Akle, V., Stankiewicz, A.J., Kharchenko, V., Yu, L., Kharchenko, P.V., Zhdanova, I.V. (2017) Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37(7):1900-1909

Appelbaum, L. Anzulovich, A., Baler, R., and Gothilf, Y. (2005) Homeobox-clock protein interaction in zebrafish: A shared mechanism for pineal-specific and circadian gene expression. The Journal of biological chemistry. 280(12):11544-11551

Bian, S.S., Zheng, X.L., Sun, H.Q., Chen, J.H., Lu, Y.L., Liu, Y.Q., Tao, D.C., Ma, Y.X. (2017) Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signalings in the zebrafish embryo. The Journal of biological chemistry. 292(34):14165-14175

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

Cahill, G.M. (2002) Clock mechanisms in zebrafish. Cell and tissue research. 309(1):27-34

Catchen, J.M., Conery, J.S., and Postlethwait, J.H. (2009) Automated identification of conserved synteny after whole-genome duplication. Genome research. 19(8):1497-1505

Chen, S., Oikonomou, G., Chiu, C.N., Niles, B.J., Liu, J., Lee, D.A., Antoshechkin, I., and Prober, D.A. (2013) A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic acids research. 41(4):2769-2778

D'Agostino, Y., Frigato, E., Noviello, T.M.R., Toni, M., Frabetti, F., Cigliano, L., Ceccarelli, M., Sordino, P., Cerulo, L., Bertolucci, C., D'Aniello, S. (2022) Loss of circadian rhythmicity in bdnf knockout zebrafish larvae. iScience. 25:104054

Dekens, M.P., and Whitmore, D. (2008) Autonomous onset of the circadian clock in the zebrafish embryo. The EMBO journal. 27(20):2757-2765

Di Rosa, V., Frigato, E., López-Olmeda, J.F., Sánchez-Vázquez, F.J., Bertolucci, C. (2015) The Light Wavelength Affects the Ontogeny of Clock Gene Expression and Activity Rhythms in Zebrafish Larvae. PLoS One. 10:e0132235

Hirayama, J., Miyamura, N., Uchida, Y., Asaoka, Y., Honda, R., Sawanobori, K., Todo, T., Yamamoto, T., Sassone-Corsi, P., and Nishina, H. (2009) Common light signaling pathways controlling DNA repair and circadian clock entrainment in zebrafish. Cell cycle (Georgetown, Tex.). 8(17):2794-2801

Hung, I.C., Hsiao, Y.C., Sun, H.S., Chen, T.M., Lee, S.J. (2016) MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae. BMC Genomics. 17:922

Jensen, L.D., Cao, Z., Nakamura, M., Yang, Y., Bräutigam, L., Andersson, P., Zhang, Y., Wahlberg, E., Länne, T., Hosaka, K., and Cao, Y. (2012) Opposing Effects of Circadian Clock Genes Bmal1 and Period2 in Regulation of VEGF-Dependent Angiogenesis in Developing Zebrafish. Cell Reports. 2(2):231-241

Kajimura, S., Aida, K., and Duan, C. (2006) Understanding hypoxia-induced gene expression in early development: in vitro and in vivo analysis of hypoxia-inducible factor 1-regulated zebra fish insulin-like growth factor binding protein 1 gene expression. Molecular and cellular biology. 26 (3):1142-1155

Khan, Z.A., Labala, R.K., Yumnamcha, T., Devi, S.D., Mondal, G., Sanjita Devi, H., Rajiv, C., Bharali, R., Chattoraj, A. (2018) Artificial Light at Night (ALAN), an alarm to ovarian physiology: A study of possible chronodisruption on zebrafish (Danio rerio). The Science of the total environment. 628-629:1407-1421

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, C., Hu, J., Qu, C., Wang, L., Huang, G., Niu, P., Zhong, Z., Hong, F., Wang, G., Postlethwait, J.H., Wang, H. (2015) Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes. Scientific Reports. 5:8113

Liu, H., Ma, Z., Zhang, T., Yu, N., Su, G., Giesy, J.P., Yu, H. (2018) Pharmacokinetics and effects of tetrabromobisphenol a (TBBPA) to early life stages of zebrafish (Danio rerio). Chemosphere. 190:243-252

Ma, Z., Yu, Y., Tang, S., Liu, H., Su, G., Xie, Y., Giesy, J.P., Hecker, M., Yu, H. (2015) Differential modulation of expression of nuclear receptor mediated genes by tris(2-butoxyethyl) phosphate (TBOEP) on early life stages of zebrafish (Danio rerio). Aquatic toxicology (Amsterdam, Netherlands). 169:196-203

Morbiato, E., Frigato, E., Dinarello, A., Maradonna, F., Facchinello, N., Argenton, F., Carnevali, O., Dalla Valle, L., Bertolucci, C. (2019) Feeding Entrainment of the Zebrafish Circadian Clock Is Regulated by the Glucocorticoid Receptor. Cells. 8(11):

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

Ren, D.L., Ji, C., Wang, X.B., Wang, H., Hu, B. (2017) Endogenous melatonin promotes rhythmic recruitment of neutrophils toward an injury in zebrafish. Scientific Reports. 7:4696

Sbragaglia, V., López-Olmeda, J.F., Frigato, E., Bertolucci, C., Arlinghaus, R. (2020) Size-selective mortality induces evolutionary changes in group risk-taking behavior and the circadian system in a fish. The Journal of animal ecology. 90(2):387-403

Stankiewicz, A.J., McGowan, E.M., Yu, L., Zhdanova, I.V. (2017) Impaired Sleep, Circadian Rhythms and Neurogenesis in Diet-Induced Premature Aging. International Journal of Molecular Sciences. 18(11)

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, H. (2009) Comparative genomic analysis of teleost fish bmal genes. Genetica. 136(1):149-161

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

Weger, B.D., Weger, M., Görling, B., Schink, A., Gobet, C., Keime, C., Poschet, G., Jost, B., Krone, N., Hell, R., Gachon, F., Luy, B., Dickmeis, T. (2016) Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids. PLoS Genetics. 12:e1006512

Yang, Y., Dong, F., Liu, X., Xu, J., Wu, X., Zheng, Y. (2019) Dysregulation of circadian rhythm in zebrafish (Danio rerio) by thifluzamide: Involvement of positive and negative regulators. Chemosphere. 235:280-287

Zebrafish Nomenclature Committee (2024) Nomenclature Data Curation (2024). Nomenclature Committee Submission.

Zhang, L., Fang, Y., Lu, X., Xu, S., Cai, F., Yu, M., Li, X., Zhong, S. (2020) Transcriptional response of zebrafish larvae exposed to lindane reveals two detoxification genes of ABC transporter family (abcg5 and abcg8). Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 232:108755

Zhang, Z., Ran, C., Ding, Q.W., Liu, H.L., Xie, M.X., Yang, Y.L., Xie, Y.D., Gao, C.C., Zhang, H.L., Zhou, Z.G. (2019) Ability of prebiotic polysaccharides to activate a HIF1α-antimicrobial peptide axis determines liver injury risk in zebrafish. Communications biology. 2:274

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

Zebrafish Nomenclature Committee (2024) Nomenclature Data Curation (2024). Nomenclature Committee Submission.

Dao, P., Hajny, S., Mekis, R., Orel, L., Dinhopl, N., Tessmar-Raible, K., Nowikovsky, K. (2022) The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish. Life science alliance. 5(9)

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

Meng, Q., Yeung, K., Kwok, M.L., Chung, C.T., Hu, X.L., Chan, K.M. (2020) Toxic effects and transcriptome analyses of zebrafish (Danio rerio) larvae exposed to benzophenones. Environmental pollution (Barking, Essex : 1987). 265:114857

Wang, H., Yang, Z., Li, X., Huang, D., Yu, S., He, J., Li, Y., Yan, J. (2020) Single-cell in vivo imaging of cellular circadian oscillators in zebrafish. PLoS Biology. 18:e3000435

Liang, Y.Q., Huang, G.Y., Zhen, Z., Tian, F., Hou, L., Lin, Z., Ying, G.G. (2019) The effects of binary mixtures of estradiol and progesterone on transcriptional expression profiles of genes involved in hypothalamic-pituitary-gonadal axis and circadian rhythm signaling in embryonic zebrafish (Danio rerio). Ecotoxicology and environmental safety. 174:540-548

Onoue, T., Nishi, G., Hikima, J.I., Sakai, M., Kono, T. (2019) Circadian oscillation of TNF-α gene expression regulated by clock gene, BMAL1 and CLOCK1, in the Japanese medaka (Oryzias latipes). International Immunopharmacology. 70:362-371

Yang, Y., Dong, F., Liu, X., Xu, J., Wu, X., Zheng, Y. (2019) Dysregulation of circadian rhythm in zebrafish (Danio rerio) by thifluzamide: Involvement of positive and negative regulators. Chemosphere. 235:280-287

Zhang, Z., Ran, C., Ding, Q.W., Liu, H.L., Xie, M.X., Yang, Y.L., Xie, Y.D., Gao, C.C., Zhang, H.L., Zhou, Z.G. (2019) Ability of prebiotic polysaccharides to activate a HIF1α-antimicrobial peptide axis determines liver injury risk in zebrafish. Communications biology. 2:274

Liu, H., Ma, Z., Zhang, T., Yu, N., Su, G., Giesy, J.P., Yu, H. (2018) Pharmacokinetics and effects of tetrabromobisphenol a (TBBPA) to early life stages of zebrafish (Danio rerio). Chemosphere. 190:243-252

Akle, V., Stankiewicz, A.J., Kharchenko, V., Yu, L., Kharchenko, P.V., Zhdanova, I.V. (2017) Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37(7):1900-1909

Carmona-Antoñanzas, G., Santi, M., Migaud, H., Vera, L.M. (2017) Light- and clock-control of genes involved in detoxification. Chronobiology International. 34(8):1026-1041

Jerônimo, R., Moraes, M.N., de Assis, L.V.M., Ramos, B.C., Rocha, T., Castrucci, A.M.L. (2017) Thermal stress in Danio rerio: a link between temperature, light, thermo-TRP channels, and clock genes. Journal of thermal biology. 68:128-138

Ren, D.L., Ji, C., Wang, X.B., Wang, H., Hu, B. (2017) Endogenous melatonin promotes rhythmic recruitment of neutrophils toward an injury in zebrafish. Scientific Reports. 7:4696

Zhang, L., Jin, Y., Han, Z., Liu, H., Shi, L., Hua, X., A Doering, J., Tang, S., P Giesy, J., Yu, H. (2017) INTEGRATED IN SILICO AND IN VIVO APPROACHES TO INVESTIGATE EFFECTS OF BDE-99 MEDIATED BY THE NUCLEAR RECEPTORS ON DEVELOPING ZEBRAFISH. Environmental toxicology and chemistry. 37(3):780-787

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

Hung, I.C., Hsiao, Y.C., Sun, H.S., Chen, T.M., Lee, S.J. (2016) MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae. BMC Genomics. 17:922

Weger, B.D., Weger, M., Görling, B., Schink, A., Gobet, C., Keime, C., Poschet, G., Jost, B., Krone, N., Hell, R., Gachon, F., Luy, B., Dickmeis, T. (2016) Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids. PLoS Genetics. 12:e1006512

Zhao, Y., Zhang, K., Fent, K. (2016) Corticosteroid Fludrocortisone Acetate Targets Multiple End Points in Zebrafish (Danio rerio) at Low Concentrations. Environmental science & technology. 50(18):10245-54

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

Liu, H., Tang, S., Zheng, X., Zhu, Y., Ma, Z., Liu, C., Hecker, M., Saunders, D.M., Giesy, J.P., Zhang, X., Yu, H. (2015) Bioaccumulation, biotransformation and toxicity of BDE-47, 6-OH-BDE-47 and 6-MeO-BDE-47 in early life-stages of zebrafish (Danio rerio). Environmental science & technology. 49(3):1823-33

Toloza-Villalobos, J., Arroyo, J.I., Opazo, J.C. (2015) The Circadian Clock of Teleost Fish: A Comparative Analysis Reveals Distinct Fates for Duplicated Genes. Journal of molecular evolution. 80(1):57-64

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

Briolat, V., Jouneau, L., Carvalho, R., Palha, N., Langevin, C., Herbomel, P., Schwartz, O., Spaink, H.P., Levraud, J.P., Boudinot, P. (2014) Contrasted Innate Responses to Two Viruses in Zebrafish: Insights into the Ancestral Repertoire of Vertebrate IFN-Stimulated Genes. Journal of immunology (Baltimore, Md. : 1950). 192:4328-41

Liu, C., Wang, Q., Liang, K., Liu, J., Zhou, B., Zhang, X., Liu, H., Giesy, J.P., and Yu, H. (2013) Effects of tris(1,3-dichloro-2-propyl) phosphate and triphenyl phosphate on receptor-associated mRNA expression in zebrafish embryos/larvae. Aquatic toxicology (Amsterdam, Netherlands). 128-129C:147-157

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

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

Hirayama, J., Miyamura, N., Uchida, Y., Asaoka, Y., Honda, R., Sawanobori, K., Todo, T., Yamamoto, T., Sassone-Corsi, P., and Nishina, H. (2009) Common light signaling pathways controlling DNA repair and circadian clock entrainment in zebrafish. Cell cycle (Georgetown, Tex.). 8(17):2794-2801

Wang, Y., Chen, K., Yao, Q., Zheng, X., and Yang, Z. (2009) Phylogenetic Analysis of Zebrafish Basic Helix-Loop-Helix Transcription Factors. Journal of molecular evolution. 68(6):629-640

Shang, E.H., and Zhdanova, I.V. (2007) The circadian system is a target and modulator of prenatal cocaine effects. PLoS One. 2(1):e587

Kajimura, S., Aida, K., and Duan, C. (2006) Understanding hypoxia-induced gene expression in early development: in vitro and in vivo analysis of hypoxia-inducible factor 1-regulated zebra fish insulin-like growth factor binding protein 1 gene expression. Molecular and cellular biology. 26 (3):1142-1155

Triqueneaux, G., Thenot, S., Kakizawa, T., Antoch, M.P., Safi, R., Takahashi, J.S., Delaunay, F., and Laudet, V. (2004) The orphan receptor Rev-erb{alpha} gene is a target of the circadian clock pacemaker. Journal of molecular endocrinology. 33(3):585-608

Cahill, G.M. (2002) Clock mechanisms in zebrafish. Cell and tissue research. 309(1):27-34

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