Ahn, D., and Ho, R.K. (2008) Tri-phasic expression of posterior Hox genes during development of pectoral fins in zebrafish: Implications for the evolution of vertebrate paired appendages. Developmental Biology. 322(1):220-233

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

Chestnut, B., Casie Chetty, S., Koenig, A.L., Sumanas, S. (2020) Single-cell transcriptomic analysis identifies the conversion of zebrafish Etv2-deficient vascular progenitors into skeletal muscle. Nature communications. 11:2796

Chiu, C.-H., Nonaka, D., Xue, L., Amemiya, C.T., and Wagner, G.P. (2000) Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition. Molecular phylogenetics and evolution. 17(2):305-316

Chiu, C.H., Dewar, K., Wagner, G.P., Takahashi, K., Ruddle, F., Ledje, C., Bartsch, P., Scemama, J.L., Stellwag, E., Fried, C., Prohaska, S.J., Stadler, P.F., and Amemiya, C.T. (2004) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome research. 14(1):11-17

Crow, K.D., Smith, C.D., Cheng, J.F., Wagner, G.P., and Amemiya, C.T. (2012) An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference. Genome biology and evolution. 4(9):937-953

Elkon, R., Milon, B., Morrison, L., Shah, M., Vijayakumar, S., Racherla, M., Leitch, C.C., Silipino, L., Hadi, S., Weiss-Gayet, M., Barras, E., Schmid, C.D., Ait-Lounis, A., Barnes, A., Song, Y., Eisenman, D.J., Eliyahu, E., Frolenkov, G.I., Strome, S.E., Durand, B., Zaghloul, N.A., Jones, S.M., Reith, W., Hertzano, R. (2015) RFX transcription factors are essential for hearing in mice. Nature communications. 6:8549

Géraudie, J., and Borday-Birraux, V. (2003) Posterior hoxa genes expression during zebrafish bony fin ray development and regeneration suggests their involvement in scleroblast differentiation. Development genes and evolution. 213(4):182-186

Ishizaka, M., Maeno, A., Nakazawa, H., Fujii, R., Oikawa, S., Tani, T., Kanno, H., Koita, R., Kawamura, A. (2024) The functional roles of zebrafish HoxA- and HoxD-related clusters in the pectoral fin development. Scientific Reports. 14:2360223602

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

Kurosawa, G., Takamatsu, N., Takahashi, M., Sumitomo, M., Sanaka, E., Yamada, K., Nishii, K., Matsuda, M., Asakawa, S., Ishiguro, H., Miura, K., Kurosawa, Y., Shimizu, N., Kohara, Y., and Hori, H. (2006) Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene. 370:75-82

Langellotto, F., Fiorentino, M., De Felice, E., Caputi, L., Nittoli, V., Joss, J.M.P., Sordino, P. (2018) Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages.. EvoDevo. 9:11

Lindeman, L.C., Andersen, I.S., Reiner, A.H., Li, N., Aanes, H., Ostrup, O., Winata, C., Mathavan, S., Muller, F., Aleström, P., and Collas, P. (2011) Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Developmental Cell. 21(6):993-1004

Mehta, T.K., Ravi, V., Yamasaki, S., Lee, A.P., Lian, M.M., Tay, B.H., Tohari, S., Yanai, S., Tay, A., Brenner, S., and Venkatesh, B. (2013) Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proceedings of the National Academy of Sciences of the United States of America. 110(40):16044-16049

Neumann, C.J., Grandel, H., Gaffield, W., Schulte-Merker, S., Nüsslein-Volhard, C. (1999) Transient establishment of anteroposterior polarity in the zebrafish pectoral fin bud in the absence of sonic hedgehog activity. Development (Cambridge, England). 126(21):4817-4826

Prohaska, S.J., and Stadler, P.F. (2004) The duplication of the Hox gene clusters in teleost fishes. Theory in biosciences = Theorie in den Biowissenschaften. 123(1):89-110

Santini, S., and Bernardi, G. (2005) Organization and base composition of tilapia Hox genes: implications for the evolution of Hox clusters in fish. Gene. 346:51-61

Schiller, V., Wichmann, A., Kriehuber, R., Muth-Köhne, E., Giesy, J.P., Hecker, M., and Fenske, M. (2013) Studying the effects of genistein on gene expression of fish embryos as an alternative testing approach for endocrine disruption. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 157(1):41-53

Smeeton, J., Natarajan, N., Naveen Kumar, A., Miyashita, T., Baddam, P., Fabian, P., Graf, D., Crump, J.G. (2021) Zebrafish Model for Spondylo-Megaepiphyseal-Metaphyseal Dysplasia Reveals Post-Embryonic Roles of Nkx3.2 in the Skeleton. Development (Cambridge, England). 148(2):

Sordino, P., van der Hoeven, F., and Duboule, D. (1995) Hox gene expression in teleost fins and the origin of vertebrate digits. Nature. 375:678-681

Sundaramoorthi, H., Fallatah, W., Mary, J., Jagadeeswaran, P. (2023) Discovery of seven hox genes in zebrafish thrombopoiesis. Blood cells, molecules & diseases. 104:102796102796

Wagner, G.P., Takahashi, K., Lynch, V., Prohaska, S.J., Fried, C., Stadler, P.F., and Amemiya, C. (2005) Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences. Journal of molecular evolution. 60(5):665-676

Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K., Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., and Talbot, W.S. (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome research. 15(9):1307-1314

Zhang, H., Wang, X., Lv, K., Gao, S., Wang, G., Fan, C., Zhang, X.A., Yan, J. (2015) Time Point-based Integrative Analyses of Deep-transcriptome Identify Four Signal Pathways in Blastemal Regeneration of Zebrafish Lower Jaw. Stem cells (Dayton, Ohio). 33(3):806-18

Ishizaka, M., Maeno, A., Nakazawa, H., Fujii, R., Oikawa, S., Tani, T., Kanno, H., Koita, R., Kawamura, A. (2024) The functional roles of zebrafish HoxA- and HoxD-related clusters in the pectoral fin development. Scientific Reports. 14:2360223602

Hawkins, M.B., Henke, K., Harris, M.P. (2021) Latent developmental potential to form limb-like skeletal structures in zebrafish. Cell. 184(4):899-911.e13

Yamada, K., Maeno, A., Araki, S., Kikuchi, M., Suzuki, M., Ishizaka, M., Satoh, K., Akama, K., Kawabe, Y., Suzuki, K., Kobayashi, D., Hamano, N., Kawamura, A. (2021) An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters. Development (Cambridge, England). 148(11):

Rougeot, J., Chrispijn, N.D., Aben, M., Elurbe, D.M., Andralojc, K.M., Murphy, P.J., Jansen, P.W.T.C., Vermeulen, M., Cairns, B.R., Kamminga, L.M. (2019) Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan. Development (Cambridge, England). 146(19):

Langellotto, F., Fiorentino, M., De Felice, E., Caputi, L., Nittoli, V., Joss, J.M.P., Sordino, P. (2018) Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages.. EvoDevo. 9:11

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

Kherdjemil, Y., Lalonde, R.L., Sheth, R., Dumouchel, A., de Martino, G., Pineault, K.M., Wellik, D.M., Stadler, H.S., Akimenko, M.A., Kmita, M. (2016) Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state. Nature. 539(7627):89-92

Zhang, H., Wang, X., Lv, K., Gao, S., Wang, G., Fan, C., Zhang, X.A., Yan, J. (2015) Time Point-based Integrative Analyses of Deep-transcriptome Identify Four Signal Pathways in Blastemal Regeneration of Zebrafish Lower Jaw. Stem cells (Dayton, Ohio). 33(3):806-18

Pascoal, S., Esteves de Lima, J., Leslie, J.D., Hughes, S.M., and Saúde, L. (2013) Notch signalling is required for the formation of structurally stable muscle fibres in zebrafish. PLoS One. 8(6):e68021

Schiller, V., Wichmann, A., Kriehuber, R., Schäfers, C., Fischer, R., and Fenske, M. (2013) Transcriptome alterations in zebrafish embryos after exposure to environmental estrogens and anti-androgens can reveal endocrine disruption. Reproductive toxicology (Elmsford, N.Y.). 42:210-23

Wang, X., He, H., Tang, W., Zhang, X.A., Hua, X., and Yan, J. (2012) Two origins of blastemal progenitors define blastemal regeneration of zebrafish lower jaw. PLoS One. 7(9):e45380

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

Zou, S.M., Jiang, X.Y., He, Z.Z., Yuan, J., Yuan, X.N., and Li, S.F. (2007) Hox gene clusters in blunt snout bream, Megalobrama amblycephala and comparison with those of zebrafish, fugu and medaka genomes. Gene. 400(1-2):60-70

Kurosawa, G., Takamatsu, N., Takahashi, M., Sumitomo, M., Sanaka, E., Yamada, K., Nishii, K., Matsuda, M., Asakawa, S., Ishiguro, H., Miura, K., Kurosawa, Y., Shimizu, N., Kohara, Y., and Hori, H. (2006) Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene. 370:75-82

Metscher, B.D., Takahashi, K., Crow, K., Amemiya, C., Nonaka, D.F., and Wagner, G.P. (2005) Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray-finned fish, Polyodon spathula: implications for the origin of tetrapod limbs. Evolution & development. 7(3):186-195

Wagner, G.P., Takahashi, K., Lynch, V., Prohaska, S.J., Fried, C., Stadler, P.F., and Amemiya, C. (2005) Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences. Journal of molecular evolution. 60(5):665-676

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

Prohaska, S.J., and Stadler, P.F. (2004) The duplication of the Hox gene clusters in teleost fishes. Theory in biosciences = Theorie in den Biowissenschaften. 123(1):89-110

Lavoie, H., Debeane, F., Trinh, Q.D., Turcotte, J.F., Corbeil-Girard, L.P., Dicaire, M.J., Saint-Denis, A., Page, M., Rouleau, G.A., and Brais, B. (2003) Polymorphism, shared functions and convergent evolution of genes with sequences coding for polyalanine domains. Human molecular genetics. 12(22):2967-2979

Chiu, C.-H., Amemiya, C., Dewar, K., Kim, C.-B., Ruddle, F.H., and Wagner, G.P. (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proceedings of the National Academy of Sciences of the United States of America. 99(8):5492-5497

Chiu, C.-H., Nonaka, D., Xue, L., Amemiya, C.T., and Wagner, G.P. (2000) Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition. Molecular phylogenetics and evolution. 17(2):305-316

Grandel, H., Draper, B.W., and Schulte-Merker, S. (2000) dackel acts in the ectoderm of the zebrafish pectoral fin bud to maintain AER signaling. Development (Cambridge, England). 127(19):4169-4178

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

van der, Hoeven, F., Sordino, P., Fraudeau, N., Izpisúa Belmonte, J.C., and Duboule, D. (1996) Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex. Mechanisms of Development. 54(1):9-21