Babin, P.J. (2008) Conservation of a vitellogenin gene cluster in oviparous vertebrates and identification of its traces in the platypus genome. Gene. 413(1-2):76-82

Bayés, À., Collins, M.O., Reig-Viader, R., Gou, G., Goulding, D., Izquierdo, A., Choudhary, J.S., Emes, R.D., Grant, S.G. (2017) Evolution of complexity in the zebrafish synapse proteome. Nature communications. 8:14613

Chen, Z., He, M., Wang, H., Li, X., Qin, R., Ye, D., Zhai, X., Zhu, J., Zhang, Q., Hu, P., Shui, G., Sun, Y. (2024) Intestinal DHA-PA-PG axis promotes digestive organ expansion by mediating usage of maternally deposited yolk lipids. Nature communications. 15:97699769

Cuello, S., Ximénez-Embún, P., Ruppen, I., Schonthaler, H.B., Ashman, K., Madrid, Y., Luque-Garcia, J.L., and Cámara, C. (2012) Analysis of protein expression in developmental toxicity induced by MeHg in zebrafish. The Analyst. 137(22):5302-5311

Feltes, M., Zimin, A.V., Angel, S., Pansari, N., Hensley, M.R., Anderson, J.L., Shen, M.C., Klemek, M., Shen, Y., Ginde, V.S., Kozan, H., Le, N.V., Truong, V.P., Wilson, M.H., Salzberg, S.L., Farber, S.A. (2025) Phenotype to genotype: A new and rapid approach using whole-genome sequencing. PLoS Genetics. 21:e1011702e1011702

Gomez, G.A., Veldman, M.B., Zhao, Y., Burgess, S., and Lin, S. (2009) Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish. PLoS One. 4(3):e4994

Hu, P., Liu, M., Zhang, D., Wang, J., Niu, H., Liu, Y., Wu, Z., Han, B., Zhai, W., Shen, Y., Chen, L. (2015) Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish. Nucleic acids research. 43(19):9198-213

Höijer, I., Emmanouilidou, A., Östlund, R., van Schendel, R., Bozorgpana, S., Tijsterman, M., Feuk, L., Gyllensten, U., den Hoed, M., Ameur, A. (2022) CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations. Nature communications. 13:627

Jin, Y., Kozan, D., Young, E.D., Hensley, M., Shen, M.C., Wen, J., Moll, T., Anderson, J.L., Kozan, H., Rawls, J.F., Farber, S.A. (2024) A high-cholesterol zebrafish diet promotes hypercholesterolemia and fasting-associated liver steatosis. Journal of Lipid Research. 65(10):100637

Lam, S.H., Mathavan, S., Tong, Y., Li, H., Karuturi, R.K., Wu, Y., Vega, V.B., Liu, E.T., and Gong, Z. (2008) Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology. PLoS Genetics. 4(7):e1000121

Li, C., Tan, X.F., Lim, T.K., Lin, Q., Gong, Z. (2016) Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human. Scientific Reports. 6:24329

Martínez, R., Tu, W., Eng, T., Allaire-Leung, M., Piña, B., Navarro-Martín, L., Mennigen, J.A. (2020) Acute and long-term metabolic consequences of early developmental Bisphenol A exposure in zebrafish (Danio rerio). Chemosphere. 256:127080

Otis, J.P., Zeituni, E.M., Thierer, J.H., Anderson, J.L., Brown, A.C., Boehm, E.D., Cerchione, D.M., Ceasrine, A.M., Avraham-Davidi, I., Tempelhof, H., Yaniv, K., Farber, S.A. (2015) Zebrafish as a model for apolipoprotein biology: Comprehensive expression analysis and a role for ApoA-IV in regulating food intake. Disease models & mechanisms. 8(3):295-309

Seth, A., Machingo, Q.J., Fritz, A., and Shur, B.D. (2010) Core fucosylation is required for midline patterning during zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(12):3380-3390

Sweeney, D.W., Shen, M.C., Farber, S.A. (2025) Creb3l3 deficiency promotes intestinal lipid accumulation and alters ApoB-containing lipoprotein kinetics. Journal of Lipid Research. :100833100833

Thierer, J.H., Ekker, S.C., Farber, S.A. (2019) The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 10:3426

Ton, C., Hwang, D.M., Dempsey, A.A., Tang, H.C., Yoon, J., Lim, M., Mably, J.D., Fishman, M.C., and Liew, C.C. (2000) Identification, characterization, and mapping of expressed sequence tags from an embryonic zebrafish heart cDNA library. Genome research. 10(12):1915-1927

Wang, W., Zhang, X., Qin, J., Wei, P., Jia, Y., Wang, J., Ru, S. (2019) Long-term bisphenol S exposure induces fat accumulation in liver of adult male zebrafish (Danio rerio) and slows yolk lipid consumption in F1 offspring. Chemosphere. 221:500-510

Wilson, M.H., Hensley, M.R., Shen, M.C., Lu, H.Y., Quinlivan, V.H., Busch-Nentwich, E.M., Rawls, J.F., Farber, S.A. (2024) Zebrafish are resilient to the loss of major diacylglycerol acyltransferase enzymes. The Journal of biological chemistry. 300(12):107973

Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F. (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports. 27:1567-1578.e5

Zeng, T., Lv, J., Liang, J., Xie, B., Liu, L., Tan, Y., Zhu, J., Jiang, J., Xie, H. (2024) Zebrafish cobll1a regulates lipid homeostasis via the RA signaling pathway. Frontiers in cell and developmental biology. 12:13813621381362

Zhao, Q., Chang, H., Zheng, J., Li, P., Ye, L., Pan, R., Li, D., Shao, J.Z., Zhao, R.C., Chen, Y. (2023) A novel Trmt5-deficient zebrafish model with spontaneous inflammatory bowel disease-like phenotype. Signal transduction and targeted therapy. 8:8686

Zheng, W., Li, Z., Nguyen, A.T., Li, C., Emelyanov, A., Gong, Z. (2014) Xmrk, kras and myc transgenic zebrafish liver cancer models share molecular signatures with subsets of human hepatocellular carcinoma. PLoS One. 9:e91179

Feltes, M., Zimin, A.V., Angel, S., Pansari, N., Hensley, M.R., Anderson, J.L., Shen, M.C., Klemek, M., Shen, Y., Ginde, V.S., Kozan, H., Le, N.V., Truong, V.P., Wilson, M.H., Salzberg, S.L., Farber, S.A. (2025) Phenotype to genotype: A new and rapid approach using whole-genome sequencing. PLoS Genetics. 21:e1011702e1011702

Chen, Z., He, M., Wang, H., Li, X., Qin, R., Ye, D., Zhai, X., Zhu, J., Zhang, Q., Hu, P., Shui, G., Sun, Y. (2024) Intestinal DHA-PA-PG axis promotes digestive organ expansion by mediating usage of maternally deposited yolk lipids. Nature communications. 15:97699769

Wilson, M.H., Hensley, M.R., Shen, M.C., Lu, H.Y., Quinlivan, V.H., Busch-Nentwich, E.M., Rawls, J.F., Farber, S.A. (2024) Zebrafish are resilient to the loss of major diacylglycerol acyltransferase enzymes. The Journal of biological chemistry. 300(12):107973

Guirgis, F.W., Jacob, V., Wu, D., Henson, M., Daly-Crews, K., Hopson, C., Black, L.P., DeVos, E.L., Sulaiman, D., Labilloy, G., Brusko, T.M., Shavit, J.A., Bertrand, A., Feldhammer, M., Baskovich, B., Graim, K., Datta, S., Reddy, S.T. (2023) DHCR7 Expression Predicts Porsusor Outcomes and Mortality From Sepsis. Critical care explorations. 5:e0929e0929

Buerger, A.N., Parente, C.E., Harris, J.P., Watts, E.G., Wormington, A.M., Bisesi, J.H. (2022) Impacts of diethylhexyl phthalate and overfeeding on physical fitness and lipid mobilization of Danio rerio (zebrafish). Chemosphere. 295:133703

Ivanovics, B., Gazsi, G., Reining, M., Berta, I., Poliska, S., Toth, M., Domokos, A., Nagy, B., Staszny, A., Cserhati, M., Csosz, E., Bacsi, A., Csenki-Bakos, Z., Acs, A., Urbanyi, B., Czimmerer, Z. (2021) Embryonic exposure to low concentrations of aflatoxin B1 triggers global transcriptomic changes, defective yolk lipid mobilization, abnormal gastrointestinal tract development and inflammation in zebrafish. Journal of hazardous materials. 416:125788

Wang, W., Zhang, J., Li, Z., Gu, J., Qin, J., Li, J., Zhang, X., Ru, S. (2021) Bisphenol S exposure accelerates the progression of atherosclerosis in zebrafish embryo-larvae. Journal of hazardous materials. 426:128042

Martínez, R., Tu, W., Eng, T., Allaire-Leung, M., Piña, B., Navarro-Martín, L., Mennigen, J.A. (2020) Acute and long-term metabolic consequences of early developmental Bisphenol A exposure in zebrafish (Danio rerio). Chemosphere. 256:127080

Thierer, J.H., Ekker, S.C., Farber, S.A. (2019) The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 10:3426

Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F. (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports. 27:1567-1578.e5

Bayés, À., Collins, M.O., Reig-Viader, R., Gou, G., Goulding, D., Izquierdo, A., Choudhary, J.S., Emes, R.D., Grant, S.G. (2017) Evolution of complexity in the zebrafish synapse proteome. Nature communications. 8:14613

Baker, B.B., Yee, J.S., Meyer, D.N., Yang, D., Baker, T.R. (2016) Histological and Transcriptomic Changes in Male Zebrafish Testes Due to Early Life Exposure to Low Level 2,3,7,8-Tetrachlorodibenzo-p-Dioxin. Zebrafish. 13:413-423

Lui, E.Y., Li, C., Li, Z.H., Gong, Z., Lam, S.H. (2016) Molecular insights of organochlorine biocide-induced toxicity in zebrafish: Whole-adult-organism toxicogenomics, targeted gene expression and histological analyses. Journal of genetics and genomics = Yi chuan xue bao. 43(8):525-8

Zeituni, E.M., Wilson, M.H., Zheng, X., Iglesias, P.A., Sepanski, M., Siddiqi, M.A., Anderson, J.L., Zheng, Y., Farber, S.A. (2016) Endoplasmic reticulum lipid flux influences enterocyte nuclear morphology and lipid-dependent transcriptional responses. The Journal of biological chemistry. 291(45):23804-23816

Hu, P., Liu, M., Zhang, D., Wang, J., Niu, H., Liu, Y., Wu, Z., Han, B., Zhai, W., Shen, Y., Chen, L. (2015) Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish. Nucleic acids research. 43(19):9198-213

Otis, J.P., Zeituni, E.M., Thierer, J.H., Anderson, J.L., Brown, A.C., Boehm, E.D., Cerchione, D.M., Ceasrine, A.M., Avraham-Davidi, I., Tempelhof, H., Yaniv, K., Farber, S.A. (2015) Zebrafish as a model for apolipoprotein biology: Comprehensive expression analysis and a role for ApoA-IV in regulating food intake. Disease models & mechanisms. 8(3):295-309

Zhang, X., Li, C., Gong, Z. (2014) Development of a convenient in vivo hepatotoxin assay using a transgenic zebrafish line with liver-specific DsRed expression. PLoS One. 9:e91874

Ordas, A., Kanwal, Z., Lindenberg, V., Rougeot, J., Mink, M., Spaink, H.P., and Meijer, A.H. (2013) MicroRNA-146 function in the innate immune transcriptome response of zebrafish embryos to Salmonella typhimurium infection. BMC Genomics. 14(1):696

Cuello, S., Ximénez-Embún, P., Ruppen, I., Schonthaler, H.B., Ashman, K., Madrid, Y., Luque-Garcia, J.L., and Cámara, C. (2012) Analysis of protein expression in developmental toxicity induced by MeHg in zebrafish. The Analyst. 137(22):5302-5311

Seth, A., Machingo, Q.J., Fritz, A., and Shur, B.D. (2010) Core fucosylation is required for midline patterning during zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(12):3380-3390

Zheng, D., Kille, P., Feeney, G.P., Cunningham, P., Handy, R.D., and Hogstrand, C. (2010) Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion. BMC Genomics. 11:548

Babin, P.J. (2008) Conservation of a vitellogenin gene cluster in oviparous vertebrates and identification of its traces in the platypus genome. Gene. 413(1-2):76-82

Ton, C., Hwang, D.M., Dempsey, A.A., Tang, H.C., Yoon, J., Lim, M., Mably, J.D., Fishman, M.C., and Liew, C.C. (2000) Identification, characterization, and mapping of expressed sequence tags from an embryonic zebrafish heart cDNA library. Genome research. 10(12):1915-1927