Amsterdam, A., Nissen, R.M., Sun, Z., Swindell, E., Farrington, S., and Hopkins, N. (2004) Identification of 315 genes essential for early zebrafish development. Proceedings of the National Academy of Sciences of the United States of America. 101(35):12792-12797
|
|
Barresi, M.J., Burton, S., Dipietrantonio, K., Amsterdam, A., Hopkins, N., and Karlstrom, R.O. (2010) Essential genes for astroglial development and axon pathfinding during zebrafish embryogenesis. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(10):2603-2618
|
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
|
Chambers, B.E., Gerlach, G.F., Clark, E.G., Chen, K.H., Levesque, A.E., Leshchiner, I., Goessling, W., Wingert, R.A. (2019) Tfap2a is a novel gatekeeper of nephron differentiation during kidney development. Development (Cambridge, England). 146(13):
|
Chi, N.C., Shaw, R.M., Jungblut, B., Huisken, J., Ferrer, T., Arnaout, R., Scott, I., Beis, D., Xiao, T., Baier, H., Jan, L.Y., Tristani-Firouzi, M., and Stainier, D.Y. (2008) Genetic and Physiologic Dissection of the Vertebrate Cardiac Conduction System. PLoS Biology. 6(5):e109
|
|
|
|
|
|
|
Drummond, D.L., Cheng, C.S., Selland, L.G., Hocking, J.C., Prichard, L.B., and Waskiewicz, A.J. (2013) The role of Zic transcription factors in regulating hindbrain retinoic acid signaling. BMC Developmental Biology. 13:31
|
Dutton, K., Abbas, L., Spencer, J., Brannon, C., Mowbray, C., Nikaido, M., Kelsh, R.N., and Whitfield, T.T. (2009) A zebrafish model for Waardenburg syndrome type IV reveals diverse roles for Sox10 in the otic vesicle. Disease models & mechanisms. 2(1-2):68-83
|
Fodor, E., Zsigmond, A., Horváth, B., Molnár, J., Nagy, I., Tóth, G., Wilson, S.W., and Varga, M. (2013) Full transcriptome analysis of early dorsoventral patterning in zebrafish. PLoS One. 8(7):e70053
|
|
|
Golling, G., Amsterdam, A., Sun, Z., Antonelli, M., Maldonado, E., Chen, W., Burgess, S., Haldi, M., Artzt, K., Farrington, S., Lin, S.Y., Nissen, R.M., and Hopkins, N. (2002) Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nature Genetics. 31(2):135-140
|
Gong, H.Y., Lin, C.J., Chen, M.H., Hu, M.C., Lin, G.H., Zhou, Y., Zon, L.I., and Wu, J.L. (2004) Two distinct teleost hepatocyte nuclear factor 1 genes, hnf1alpha/tcf1 and hnf1beta/tcf2, abundantly expressed in liver, pancreas, gut and kidney of zebrafish. Gene. 338(1):35-46
|
|
Gongal, P.A., March, L.D., Holly, V.L., Pillay, L.M., Berry-Wynne, K.M., Kagechika, H., and Waskiewicz, A.J. (2011) Hmx4 regulates Sonic hedgehog signaling through control of retinoic acid synthesis during forebrain patterning. Developmental Biology. 355(1):55-64
|
|
Her, G.M., Cheng, C.H., Hon, J.R., Sundaram, G.S., and Wu, J.L. (2006) Imbalance in liver homeostasis leading to hyperplasia by overexpressing either one of the Bcl-2-related genes, zfBLP1 and zfMcl-1a. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(2):515-523
|
Hernandez, R.E., Putzke, A.P., Myers, J.P., Margaretha, L., and Moens, C.B. (2007) Cyp26 enzymes generate the retinoic acid response pattern necessary for hindbrain development. Development (Cambridge, England). 134(1):177-187
|
|
Hong, S.K., Levin, C.S., Brown, J.L., Wan, H., Sherman, B.T., Huang, D.W., Lempicki, R.A., and Feldman, B. (2010) Pre-gastrula expression of zebrafish extraembryonic genes. BMC Developmental Biology. 10:42
|
|
Kim, H.J., Sumanas, S., Palencia-Desai, S., Dong, Y., Chen, J.N., and Lin, S. (2006) Genetic analysis of early endocrine pancreas formation in zebrafish. Molecular endocrinology (Baltimore, Md.). 20(1):194-203
|
Lancman, J.J., Zvenigorodsky, N., Gates, K.P., Zhang, D., Solomon, K., Humphrey, R.K., Kuo, T., Setiawan, L., Verkade, H., Chi, Y.I., Jhala, U.S., Wright, C.V., Stainier, D.Y., and Dong, P.D. (2013) Specification of hepatopancreas progenitors in zebrafish by hnf1ba and wnt2bb. Development (Cambridge, England). 140(13):2669-2679
|
|
Lecaudey, V., Ulloa, E., Anselme, I., Stedman, A., Schneider-Maunoury, S., and Pujades C. (2007) Role of the hindbrain in patterning the otic vesicle: A study of the zebrafish vhnf1 mutant. Developmental Biology. 303(1):134-143
|
|
Lokmane, L., Haumaitre, C., Garcia-Villalba, P., Anselme, I., Schneider-Maunoury, S., and Cereghini, S. (2008) Crucial role of vHNF1 in vertebrate hepatic specification. Development (Cambridge, England). 135(16):2777-2786
|
Matthews, R.P., Eauclaire, S.F., Mugnier, M., Lorent, K., Cui, S., Ross, M.M., Zhang, Z., Russo, P., and Pack, M. (2011) DNA hypomethylation causes bile duct defects in zebrafish and is a distinguishing feature of infantile biliary atresia. Hepatology (Baltimore, Md.). 53(3):905-914
|
|
|
|
|
|
|
|
|
O'Hare, E.A., Yerges-Armstrong, L.M., Perry, J.A., Shuldiner, A.R., Zaghloul, N.A. (2016) Assignment of Functional Relevance to Genes at Type 2 Diabetes-Associated Loci Through Investigation of β-Cell Mass Deficits. Molecular endocrinology (Baltimore, Md.). 30(4):429-45
|
|
|
Rai, K., Nadauld, L.D., Chidester, S., Manos, E.J., James, S.R., Karpf, A.R., Cairns, B.R., and Jones, D.A. (2006) Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Molecular and cellular biology. 26(19):7077-7085
|
|
Sander, V., Patke, S., Sahu, S., Teoh, C.L., Peng, Z., Chang, Y.T., Davidson, A.J. (2015) The small molecule probe PT-Yellow labels the renal proximal tubules in zebrafish. Chemical communications (Cambridge, England). 51(2):395-8
|
Sander, V., Salleh, L., Naylor, R.W., Schierding, W., Sontam, D.M., O'Sullivan, J.M., Davidson, A.J. (2019) Transcriptional profiling of the zebrafish proximal tubule. American journal of physiology. Renal physiology. 317(2):F478-F488
|
|
|
Song, J., Kim, H.J., Gong, Z., Liu, N.A., and Lin, S. (2007) Vhnf1 acts downstream of Bmp, Fgf, and RA signals to regulate endocrine beta cell development in zebrafish. Developmental Biology. 303(2):561-575
|
Stedman, A., Lecaudey, V., Havis, E., Anselme, I., Wassef, M., Gilardi-Hebenstreit, P., and Schneider-Maunoury, S. (2009) A functional interaction between Irx and Meis patterns the anterior hindbrain and activates krox20 expression in rhombomere 3. Developmental Biology. 327(2):566-577
|
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
|
Sukardi, H., Zhang, X., Lui, E.Y., Ung, C.Y., Mathavan, S., Gong, Z., and Lam, S.H. (2012) Liver X receptor agonist T0901317 induced liver perturbation in zebrafish: Histological, gene set enrichment and expression analyses. Biochimica et biophysica acta. General subjects. 1820(1):33-43
|
|
Sun, Z., Amsterdam, A., Pazour, G.J., Cole, D.G., Miller, M.S. and Hopkins, N. (2004) A Genetic Screen in Zebrafish Identifies Cilia Genes as a Principal Cause of Cystic Kidney Development. Development (Cambridge, England). 131(16):4085-4093
|
Tang, V., Cofer, Z.C., Cui, S., Sapp, V., Loomes, K.M., Matthews, R.P. (2016) Loss of a Candidate Biliary Atresia Susceptibility Gene, add3a, Causes Biliary Developmental Defects in Zebrafish. Journal of pediatric gastroenterology and nutrition. 63(5):524-530
|
|
|
Varshney, G.K., Lu, J., Gildea, D., Huang, H., Pei, W., Yang, Z., Huang, S.C., Schoenfeld, D.S., Pho, N., Casero, D., Hirase, T., Mosbrook-Davis, D.M., Zhang, S., Jao, L.E., Zhang, B., Woods, I.G., Zimmerman, S., Schier, A.F., Wolfsberg, T., Pellegrini, M., Burgess, S.M., and Lin, S. (2013) A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 23(4):727-735
|
Wang, D., Jao, L.E., Zheng, N., Dolan, K., Ivey, J., Zonies, S., Wu, X., Wu, K., Yang, H., Meng, Q., Zhu, Z., Zhang, B., Lin, S., and Burgess, S.M. (2007) Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proceedings of the National Academy of Sciences of the United States of America. 104(30):12428-12433
|
|
|
|
|
|
|
Xu, L., Feng, Z., Sinha, D., Ducos, B., Ebenstein, Y., Tadmor, A.D., Gauron, C., Le Saux, T., Lin, S., Weiss, S., Vriz, S., Jullien, L., and Bensimon, D. (2012) Spatiotemporal manipulation of retinoic acid activity in zebrafish hindbrain development via photo-isomerization. Development (Cambridge, England). 139(18):3355-3362
|
Zhang, W., Scerbo, P., Delagrange, M., Candat, V., Mayr, V., Vriz, S., Distel, M., Ducos, B., Bensimon, D. (2022) Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis. Communications biology. 5:113
|
Zhao, C., Lancman, J.J., Yang, Y., Gates, K.P., Cao, D., Barske, L., Matalonga, J., Pan, X., He, J., Graves, A., Huisken, J., Chen, C., Dong, P.D.S. (2021) Intrahepatic cholangiocyte regeneration from an Fgf-dependent extrahepatic progenitor niche in a zebrafish model of Alagille Syndrome. Hepatology (Baltimore, Md.). 75(3):567-583
|