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Zebrafish Information Network

Background:

A group of us were appointed at the 1994 Cold Spring Harbor meeting on zebrafish genetics and development, to establish an on-line database of information for zebrafish researchers.

The resulting database, The Zebrafish Information Network (ZFIN) (https://zfin.org/), is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, phenotypes, orthology, human disease models, nomenclature and reagents.

In 2016, ZFIN joined together with five other model organism databases (WormBase, FlyBase, Mouse Genome Database, Rat Genome Database, Saccharomyces Genome Database) and the Gene Ontology Consortium to form the Alliance of Genome Resources (The Alliance).  The primary mission of the Alliance is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.


Goals:

The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.

ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.


Citing ZFIN:

We recommend the following formats for citing ZFIN in publications:

1. For a general reference to the database:

Ruzicka L, Howe DG, Ramachandran S, Toro S, Van Slyke CE, Bradford YM, Eagle A, Fashena D, Frazer K, Kalita P, Mani P, Martin R, Moxon ST, Paddock H, Pich C, Schaper K, Shao X, Singer A, Westerfield M. (2019). The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic Acids Res. Jan 8;47(D1):D867-D873.

doi: 10.1093/nar/gky1090.      PubMed PMID:30407545      PubMed Central PMCID:PMC6323962

2. For citing a specific entry in ZFIN:

[Type of] data for this paper were retrieved from the Zebrafish Information Network (ZFIN), University of Oregon, Eugene, OR 97403-5274; URL: http://zfin.org/; [the date you retrieved the data cited].


Research staff:

Monte Westerfield, P.I.; Doug Howe, Data Curation Manager; Anne Eagle, Technical Manager; and the rest of the ZFIN Database Team.


Advisory board:

  • Carol Bult, The Jackson Laboratory Cancer Center
  • Shawn Burgess, National Human Genome Research Center, National Institutes of Health
  • Jeffrey De Pons, Medical College of Wisconsin
  • Richard Dorsky, Director of Neuroscience, University of Utah
  • John Postlethwait, University of Oregon
  • Paul Sternberg, Wormbase. 


Publications:

Burrage, L.C., Reynolds, J.J., Baratang, N.V., Phillips, J.B., Wegner, J., McFarquhar, A., Higgs, M.R., Christiansen, A.E., Lanza, D.G., Seavitt, J.R., Jain, M., Li, X., Parry, D.A., Raman, V., Chitayat, D., Chinn, I.K., Bertuch, A.A., Karaviti, L., Schlesinger, A.E., Earl, D., Bamshad, M., Savarirayan, R., Doddapaneni, H., Muzny, D., Jhangiani, S.N., Eng, C.M., Gibbs, R.A., Bi, W., Emrick, L., Rosenfeld, J.A., Postlethwait, J., Westerfield, M., Dickinson, M.E., Beaudet, A.L., Ranza, E., Huber, C., Cormier-Daire, V., Shen, W., Mao, R., Heaney, J.D., Orange, J.S., University of Washington Center for Mendelian Genomics, Undiagnosed Diseases Network, Bertola, D., Yamamoto, G.L., Baratela, W.A.R., Butler, M.G., Ali, A., Adeli, M., Cohn, D.H., Krakow, D., Jackson, A.P., Lees, M., Offiah, A.C., Carlston, C.M., Carey, J.C., Stewart, G.S., Bacino, C.A., Campeau, P.M., Lee, B. (2019) Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes. American journal of human genetics. 104(3):422-438

Ruzicka, L., Howe, D.G., Ramachandran, S., Toro, S., Van Slyke, C.E., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Schaper, K., Shao, X., Singer, A., Westerfield, M. (2018) The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic acids research. 47(D1):D867-D873

Blanco-Sánchez, B., Clément, A., Fierro, J., Stednitz, S., Phillips, J.B., Wegner, J., Panlilio, J.M., Peirce, J.L., Washbourne, P., Westerfield, M. (2018) Grxcr1 Promotes Hair Bundle Development by Destabilizing the Physical Interaction between Harmonin and Sans Usher Syndrome Proteins. Cell Reports. 25:1281-1291.e4

Ferreira, C.R., Xia, Z.J., Clément, A., Parry, D.A., Davids, M., Taylan, F., Sharma, P., Turgeon, C.T., Blanco-Sánchez, B., Ng, B.G., Logan, C.V., Wolfe, L.A., Solomon, B.D., Cho, M.T., Douglas, G., Carvalho, D.R., Bratke, H., Haug, M.G., Phillips, J.B., Wegner, J., Tiemeyer, M., Aoki, K., Undiagnosed Diseases Network, Scottish Genome Partnership, Nordgren, A., Hammarsjö, A., Duker, A.L., Rohena, L., Hove, H.B., Ek, J., Adams, D., Tifft, C.J., Onyekweli, T., Weixel, T., Macnamara, E., Radtke, K., Powis, Z., Earl, D., Gabriel, M., Russi, A.H.S., Brick, L., Kozenko, M., Tham, E., Raymond, K.M., Phillips, J.A., Tiller, G.E., Wilson, W.G., Hamid, R., Malicdan, M.C.V., Nishimura, G., Grigelioniene, G., Jackson, A., Westerfield, M., Bober, M.B., Gahl, W.A., Freeze, H.H. (2018) A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation. American journal of human genetics. 103:553-567

Clément, A., Blanco-Sánchez, B., Peirce, J.L., Westerfield, M. (2018) Cog4 is required for protrusion and extension of the epithelium in the developing semicircular canals. Mechanisms of Development. 155:1-7

Howe, D.G., Blake, J.A., Bradford, Y.M., Bult, C.J., Calvi, B.R., Engel, S.R., Kadin, J.A., Kaufman, T.C., Kishore, R., Laulederkind, S.J.F., Lewis, S.E., Moxon, S.A.T., Richardson, J.E., Smith, C. (2018) Model organism data evolving in support of translational medicine. Lab animal. 47(10):277-289

Dona, M., Slijkerman, R., Lerner, K., Broekman, S., Wegner, J., Howat, T., Peters, T., Hetterschijt, L., Boon, N., de Vrieze, E., Sorusch, N., Wolfrum, U., Kremer, H., Neuhauss, S., Zang, J., Kamermans, M., Westerfield, M., Phillips, J., van Wijk, E. (2018) Usherin defects lead to early-onset retinal dysfunction in zebrafish. Experimental Eye Research. 173:148-159

Howe, D.G. (2018) A statistical approach to identify, monitor, and manage incomplete curated data sets. BMC Bioinformatics. 19:110

Matthews, J.L., Murphy, J.M., Carmichael, C., Yang, H., Tiersch, T., Westerfield, M., Varga, Z.M. (2018) Changes to Extender, Cryoprotective Medium, and In Vitro Fertilization Improve Zebrafish Sperm Cryopreservation. Zebrafish. 15(3):279-290

Postlethwait, J., Batzel, P., and Westerfield, M. (2018) Bioinformatics and Literature Analysis Gene Expression Data Submission. ZFIN Direct Data Submission.

Van Slyke, C.E., Bradford, Y.M., Howe, D.G., Fashena, D.S., Ramachandran, S., Ruzicka, L., ZFIN Staff* (2018) Using ZFIN: Data Types, Organization, and Retrieval. Methods in molecular biology (Clifton, N.J.). 1757:307-347

Wangler, M.F., Yamamoto, S., Chao, H.T., Posey, J.E., Westerfield, M., Postlethwait, J., Hieter, P., Boycott, K.M., Campeau, P.M., Bellen, H.J. (2017) Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics. 207:9-27

Bradford, Y.M., Toro, S., Ramachandran, S., Ruzicka, L., Howe, D.G., Eagle, A., Kalita, P., Martin, R., Taylor Moxon, S.A., Schaper, K., Westerfield, M. (2017) Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN. ILAR journal. 58:4-16

Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2017) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic acids research. 45(D1):D758-D768

Blanco-Sánchez, B., Clément, A., Phillips, J.B., Westerfield, M. (2017) Zebrafish models of human eye and inner ear diseases. Methods in cell biology. 138:415-467

Li, T., Fan, J., Blanco-Sánchez, B., Giagtzoglou, N., Lin, G., Yamamoto, S., Jaiswal, M., Chen, K., Zhang, J., Wei, W., Lewis, M.T., Groves, A.K., Westerfield, M., Jia, J., Bellen, H.J. (2016) Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-2 and Kif7 through Poly-ubiquitination. PLoS Genetics. 12:e1006054

Edmunds, R.C., Su, B., Balhoff, J.P., Eames, B.F., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. (2016) Phenoscape: Identifying candidate genes for evolutionary phenotypes. Molecular Biology and Evolution. 33(1):13-24

Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-81

Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic acids research. 45(D1):D758-D768

Desvignes, T., Batzel, P., Berezikov, E., Eilbeck, K., Eppig, J.T., McAndrews, M.S., Singer, A., Postlethwait, J.H. (2015) miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends in genetics : TIG. 31:613-26Ruzicka, L., Bradford, Y.M., Frazer, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.E., Fashena, D., Kalita, P., Knight, J., Mani, P., Martin, R., Moxon, S.A., Pich, C., Schaper, K., Shao, X., Westerfield, M. (2015) ZFIN, the Zebrafish Model Organism Database: Updates and new directions. Genesis (New York, N.Y. : 2000). 53(8):498-509

Lyne, R., Sullivan, J., Butano, D., Contrino, S., Heimbach, J., Hu, F., Kalderimis, A., Lyne, M., Smith, R.N., Štěpán, R., Balakrishnan, R., Binkley, G., Harris, T., Karra, K., Moxon, S.A., Motenko, H., Neuhauser, S., Ruzicka, L., Cherry, M., Richardson, J., Stein, L., Westerfield, M., Worthey, E., Micklem, G. (2015) Cross-Organism Analysis Using InterMine. Genesis (New York, N.Y. : 2000). 53(8):547-60

Elsayed, S.M., Phillips, J.B., Heller, R., Thoenes, M., Elsobky, E., Nürnberg, G., Nürnberg, P., Seland, S., Ebermann, I., Altmüller, J., Thiele, H., Toliat, M., Körber, F., Hu, X., Wu, Y.D., Zaki, M.S., Abdel-Salam, G., Gleeson, J., Boltshauser, E., Westerfield, M., Bolz, H.J. (2015) Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene. Human molecular genetics. 24(9):2594-603

Van Slyke, C.E., Bradford, Y.M., Westerfield, M., Haendel, M.A. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. Journal of biomedical semantics. 5:12

Beck, B.B., Phillips, J.B., Bartram, M.P., Wegner, J., Thoenes, M., Pannes, A., Sampson, J., Heller, R., Göbel, H., Koerber, F., Neugebauer, A., Hedergott, A., Nürnberg, G., Nürnberg, P., Thiele, H., Altmüller, J., Toliat, M.R., Staubach, S., Boycott, K.M., Valente, E.M., Janecke, A.R., Eisenberger, T., Bergmann, C., Tebbe, L., Wang, Y., Wu, Y., Fry, A.M., Westerfield, M., Wolfrum, U., Bolz, H.J. (2014) Mutation of POC1B in a Severe Syndromic Retinal Ciliopathy. Human Mutation. 35(10):1153-62

Phillips, J.B., Westerfield, M. (2014) Zebrafish models in translational research: tipping the scales toward advancements in human health. Disease models & mechanisms. 7:739-743

Alam-Faruque, Y., Hill, D.P., Dimmer, E.C., Harris, M.A., Foulger, R.E., Tweedie, S., Attrill, H., Howe, D.G., Thomas, S.R., Davidson, D., Woolf, A.S., Blake, J.A., Mungall, C.J., O'Donovan, C., Apweiler, R., Huntley, R.P. (2014) Representing Kidney Development Using the Gene Ontology. PLoS One. 9:e99864

Haendel, M.A., Balhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Bradford, Y., Comte, A., Dahdul, W.M., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C.J. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of biomedical semantics. 5:21

Blanco-Sánchez, B., Clément, A., Fierro, J., Washbourne, P., Westerfield, M. (2014) Complexes of Usher proteins preassemble at the endoplasmic reticulum and are required for trafficking and ER homeostasis. Disease models & mechanisms. 7:547-59

Köhler, S., Doelken, S.C., Mungall, C.J., Bauer, S., Firth, H.V., Bailleul-Forestier, I., Black, G.C., Brown, D.L., Brudno, M., Campbell, J., Fitzpatrick, D.R., Eppig, J.T., Jackson, A.P., Freson, K., Girdea, M., Helbig, I., Hurst, J.A., Jähn, J., Jackson, L.G., Kelly, A.M., Ledbetter, D.H., Mansour, S., Martin, C.L., Moss, C., Mumford, A., Ouwehand, W.H., Park, S.M., Riggs, E.R., Scott, R.H., Sisodiya, S., Vooren, S.V., Wapner, R.J., Wilkie, A.O., Wright, C.F., Vulto-van Silfhout, A.T., Leeuw, N.D., de Vries, B.B., Washingthon, N.L., Smith, C.L., Westerfield, M., Schofield, P., Ruef, B.J., Gkoutos, G.V., Haendel, M., Smedley, D., Lewis, S.E., and Robinson, P.N. (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic acids research. 42(1):D966-74

Phillips, J.B., Västinsalo, H., Wegner, J., Clément, A., Sankila, E.M., and Westerfield, M. (2013) The cone-dominant retina and the inner ear of zebrafish express the ortholog of CLRN1, the causative gene of human Usher syndrome type 3A. Gene expression patterns : GEP. 13(8):473-81

Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M. (2013).  ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. Jan;41(Database issue):D854-60.

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. Scientific Reports. 3:1802

Köhler, S., Doelken, S.C., Ruef, B.J., Bauer, S., Washington, N., Westerfield, M., Gkoutos, G., Schofield, P., Smedley, D., Lewis, S.E., Robinson, P.N., and Mungall, C.J. (2013) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000 Research. 2:30

Khodiyar, V.K., Howe, D., Talmud, P.J., Breckenridge, R., Lovering, R.C. (2013) From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.. F1000 Research. 2:1-17

Vasilevsky, N.A., Brush, M.H., Paddock, H., Ponting, L., Tripathy, S.J., Larocca, G.M., and Haendel, M.A. (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ. 1:e148

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. Nature. 496:498-503

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 revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Disease models & mechanisms. 6(2):358-372

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 research. 41(D1):D854-860

Mabee, 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. Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology. 28(3):300-305

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 One. 7(12):e51070

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 One. 7(5):e36516

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. Disease models & mechanisms. 4(6):786-800

Howe DG, Frazer K, Fashena D, Ruzicka L, Bradford Y, Ramachandran S, Ruef BJ, Van Slyke C, Singer A, Westerfield M. (2011).  Data extraction, transformation, and dissemination through ZFIN. Methods Cell Biol.104:311-25.

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.

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. Journal of the American Association for Laboratory Animal Science : JAALAS. 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. Comparative medicine. 61(4):322-329

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 in cell biology. 104:311-325

Detrich, H.W., Westerfield, M., Zon, L.I. (2010) The Zebrafish: Cellular and Developmental Biology, Part A. Methods in cell biology. 100:1-347

Zhang, C., Song, Y., Thompson, D.A., Madonna, M.A., Millhauser, G.L., Toro, S., Varga, Z., Westerfield, M., Gamse, J., Chen, W., Cone, R.D. (2010) Pineal-specific agouti protein regulates teleost background adaptation. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20164-71

Ramachandran, S., Ruef, B., Pich, C., and Sprague, J. (2010) Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Current protocols in bioinformatics. Chapter 1:Unit 1.18

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. Genesis (New York, N.Y. : 2000). 48(8):505-511

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 One. 5(5):e10708

Eames, B.F., Singer, A., Smith, G.A., Wood, Z.A., Yan, Y.L., He, X., Polizzi, S.J., Catchen, J.M., Rodriguez-Mari, A., Linbo, T., Raible, D.W., and Postlethwait, J.H. (2010) UDP xylose synthase 1 is required for morphogenesis and histogenesis of the craniofacial skeleton. Developmental Biology. 341(2):400-415

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. Systematic biology. 59(4):369-383

Ramachandran S, Ruef B, Pich C, Sprague J. (2010). Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Curr. Protoc. Bioinformatics. Chapter 1:Unit 1.18.

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 Biology. 7(11):e1000247

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 Expression Patterns. 9(4):200-208

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. Aquaculture (Amsterdam, Netherlands). 297(1-4):157-162

Viktorin, G., Chiuchitu, C., Rissler, M., Varga, Z.M., and Westerfield, M. (2009) Emx3 is required for the differentiation of dorsal telencephalic neurons. Developmental dynamics : an official publication of the American Association of Anatomists. 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 expression patterns : GEP. 9(4):200-208

Ochi, H., and Westerfield, M. (2009) Lbx2 regulates formation of myofibrils. BMC Developmental Biology. 9:13

Carmichael, C., Westerfield, M., and Varga, Z.M. (2009) Cryopreservation and in vitro fertilization at the zebrafish international resource center. Methods in molecular biology (Clifton, N.J.). 546:45-65

Dutta, S., Dietrich, J.E., Westerfield, M., and Varga, Z.M. (2008) Notch signaling regulates endocrine cell specification in the zebrafish anterior pituitary. Developmental Biology. 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 biology : journal of the International Society for Matrix Biology. 27(6):561-572

Ochi, H., Hans, S., and Westerfield, M. (2008) Smarcd3 regulates the timing of zebrafish myogenesis onset. The Journal of biological chemistry. 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 research. 36:D768-772

Toro, S., and Varga, Z.M. (2007) Equivalent progenitor cells in the zebrafish anterior preplacodal field give rise to adenohypophysis, lens, and olfactory placodes. Seminars in cell & developmental biology. 18(4):534-542

Hans, S., and Westerfield, M. (2007) Changes in retinoic acid signaling alter otic patterning. Development (Cambridge, England). 134(13):2449-2458

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. Journal of Cell Science. 120(13):2151-2161

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 and differentiation. 14(6):1095-1105

Hans, S., Christison, J., Liu, D., and Westerfield, M. (2007) Fgf-dependent otic induction requires competence provided by Foxi1 and Dlx3b. BMC Developmental Biology. 7(1):5

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 in Ecology & Evolution. 22(7):345-350

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. Journal of experimental zoology. Part B, Molecular and developmental evolution. 308(5):655-668

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 Developmental Biology. 7(1):1

Ochi, H., and Westerfield, M. (2007) Signaling networks that regulate muscle development: lessons from zebrafish. Development, growth & differentiation. 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.

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. Developmental Biology. 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. Aquaculture (Amsterdam, Netherlands). 258(1-4):565-574

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. Jan 1;34(Database issue):D581-5.

Peng, G., and Westerfield, M. (2006) Lhx5 promotes forebrain development and activates transcription of secreted Wnt antagonists. Development (Cambridge, England). 133(16):3191-3200

Zon, L.I., Traver, D., Davidson,A.J., Van Slyke, C. (2006) ZFIN Anatomy Working Group: Blood. Manually curated data.

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. Development (Cambridge, England). 133(4):725-735

Bradford, Y.M. (2006) Expression and development of zebrafish Ribeye. Ph.D. Thesis. :113p

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 research. 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. Human molecular genetics. 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. Development (Cambridge, England). 132(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. Development (Cambridge, England). 132(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. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 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. Genesis (New York, N.Y. : 2000). 40(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. Developmental Biology. 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. Development (Cambridge, England). 131(20):5091-5102

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. Current biology : CB. 14(8):711-717

Amores, A., Suzuki, T., Yan, Y.-L., Pomeroy, J., Singer, A., Amemiya, C., and Postlethwait, J.H. (2004) Developmental roles of pufferfish hox clusters and genome evolution in ray-fin fish. Genome research. 14(1):1-10

Henrich, T., Ramialison, M., Segerdell, E., Westerfield, M., Furutani-Seiki, M., Wittbrodt, J., Kondoh, H. (2004) GSD: a genetic screen database. Mechanisms of Development. 121(7-8):959-963

Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. Jan 1;31(1):241-3.

Cresko, W.A., Yan, Y.L., Baltrus, D.A., Amores, A., Singer, A., Rodriguez-Mari, A., and Postlethwait, J.H. (2003) Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish. Developmental dynamics : an official publication of the American Association of Anatomists. 228(3):480-489

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. Development (Cambridge, England). 130(10):2213-2224

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 research. 31(1):241-243

  Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. Jan 1;31(1):241-3.

Close, R., Toro, S., Martial, J., and Muller, M. (2002) Expression of the zinc finger Egr1 gene during zebrafish embryonic development. Mechanisms of Development. 118(1-2):269-272

Singer, A., Perlman, H., Yan, Y.-L., Walker, C., Corley-Smith, G., Brandhorst, B., and Postlethwait, J. (2002) Sex-specific recombination rates in zebrafish (Danio rerio). Genetics. 160(2):649-657

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. Development (Cambridge, England). 129(21):5065-5079

Judy Sprague, Eckehard Doerry, Sarah Douglas and Monte Westerfield. (2001). The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acid Res. 29:87-90.

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. Marine biotechnology (New York, N.Y.). 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. Development (Cambridge, England). 128(18):3497-3509

Hirsinger, E. and Westerfield, M. (2001) Segregation of zebrafish muscle lineages: lineage relationships and cellular commitment. Developmental Biology. 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. Developmental Biology. 235(1):181 (#46)

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. Development (Cambridge, England). 128(1):95-105

Singer, A.G. (2001) Sex-specific differences of recombination rates in zebrafish. Master's Thesis.

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 research. 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. Development (Cambridge, England). 127(17):3645-3653

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. Development (Cambridge, England). 126:5533-5546

Westerfield, M., Doerry, E., and Douglas, S. (1999) Zebrafish in the net. Trends in genetics : TIG. 15(6):248-249

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. Current biology : CB. 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 in cell biology. 59:3-10

Detrich, H.W. III, Westerfield, M., and Zon, L.I., eds. (1999) The Zebrafish: Genetics and Genomics. San Diego: Academic Press. 60:407

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

Fashena, D. and Westerfield, M. (1999) Secondary motoneuron axons localize DM-GRASP on their fasciculated segments. The Journal of comparative neurology. 406(3):415-424

Westerfield, M., Doerry, E., and Douglas, S. (1999). Zebrafish in the net. Trends Genet. 15(6):248-249. This manuscript describes the history of the ZFIN database project.

Monte Westerfield, Eckehard Doerry, Arthur E. Kirkpatrick and Sarah A. Douglas. (1999). Zebrafish informatics and the ZFIN database. Meth. Cell Biol. 60:339-355. This paper describes the data model and structure of the database.

Edwards, P. (1999). Zebrafish Web Site Listings. In The Zebrafish: Genetics and Genomics, H.W. Detrich, III, M. Westerfield, and L.I. Zon, eds., San Diego: Academic Press, Meth. Cell Biol. 60:373-385.

Eckehard Doerry, Monte Westerfield, Sarah A. Douglas and Arthur E. Kirkpatrick. (1998). The zebrafish information network project. ACM Interactions 3:69. This report describes our design process.

Doerry, E., Douglas, S.A., Kirkpatrick, A.E., and Westerfield, M. (1998) The zebrafish information network project. Interactions. 3:69

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. Science (New York, N.Y.). 282:1711-1714

Whitlock, K.E. and Westerfield, M. (1998) A transient population of neurons pioneers the olfactory pathway in the zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 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 Genetics. 18:345-349

Houart, C., M. Westerfield, and S.W. Wilson (1998) A small population of anterior cells patterns the forebrain during zebrafish gastrulation. Nature. 391:788-792

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. Genetics. 184:361-372

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. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17(20):7796-7804

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-β Gene Families. The Journal of cell biology. 139(1):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

Westerfield, M., E. Doerry, A.E. Kirkpatrick, W. Driever, and S.A. Douglas (1997) An on-line database for zebrafish development and genetics research. Seminars in cell & developmental biology. 8:477-488

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.

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.

Fishman, M., D.Y. Stainier, R. Breitbart, and M. Westerfield (1997) Zebrafish: Genetic and embryological methods in a transparent vertebrate embryo. Methods in cell biology. 52:67-82

Eckehard Doerry, Sarah A. Douglas, Arthur E. Kirkpatrick, Monte Westerfield. (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 Dept., University of Oregon. This paper describes the design methodology used to create the ZFIN system, and the hybrid, web-accessible interface developed to satisfy stringent usability requirements.

Eckehard Doerry, Sarah A. Douglas, Arthur E. Kirkpatrick, Monte Westerfield. (1997). Participatory Design for Widely-Distributed Scientific Communities. Proceedings of the 3rd Conference on Human Factors and the Web. This paper briefly examines the special challenges of applying the user-centered design methodology to widely-distributed scientific communities.

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. Devel. Biol. 8:477-488. The Zebrafish Database contents and use are described with examples written for both biologists and computer scientists.

Eckehard Doerry, Sarah A. Douglas, Ted Kirkpatrick, Monte Westerfield. (1997). Task-centered Navigation in Web-accessible Dataspaces. Position Paper submitted to the WebNet97 Conference, Oct. 31-Nov.5, 1997, Toronto, Canada. This short paper introduces the notion of using a representation of known user tasks to provide navigational feedback during multi-step transactions with a web-accessible database.

Fritz, A., Rozowski, M., Walker, C., and Westerfield, M. (1996) Identification of selected gamma-ray induced deficiencies in zebrafish using multiplex polymerase chain reaction. Genetics. 144(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. Development (Cambridge, England). 122(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. Developmental Biology. 175(2):386

Fashena, D.S. (1996) A neuron's reach can exceed its grasp: expression of a cell adhesion molecule in the zebrafish embryo. Ph.D. Thesis.

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. Development (Cambridge, England). 121:347-357

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

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. Development (Cambridge, England). 120:1767-1775

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. The Journal of neuroscience : the official journal of the Society for Neuroscience. 14:3475-3486

Sepich, D.S., Ho, R.K., and Westerfield, M. (1994) Autonomous expression of the nic1 acetylcholine receptor mutation in zebrafish muscle cells. Developmental Biology. 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., 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. 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., 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., Wegner, J., Akimenko, M.A., and Westerfield, M. (1992) Coordinate embryonic expression of three zebrafish engrailed genes. Development (Cambridge, England). 116:1001-1010

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. Genomics. 14:200-202

Püschel, A.W., Westerfield, M., and Dressler, G.R. (1992) Comparative analysis of Pax-2 protein distributions during neurulation in mice and zebrafish. Mechanisms of Development. 38:197-208

Ekker, M., Fritz, A., and Westerfield, M. (1992) Identification of two families of satellite-like repetitive DNA sequences from the zebrafish (Brachydanio rerio). Genomics. 13:1169-1173

Ekker, M., Akimenko, M.A., BreMiller, R., and Westerfield, M. (1992) Regional expression of three homeobox transcripts in the inner ear of zebrafish embryos. Neuron. 9:27-35

Liu, D.W. and Westerfield, M. (1992) Clustering of muscle acetylcholine receptors requires motoneurons in live embryos but not in cell culture. The Journal of neuroscience : the official journal of the Society for Neuroscience. 12:1859-1866

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 & Development. 6:591-598

Püschel, A.W., Gruss, P., and Westerfield, M. (1992) Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice. Development (Cambridge, England). 114:643-651

Westerfield, M. (1992) Motor axon pathfinding. Current opinion in neurobiology. 2:28-30

Westerfield, M. (1992) Zebrafish Hox and Pax genes. Neurosci. Facts. 3:3

Hatta, K., BreMiller, R.A., Westerfield, M., and Kimmel, C.B. (1991) Diversity of expression of engrailed-like antigens in zebrafish. Development (Cambridge, England). 112:821-832

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

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

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. The Journal of neuroscience : the official journal of the Society for Neuroscience. 10:3947-3959

Stuart, G.W., Vielkind, J.R., McMurray, J.V., and Westerfield, M. (1990) Stable lines of transgenic zebrafish exhibit reproducible patterns of transgene expression. Development (Cambridge, England). 109:577-584

Westerfield, M., Liu, D.W., Kimmel, C.B., and Walker, C. (1990) Pathfinding and synapse formation in a zebrafish mutant lacking functional acetylcholine receptors. Neuron. 4:867-874

Felsenfeld, A.L., Walker, C., Westerfield, M., Kimmel, C., and Streisinger, G. (1990) Mutations affecting skeletal muscle myofibril structure in the zebrafish. Development (Cambridge, England). 108:443-459

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

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

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 Press. 192:41-47

Westerfield, M. (1990) Does the mesoderm induce Hox gene expression in the zebrafish nervous system?. Soc. Neurosci. Abstr.. 16:302

Hanneman, E. and Westerfield, M. (1989) Early expression of acetylcholinesterase activity in functionally distinct neurons of the zebrafish. The Journal of comparative neurology. 284:350-361

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.

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.

Liu, D.W. and Westerfield, M. (1988) Function of identified motoneurones and co-ordination of primary and secondary motor systems during zebra fish swimming. The Journal of physiology. 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. Development (Cambridge, England). 103:403-412

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. Development (Cambridge, England). 103:49-58

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. Developmental Biology. 126:115-128

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.

Stuart, G.W., McMurray, J.V., and Westerfield, M. (1988) Germ-line transformation of the zebrafish Brachydanio-rerio. Journal of cellular biochemistry. (Suppl.) 12:195

Westerfield, M. and Eisen, J.S. (1988) Neuromuscular specificity: pathfinding by identified motor growth cones in a vertebrate embryo. Trends in neurosciences. 11:18-22

Westerfield, M. (1987) Substrate interactions affecting motor growth cone guidance during development and regeneration. The Journal of experimental biology. 132:161-176

Liu, D.W. and Westerfield, M. (1987) The formation of terminal fields by identified motoneurons in the zebrafish. Animal behaviour. 35:1875-1882

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

Myers, P.Z., Eisen, J.S., and Westerfield, M. (1986) Development and axonal outgrowth of identified motoneurons in the zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 6:2278-2289

Westerfield, M., McMurray, J.V., and Eisen, J.S. (1986) Identified motoneurons and their innervation of axial muscles in the zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 6:2267-2277

Eisen, J.S., Myers, P.Z., and Westerfield, M. (1986) Pathway selection by growth cones of identified motoneurones in live zebra fish embryos. Nature. 320(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

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. and Eisen, J.S. (1985) The growth of motor axons in the spinal cord of Xenopus embryos. Developmental Biology. 109:96-121

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

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


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