High-resolution in situ hybridization to whole-mount zebrafish embryos

Generating Transparent Zebrafish: A Refined Method to Improve Detection of Gene Expression During Embryonic Development

Karlsson, J., von Hofsten, J., & Olsson, P.-E. (2001) · Marine Biotechnology · doi:10.1007/s1012601-0053-4 · Cited by 328

Identification of Sef, a novel modulator of FGF signalling

Tsang, M., Friesel, R., Kudoh, T., & Dawid, I. B. (2002) · Nature Cell Biology · doi:10.1038/ncb749 · Cited by 304

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

Choi, H. M. T., Schwarzkopf, M., Fornace, M. E., Acharya, A., Artavanis, G., Stegmaier, J., Cunha, A., & Pierce, N. A. (2018) · Development · doi:10.1242/dev.165753 · Cited by 1,495

Dissecting cell identity via network inference and in silico gene perturbation

Kamimoto, K., Stringa, B., Hoffmann, C. M., Jindal, K., Solnica-Krezel, L., & Morris, S. A. (2023) · Nature · doi:10.1038/s41586-022-05688-9 · Cited by 677

Loss of function of C9orf72 causes motor deficits in a zebrafish model of amyotrophic lateral sclerosis

Ciura, S., Lattante, S., Le Ber, I., Latouche, M., Tostivint, H., Brice, A., & Kabashi, E. (2013) · Annals of Neurology · doi:10.1002/ana.23946 · Cited by 333

Early steps in primary cilium assembly require EHD1/EHD3-dependent ciliary vesicle formation

Lu, Q., Insinna, C., Ott, C., Stauffer, J., Pintado, P. A., Rahajeng, J., Baxa, U., Walia, V., Cuenca, A., Hwang, Y.-S., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3109 · Cited by 279

Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration

Wan, J., Yourshaw, M., Mamsa, H., Rudnik-Schöneborn, S., Menezes, M. P., Hong, J. E., Leong, D. W., Senderek, J., Salman, M. S., Chitayat, D., et al. (2012) · Nature Genetics · doi:10.1038/ng.2254 · Cited by 257

Polystyrene nanoplastics disrupt glucose metabolism and cortisol levels with a possible link to behavioural changes in larval zebrafish

Brun, N. R., van Hage, P., Hunting, E. R., Haramis, A.-P. G., Vink, S. C., Vijver, M. G., Schaaf, M. J. M., & Tudorache, C. (2019) · Communications Biology · doi:10.1038/s42003-019-0629-6 · Cited by 246

TMEM237 is mutated in individuals with a Joubert syndrome related disorder and expands the role of the TMEM family at the ciliary transition zone.

Huang, L., Szymanska, K., Jensen, V. L., Janecke, A. R., Innes, A. M., Davis, E. E., Frosk, P., Li, C., Willer, J. R., Chodirker, B. N., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.005 · Cited by 194

Control of angiogenesis by AIBP-mediated cholesterol efflux

Fang, L., Choi, S.-H., Baek, J. S., Liu, C., Almazan, F., Ulrich, F., Wiesner, P., Taleb, A., Deer, E., Pattison, J., et al. (2013) · Nature · doi:10.1038/nature12166 · Cited by 192

The histone variant macroH2A is an epigenetic regulator of key developmental genes

Buschbeck, M., Uribesalgo, I., Wibowo, I., Rué, P., Martin, D., Gutierrez, A., Morey, L., Guigó, R., López-Schier, H., & Di Croce, L. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1665 · Cited by 192

Deep conservation of the enhancer regulatory code in animals

Wong, E. S., Zheng, D., Tan, S. Z., Bower, N. I., Garside, V., Vanwalleghem, G., Gaiti, F., Scott, E., Hogan, B. M., Kikuchi, K., et al. (2020) · Science · doi:10.1126/science.aax8137 · Cited by 176

Mechanically activated piezo channels modulate outflow tract valve development through the Yap1 and Klf2-Notch signaling axis

Duchemin, A.-L., Vignes, H., & Vermot, J. (2019) · eLife · doi:10.7554/elife.44706 · Cited by 170

Hemodynamic Forces Sculpt Developing Heart Valves through a KLF2-WNT9B Paracrine Signaling Axis

Goddard, L. M., Duchemin, A.-L., Ramalingan, H., Wu, B., Chen, M., Bamezai, S., Yang, J., Li, L., Morley, M. P., Wang, T., et al. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.09.023 · Cited by 156

Microglial transglutaminase-2 drives myelination and myelin repair via GPR56/ADGRG1 in oligodendrocyte precursor cells

Giera, S., Luo, R., Ying, Y., Ackerman, S. D., Jeong, S.-J., Stoveken, H. M., Folts, C. J., Welsh, C. A., Tall, G. G., Stevens, B., et al. (2018) · eLife · doi:10.7554/elife.33385 · Cited by 145

p63 is a cereblon substrate involved in thalidomide teratogenicity

Asatsuma-Okumura, T., Ando, H., De Simone, M., Yamamoto, J., Sato, T., Shimizu, N., Asakawa, K., Yamaguchi, Y., Ito, T., Guerrini, L., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0366-7 · Cited by 134

Organelle degradation in the lens by PLAAT phospholipases

Morishita, H., Eguchi, T., Tsukamoto, S., Sakamaki, Y., Takahashi, S., Saito, C., Koyama-Honda, I., & Mizushima, N. (2021) · Nature · doi:10.1038/s41586-021-03439-w · Cited by 111

mitfa is required at multiple stages of melanocyte differentiation but not to establish the melanocyte stem cell

Johnson, S. L., Nguyen, A. N., & Lister, J. A. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2010.12.004 · Cited by 85

ESCRT proteins restrict constitutive NF-κB signaling by trafficking cytokine receptors

Mamińska, A., Bartosik, A., Banach-Orłowska, M., Pilecka, I., Jastrzębski, K., Zdżalik-Bielecka, D., Castanon, I., Poulain, M., Neyen, C., Wolińska-Nizioł, L., et al. (2016) · Science Signaling · doi:10.1126/scisignal.aad0848 · Cited by 74

Heterozygous germline mutations in A2ML1 are associated with a disorder clinically related to Noonan syndrome

Vissers, L. E., Bonetti, M., Paardekooper Overman, J., Nillesen, W. M., Frints, S. G. M., de Ligt, J., Zampino, G., Justino, A., Machado, J. C., Schepens, M., et al. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.115 · Cited by 75

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution

Lambert, N., Lambot, M.-A., Bilheu, A., Albert, V., Englert, Y., Libert, F., Noel, J.-C., Sotiriou, C., Holloway, A. K., Pollard, K. S., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017753 · Cited by 73

Reticular dysgenesis–associated AK2 protects hematopoietic stem and progenitor cell development from oxidative stress

Rissone, A., Weinacht, K. G., la Marca, G., Bishop, K., Giocaliere, E., Jagadeesh, J., Felgentreff, K., Dobbs, K., Al-Herz, W., Jones, M., et al. (2015) · Journal of Experimental Medicine · doi:10.1084/jem.20141286 · Cited by 63

Embryonic expression of zebrafish MiT family genes tfe3b, tfeb, and tfec

Lister, J. A., Lane, B. M., Nguyen, A., & Lunney, K. (2011) · Developmental Dynamics · doi:10.1002/dvdy.22743 · Cited by 61

Loss of cardiac Wnt/β-catenin signalling in desmoplakin-deficient AC8 zebrafish models is rescuable by genetic and pharmacological intervention

Giuliodori, A., Beffagna, G., Marchetto, G., Fornetto, C., Vanzi, F., Toppo, S., Facchinello, N., Santimaria, M., Vettori, A., Rizzo, S., et al. (2018) · Cardiovascular Research · doi:10.1093/cvr/cvy057 · Cited by 57

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development

Yuan, X., Song, M., Devine, P., Bruneau, B. G., Scott, I. C., & Wilson, M. D. (2018) · Nature Communications · doi:10.1038/s41467-018-07451-z · Cited by 51

Quantitative proteomics identify DAB2 as a cardiac developmental regulator that inhibits WNT/β-catenin signaling

Hofsteen, P., Robitaille, A. M., Chapman, D. P., Moon, R. T., & Murry, C. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523930113 · Cited by 50

A lysosomal regulatory circuit essential for the development and function of microglia

Iyer, H., Shen, K., Meireles, A. M., & Talbot, W. S. (2022) · Science Advances · doi:10.1126/sciadv.abp8321 · Cited by 49

Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development

Shestopalov, I. A., Pitt, C. L. W., & Chen, J. K. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.772 · Cited by 42

Otx but not mitf transcription factors are required for zebrafish retinal pigment epithelium development

Lane, B. M., & Lister, J. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049357 · Cited by 40

FoxA transcription factors are essential for the development of dorsal axial structures

Dal-Pra, S., Thisse, C., & Thisse, B. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2010.12.018 · Cited by 35

An ongoing role for Wnt signaling in differentiating melanocytes in vivo

Vibert, L., Aquino, G., Gehring, I., Subkankulova, T., Schilling, T. F., Rocco, A., & Kelsh, R. N. (2017) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12568 · Cited by 35

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

Nepal, C., Coolen, M., Hadzhiev, Y., Cussigh, D., Mydel, P., Steen, V. M., Carninci, P., Andersen, J. B., Bally-Cuif, L., Müller, F., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1354 · Cited by 35

snow white, a Zebrafish Model of Hermansky-Pudlak Syndrome Type 5

Daly, C. M. S., Willer, J., Gregg, R., & Gross, J. M. (2013) · Genetics · doi:10.1534/genetics.113.154898 · Cited by 33

Motor neuron‐expressed micro RNA s 218 and their enhancers are nested within introns of Slit2/3 genes

Punnamoottil, B., Rinkwitz, S., Giacomotto, J., Svahn, A. J., & Becker, T. S. (2015) · genesis · doi:10.1002/dvg.22852 · Cited by 28

Gag proteins encoded by endogenous retroviruses are required for zebrafish development

Chang, N.-C., Wells, J. N., Wang, A. Y., Schofield, P., Huang, Y.-C., Truong, V. H., Simoes-Costa, M., & Feschotte, C. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2411446122 · Cited by 27

Rab32 and Rab38 genes in chordate pigmentation: An evolutionary perspective

Coppola, U., Annona, G., D’Aniello, S., & Ristoratore, F. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0596-1 · Cited by 23

Distant Insulin Signaling Regulates Vertebrate Pigmentation through the Sheddase Bace2

Zhang, Y. M., Zimmer, M. A., Guardia, T., Callahan, S. J., Mondal, C., Di Martino, J., Takagi, T., Fennell, M., Garippa, R., Campbell, N. R., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.04.025 · Cited by 22

A p21-GFP zebrafish model of senescence for rapid testing of senolytics in vivo

Morsli, S., Henriques, C. M., Ellis, P. S., Mortiboys, H., Baxendale, S., Loynes, C. A., Renshaw, S. A., & Bellantuono, I. (2023) · Aging Cell · doi:10.1111/acel.13835 · Cited by 21

SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics

Trachsel-Moncho, L., Veroni, C., Mathai, B. J., Lapao, A., Singh, S., Asp, N. T., Schultz, S. W., Pankiv, S., & Simonsen, A. (2025) · Journal of Cell Biology · doi:10.1083/jcb.202404009 · Cited by 16

GRG5/AES Interacts with T-Cell Factor 4 (TCF4) and Downregulates Wnt Signaling in Human Cells and Zebrafish Embryos

Costa, Â. M. S., Pereira-Castro, I., Ricardo, E., Spencer, F., Fisher, S., & Costa, L. T. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067694 · Cited by 13

Molecular mechanisms controlling the biogenesis of the TGF-β signal Vg1

Dingal, P. C. D. P., Carte, A. N., Montague, T. G., Lim Suan, M. B., & Schier, A. F. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307203120 · Cited by 4

The zebrafish mutant dreammist implicates sodium homeostasis in sleep regulation

(2020) · doi:10.1101/2020.11.18.388736 · Cited by 4

CCSer2 gates dynein activity at the cell periphery

Zang, J. L., Gibson, D., Zheng, A.-M., Shi, W., Gillies, J. P., Stein, C., Drerup, C. M., & DeSantis, M. E. (2025) · Journal of Cell Biology · doi:10.1083/jcb.202406153 · Cited by 3

Tribbles1 is host protective during in vivo mycobacterial infection

Hammond, F. R., Lewis, A., Pollara, G., Tomlinson, G. S., Noursadeghi, M., Kiss-Toth, E., & Elks, P. M. (2024) · eLife · doi:10.7554/elife.95980 · Cited by 2

Molecular and Functional Divergence of Zebrafish Sox Paralogs Controlling Endoderm Formation and Left–Right Patterning

Johal, S., Elsayed, R., Wang, D., Talbot, C. D., Feuda, R., Panfilio, K. A., & Nelson, A. C. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf213 · Cited by 1

The zebrafish mutant dreammist implicates sodium homeostasis in sleep regulation

Barlow, I. L., Mackay, E., Wheater, E., Goel, A., Lim, S., Zimmerman, S., Woods, I., Prober, D. A., & Rihel, J. (2023) · doi:10.7554/elife.87521.2