng, G., He, X., Swartz, M.E., Ullmann, B., Westerfield, M., and Kimmel, C.B. (2010) Zebrafish sp7:EGFP: A transgenic for studying otic vesicle formation, skeletogenesis, and bone regeneration Genesis48(8):505-511.
Sanders, J.L., Lawrence, C., Nichols, D.K., Brubaker, J.F., Peterson, T.S., Murray, K.N., and Kent, M.L. (2010) Pleistophora hyphessobryconis (Microsporidia) infecting zebrafish Danio rerio in research facilities Dis. Aquat. Organ.91(1):47-56.
Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., and Mabee, P.M. (2010) The teleost anatomy ontology: anatomical representation for the genomics age Syst. Biol.59(4):369-383.
Ebermann, I., Phillips, J.B., Liebau, M.C., Koenekoop, R.K., Schermer, B., Lopez, I., Schäfer, E., Roux, A.F., Dafinger, C., Bernd, A., Zrenner, E., Claustres, M., Blanco, B., Nürnberg, G., Nürnberg, P., Ruland, R., Westerfield, M., Benzing, T., and Bolz, H.J. (2010) PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome J. Clin. Invest.120(6):1812-1823.
Dahdul, W.M., Balhoff, J.P., Engeman, J., Grande, T., Hilton, E.J., Kothari, C., Lapp, H., Lundberg, J.G., Midford, P.E., Vision, T.J., Westerfield, M., and Mabee, P.M. (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature PLoS One5(5):e10708.
Ramsay, J.M., Watral, V., Schreck, C.B., and Kent, M.L. (2009) Pseudoloma neurophilia infections in zebrafish Danio rerio: effects of stress on survival, growth, and reproduction Dis. Aquat. Organ.88(1):69-84.
Lawrence, C., Sanders, G.E., Varga, Z.M., Baumann, D.P., Freeman, A., Baur, B., and Francis, M. (2009) Regulatory Compliance and the Zebrafish Zebrafish6(4):453-456.
Ramsay, J.M., Feist, G.W., Varga, Z.M., Westerfield, M., Kent, M.L., and Schreck, C.B. (2009) Whole-body cortisol response of zebrafish to acute net handling stress Aquaculture297(1-4):157-162.
Washington, N.L., Haendel, M.A., Mungall, C.J., Ashburner, M., Westerfield, M., and Lewis, S.E. (2009) Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation PLoS Biol.7(11):e1000247.
Viktorin, G., Chiuchitu, C., Rissler, M., Varga, Z.M., and Westerfield, M. (2009) Emx3 is required for the differentiation of dorsal telencephalic neurons Dev. Dyn.238(8):1984-1998.
Toro, S., Wegner, J., Muller, M., Westerfield, M., and Varga, Z.M. (2009) Identification of differentially expressed genes in the zebrafish hypothalamic-pituitary axis Gene Expr. Patterns9(4):200-208.
Ochi, H., and Westerfield, M. (2009) Lbx2 regulates formation of myofibrils BMC Dev. Biol.9:13.
Hagedorn, M., Ricker, J., McCarthy, M., Meyers, S.A., Tiersch, T.R., Varga, Z.M., and Kleinhans, F.W. (2009) Biophysics of zebrafish (Danio rerio) sperm Cryobiology58(1):12-19.
Carmichael, C., Westerfield, M., and Varga, Z.M. (2009) Cryopreservation and in vitro fertilization at the zebrafish international resource center Methods Mol. Biol.546:45-65.
Whipps, C.M., Matthews, J.L., and Kent, M.L. (2008) Distribution and genetic characterization of Mycobacterium chelonae in laboratory zebrafish Danio rerio Dis. Aquat. Organ.82(1):45-54.
Dutta, S., Dietrich, J.E., Westerfield, M., and Varga, Z.M. (2008) Notch signaling regulates endocrine cell specification in the zebrafish anterior pituitary Dev. Biol.319(2):248-257.
Rotllant, J., Liu, D., Yan, Y.L., Postlethwait, J.H., Westerfield, M., and Du, S.J. (2008) Sparc (Osteonectin) functions in morphogenesis of the pharyngeal skeleton and inner ear Matrix Biol.27(6):561-572.
Ostland, V.E., Watral, V., Whipps, C.M., Austin, F.W., St-Hilaire, S., Westerman, M.E., and Kent, M.L. (2008) Biochemical, molecular, and virulence characteristics of select Mycobacterium marinum isolates in hybrid striped bass Morone chrysops x M. saxatilis and zebrafish Danio rerio Dis. Aquat. Organ.79(2):107-118.
Ochi, H., Hans, S., and Westerfield, M. (2008) Smarcd3 regulates the timing of zebrafish myogenesis onset J. Biol. Chem.283(6):3529-3536.
Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J., Mani, P., Moxon, S.A., Pich, C., Ramachandran, S., Schaper, K., Segerdell, E., Shao, X., Singer, A., Song, P., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes Nucleic Acids Res.36:D768-772.
Baden, K.N., Murray, J., Capaldi, R.A., and Guillemin, K. (2007) Early developmental pathology due to cytochrome c oxidase deficiency is revealed by a new zebrafish model J. Biol. Chem.282(48):34839-34849.
Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish J. Exp. Zoolog. B Mol. Dev. Evol.308(5):655-668.
Toro, S., and Varga, Z.M. (2007) Equivalent progenitor cells in the zebrafish anterior preplacodal field give rise to adenohypophysis, lens, and olfactory placodes Semin. Cell Dev. Biol.18(4):534-542.
Yang, H., Carmichael, C., Varga, Z.M., and Tiersch, T.R. (2007) Development of a simplified and standardized protocol with potential for high-throughput for sperm cryopreservation in zebrafish Danio rerio Theriogenology68(2):128-136.
Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C., and Westerfield, M. (2007) Phenotype ontologies: the bridge between genomics and evolution Trends Ecol. Evol.22(7):345-350.
Nixon, S.J., Carter, A., Wegner, J., Ferguson, C., Floetenmeyer, M., Riches, J., Key, B., Westerfield, M., and Parton, R.G. (2007) Caveolin-1 is required for lateral line neuromast and notochord development J. Cell Sci.120(13):2151-2161.
Hans, S., and Westerfield, M. (2007) Changes in retinoic acid signaling alter otic patterning Development134(13):2449-2458.
Schlueter, P.J., Peng, G., Westerfield, M., and Duan, C. (2007) Insulin-like growth factor signaling regulates zebrafish embryonic growth and development by promoting cell survival and cell cycle progression Cell Death Differ.14(6):1095-1105.
Whipps, C.M., Dougan, S.T., and Kent, M.L. (2007) Mycobacterium haemophilum infections of zebrafish (Danio rerio) in research facilities FEMS Microbiol. Lett.270(1):21-26.
Watral, V., and Kent, M.L. (2007) Pathogenesis of Mycobacterium spp. in zebrafish (Danio rerio) from research facilities Comp. Biochem. Physiol. C Toxicol. Pharmacol.145(1):55-60.
Hans, S., Christison, J., Liu, D., and Westerfield, M. (2007) Fgf-dependent otic induction requires competence provided by Foxi1 and Dlx3b BMC Dev. Biol.7(1):5.
Chen, Y.H., Wang, Y.H., Chang, M.Y., Lin, C.Y., Weng, C.W., Westerfield, M., and Tsai, H.J. (2007) Multiple upstream modules regulate zebrafish myf5 expression BMC Dev. Biol.7(1):1.
Ochi, H., and Westerfield, M. (2007) Signaling networks that regulate muscle development: lessons from zebrafish Dev. Growth Differ.49(1):1-11.
Westerfield, M. (2007) The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio), 5th Edition University of Oregon Press, Eugene.
Bates, J.M., Mittge, E., Kuhlman, J., Baden, K.N., Cheesman, S.E., and Guillemin, K. (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation Dev. Biol.297(2):374-386.
Ochi, H., Pearson, B.J., Chuang, P.T., Hammerschmidt, M., and Westerfield, M. (2006) Hhip regulates zebrafish muscle development by both sequestering Hedgehog and modulating localization of Smoothened Dev. Biol.297(1):127-140.
Ramsay, J.M., Feist, G.W., Varga, Z.M., Westerfield, M., Kent, M.L., and Schreck, C.B. (2006) Whole-body cortisol is an indicator of crowding stress in adult zebrafish, Danio rerio Aquaculture258(1-4):565-574.
Peng, G., and Westerfield, M. (2006) Lhx5 promotes forebrain development and activates transcription of secreted Wnt antagonists Development133(16):3191-3200.
Seth, A., Culverwell, J., Walkowicz, M., Toro, S., Rick, J.M., Neuhauss, S.C., Varga, Z.M., and Karlstrom, R.O. (2006) belladonna/(lhx2) is required for neural patterning and midline axon guidance in the zebrafish forebrain Development133(4):725-735.
Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (2006) The Zebrafish Information Network: the zebrafish model organism database Nucleic Acids Res.34:D581-585.
Nixon, S.J., Wegner, J., Ferguson, C., Méry, P.F., Hancock, J.F., Currie, P.D., Key, B., Westerfield, M., and Parton, R.G. (2005) Zebrafish as a model for caveolin-associated muscle disease; caveolin-3 is required for myofibril organization and muscle cell patterning Hum. Mol. Genet.14(13):1727-1743.
Dutta, S., Dietrich, J.E., Aspock, G., Burdine, R.D., Schier, A., Westerfield, M., and Varga, Z.M. (2005) pitx3 defines an equivalence domain for lens and anterior pituitary placode Development132(7):1579-1590.
Yan, Y.L., Willoughby, J., Liu, D., Crump, J.G., Wilson, C., Miller, C.T., Singer, A., Kimmel, C., Westerfield, M., and Postlethwait, J.H. (2005) A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development Development132(5):1069-1083.
Wang-Buhler, J.L., Lee, S.J., Chung, W.G., Stevens, J.F., Tseng, H.P., Hseu, T.H., Hu, C.H., Westerfield, M., Yang, Y.H., Miranda, C.L., and Buhler, D.R. (2005) CYP2K6 from zebrafish (Danio rerio): Cloning, mapping, developmental/tissue expression, and aflatoxin B1 activation by baculovirus expressed enzyme Comp. Biochem. Physiol. C Toxicol. Pharmacol.140(2):207-219.
Wiellette, E., Grinblat, Y., Austen, M., Hirsinger, E., Amsterdam, A., Walker, C., Westerfield, M., and Sive, H. (2004) Combined haploid and insertional mutation screen in the zebrafish Genesis40(4):231-240.
Hirsinger, E., Stellabotte, F., Devoto, S.H., and Westerfield, M. (2004) Hedgehog signaling is required for commitment but not initial induction of slow muscle precursors Dev. Biol.275(1):143-157.
Hans, S., Liu, D., and Westerfield, M. (2004) Pax8 and Pax2a function synergistically in otic specification, downstream of the Foxi1 and Dlx3b transcription factors Development131(20):5091-5102.
Herzog, W., Sonntag, C., Von Der Hardt, S., Roehl, H.H., Varga, Z.M., and Hammerschmidt, M. (2004) Fgf3 signaling from the ventral diencephalon is required for early specification and subsequent survival of the zebrafish adenohypophysis Development131(15):3681-3692.
Henrich, T., Ramialison, M., Segerdell, E., Westerfield, M., Furutani-Seiki, M., Wittbrodt, J., Kondoh, H. (2004) GSD: a genetic screen database Mech. Dev.121(7-8):959-963.
Kent, M.L., Whipps, C.M., Matthews, J.L., Florio, D., Watral, V., Bishop-Stewart, J.K., Poort, M., and Bermudez, L. (2004) Mycobacteriosis in zebrafish (Danio rerio) research facilities Comp. Biochem. Physiol. C Toxicol. Pharmacol.138(3):383-390.
Jensen, A.M., and Westerfield, M. (2004) Zebrafish Mosaic Eyes Is a Novel FERM Protein Required for Retinal Lamination and Retinal Pigmented Epithelial Tight Junction Formation Curr. Biol.14(8):711-717.
Matthews, J.L. (2004) Common diseases of laboratory zebrafish The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.77:617-643.
Kent, M.L. and Bishop-Stewart, J.K. (2003) Transmission and tissue distribution of Pseudoloma neurophilia (Microsporidia) of zebrafish, Danio rerio (Hamilton) J. Fish Dis.26(7):423-426.
Liu, D., Chu, H., Maves, L., Yan, Y.-L., Morcos, P.A., Postlethwait, J.H., and Westerfield, M. (2003) Fgf3 and Fgf8 dependent and independent transcription factors are required for otic placode specification Development130(10):2213-2224.
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 Toxicol. Pathol.(Suppl.) 31:62-87.
Sprague, J., Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E., Song, P., Sprunger, B., and Westerfield, M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database Nucleic Acids Res.31(1):241-243.
Yan, Y.-L., Miller, C.T., Nissen, R.M., Singer, A., Liu, D., Kirn, A., Draper, B., Willoughby, J., Morcos, P.A., Amsterdam, A., Chung, B.-C., Westerfield, M., Haffter, P., Hopkins, N., Kimmel, C., and Postlethwait, J.H. (2002) A zebrafish sox9 gene required for cartilage morphogenesis Development129(21):5065-5079.
Matthews, M., Trevarrow, B., and Matthews, J. (2002) A virtual tour of the guide for zebrafish users Lab Anim. (NY)31(3):34-40.
Byers, K.B. and Matthews, J.L. (2002) Use of zebrafish and zoonoses Appl. Biosaf.7(3):117-119.
Kent, M.L., Bishop-Stewart, J.K., Matthews, J.L., and Spitsbergen, J.M. (2002) Pseudocapillaria tomentosa, a nematode pathogen, and associated neoplasms of zebrafish (Danio rerio) kept in research colonies Comp. Med.52(4):354-358.
Jensen, A.M., Walker, C., and Westerfield, M. (2001) mosaic eyes: a zebrafish gene required in pigmented epithelium for apical localization of retinal cell division and lamination Development128(1):95-105.
Hawkins, W.E., Clark, M.S., Shima, A., Walter, R.B., Winn, R.N., and Westerfield, M. (2001) Four resource centers for fishes: specifies, stocks, and services Mar. Biotechnol.3:S239-S248.
Varga, Z.M., Amores, A., Lewis, K.E., Yan, Y.-L., Postlethwait, J.H., Eisen, J.S., and Westerfield, M. (2001) Zebrafish smoothened functions in ventral neural tube specification and axon tract formation Development128(18):3497-3509.
Hirsinger, E. and Westerfield, M. (2001) Segregation of zebrafish muscle lineages: lineage relationships and cellular commitment Dev. Biol.235(1):180 (#40).
Jensen, A.M. and Westerfield, M. (2001) Zebrafish mosaic eyes gene is required for tight junction formation in the retinal pigmented epithelium Dev. Biol.235(1):181 (#46).
Matthews, J.L., Brown, A.M.V., Larison, K., Bishop-Stewart, J.K., Rogers, P., and Kent, M.L. (2001) Pseudoloma neurophilia n. g., n. sp., a new microsporidium from the central nervous system of the zebrafish (Danio rerio) J. Eukaryot. Microbiol.48(2):227-233.
Rohr, K.B., Barth, K.A., Varga, Z.M., and Wilson, S.W. (2001) The nodal pathway acts upstream of hedgehog signaling to specify ventral telencephalic identity Neuron29(2):341-351.
Sprague, J., Doerry, E., Douglas, S., Westerfield, M., and ZFIN GRP, (Conlin, T., Clements, D., Edwards, P., Frazer, K., Schaper, K., Segerdell, E.) (2001) The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research Nucleic Acids Res.29(1):87-90.
Whitlock, K.E. and Westerfield, M. (2000) The olfactory placodes of the zebrafish form by convergence of cellular fields at the edge of the neural plate Development127(17):3645-3653.
De Martino, S., Yan, Y.-L., Jowett, T., Postlethwait, J.H., Varga, Z.M., Ashworth, A., and Austin, C.A. (2000) Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development Dev. Dyn.217(3):279-292.
Westerfield, M. (2000) The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio), 4th Edition University of Oregon Press, Eugene.
Varga, Z.M., Wegner, J., and Westerfield, M. (1999) Anterior movement of ventral diencephalic precursors separates the primordial eye field in the neural plate and requires cyclops Development126:5533-5546.
Westerfield, M., Doerry, E., and Douglas, S. (1999) Zebrafish in the net Trends Genet.15(6):248-249.
Fashena, D. and Westerfield, M. (1999) Secondary motoneuron axons localize DM-GRASP on their fasciculated segments J. Comp. Neurol.406(3):415-424.
Appel, B., Fritz, A., Westerfield, M., Grunwald, D.J., Eisen, J.S., and Riley, B.B. (1999) Delta-mediated specification of midline cell fates in zebrafish embryos Curr. Biol.9:247-256.
Detrich, H.W. III, Westerfield, M., and Zon, L.I. (1999) Overview of the zebrafish system. In The Zebrafish: Biology. H.W. Detrich, L.I. Zon, and M. Westerfield, eds Methods Cell Biol.59:3-10.
Detrich, H.W. III, Westerfield, M., and Zon, L.I., eds. (1999) The Zebrafish: Genetics and Genomics San Diego: Academic Press60:407.
Detrich, H.W. III, Westerfield, M., and Zon, L.I., eds. (1999) The Zebrafish: Biology San Diego: Academic Press, Methods Cell Biol.59:391.
Westerfield, M., Doerry, E., Kirkpatrick, A.E., and Douglas, S.A. (1999) Zebrafish informatics and the ZFIN database In The Zebrafish: Genetics and Genomics, H.W. Detrich, III, M. Westerfield, and L.I. Zon, eds., San Diego, CA: Academic Press, Methods Cell Biol.60:339-355.
Doerry, E., Douglas, S.A., Kirkpatrick, A.E., and Westerfield, M. (1998) The zebrafish information network project Interactions3:69.
Amores, A., Force, A., Yan, Y.-L. Joly, L., Amemiya, C., Fritz, A., Ho, R., Langeland, J., Prince, V., Wang, Y.-L., Westerfield, M., Ekker, M., and Postlethwait, J.H. (1998) Zebrafish hox clusters and vertebrate genome evolution Science282:1711-1714.
Whitlock, K.E. and Westerfield, M. (1998) A transient population of neurons pioneers the olfactory pathway in the zebrafish J. Neurosci.18:8919-8927.
Postlethwait, J.H, Yan, Y.-L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.-S., Larhammar, D., Rosa, F., Westerfield, M., Zon, L.I., Johnson, S.L., and Talbot, W.S. (1998) Vertebrate genome evolution and the zebrafish gene map Nature Genet.18:345-349.
Houart, C., M. Westerfield, and S.W. Wilson (1998) A small population of anterior cells patterns the forebrain during gastrulation Nature391:788-792.
Sepich, D.S., Wegner, J., O'Shea, S., and Westerfield, M. (1998) An altered intron inhibits synthesis of the acetylcholine receptor alpha-subunit in the paralyzed zebrafish mutant nic1 Genetics184:361-372.
Doerry, E., Kirkpatrick, A.E., Douglas, S.A., and Westerfield, M. (1997) Task-centered Navigation in a Web-accessible Data Space AACE/WebNet97 conference on WWW, Internet, and Intranet, Toronto, Canada, Nov. 1,1997.
Melançon, E., Liu, D.W.C., Westerfield, M., and Eisen, J.S. (1997) Pathfinding by identified zebrafish motoneurons in the absence of muscle pioneers J. Neurosci.17(20):7796-7804.
Doerry, E., Douglas, S., Kirkpatrick, T., and Westerfield, M. (1997) Moving beyond html to create a multimedia database with user-centered design: a case study of a biological database Tech. Report CIS-TR-97-02, Computer and Information Science Department, University of Oregon.
Doerry, E., Douglas, S.A., Kirkpatrick, A.E., and Westerfield, M. (1997) Participatory design for widely-distributed scientific communities Proc. 3rd Conf. Human Factors and the Web.
Du, S.J., S.H. Devoto, M. Westerfield, and R.T. Moon (1997) Positive and negative regulation of muscle cell identity by members of the hedgehog and TGF-b gene families J. Cell Biol.139:145-156.
Ekker, M., Akimenko, M.-A., Allende, M.L., Smith, R., Drouin, G., Langille, R.M., Weinberg, E.S., and Westerfield, M. (1997) Relationships among msx gene structure and function in zebrafish and other vertebrates Mol. Biol. Evol.14:1008-1022.
Fishman, M., D.Y. Stainier, R. Breitbart, and M. Westerfield (1997) Zebrafish: Genetic and embryological methods in a transparent vertebrate embryo Methods Cell Biol.52:67-82.
Westerfield, M., E. Doerry, A.E. Kirkpatrick, W. Driever, and S.A. Douglas (1997) An on-line database for zebrafish development and genetics research Sem. Cell Dev. Biol.8:477-488.
Fritz, A., Rozowski, M., Walker, C., and Westerfield, M. (1996) Identification of selected gamma-ray induced deficiencies in zebrafish using multiplex polymerase chain reaction Genetics144(4):1735-1745.
Devoto, S.H., Melancon, E., Eisen, J.S., and Westerfield, M. (1996) Identification of separate slow and fast muscle precursor cells in vivo, prior to somite formation Development122(11):3371-3380.
Devoto, S.H., Melancon, E., Amacher, S.L., Eisen, J.S., and Westerfield, M. (1996) Influence of axial mesoderm on the development of slow muscle precursors Dev. Biol.175(2):386.
Akimenko, M.A., Johnson, S.L., Westerfield, M., and Ekker, M. (1995) Differential induction of four msx homeobox genes during fin development and regeneration in zebrafish Development121:347-357.
Westerfield, M. (1995) The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio), 3rd Edition Eugene, OR, University of Oregon Press,:385.
Akimenko, M.A., Ekker, M., Wegner, J., Lin, W., and Westerfield, M. (1994) Combinatorial expression of three zebrafish genes related to distal-less: part of a homeobox gene code for the head J. Neurosci.14:3475-3486.
Reinhard, E., Nedivi, E., Wegner, J., Skene, J.H.P., and Westerfield, M. (1994) Neural selective activation and temporal regulation of a mammalian GAP-43 promoter in zebrafish Development120:1767-1775.
Sepich, D.S., Ho, R.K., and Westerfield, M. (1994) Autonomous expression of the nic1 acetylcholine receptor mutation in zebrafish muscle cells Dev. Biol.161:84-90.
Westerfield, M. (1993) The Zebrafish Book; A Guide for the Laboratory Use of Zebrafish (Brachydanio rerio) University of Oregon Press, Eugene,2nd edition:300P.
Westerfield, M. and Liu, D.W. (1993) Cellular interactions regulating the formation of terminal arbors by primary motoneurons in the zebrafish In Cell-Cell Signaling in Vertebrate Development, E. Robertson, F.R. Maxfield, and H.J. Vogel, eds., Academic Press:113-122.
Westerfield, M., Akimenko, M.A., Ekker, M., and Püschel, A. (1993) Eyes, ears and homeobox genes in zebrafish embryos In Molecular Basis of Morphogenesis, M. Bernfield, ed., New York, NY: John Wiley & Sons, Wiley-Liss Division:67-75.
Westerfield, M., Stuart, G., and Wegner, J. (1993) Expression of foreign genes in zebrafish embryos In Devel. Ind. Microbiol., Vol II, William C. Brown, ed., New York:658-665.
Ekker, M., Akimenko, M.A., BreMiller, R., and Westerfield, M. (1992) Regional expression of three homeobox transcripts in the inner ear of zebrafish embryos Neuron9:27-35.
Ekker, M., Fritz, A., and Westerfield, M. (1992) Identification of two families of satellite-like repetitive DNA sequences from the zebrafish (Brachydanio rerio) Genomics13:1169-1173.
Ekker, M., Wegner, J., Akimenko, M.A., and Westerfield, M. (1992) Coordinate embryonic expression of three zebrafish engrailed genes Development116:1001-1010.
Goff, D.J., Galvin, K., Katz, H., Westerfield, M., Lander, E.S., and Tabin, C.J. (1992) Identification of polymorphic simple sequence repeats in the genome of the zebrafish Genomics14:200-202.
Liu, D.W. and Westerfield, M. (1992) Clustering of muscle acetylcholine receptors requires motoneurons in live embryos but not in cell culture J. Neurosci.12:1859-1866.
Püschel, A.W., Gruss, P., and Westerfield, M. (1992) Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice Development114:643-651.
Püschel, A.W., Westerfield, M., and Dressler, G.R. (1992) Comparative analysis of Pax-2 protein distributions during neurulation in mice and zebrafish Mech. Dev.38:197-208.
Westerfield, M. (1992) Motor axon pathfinding Curr. Opin. Neurobiol.2:28-30.
Westerfield, M. (1992) Zebrafish Hox and Pax genes Neurosci. Facts3:3.
Westerfield, M., Wegner, J., Jegalian, B.G., De Robertis, E.M., and Püschel, A.W. (1992) Specific activation of mammalian Hox promoters in mosaic transgenic zebrafish Genes Dev.6:591-598.
Ekker, M., Akimenko, M.A., BreMiller, R., and Westerfield, M. (1991) Characterization of four homeobox genes expressed in zebrafish neural crest Soc. Neurosci. Abstr.17:924.
Hatta, K., BreMiller, R.A., Westerfield, M., and Kimmel, C.B. (1991) Diversity of expression of engrailed-like antigens in zebrafish Development112:821-832.
Westerfield, M., Wegner, J., Akimenko, M., Ekker, M., Eisen, J., and Halpern, M. (1991) A role for engrailed gene in zebrafish muscle patterning Soc. Neurosci. Abstr.17:761.
Akimenko, M.A., Ekker, M., and Westerfield, M. (1990) Characterization of three zebrafish genes related to Hox-7 In Developmental Patterning of the Vertebrate Limb, J.R. Hinchliffe, J. Hurle and D. Summerbell, eds., New York: Plenum Press:61-63.
Felsenfeld, A.L., Walker, C., Westerfield, M., Kimmel, C., and Streisinger, G. (1990) Mutations affecting skeletal muscle myofibril structure in the zebrafish Development108:443-459.
Kimmel, C.B. and Westerfield, M. (1990) Primary neurons of the zebrafish In Signal and Sense, G.M. Edelman, W.E. Gall, and M.W. Cowan, eds., New York: Wiley-Liss:561-588.
Liu, D.W.C. and Westerfield, M. (1990) The formation of terminal fields in the absence of competitive interactions among primary motoneurons in the zebrafish J. Neurosci.10:3947-3959.
Metcalfe, W.K. and Westerfield, M. (1990) Primary motoneurons of the zebrafish In Systems Approaches to Developmental Neurobiology, P.A. Raymond, S.S. Easter and G.M. Innocenti, eds., NATO ASI Series A,New York: Plenum Press192:41-47.
Stuart, G.W., Vielkind, J.R., McMurray, J.V., and Westerfield, M. (1990) Stable lines of transgenic zebrafish exhibit reproducible patterns of transgene expression Development109:577-584.
Westerfield, M. (1990) Does the mesoderm induce Hox gene expression in the zebrafish nervous system? Soc. Neurosci. Abstr.16:302.
Westerfield, M., Liu, D.W., Kimmel, C.B., and Walker, C. (1990) Pathfinding and synapse formation in a zebrafish mutant lacking functional acetylcholine receptors Neuron4:867-874.
Debu B., Frost, D., Westerfield M., Eisen J.S. (1989) Patterning of primary motoneuron axonal outgrowth by extracellular matrix molecules in zebrafish embryos Soc. Dev. Biol. Mtg. Abstr.
Hanneman, E. and Westerfield, M. (1989) Early expression of acetylcholinesterase activity in functionally distinct neurons of the zebrafish J. Comp. Neurol.284:350-361.
Liu, D.W. and Westerfield, M. (1989) Primary motoneurons instruct muscle acetylcholine receptor placement but receptors don't instruct motoneuronal synapse placement in live zebrafish Soc. Neurosci. Abstr.15:1262.
Stuart, G.W., McMurray, J.V., and Westerfield, M. (1989) Germ-line transformation of the zebrafish In Gene Transfer and Gene Therapy, A.L. Beaudet, R. Mulligan, and I. M. Verma, eds., New York, NY, USA: Alan R. Liss, Inc.:19-28.
Westerfield, M. (1989) Establishment of cell-specific differences among primary motoneurons in the zebrafish In The Assembly of the Nervous System. Landmesser, L.T., ed., New York, NY, USA: Alan R. Liss, Inc.:189-198.
Westerfield, M. (1989) The Zebrafish Book; A Guide for the Laboratory Use of Zebrafish (Brachydanio rerio) University of Oregon Press, Eugene.
Bass, M.B. and Westerfield, M. (1988) Purification of neuron-specific antigens from zebrafish Soc. Neurosci. Abstr.14:1267.
Frost, D., Debu B., Eisen J.S., and Westerfield M. (1988) Axonal outgrowth in embryonic zebrafish is perturbed by ectopic localization of fibronectin in vivo Soc. Dev. Biol. Mtg. Abstr.
Grunwald, D.J., Kimmel, C.B., Westerfield, M., Walker, C., and Streisinger, G. (1988) A neural degeneration mutation that spares primary neurons in the zebrafish Dev. Biol.126:115-128.
Hanneman, E., Trevarrow, B., Metcalfe, W.K., Kimmel, C.B., and Westerfield, M. (1988) Segmental pattern of development of the hindbrain and spinal cord of the zebrafish embryo Development103:49-58.
Liu, D.W. and Westerfield, M. (1988) Function of identified motoneurones and co-ordination of primary and secondary motor systems during zebra fish swimming J. Physiol. Lond.403:73-89.
Stuart, G.W., McMurray, J.V., and Westerfield, M. (1988) Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos Development103:403-412.
Stuart, G.W., McMurray, J.V., and Westerfield, M. (1988) Germ-line transformation of the zebrafish Brachydanio-rerio J. Cell. Biochem.(Suppl.) 12:195.
Westerfield, M. and Eisen, J.S. (1988) Neuromuscular specificity: pathfinding by identified motor growth cones in a vertebrate embryo Trends Neurosci.11:18-22.
Liu, D.W. and Westerfield, M. (1987) The formation of terminal fields by identified motoneurons in the zebrafish Anim. Behav.35:1875-1882.
Westerfield, M. (1987) Substrate interactions affecting motor growth cone guidance during development and regeneration J. Exp. Biol.132:161-176.
Westerfield, M. and Eisen, J.S. (1987) Common mechanisms of growth cone guidance during axonal pathfinding In From Message to Mind: New Directions in the Developmental Neurobiology, Sinauer Assoc.:110-120.
Westerfield, M., Kimmel, C.B., and Walker, C. (1987) Normal pathfinding by pioneer motor growth cones in mutant zebrafish lacking functional acetylcholine receptors Soc. Neurosci. Abstr.13:5.
Eisen, J.S., Myers, P.Z., and Westerfield, M. (1986) Pathway selection by growth cones of identified motoneurones in live zebra fish embryos Nature320(6059):269-271.
Felsenfeld, A. and Westerfield, M. (1986) Normal pathfinding and synapse formation by motoneurons in a non-motile mutant zebrafish embryo Soc. Neurosci. Abstr.147:12.
Frost, D. and Westerfield, M. (1986) Axonal outgrowth of embryonic zebrafish neurons is promoted by laminin and inhibited by fibronectin Soc. Neurosci. Abstr.12:1114.
Liu, D. and Westerfield, M. (1986) Coactivation of two motor systems in the zebrafish Soc. Neurosci. Abstr.2:790.
Myers, P.Z., Eisen, J.S., and Westerfield, M. (1986) Development and axonal outgrowth of identified motoneurons in the zebrafish J. Neurosci.6:2278-2289.
Westerfield, M., Eisen, J.S., Myers, P.Z., McMurray, J.V., and Kimmel, C.B. (1986) Early neurogenesis in the zebrafish Proc. Int. Union Physiol. Sci.16:20.
Westerfield, M., McMurray, J.V., and Eisen, J.S. (1986) Identified motoneurons and their innervation of axial muscles in the zebrafish J. Neurosci.6:2267-2277.
Eisen, J.S., Myers, P.Z., and Westerfield, M. (1985) Functional interactions between identified growth cones and muscles in embryonic zebrafish Soc. Neurosci. Abstr.11:586.
Kimmel, C.B., Grunwald, D.J., Walker, C., Westerfield, M., and Streisinger, G. (1985) Neuronal degeneration mutations that spare primary neurons in the zebrafish Soc. Neurosci. Abstr.11:647.
Westerfield, M. and Eisen, J.S. (1985) The growth of motor axons in the spinal cord of Xenopus embryos Dev. Biol.109:96-121.
Eisen, J.S., Myers, P.Z., and Westerfield, M. (1984) Segmentally specific growth of motor axons in live zebrafish embryos Soc. Neurosci. Abstr.10:371.
Hanneman, E. and Westerfield, M. (1984) Identified neurons produce acetylcholinesterase before they sprout axons in the zebrafish Soc. Neurosci. Abstr.10:1043.
Westerfield, M., Myers, P.Z., and Eisen, J.S. (1984) Polyneuronal and intersegmental innervation of body muscles in the zebrafish Soc. Neurosci. Abstr.10:371.