Anderson, R.A., Schwalbach, K.T., Mui, S.R., LeClair, E.E., Topczewska, J.M., Topczewski, J. (2020) Zebrafish models of skeletal dysplasia induced by cholesterol biosynthesis deficiency. Disease models & mechanisms. 13(6):

Avaron, F., Hoffman, L., Guay, D., and Akimenko, M.A. (2006) Characterization of two new zebrafish members of the hedgehog family: Atypical expression of a zebrafish indian hedgehog gene in skeletal elements of both endochondral and dermal origins. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(2):478-489

Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48(4):427-37

Cheesman, S.E., Layden, M.J., Von Ohlen, T., Doe, C.Q., and Eisen, J.S. (2004) Zebrafish and fly Nkx6 proteins have similar CNS expression patterns and regulate motoneuron formation. Development (Cambridge, England). 131(21):5221-5232

Corallo, D., Schiavinato, A., Trapani, V., Moro, E., Argenton, F., and Bonaldo, P. (2013) Emilin3 is required for notochord sheath integrity and interacts with Scube2 to regulate notochord-derived Hedgehog signals. Development (Cambridge, England). 140(22):4594-4601

Currie, P.D. and Ingham, P.W. (1996) Induction of a specific muscle cell type by a hedgehog-like protein in zebrafish. Nature. 382(6590):452-455

Du, S.J. and Dienhart, M. (2001) Gli2 mediation of Hedgehog signals in slow muscle induction in zebrafish. Differentiation; research in biological diversity. 67(3):84-91

Eames, B.F., Yan, Y.L., Swartz, M.E., Levic, D.S., Knapik, E.W., Postlethwait, J.H., and Kimmel, C.B. (2011) Mutations in fam20b and xylt1 Reveal That Cartilage Matrix Controls Timing of Endochondral Ossification by Inhibiting Chondrocyte Maturation. PLoS Genetics. 7(8):e1002246

Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., and Talbot, W.S. (1999) A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome research. 9(4):334-347

Haga, Y., Dominique, V.J. 3rd, and Du, S.J. (2009) Analyzing notochord segmentation and intervertebral disc formation using the twhh:gfp transgenic zebrafish model. Transgenic Research. 18(5):669-683

Hawkins, T.A., Cavodeassi, F., Erdelyi, F., Szabo, G., and Lele, Z. (2008) The small molecule Mek1/2 inhibitor U0126 disrupts the chordamesoderm to notochord transition in zebrafish. BMC Developmental Biology. 8(1):42

Huycke, T.R., Eames, B.F., and Kimmel, C.B. (2012) Hedgehog-dependent proliferation drives modular growth during morphogenesis of a dermal bone. Development (Cambridge, England). 139(13):2371-2380

Ingham, P.W., and McMahon, A.P. (2001) Hedgehog signaling in animal development: paradigms and principles. Genes & Development. 15(23):3059-3087

Kague, E., Roy, P., Asselin, G., Hu, G., Stanley, A., Albertson, C., Simonet, J., Fisher, S. (2016) Osterix/sp7 limits cranial bone initiation sites and is required for formation of sutures. Developmental Biology. 413(2):160-72

Kassahn, K.S., Dang, V.T., Wilkins, S.J., Perkins, A.C., and Ragan, M.A. (2009) Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome research. 19(8):1404-1418

Lam, C.S., Sleptsova-Friedrich, I., Munro, A.D., and Korzh, V. (2003) SHH and FGF8 play distinct roles during development of noradrenergic neurons in the locus coeruleus of the zebrafish. Molecular and cellular neurosciences. 22(4):501-515

Lele, Z., Hartson, S.D., Martin, C.C., Whitesell, L., Matts, R.L., and Krone, P.H. (1999) Disruption of zebrafish somite development by pharmacologic inhibition of hsp90. Developmental Biology. 210(1):56-70

Lewis, K.E. and Eisen, J.S. (2003) From cells to circuits: development of the zebrafish spinal cord. Prog. Neurobiol.. 69(6):419-449

Lewis, K.E., Concordet, J.P., and Ingham, P.W. (1999) Characterisation of a second patched gene in the zebrafish Danio rerio and the differential response of patched genes to hedgehog signalling. Developmental Biology. 208:14-29

Lin, Y.Y., White, R.J., Torelli, S., Cirak, S., Muntoni, F., and Stemple, D.L. (2011) Zebrafish Fukutin family proteins link the unfolded protein response with dystroglycanopathies. Human molecular genetics. 20(9):1763-75

Pagnon-Minot, A., Malbouyres, M., Haftek-Terreau, Z., Kim, H.R., Sasaki, T., Thisse, C., Thisse, B., Ingham, P.W., Ruggiero, F., and Le Guellec, D. (2008) Collagen XV, a novel factor in zebrafish notochord differentiation and muscle development. Developmental Biology. 316(1):21-35

Parsons, M.J., Pollard, S.M., Saude, L., Feldman, B., Coutinho, P., Hirst, E.M., and Stemple, D.L. (2002) Zebrafish mutants identify an essential role for laminins in notochord formation. Development (Cambridge, England). 129(13):3137-3146

Phillips, R.B., Amores, A., Morasch, M.R., Wilson, C., and Postlethwait, J.H. (2006) Assignment of zebrafish genetic linkage groups to chromosomes. Cytogenetic and genome research. 114(2):155-162

Pollard, S.M., Parsons, M.J., Kamei, M., Kettleborough, R.N., Thomas, K.A., Pham, V.N., Bae, M.K., Scott, A., Weinstein, B.M., and Stemple, D.L. (2006) Essential and overlapping roles for laminin alpha chains in notochord and blood vessel formation. Developmental Biology. 289(1):64-76

Romero, M.M.G., McCathie, G., Jankun, P., Roehl, H.H. (2018) Damage-induced reactive oxygen species enable zebrafish tail regeneration by repositioning of Hedgehog expressing cells. Nature communications. 9:4010

Ryckebüsch, L., Hernandez, L., Wang, C., Phan, J., Yelon, D. (2016) Tmem2 regulates cell-matrix interactions that are essential for muscle fiber attachment. Development (Cambridge, England). 143(16):2965-72

Shestopalov, I.A., Pitt, C.L., and Chen, J.K. (2012) Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nature Chemical Biology. 8(3):270-276

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Sun, S., Gui, Y., Jiang, Q., and Song, H. (2011) Dihydrofolate reductase is required for the development of heart and outflow tract in zebrafish. Acta biochimica et biophysica Sinica. 43(12):957-969

Wang, N., Sun, Y.H., Liu, J., Wang, Y.P., and Zhu, Z.Y. (2007) Molecular characterization of common carp (Cyprinus carpio) Sonic Hedgehog and discovery of its maternal expression. Development genes and evolution. 217(4):299-305

Wen, W., Pillai-Kastoori, L., Wilson, S.G., Morris, A.C. (2015) Sox4 regulates choroid fissure closure by limiting hedgehog signaling during ocular morphogenesis. Developmental Biology. 399(1):139-53

Wolff, C., Roy, S., and Ingham, P.W. (2003) Multiple muscle cell identities induced by distinct levels and timing of hedgehog activity in the zebrafish embryo. Current biology : CB. 13(14):1169-1181

Wu, Y., Li, W., Yuan, M., Liu, X. (2019) The synthetic pyrethroid deltamethrin impairs zebrafish (Danio rerio) swim bladder development. The Science of the total environment. 701:134870

Zardoya, R., Abouheif, E., and Meyer, A. (1996) Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 93:13036-13041

Nie, C.H., Wan, S.M., Chen, Y.L., Huysseune, A., Wu, Y.M., Zhou, J.J., Hilsdorf, A.W.S., Wang, W.M., Witten, P.E., Lin, Q., Gao, Z.X. (2022) Single-cell transcriptomes and runx2b^-/- mutants reveal the genetic signatures of intermuscular bone formation in zebrafish. National science review. 9:nwac152nwac152

Anderson, R.A., Schwalbach, K.T., Mui, S.R., LeClair, E.E., Topczewska, J.M., Topczewski, J. (2020) Zebrafish models of skeletal dysplasia induced by cholesterol biosynthesis deficiency. Disease models & mechanisms. 13(6):

Romero, M.M.G., McCathie, G., Jankun, P., Roehl, H.H. (2018) Damage-induced reactive oxygen species enable zebrafish tail regeneration by repositioning of Hedgehog expressing cells. Nature communications. 9:4010

Sugimoto, K., Hui, S.P., Sheng, D.Z., Kikuchi, K. (2017) Dissection of zebrafish shha function using site-specific targeting with a Cre-dependent genetic switch.. eLIFE. 6

Kague, E., Roy, P., Asselin, G., Hu, G., Stanley, A., Albertson, C., Simonet, J., Fisher, S. (2016) Osterix/sp7 limits cranial bone initiation sites and is required for formation of sutures. Developmental Biology. 413(2):160-72

Ryckebüsch, L., Hernandez, L., Wang, C., Phan, J., Yelon, D. (2016) Tmem2 regulates cell-matrix interactions that are essential for muscle fiber attachment. Development (Cambridge, England). 143(16):2965-72

Wen, W., Pillai-Kastoori, L., Wilson, S.G., Morris, A.C. (2015) Sox4 regulates choroid fissure closure by limiting hedgehog signaling during ocular morphogenesis. Developmental Biology. 399(1):139-53

Chung, A.Y., Kim, S., Kim, E., Kim, D., Jeong, I., Cha, Y.R., Bae, Y.K., Park, S.W., Lee, J., and Park, H.C. (2013) Indian hedgehog B function is required for the specification of oligodendrocyte progenitor cells in the zebrafish CNS. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33(4):1728-1733

Williams, L.M., Timme-Laragy, A.R., Goldstone, J.V., McArthur, A.G., Stegeman, J.J., Smolowitz, R.M., and Hahn, M.E. (2013) Developmental expression of the Nfe2-related factor (Nrf) transcription factor family in the zebrafish, Danio rerio. PLoS One. 8(10):e79574

Shestopalov, I.A., Pitt, C.L., and Chen, J.K. (2012) Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nature Chemical Biology. 8(3):270-276

Eames, B.F., Yan, Y.L., Swartz, M.E., Levic, D.S., Knapik, E.W., Postlethwait, J.H., and Kimmel, C.B. (2011) Mutations in fam20b and xylt1 Reveal That Cartilage Matrix Controls Timing of Endochondral Ossification by Inhibiting Chondrocyte Maturation. PLoS Genetics. 7(8):e1002246

Sun, S., Gui, Y., Jiang, Q., and Song, H. (2011) Dihydrofolate reductase is required for the development of heart and outflow tract in zebrafish. Acta biochimica et biophysica Sinica. 43(12):957-969

Jackman, W.R., Yoo, J.J., and Stock, D.W. (2010) Hedgehog signaling is required at multiple stages of zebrafish tooth development. BMC Developmental Biology. 10:119

Yamamoto, M., Morita, R., Mizoguchi, T., Matsuo, H., Isoda, M., Ishitani, T., Chitnis, A.B., Matsumoto, K., Crump, J.G., Hozumi, K., Yonemura, S., Kawakami, K., and Itoh, M. (2010) Mib-Jag1-Notch signalling regulates patterning and structural roles of the notochord by controlling cell-fate decisions. Development (Cambridge, England). 137(15):2527-2537

Kassahn, K.S., Dang, V.T., Wilkins, S.J., Perkins, A.C., and Ragan, M.A. (2009) Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome research. 19(8):1404-1418

Hawkins, T.A., Cavodeassi, F., Erdelyi, F., Szabo, G., and Lele, Z. (2008) The small molecule Mek1/2 inhibitor U0126 disrupts the chordamesoderm to notochord transition in zebrafish. BMC Developmental Biology. 8(1):42

Park, S.W., Davison, J.M., Rhee, J., Hruban, R.H., Maitra, A., and Leach, S.D. (2008) Oncogenic KRAS Induces Progenitor Cell Expansion and Malignant Transformation in Zebrafish Exocrine Pancreas. Gastroenterology. 134(7):2080-2090

Wang, N., Sun, Y.H., Liu, J., Wang, Y.P., and Zhu, Z.Y. (2007) Molecular characterization of common carp (Cyprinus carpio) Sonic Hedgehog and discovery of its maternal expression. Development genes and evolution. 217(4):299-305

Phillips, R.B., Amores, A., Morasch, M.R., Wilson, C., and Postlethwait, J.H. (2006) Assignment of zebrafish genetic linkage groups to chromosomes. Cytogenetic and genome research. 114(2):155-162

Wang, Y., Qian, L., Dong, Y., Jiang, Q., Gui, Y., Zhong, T.P., and Song, H. (2006) Myocyte-specific enhancer factor 2A is essential for zebrafish posterior somite development. Mechanisms of Development. 123(10):783-791

Lewis, K.E., Bates, J., and Eisen, J.S. (2005) Regulation of iro3 expression in the zebrafish spinal cord. Developmental Dynamics : an official publication of the American Association of Anatomists. 232(1):140-148

Cheesman, S.E., Layden, M.J., Von Ohlen, T., Doe, C.Q., and Eisen, J.S. (2004) Zebrafish and fly Nkx6 proteins have similar CNS expression patterns and regulate motoneuron formation. Development (Cambridge, England). 131(21):5221-5232

Hammond, K.L., Loynes, H.E., Folarin, A.A., Smith, J., and Whitfield, T.T. (2003) Hedgehog signalling is required for correct anteroposterior patterning of the zebrafish otic vesicle. Development (Cambridge, England). 130(7):1403-1417

Lewis, K.E. and Eisen, J.S. (2003) From cells to circuits: development of the zebrafish spinal cord. Prog. Neurobiol.. 69(6):419-449

Parsons, M.J., Pollard, S.M., Saude, L., Feldman, B., Coutinho, P., Hirst, E.M., and Stemple, D.L. (2002) Zebrafish mutants identify an essential role for laminins in notochord formation. Development (Cambridge, England). 129(13):3137-3146

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Ingham, P.W., and McMahon, A.P. (2001) Hedgehog signaling in animal development: paradigms and principles. Genes & Development. 15(23):3059-3087

Roy, S., Qiao, T., Wolff, C., and Ingham, P.W. (2001) Hedgehog signaling pathway is essential for pancreas specification in the zebrafish embryo. Current biology : CB. 11(17):1358-1363

Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., and Talbot, W.S. (1999) A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome research. 9(4):334-347

Lewis, K.E., Concordet, J.P., and Ingham, P.W. (1999) Characterisation of a second patched gene in the zebrafish Danio rerio and the differential response of patched genes to hedgehog signalling. Developmental Biology. 208:14-29

Lauderdale, J.D., Pasquali, S.K., Fazel, R., van Eeden, F.J., Schauerte, H.E., Haffter, P., and Kuwada, J.Y. (1998) Regulation of netrin-1a expression by hedgehog proteins. Molecular and cellular neurosciences. 11:194-205

Schauerte, H.E., van Eeden, F.J.M., Fricke, C., Odenthal, J., Strähle, U., Haffter, P. (1998) Sonic hedgehog is not required for the induction of medial floor plate cells in the zebrafish. Development (Cambridge, England). 125:2983-2993

Currie, P.D. and Ingham, P.W. (1996) Induction of a specific muscle cell type by a hedgehog-like protein in zebrafish. Nature. 382(6590):452-455

Krauss, S., Concordet, J.P., and Ingham, P.W. (1993) A functionally conserved homolog of the Drosophila segment polarity gene hh is expressed in tissues with polarizing activity in zebrafish embryos. Cell. 75(7):1431-1444