Amaral, I.P., and Johnston, I.A. (2012) Circadian expression of clock and putative clock-controlled genes in skeletal muscle of the zebrafish. American journal of physiology. Regulatory, integrative and comparative physiology. 302(1):R193-206

Ben-Moshe Livne, Z., Alon, S., Vallone, D., Bayleyen, Y., Tovin, A., Shainer, I., Nisembaum, L.G., Aviram, I., Smadja-Storz, S., Fuentes, M., Falcón, J., Eisenberg, E., Klein, D.C., Burgess, H.A., Foulkes, N.S., Gothilf, Y. (2016) Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior. PLoS Genetics. 12:e1006445

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

Cavallari, N., Frigato, E., Vallone, D., Fröhlich, N., Lopez-Olmeda, J.F., Foà, A., Berti, R., Sánchez-Vázquez, F.J., Bertolucci, C., and Foulkes, N.S. (2011) A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception. PLoS Biology. 9(9):e1001142

Cruz, B.P., Brongar, L.F., Popiolek, P., Gonçalvez, B.S.B., Figueiredo, M.A., Amaral, I.P.G., Da Rosa, V.S., Nery, L.E.M., Marins, L.F. (2017) Clock genes expression and locomotor activity are altered along the light-dark cycle in transgenic zebrafish overexpressing growth hormone. Transgenic Research. 26(6):739-752

Delaunay, F., Thisse, C., Marchand, O., Laudet, V., and Thisse, B. (2000) An inherited functional circadian clock in zebrafish embryos. Science (New York, N.Y.). 289(5477):297-300

Du, L.Y., Darroch, H., Keerthisinghe, P., Ashimbayeva, E., Astin, J.W., Crosier, K.E., Crosier, P.S., Warman, G., Cheeseman, J., Hall, C.J. (2017) The innate immune cell response to bacterial infection in larval zebrafish is light-regulated. Scientific Reports. 7:12657

Garcia-Concejo, A., Larhammar, D. (2021) Protein kinase C family evolution in jawed vertebrates. Developmental Biology. 479:77-90

Hua, Y., Wang, C., Huang, J., Wang, K. (2017) A simple and efficient method for CRISPR/Cas9-induced mutant screening. Journal of genetics and genomics = Yi chuan xue bao. 44(4):207-213

Huang, G., Zhang, F., Ye, Q., Wang, H. (2016) The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbα and indirectly via Cebpb/(C/ebpβ) in zebrafish. Autophagy. 12(8):1292-309

Idda, M.L., Kage, E., Lopez-Olmedam, J.F., Mracek, P., Foulkes, N.S., and Vallone, D. (2012) Circadian timing of injury-induced cell proliferation in zebrafish. PLoS One. 7(3):e34203

Li, P., Chaurasia, S.S., Gao, Y., Carr, A.L., Iuvone, P.M., and Li, L. (2008) CLOCK is required for maintaining the circadian rhythms of opsin mRNA expression in photoreceptor cells. The Journal of biological chemistry. 283(46):31673-31678

Liang, Y.Q., Huang, G.Y., Zhao, J.L., Shi, W.J., Hu, L.X., Tian, F., Liu, S.S., Jiang, Y.X., Ying, G.G. (2017) Transcriptional alterations induced by binary mixtures of ethinylestradiol and norgestrel during the early development of zebrafish (Danio rerio). Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 195:60-67

Liu, T., He, W., Zhong, Z., Lu, C., Wu, L., Wang, Z., Smith, W.K., Shi, Q., Long, Q., Wang, H. (2024) The circadian clock orchestrates spermatogonial differentiation and fertilization by regulating retinoic acid signaling in vertebrates. National science review. 12:nwae456nwae456

Long, Y., Song, G., Yan, J., He, X., Li, Q., and Cui, Z. (2013) Transcriptomic characterization of cold acclimation in larval zebrafish. BMC Genomics. 14(1):612

Moore, H.A., and Whitmore, D. (2014) Circadian rhythmicity and light sensitivity of the zebrafish brain. PLoS One. 9(1):e86176

Mosser, E.A., Chiu, C.N., Tamai, T.K., Hirota, T., Li, S., Hui, M., Wang, A., Singh, C., Giovanni, A., Kay, S.A., Prober, D.A. (2019) Identification of pathways that regulate circadian rhythms using a larval zebrafish small molecule screen. Scientific Reports. 9:12405

Pando, M.P., Pinchak, A.B., Cermakian, N., and Sassone-Corsi, P. (2001) A cell-based system that recapitulates the dynamic light-dependent regulation of the vertebrate clock. Proceedings of the National Academy of Sciences of the United States of America. 98(18):10178-10183

Pierce, L.X., Noche, R.R., Ponomareva, O., Chang, C., and Liang, J.O. (2008) Novel functions for Period 3 and Exo-rhodopsin in rhythmic transcription and melatonin biosynthesis within the zebrafish pineal organ. Brain research. 1223:11-24

Reichert, S., Pavón Arocas, O., Rihel, J. (2019) The Neuropeptide Galanin Is Required for Homeostatic Rebound Sleep following Increased Neuronal Activity. Neuron. 104(2):370-384.e5

Safarian, N., Houshangi-Tabrizi, S., Zoidl, C., Zoidl, G.R. (2021) Panx1b Modulates the Luminance Response and Direction of Locomotion in the Zebrafish. International Journal of Molecular Sciences. 22(21):

Sloan, J.L., Achilly, N.P., Arnold, M.L., Catlett, J.L., Blake, T., Bishop, K., Jones, M., Harper, U., English, M.A., Anderson, S., Trivedi, N.S., Elkahloun, A., Hoffmann, V., Brooks, B.P., Sood, R., Venditti, C.P. (2020) The vitamin B12 processing enzyme, mmachc, is essential for zebrafish survival, growth and retinal morphology. Human molecular genetics. 29(13):2109-2123

Tamai, T.K., Young, L.C., and Whitmore, D. (2007) Light signaling to the zebrafish circadian clock by Cryptochrome 1a. Proceedings of the National Academy of Sciences of the United States of America. 104(37):14712-14717

Tovin, A., Alon, S., Ben-Moshe, Z., Mracek, P., Vatine, G., Foulkes, N.S., Jacob-Hirsch, J., Rechavi, G., Toyama, R., Coon, S.L., Klein, D.C., Eisenberg, E., and Gothilf, Y. (2012) Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork. PLoS Genetics. 8(12):e1003116

Wang, M., Zhong, Z., Zhong, Y., Zhang, W., Wang, H. (2015) The Zebrafish Period2 Protein Positively Regulates the Circadian Clock through Mediation of Retinoic Acid Receptor (RAR)-related Orphan Receptor α (Rorα). The Journal of biological chemistry. 290(7):4367-4382

Wirbisky, S.E., Weber, G.J., Sepúlveda, M.S., Xiao, C., Cannon, J.R., Freeman, J.L. (2015) Developmental origins of neurotransmitter and transcriptome alterations in adult female zebrafish exposed to atrazine during embryogenesis. Toxicology. 333:156-67

Yang, Y., Dong, F., Liu, X., Xu, J., Wu, X., Zheng, Y. (2019) Flutolanil affects circadian rhythm in zebrafish (Danio rerio) by disrupting the positive regulators. Chemosphere. 228:649-655

Zhang, H.Y., Li, K.Y., Wang, Y.L., Wei, C.J., Gao, Y.X., Ren-Zhou, ., Zhong, Y.B., Yin, Z.J., Ren, D.L. (2025) ROS regulates circadian rhythms by modulating Ezh2 interactions with clock proteins. Redox Biology. 81:103526103526

Zhao, Y., Fent, K. (2016) Progestins alter photo-transduction cascade and circadian rhythm network in eyes of zebrafish (Danio rerio). Scientific Reports. 6:21559

Zhao, Y., Zhang, K., Fent, K. (2018) Regulation of zebrafish (Danio rerio) locomotor behavior and circadian rhythm network by environmental steroid hormones. Environmental pollution (Barking, Essex : 1987). 232:422-429

Zhang, H.Y., Li, K.Y., Wang, Y.L., Wei, C.J., Gao, Y.X., Ren-Zhou, ., Zhong, Y.B., Yin, Z.J., Ren, D.L. (2025) ROS regulates circadian rhythms by modulating Ezh2 interactions with clock proteins. Redox Biology. 81:103526103526

Men, S., Xu, J., Yang, Z., Yan, Z. (2024) DEHP-Induced Glioblastoma in Zebrafish Is Associated with Circadian Dysregulation of PER3. Toxics. 12(12):

Basnakova, A., Cheng, R.K., Chia, J.S.M., D'Agostino, G., Suryadi, ., Tan, G.J.H., Langley, S.R., Jesuthasan, S. (2021) The habenula clock influences response to a stressor. Neurobiology of stress. 15:100403

Garcia-Concejo, A., Larhammar, D. (2021) Protein kinase C family evolution in jawed vertebrates. Developmental Biology. 479:77-90

Zheng, X., Zhang, K., Zhao, Y., Fent, K. (2021) Environmental chemicals affect circadian rhythms: An underexplored effect influencing health and fitness in animals and humans. Environment International. 149:106159

Hirayama, J., Alifu, Y., Hamabe, R., Yamaguchi, S., Tomita, J., Maruyama, Y., Asaoka, Y., Nakahama, K.I., Tamaru, T., Takamatsu, K., Takamatsu, N., Hattori, A., Nishina, S., Azuma, N., Kawahara, A., Kume, K., Nishina, H. (2019) The clock components Period2, Cryptochrome1a, and Cryptochrome2a function in establishing light-dependent behavioral rhythms and/or total activity levels in zebrafish. Scientific Reports. 9:196

Mosser, E.A., Chiu, C.N., Tamai, T.K., Hirota, T., Li, S., Hui, M., Wang, A., Singh, C., Giovanni, A., Kay, S.A., Prober, D.A. (2019) Identification of pathways that regulate circadian rhythms using a larval zebrafish small molecule screen. Scientific Reports. 9:12405

Yang, Y., Dong, F., Liu, X., Xu, J., Wu, X., Zheng, Y. (2019) Flutolanil affects circadian rhythm in zebrafish (Danio rerio) by disrupting the positive regulators. Chemosphere. 228:649-655

Zhang, H., Chen, Z.F., Qi, Z., Yan, S.C., Wei, W.W., Liu, G., Cai, Z. (2019) ANALYSIS OF TRANSCRIPTIONAL RESPONSE IN ZEBRAFISH ELEUTHEROEMBRYOS EXPOSED TO CLIMBAZOLE: SIGNALING PATHWAYS AND POTENTIAL BIOMARKERS. Environmental toxicology and chemistry. 38(4):794-805

Ren, D.L., Zhang, J.L., Yang, L.Q., Wang, X.B., Wang, Z.Y., Huang, D.F., Tian, C., Hu, B. (2018) Circadian genes period1b and period2 differentially regulate inflammatory responses in zebrafish. Fish & shellfish immunology. 77:139-146

Chen, S., Reichert, S., Singh, C., Oikonomou, G., Rihel, J., Prober, D.A. (2017) Light-Dependent Regulation of Sleep and Wake States by Prokineticin 2 in Zebrafish. Neuron. 95(1):153-168.e6

Du, L.Y., Darroch, H., Keerthisinghe, P., Ashimbayeva, E., Astin, J.W., Crosier, K.E., Crosier, P.S., Warman, G., Cheeseman, J., Hall, C.J. (2017) The innate immune cell response to bacterial infection in larval zebrafish is light-regulated. Scientific Reports. 7:12657

Liang, Y.Q., Huang, G.Y., Zhao, J.L., Shi, W.J., Hu, L.X., Tian, F., Liu, S.S., Jiang, Y.X., Ying, G.G. (2017) Transcriptional alterations induced by binary mixtures of ethinylestradiol and norgestrel during the early development of zebrafish (Danio rerio). Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 195:60-67

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

Zhao, Y., Fent, K. (2016) Progestins alter photo-transduction cascade and circadian rhythm network in eyes of zebrafish (Danio rerio). Scientific Reports. 6:21559

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

Purushothaman, S., Saxena, S., Meghah, V., Meena Lakshmi, M.G., Singh, S.K., Brahmendra Swamy, C.V., Idris, M.M. (2015) Proteomic and gene expression analysis of zebrafish brain undergoing continuous light/dark stress. Journal of sleep research. 24(4):458-65

Wang, M., Zhong, Z., Zhong, Y., Zhang, W., Wang, H. (2015) The Zebrafish Period2 Protein Positively Regulates the Circadian Clock through Mediation of Retinoic Acid Receptor (RAR)-related Orphan Receptor α (Rorα). The Journal of biological chemistry. 290(7):4367-4382

Zhao, Y., Castiglioni, S., Fent, K. (2015) Environmental progestins progesterone and drospirenone alter the circadian rhythm network in zebrafish (Danio rerio). Environmental science & technology. 49(16):10155-64

Li, Y., Li, G., Wang, H., Du, J., and Yan, J. (2013) Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish. PLoS Computational Biology. 9(2):e1002940

Weger, M., Weger, B.D., Diotel, N., Rastegar, S., Hirota, T., Kay, S.A., Strähle, U., and Dickmeis, T. (2013) Real-time in vivo monitoring of circadian E-box enhancer activity: A robust and sensitive zebrafish reporter line for developmental, chemical and neural biology of the circadian clock. Developmental Biology. 380(2):259-73

Idda, M.L., Kage, E., Lopez-Olmedam, J.F., Mracek, P., Foulkes, N.S., and Vallone, D. (2012) Circadian timing of injury-induced cell proliferation in zebrafish. PLoS One. 7(3):e34203

Tovin, A., Alon, S., Ben-Moshe, Z., Mracek, P., Vatine, G., Foulkes, N.S., Jacob-Hirsch, J., Rechavi, G., Toyama, R., Coon, S.L., Klein, D.C., Eisenberg, E., and Gothilf, Y. (2012) Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork. PLoS Genetics. 8(12):e1003116

Li, P., Chaurasia, S.S., Gao, Y., Carr, A.L., Iuvone, P.M., and Li, L. (2008) CLOCK is required for maintaining the circadian rhythms of opsin mRNA expression in photoreceptor cells. The Journal of biological chemistry. 283(46):31673-31678

Wang, H. (2008) Comparative Analysis of Period Genes in Teleost Fish Genomes. Journal of molecular evolution. 67(1):29-40

Tamai, T.K., Young, L.C., and Whitmore, D. (2007) Light signaling to the zebrafish circadian clock by Cryptochrome 1a. Proceedings of the National Academy of Sciences of the United States of America. 104(37):14712-14717

Dekens, M.P.S., Santoriello, C., Vallone, D., Grassi, G., Whitmore, D., and Foulkes, N.S. (2003) Light regulates the cell cycle in zebrafish. Current biology : CB. 13(23):2051-2057

Pelegri, F. (2003) Maternal factors in zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 228(3):535-554

Pando, M.P. and Sassone-Corsi, P. (2002) Unraveling the mechanisms of the vertebrate circadian clock: zebrafish may light the way. BioEssays : news and reviews in molecular, cellular and developmental biology. 24(5):419-426

Pando, M.P., Pinchak, A.B., Cermakian, N., and Sassone-Corsi, P. (2001) A cell-based system that recapitulates the dynamic light-dependent regulation of the vertebrate clock. Proceedings of the National Academy of Sciences of the United States of America. 98(18):10178-10183