Abdelilah, S. and Driever, W. (1997) Pattern formation in janus-mutant zebrafish embryos. Developmental Biology. 184(1):70-84

Amorim, J.P., Gali-Macedo, A., Marcelino, H., Bordeira-Carriço, R., Naranjo, S., Rivero-Gil, S., Teixeira, J., Galhardo, M., Marques, J., Bessa, J. (2020) A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. Cell Reports. 32:107862

Andrzejczuk, L.A., Banerjee, S., England, S.J., Voufo, C., Kamara, K., Lewis, K.E. (2018) Tal1, Gata2a, and Gata3 Have Distinct Functions in the Development of V2b and Cerebrospinal Fluid-Contacting KA Spinal Neurons. Frontiers in neuroscience. 12:170

Auer, T.O., Duroure, K., Concordet, J.P., Del Bene, F. (2014) CRISPR/Cas9-mediated conversion of eGFP- into Gal4-transgenic lines in zebrafish. Nature Protocols. 9:2823-2840

Bakkers, J., Camacho-Carvajal, M., Nowak, M., Kramer, C., Danger, B., and Hammerschmidt, M. (2005) Destabilization of DeltaNp63alpha by Nedd4-Mediated Ubiquitination and Ubc9-Mediated Sumoylation, and Its Implications on Dorsoventral Patterning of the Zebrafish Embryo. Cell cycle (Georgetown, Tex.). 4(6):790-800

Banjo, T., Grajcarek, J., Yoshino, D., Osada, H., Miyasaka, K.Y., Kida, Y.S., Ueki, Y., Nagayama, K., Kawakami, K., Matsumoto, T., Sato, M., and Ogura, T. (2013) Haemodynamically dependent valvulogenesis of zebrafish heart is mediated by flow-dependent expression of miR-21. Nature communications. 4:1978

Barth, K.A., Kishimoto, Y., Rohr, K.B., Seydler, C., Schulte-Merker, S., and Wilson, S.W. (1999) Bmp activity establishes a gradient of positional information throughout the entire neural plate. Development (Cambridge, England). 126(22):4977-4987

Becker, P.W., Sacilotto, N., Nornes, S., Neal, A., Thomas, M., Liu, K., Preece, C., Ratnayaka, I., Davies, B., Bou-Gharios, G., De Val, S. (2016) Intronic Flk1 Enhancer Directs Arterial-Specific Expression via RBPJ-Mediated Venous Repression. Arteriosclerosis, Thrombosis, and Vascular Biology. 36(6):1209-19

Belele, C.L., English, M.A., Chahal, J., Burnetti, A., Finckbeiner, S.M., Gibney, G., Kirby, M., Sood, R., and Liu, P. (2009) Differential requirement for Gata1 DNA binding and transactivation between primitive and definitive stages of hematopoiesis in zebrafish. Blood. 114(25):5162-5172

Belting, H.G., Wendik, B., Lunde, K., Leichsenring, M., Mössner, R., Driever, W., and Onichtchouk, D. (2011) Pou5f1 contributes to dorsoventral patterning by positive regulation of vox and modulation of fgf8a expression. Developmental Biology. 356(2):323-36

Berman, J.N., Kanki, J.P., and Look, A.T. (2005) Zebrafish as a model for myelopoiesis during embryogenesis. Experimental hematology. 33(9):997-1006

Bessa, J., Luengo, M., Rivero-Gil, S., Ariza-Cosano, A., Maia, A.H., Ruiz-Ruano, F.J., Caballero, P., Naranjo, S., Carvajal, J.J., and Gómez-Skarmeta, J.L. (2014) A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates. Genome research. 24(3):487-95

Bhatia, S., Gordon, C.T., Foster, R.G., Melin, L., Abadie, V., Baujat, G., Vazquez, M.P., Amiel, J., Lyonnet, S., Heyningen, V.V., Kleinjan, D.A. (2015) Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish. PLoS Genetics. 11:e1005193

Bogdanovic, O., Fernandez-Minan, A., Tena, J.J., de Lacalle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S.J., Veenstra, G.J., and Gomez-Skarmeta, J.L. (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome research. 22(10):2043-2053

Boswell, M., Boswell, W., Lu, Y., Savage, M., Walter, R.B. (2020) Deconvoluting Wavelengths Leading to Fluorescent Light Induced Inflammation and Cellular Stress in Zebrafish (Danio rerio). Scientific Reports. 10:3321

Branam, A.M., Hoffman, G.G., Pelegri, F., and Greenspan, D.S. (2010) Zebrafish Chordin-like and Chordin Are Functionally Redundant in Regulating Patterning of the Dorsoventral Axis. Developmental Biology. 341(2):444-458

Bridoux, L., Zarrineh, P., Mallen, J., Phuycharoen, M., Latorre, V., Ladam, F., Losa, M., Baker, S.M., Sagerstrom, C., Mace, K.A., Rattray, M., Bobola, N. (2020) HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genetics. 16:e1009162

Butko, E., Distel, M., Pouget, C., Weijts, B., Kobayashi, I., Ng, K., Mosimann, C., Poulain, F.E., McPherson, A., Ni, C.W., Stachura, D.L., Del Cid, N., Espín-Palazón, R., Lawson, N.D., Dorsky, R., Clements, W.K., Traver, D. (2015) Gata2b is a restricted early regulator of hemogenic endothelium in the zebrafish embryo. Development (Cambridge, England). 142:1050-61

Cao, Y., Zhao, J., Sun, Z., Zhao, Z., Postlethwait, J., and Meng, A. (2004) fgf17b, a novel member of Fgf family, helps patterning zebrafish embryos. Developmental Biology. 271(1):130-143

Cebola, I., Rodríguez-Seguí, S.A., Cho, C.H., Bessa, J., Rovira, M., Luengo, M., Chhatriwala, M., Berry, A., Ponsa-Cobas, J., Maestro, M.A., Jennings, R.E., Pasquali, L., Morán, I., Castro, N., Hanley, N.A., Gomez-Skarmeta, J.L., Vallier, L., Ferrer, J. (2015) TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors. Nature cell biology. 17:615-26

Chan, S., Shen, D., Sang, Y., Wang, S., Wang, Y., Chen, C., Gao, B., Song, C. (2019) Development of enhancer-trapping and -detection vectors mediated by the Tol2 transposon in zebrafish. PeerJ. 7:e6862

Chen, F., Köhler, M., Cucun, G., Takamiya, M., Kizil, C., Cosacak, M.I., Rastegar, S. (2023) sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons. iScience. 26:107342107342

Chen, J.N. and Fishman, M.C. (1996) Zebrafish tinman homolog demarcates the heart field and initiates myocardial differentiation. Development (Cambridge, England). 122(12):3809-3816

Chiang, I.K., Fritzsche, M., Pichol-Thievend, C., Neal, A., Holmes, K., Lagendijk, A., Overman, J., D'Angelo, D., Omini, A., Hermkens, D., Lesieur, E., Liu, K., Ratnayaka, I., Corada, M., Bou-Gharios, G., Carroll, J., Dejana, E., Schulte-Merker, S., Hogan, B., Beltrame, M., De Val, S., Francois, M. (2017) SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development. Development (Cambridge, England). 144(14):2629-2639

Chun, C.Z., Tsai, H.J., and Chen, T.T. (2006) Trout Ea4- or human Eb-peptide of pro-IGF-I disrupts heart, red blood cell, and vasculature development in zebrafish embryos. Molecular reproduction and development. 73(9):1112-1121

Clements, W.K., Kim, A.D., Ong, K.G., Moore, J.C., Lawson, N.D., and Traver, D. (2011) A somitic Wnt16/Notch pathway specifies haematopoietic stem cells. Nature. 474(7350):220-224

Cooney, J.D., Hildick-Smith, G.J., Shafizadeh, E., McBride, P.F., Carroll, K.J., Anderson, H., Shaw, G.C., Tamplin, O.J., Branco, D.S., Dalton, A.J., Shah, D.I., Wong, C., Gallagher, P.G., Zon, L.I., North, T.E., and Paw, B.H. (2013) Teleost growth factor independence (gfi) genes differentially regulate successive waves of hematopoiesis. Developmental Biology. 373(2):431-441

Craven, S.E., French, D., Ye, W., de Sauvage, F., and Rosenthal, A. (2005) Loss of hspa9b in zebrafish recapitulates the ineffective hematopoiesis of the myelodysplastic syndromes. Blood. 105(9):3528-3534

D'haene, E., López-Soriano, V., Martínez-García, P.M., Kalayanamontri, S., Rey, A.D., Sousa-Ortega, A., Naranjo, S., Van de Sompele, S., Vantomme, L., Mahieu, Q., Vergult, S., Neto, A., Gómez-Skarmeta, J.L., Martínez-Morales, J.R., Bauwens, M., Tena, J.J., De Baere, E. (2024) Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci. Genome biology. 25:123123

Daggett, D.F., Boyd, C.A,. Gautier, P., Bryson-Richardson, R.J., Thisse, C., Thisse, B., Amacher, S.L., and Currie, P.D. (2004) Developmentally restricted actin-regulatory molecules control morphogenetic cell movements in the zebrafish gastrula. Current biology : CB. 14(18):632-638

Danilova, N., Sakamoto, K.M., and Lin, S. (2008) Ribosomal protein S19 deficiency in zebrafish leads to developmental abnormalities and defective erythropoiesis through activation of p53 protein family. Blood. 112(13):5228-5237

Davidson, A.J., and Zon, L.I. (2004) The 'definitive' (and 'primitive') guide to zebrafish hematopoiesis. Oncogene. 23(43):7233-7246

Dee, C.T., Gibson, A., Rengifo, A., Sun, S.K., Patient, R.K., and Scotting, P.J. (2007) A change in response to Bmp signalling precedes ectodermal fate choice. The International journal of developmental biology. 51(1):79-84

Detrich, H.W. III., Kieran, M.W., Chan, F.Y., Barone, L.M., Yee, K., Rundstadler, J.A., Pratt, S., Ransom, D., and Zon, L.I. (1995) Intraembryonic hematopoietic cell migration during vertebrate development. Proceedings of the National Academy of Sciences of the United States of America. 92:10713-10717

Diotel, N., Viales, R.R., Armant, O., März, M., Ferg, M., Rastegar, S., Strähle, U. (2015) Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. The Journal of comparative neurology. 523(8):1202-21

Dobrzycki, T., Krecsmarik, M., Bonkhofer, F., Patient, R., Monteiro, R. (2018) An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation.. Biology Open. 7(4)

Dong, X., Navratilova, P., Fredman, D., Drivenes, Ø., Becker, T.S., and Lenhard, B. (2010) Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic acids research. 38(4):1071-1085

Eimon, P.M., Kratz, E., Varfolomeev, E., Hymowitz, S.G., Stern, H., Zha, J., and Ashkenazi, A. (2006) Delineation of the cell-extrinsic apoptosis pathway in the zebrafish. Cell death and differentiation. 13(10):1619-1630

Ellingsen, S., Laplante, M.A., Konig, M., Kikuta, H., Furmanek, T., Hoivik, E.A., and Becker, T.S. (2005) Large-scale enhancer detection in the zebrafish genome. Development (Cambridge, England). 132(17):3799-3811

Ernest, S., Rosa, F.M. (2015) A genomic region encompassing a newly identified exon provides enhancing activity sufficient for normal myo7aa expression in zebrafish sensory hair cells. Developmental Neurobiology. 75(9):961-83

Fan, C., Ouyang, Y., Yuan, X., Wang, J. (2022) An enhancer trap zebrafish line for lateral line development and regulation of six2b expression. Gene expression patterns : GEP. 43:119231

Fang, Y., Gupta, V., Karra, R., Holdway, J.E., Kikuchi, K., and Poss, K.D. (2013) Translational profiling of cardiomyocytes identifies an early Jak1/Stat3 injury response required for zebrafish heart regeneration. Proceedings of the National Academy of Sciences of the United States of America. 110(33):13416-13421

Fekany-Lee, K., Gonzalez, E., Miller-Bertoglio, V., and Solnica-Krezel, L. (2000) The homeobox gene bozozok promotes anterior neuroectoderm formation in zebrafish through negative regulation of BMP2/4 and Wnt pathways. Development (Cambridge, England). 127(11):2333-2345

Ferri-Lagneau, K.F., Moshal, K.S., Grimes, M., Zahora, B., Lv, L., Sang, S., and Leung, T. (2012) Ginger Stimulates Hematopoiesis via Bmp Pathway in Zebrafish. PLoS One. 7(6):e39327

Fisher, S., Amacher, S.L., and Halpern, M.E. (1997) Loss of cerebum function ventralizes the zebrafish embryo. Development (Cambridge, England). 124(7):1301-1311

Folgueira, M., Bayley, P., Navratilova, P., Becker, T.S., Wilson, S.W., and Clarke, J.D. (2012) Morphogenesis underlying the development of the everted teleost telencephalon. Neural Development. 7(1):32

Gago-Rodrigues, I., Fernández-Miñán, A., Letelier, J., Naranjo, S., Tena, J.J., Gómez-Skarmeta, J.L., Martinez-Morales, J.R. (2015) Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis. Nature communications. 6:7054

Galloway, J.L., Wingert, R.A., Thisse, C., Thisse, B., and Zon, L.I. (2005) Loss of gata1 but not gata2 converts erythropoiesis to myelopoiesis in zebrafish embryos. Developmental Cell. 8(1):109-116

Gao, Y., de Wit, M., Struys, E.A., van der Linde, H.C.Z., Salomons, G.S., Lamfers, M.L.M., Willemsen, R., Sillevis Smitt, P.A.E., French, P.J. (2018) IDH1-mutated transgenic zebrafish lines: An in-vivo model for drug screening and functional analysis. PLoS One. 13:e0199737

Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., and Talbot, W.S. (1999) A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome research. 9(4):334-347

Gering, M., Rodaway, A.R.F., Göttgens, B., Patient, R.K., and Green, A.R. (1998) The SCL gene specifies haemangioblast development from early mesoderm. The EMBO journal. 17:4029-4045

Giacomotto, J., Carroll, A.P., Rinkwitz, S., Mowry, B., Cairns, M.J., Becker, T.S. (2016) Developmental suppression of schizophrenia-associated miR-137 alters sensorimotor function in zebrafish. Translational psychiatry. 6:e818

Gioacchino, E., Koyunlar, C., Zink, J., de Looper, H., de Jong, M., Dobrzycki, T., Mahony, C.B., Hoogenboezem, R., Bosch, D., van Strien, P.M.H., van Royen, M.E., French, P.J., Bindels, E., Gussinklo, K.J., Monteiro, R., Touw, I.P., de Pater, E. (2021) Essential role for Gata2 in modulating lineage output from hematopoietic stem cells in zebrafish. Blood advances. 5:2687-2700

Grimm, L., Mason, E., Yu, H., Dudczig, S., Panara, V., Chen, T., Bower, N.I., Paterson, S., Rondon Galeano, M., Kobayashi, S., Senabouth, A., Lagendijk, A.K., Powell, J., Smith, K.A., Okuda, K.S., Koltowska, K., Hogan, B.M. (2023) Single-cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development. The EMBO journal. 42(11):e112590

Guo, L., Yamashita, H., Kou, I., Takimoto, A., Meguro-Horike, M., Horike, S.I., Sakuma, T., Miura, S., Adachi, T., Yamamoto, T., Ikegawa, S., Hiraki, Y., Shukunami, C. (2016) Functional Investigation of a Non-coding Variant Associated with Adolescent Idiopathic Scoliosis in Zebrafish: Elevated Expression of the Ladybird Homeobox Gene Causes Body Axis Deformation. PLoS Genetics. 12:e1005802

Gálvez-Santisteban, M., Chen, D., Zhang, R., Serrano, R., Nguyen, C., Zhao, L., Nerb, L., Masutani, E.M., Vermot, J., Burns, C.G., Burns, C.E., Del Álamo, J.C., Chi, N.C. (2019) Hemodynamic-mediated endocardial signaling controls in vivo myocardial reprogramming. eLIFE. 8:

Hammerschmidt, M., Pelegri, F., Mullins, M.C., Kane, D.A., van Eeden, F.J., Granato, M., Brand, M., Furutani-Seiki, M., Haffter, P., Heisenberg, C.P., Jiang, Y.J., Kelsh, R.N., Odenthal, J., Warga, R.M., and Nüsslein-Volhard, C. (1996) dino and mercedes, two genes regulating dorsal development in the zebrafish embryo. Development (Cambridge, England). 123:95-102

Hart, D.O., Raha, T., Lawson, N.D., and Green, M.R. (2007) Initiation of zebrafish haematopoiesis by the TATA-box-binding protein-related factor Trf3. Nature. 450(7172):1082-1085

Harvey, S.A., Tümpel, S., Dubrulle, J., Schier, A.F., and Smith, J.C. (2010) no tail integrates two modes of mesoderm induction. Development (Cambridge, England). 137(7):1127-1135

Heicklen-Klein, A., McReynolds, L.J., and Evans, T. (2005) Using the zebrafish model to study GATA transcription factors. Seminars in cell & developmental biology. 16(1):95-106

Hsia, N., and Zon, L.I. (2005) Transcriptional regulation of hematopoietic stem cell development in zebrafish. Experimental hematology. 33(9):1007-1014

Hsu, J., Huang, H.T., Lee, C.T., Choudhuri, A., Wilson, N.K., Abraham, B.J., Moignard, V., Kucinski, I., Yu, S., Hyde, R.K., Tober, J., Cai, X., Li, Y., Guo, Y., Yang, S., Superdock, M., Trompouki, E., Calero-Nieto, F.J., Ghamari, A., Jiang, J., Gao, P., Gao, L., Nguyen, V., Robertson, A.L., Durand, E.M., Kathrein, K.L., Aifantis, I., Gerber, S.A., Tong, W., Tan, K., Cantor, A.B., Zhou, Y., Liu, P.P., Young, R.A., Göttgens, B., Speck, N.A., Zon, L.I. (2020) CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. Proceedings of the National Academy of Sciences of the United States of America. 117(38):23626-23635

Huang, C., Gu, S., Yu, P., Yu, F., Feng, C., Gao, N., and Du, J. (2010) Deficiency of smarcal1 causes cell cycle arrest and developmental abnormalities in zebrafish. Developmental Biology. 339(1):89-100

Imai,Y. and Talbot, W.S. (2001) Morpholino phenocopies of the bmp2b/swirl and bmp7/snailhouse mutations. Genesis (New York, N.Y. : 2000). 30(3):160-163

Irimia, M., Royo, J.L., Burguera, D., Maeso, I., Gómez-Skarmeta, J.L., and Garcia-Fernandez, J. (2012) Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. Scientific Reports. 2:433

Ishibashi, M., Manning, E., Shoubridge, C., Krecsmarik, M., Hawkins, T.A., Giacomotto, J., Zhao, T., Mueller, T., Bader, P.I., Cheung, S.W., Stankiewicz, P., Bain, N.L., Hackett, A., Reddy, C.C., Mechaly, A.S., Peers, B., Wilson, S.W., Lenhard, B., Bally-Cuif, L., Gecz, J., Becker, T.S., Rinkwitz, S. (2015) Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. Human genetics. 134(11-12):1163-82

Issa, F.A., Mazzochi, C., Mock, A.F., and Papazian, D.M. (2011) Spinocerebellar ataxia type 13 mutant potassium channel alters neuronal excitability and causes locomotor deficits in zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31(18):6831-6841

Jagannathan-Bogdan, M., and Zon, L.I. (2013) Hematopoiesis. Development (Cambridge, England). 140(12):2463-2467

Jasuja, R., Ge, G., Voss, N.G., Lyman-Gingerich, J., Branam, A.M., Pelegri, F.J., and Greenspan, D.S. (2007) Bone morphogenetic protein 1 prodomain specifically binds and regulates signaling by bone morphogenetic proteins 2 and 4. The Journal of biological chemistry. 282(12):9053-9062

Jessen, J.R., Meng, A., McFarlane, R.J., Paw, B.H., Zon, L.I., Smith, G.R., and Lin, S. (1998) Modification of bacterial artificial chromosomes through Chi-stimulated homologous recombination and its application in zebrafish transgenesis. Proceedings of the National Academy of Sciences of the United States of America. 95:5121-5126

Jia, S., Dai, F., Wu, D., Lin, X., Xing, C., Xue, Y., Wang, Y., Xiao, M., Wu, W., Feng, X.H., and Meng, A. (2012) Protein Phosphatase 4 Cooperates with Smads to Promote BMP Signaling in Dorsoventral Patterning of Zebrafish Embryos. Developmental Cell. 22(5):1065-1078

Juarez, M.A., Su, F., Chun, S., Kiel, M.J., and Lyons, S.E. (2005) Distinct roles for Scl in erythroid specification and maturation in zebrafish. The Journal of biological chemistry. 280(50):41636-41644

Justice, C.M., Kim, J., Kim, S.D., Kim, K., Yagnik, G., Cuellar, A., Carrington, B., Lu, C.L., Sood, R., Boyadjiev, S.A., Wilson, A.F. (2017) A variant associated with sagittal nonsyndromic craniosynostosis alters the regulatory function of a non-coding element. American journal of medical genetics. Part A. 173(11):2893-2897

Kawahara, A. and Dawid, I.B. (2001) Critical role of biklf in erythroid cell differentiation in zebrafish. Current biology : CB. 11(17):1353-1357

Ketharnathan, S., Leask, M., Boocock, J., Phipps-Green, A.J., Antony, J., O'Sullivan, J.M., Merriman, T.R., Horsfield, J.A. (2018) A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression. Human molecular genetics. 27(22):3964-3973

Kimura, Y., Satou, C., and Higashijima, S.I. (2008) V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord. Development (Cambridge, England). 135(18):3001-3005

Kok, F.O., Shin, M., Ni, C., Gupta, A., Grosse, A.S., van Impel, A., Kirchmaier, B.C., Peterson-Maduro, J., Kourkoulis, G., Male, I., DeSantis, D.F., Sheppard-Tindell, S., Ebarasi, L., Betsholtz, C., Schulte-Merker, S., Wolfe, S.A., Lawson, N.D. (2015) Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish. Developmental Cell. 32(1):97-108

Konantz, M., Alghisi, E., Müller, J.S., Lenard, A., Esain, V., Carroll, K.J., Kanz, L., North, T.E., Lengerke, C. (2016) Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence. The EMBO journal. 35(21):2315-2331

Krens, S.F., He, S., Lamers, G.E., Meijer, A.H., Bakkers, J., Schmidt, T., Spaink, H.P., and Snaar-Jagalska, B.E. (2008) Distinct functions for ERK1 and ERK2 in cell migration processes during zebrafish gastrulation. Developmental Biology. 319(2):370-383

Kulkeaw, K., Inoue, T., Ishitani, T., Nakanishi, Y., Zon, L.I., Sugiyama, D. (2017) Purification of zebrafish erythrocytes as a means of identifying a novel regulator of haematopoiesis. British journal of haematology. 180(3):420-431

Kumari, J., Bogwald, J., and Dalmo, R.A. (2009) Transcription factor GATA-3 in Atlantic salmon (Salmo salar): molecular characterization, promoter activity and expression analysis. Molecular immunology. 46(15):3099-3107

Labalette, C., Bouchoucha, Y.X., Wassef, M.A., Gongal, P.A., Le Men, J., Becker, T., Gilardi-Hebenstreit, P., and Charnay, P. (2011) Hindbrain patterning requires fine-tuning of early krox20 transcription by Sprouty 4. Development (Cambridge, England). 138(2):317-326

Law, S.H., and Sargent, T.D. (2013) Maternal pak4 Expression is Required for Primitive Myelopoiesis in Zebrafish. Mechanisms of Development. 130(2-3):181-194

Letelier, J., de la Calle-Mustienes, E., Pieretti, J., Naranjo, S., Maeso, I., Nakamura, T., Pascual-Anaya, J., Shubin, N.H., Schneider, I., Martinez-Morales, J.R., Gómez-Skarmeta, J.L. (2018) A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins. Nature Genetics. 50(4):504-509

Li, G., Sun, Y., Kwok, I., Yang, L., Wen, W., Huang, P., Wu, M., Li, J., Huang, Z., Liu, Z., He, S., Peng, W., Bei, J.X., Ginhoux, F., Ng, L.G., Zhang, Y. (2024) Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish. Nature communications. 15:811811

Li, L., Chen, D., Li, J., Wang, X., Wang, N., Xu, C., and Wang, Q.K. (2014) Aggf1 acts at the top of the genetic regulatory hierarchy in specification of hemangioblasts in zebrafish. Blood. 123(4):501-8

Li, X., Jia, S., Wang, S., Wang, Y., and Meng, A. (2009) Mta3-NuRD complex is a master regulator for initiation of primitive hematopoiesis in vertebrate embryos. Blood. 114(27):5464-5472

Liang, D., Jia, W., Li, J., Li, K., and Zhao, Q. (2012) Retinoic Acid signaling plays a restrictive role in zebrafish primitive myelopoiesis. PLoS One. 7(2):e30865

Lim, S., Kumari, P., Gilligan, P., Quach, H.N., Mathavan, S., and Sampath, K. (2012) Dorsal activity of maternal squint is mediated by a non-coding function of the RNA. Development (Cambridge, England). 139(16):2903-2915

Little, S.C., and Mullins, M.C. (2009) Bone morphogenetic protein heterodimers assemble heteromeric type I receptor complexes to pattern the dorsoventral axis. Nature cell biology. 11(5):637-643

Liu, F., Walmsley, M., Rodaway, A., and Patient, R. (2008) Fli1 Acts at the Top of the Transcriptional Network Driving Blood and Endothelial Development. Current biology : CB. 18(16):1234-1240

Liu, H., Leslie, E.J., Carlson, J.C., Beaty, T.H., Marazita, M.L., Lidral, A.C., Cornell, R.A. (2017) Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting. Nature communications. 8:14759

Liu, P., Luk, K., Shin, M., Idrizi, F., Kwok, S., Roscoe, B., Mintzer, E., Suresh, S., Morrison, K., Frazão, J.B., Bolukbasi, M.F., Ponnienselvan, K., Luban, J., Zhu, L.J., Lawson, N.D., Wolfe, S.A. (2019) Enhanced Cas12a editing in mammalian cells and zebrafish. Nucleic acids research. 47(8):4169-4180

Liu, X., Xiong, C., Jia, S., Zhang, Y., Chen, Y.G., Wang, Q., and Meng, A. (2013) Araf kinase antagonizes Nodal-Smad2 activity in mesendoderm development by directly phosphorylating the Smad2 linker region. Nature communications. 4:1728

Liu, Y., Junaid, M., Wang, Y., Tang, Y.M., Bian, W.P., Xiong, W.X., Huang, H.Y., Chen, C.D., Pei, D.S. (2018) New toxicogenetic insights and ranking of the selected pharmaceuticals belong to the three different classes: A toxicity estimation to confirmation approach. Aquatic toxicology (Amsterdam, Netherlands). 201:151-161

Liu, Y., Lin, Z., Sun, H. (2020) Cystic fibrosis transmembrane conductance regulator (CFTR) regulates embryonic organizer formation during zebrafish early embryogenesis. The International journal of developmental biology. 64:409-413

Lobo, G.P., Isken, A., Hoff, S., Babino, D., and von Lintig, J. (2012) BCDO2 acts as a carotenoid scavenger and gatekeeper for the mitochondrial apoptotic pathway. Development (Cambridge, England). 139(16):2966-2977

Londin, E.R., Mentzer, L., and Sirotkin, H.I. (2007) Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling. BMC Developmental Biology. 7(1):120

Lu, Y., Xie, S., Zhang, W., Zhang, C., Gao, C., Sun, Q., Cai, Y., Xu, Z., Xiao, M., Xu, Y., Huang, X., Wu, X., Liu, W., Wang, F., Kang, Y., Zhou, T. (2017) Twa1/Gid8 is a β-catenin nuclear retention factor in Wnt signaling and colorectal tumorigenesis. Cell Research. 27(12):1422-1440

Lyman Gingerich, J., Westfall, T.A., Slusarski, D.C., and Pelegri, F. (2005) hecate, a zebrafish maternal effect gene, affects dorsal organizer induction and intracellular calcium transient frequency. Developmental Biology. 286(2):427-439

Macaulay, I.C., Svensson, V., Labalette, C., Ferreira, L., Hamey, F., Voet, T., Teichmann, S.A., Cvejic, A. (2016) Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. Cell Reports. 14(4):966-77

Mai, J., Yang, L., Wang, M., Deng, J.M., Min, M., Xie, H.J., Jiang, Y.M., Sun, H.Q., Liu, X.J. (2025) Elevated Serum Homocysteine Levels Impair Embryonic Neurodevelopment by Dysregulating the Heat Shock Proteins. Developmental Neurobiology. 85:e22958e22958

Marlétaz, F., Firbas, P.N., Maeso, I., Tena, J.J., Bogdanovic, O., Perry, M., Wyatt, C.D.R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R.D., van Heeringen, S.J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I., Permanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon, A., Subirana, L., Balwierz, P.J., Duckett, P.E., Farahani, E., Aury, J.M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutiérrez, È., Cañestro, C., Castro, F., D'Aniello, S., Ferrier, D.E.K., Huang, S., Laudet, V., Marais, G.A.B., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I., Takahashi, T., Mirabeau, O., Xu, A., Yu, J.K., Carninci, P., Martinez-Morales, J.R., Crollius, H.R., Kozmik, Z., Weirauch, M.T., Garcia-Fernàndez, J., Lister, R., Lenhard, B., Holland, P.W.H., Escriva, H., Gómez-Skarmeta, J.L., Irimia, M. (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 564:64-70

Mathewson, A.W., Berman, D., Moens, C.B. (2019) Microtubules are required for the maintenance of planar cell polarity in monociliated floorplate cells. Developmental Biology. 452(1):21-33

McFarland, K.N., Warga, R.M., and Kane, D.A. (2005) Genetic locus half baked is necessary for morphogenesis of the ectoderm. Developmental Dynamics : an official publication of the American Association of Anatomists. 233(2):390-406

McReynolds, L.J., Gupta, S., Figueroa, M.E., Mullins, M.C., and Evans, T. (2007) Smad1 and Smad5 differentially regulate embryonic hematopoiesis. Blood. 110(12):3881-3890

Meier, M., Grant, J., Dowdle, A., Thomas, A., Gerton, J., Collas, P., O'Sullivan, J.M., Horsfield, J.A. (2017) Cohesin facilitates zygotic genome activation in zebrafish. Development (Cambridge, England). 145(1)

Mintzer, K.A., Lee, M.A., Runke, G., Trout, J., Whitman, M., and Mullins, M.C. (2001) lost-a-fin encodes a type I BMP receptor, Alk8, acting maternally and zygotically in dorsoventral pattern formation. Development (Cambridge, England). 128(6):859-869

Mommaerts, H., Esguerra, C.V., Hartmann, U., Luyten, F.P., Tylzanowski, P. (2014) Smoc2 modulates embryonic myelopoiesis during zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 243(11):1375-90

Moore, J.C., Sheppard, S., Shestopalov, I.A., Chen, J.K., and Lawson, N. (2013) Post-transcriptional mechanisms contribute to Etv2 repression during vascular development. Developmental Biology. 384(1):128-40

Morley, R.H., Lachani, K., Keefe, D., Gilchrist, M.J., Flicek, P., Smith, J.C., and Wardle, F.C. (2009) A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. Proceedings of the National Academy of Sciences of the United States of America. 106(10):3829-3834

Murat El Houdigui, S., Adam-Guillermin, C., Armant, O. (2020) Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish. International Journal of Molecular Sciences. 21(11)

Naranjo, S., Voesenek, K., de la Calle-Mustienes, E., Robert-Moreno, A., Kokotas, H., Grigoriadou, M., Economides, J., Van Camp, G., Hilgert, N., Moreno, F., Alsina, B., Petersen, M.B., Kremer, H., and Gómez-Skarmeta, J.L. (2010) Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing. Human genetics. 128(4):411-419

Nasevicius, A., Hyatt, T., Kim, H., Guttman, J., Walsh, E., Sumanas, S., Wang, Y.S., and Ekker, S.C. (1998) Evidence for a fizzled-mediated wnt pathway required for zebrafish dorsal mesoderm formation. Development (Cambridge, England). 125:4283-4292

Navratilova, P., Fredman, D., Hawkins, T.A., Turner, K., Lenhard, B., and Becker, T.S. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Developmental Biology. 327(2):526-540

Neumann, J.C., Chandler, G.L., Damoulis, V.A., Fustino, N.J., Lillard, K., Looijenga, L., Margraf, L., Rakheja, D., and Amatruda, J.F. (2011) Mutation in the type IB bone morphogenetic protein receptor alk6b impairs germ-cell differentiation and causes germ-cell tumors in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 108(32):13153-8

Nishiyama, T., Kaneda, R., Ono, T., Tohyama, S., Hashimoto, H., Endo, J., Tsuruta, H., Yuasa, S., Ieda, M., Makino, S., and Fukuda, K. (2012) miR-142-3p is essential for hematopoiesis and affects cardiac cell fate in zebrafish. Biochemical and Biophysical Research Communications. 425(4):755-761

Novikov, N., and Evans, T. (2013) Tmem88a mediates GATA-dependent specification of cardiomyocyte progenitors by restricting WNT signaling. Development (Cambridge, England). 140(18):3787-98

Ogura, E., Okuda, Y., Kondoh, H., and Kamachi, Y. (2009) Adaptation of GAL4 activators for GAL4 enhancer trapping in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(3):641-655

Ong, S.L.M., de Vos, I.J.H.M., Meroshini, M., Poobalan, Y., Dunn, N.R. (2020) Microfibril-associated glycoprotein 4 (Mfap4) regulates haematopoiesis in zebrafish. Scientific Reports. 10:11801

Paik, E.J., and Zon, L.I. (2010) Hematopoietic development in the zebrafish. The International journal of developmental biology. 54(6-7):1127-1137

Parichy, D.M., Rawls, J.F., Pratt, S.J., Whitfield, T.T., and Johnson, S.L. (1999) Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development. Development (Cambridge, England). 126(15):3425-3436

Patil, P., Uechi, T., Kenmochi, N. (2015) Incomplete splicing of neutrophil-specific genes affects neutrophil development in a zebrafish model of poikiloderma with neutropenia. RNA Biology. 12:426-434

Patterson, L.J., Gering, M., Eckfeldt, C.E., Green, A.R., Verfaillie, C.M., Ekker, S.C., and Patient, R. (2007) The transcription factors, Scl and Lmo2, act together during development of the hemangioblast in zebrafish. Blood. 109(6):2389-2398

Penberthy, W.T., Zhao, C., Zhang, Y., Jessen, J.R., Yang, Z., Bricaud, O., Collazo, A., Meng, A., and Lin, S. (2004) Pur alpha and Sp8 as opposing regulators of neural gata2 expression. Developmental Biology. 275(1):225-234

Perez-Camps, M., Tian, J., Chng, S.C., Sem, K.P., Sudhaharan, T., Teh, C., Wachsmuth, M., Korzh, V., Ahmed, S., Reversade, B. (2016) Quantitative imaging reveals real-time Pou5f3-Nanog complexes driving dorsoventral mesendoderm patterning in zebrafish. eLIFE. 5

Peterkin, T., Gibson, A., and Patient, R. (2009) Common genetic control of haemangioblast and cardiac development in zebrafish. Development (Cambridge, England). 136(9):1465-1474

Peña, O.A., Lubin, A., Rowell, J., Hoade, Y., Khokhar, N., Lemmik, H., Mahony, C., Dace, P., Umamahesan, C., Payne, E.M. (2021) Differential Requirement of Gata2a and Gata2b for Primitive and Definitive Myeloid Development in Zebrafish. Frontiers in cell and developmental biology. 9:708113

Pineda, R.H., Svoboda, K.R., Wright, M.A., Taylor, A.D., Novak, A.E., Gamse, J.T., Eisen, J.S., and Ribera, A.B. (2006) Knockdown of Nav1.6a Na+ channels affects zebrafish motoneuron development. Development (Cambridge, England). 133(19):3827-3836

Prendergast, A.E., Jim, K.K., Marnas, H., Desban, L., Quan, F.B., Djenoune, L., Laghi, V., Hocquemiller, A., Lunsford, E.T., Roussel, J., Keiser, L., Lejeune, F.X., Dhanasekar, M., Bardet, P.L., Levraud, J.P., van de Beek, D., Vandenbroucke-Grauls, C.M.J.E., Wyart, C. (2023) CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection. Current biology : CB. 33(5):940-956.e10

Punnamoottil, B., Kikuta, H., Pezeron, G., Erceg, J., Becker, T.S., and Rinkwitz, S. (2008) Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(8):2195-2208

Ragvin, A., Moro, E., Fredman, D., Navratilova, P., Drivenes, O., Engström, P.G., Alonso, M.E., Mustienes, E.D., Gomez Skarmeta, J.L., Tavares, M.J., Casares, F., Manzanares, M., van Heyningen, V., Molven, A., Njølstad, P.R., Argenton, F., Lenhard, B., and Becker, T.S. (2010) Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proceedings of the National Academy of Sciences of the United States of America. 107(2):775-780

Ransom, D.G., Bahary, N., Niss, K., Traver, D., Burns, C., Trede, N.S., Paffett-Lugassy, N., Saganic, W.J., Lim, C.A., Hersey, C., Zhou, Y., Barut, B.A., Lin, S., Kingsley, P.D., Palis, J., Orkin, S.H., and Zon, L.I. (2004) The Zebrafish moonshine Gene Encodes Transcriptional Intermediary Factor 1gamma, an Essential Regulator of Hematopoiesis. PLoS Biology. 2(8):E237

Ravi, V., Bhatia, S., Gautier, P., Loosli, F., Tay, B.H., Tay, A., Murdoch, E., Coutinho, P., van Heyningen, V., Brenner, S., Venkatesh, B., and Kleinjan, D.A. (2013) Sequencing of pax6 Loci from the elephant shark reveals a family of pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. PLoS Genetics. 9(1):e1003177

Regadas, I., Matos, M.R., Monteiro, F.A., Gomez-Skarmeta, J.L., Lima, D., Bessa, J., Casares, F., and Reguenga, C. (2013) Several Cis-regulatory Elements Control mRNA Stability, Translation Efficiency, and Expression Pattern of Prrxl1 (Paired Related Homeobox Protein-like 1). The Journal of biological chemistry. 288(51):36285-301

Rentzsch, F., Bakkers, J., Kramer, C., and Hammerschmidt, M. (2004) Fgf signaling induces posterior neuroectoderm independently of Bmp signaling inhibition. Developmental Dynamics : an official publication of the American Association of Anatomists. 231(4):750-757

Rinkwitz, S., Geng, F., Manning, E., Suster, M., Kawakami, K., Becker, T.S. (2015) BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene. Genesis (New York, N.Y. : 2000). 53(10):640-51

Rohde, L.A., Oates, A.C., and Ho, R.K. (2004) A Crucial Interaction between Embryonic Red Blood Cell Progenitors and Paraxial Mesoderm Revealed in spadetail Embryos. Developmental Cell. 7(2):251-262

Ross, J.J., Shimmi, O., Vilmos, P., Petryk, A., Kim, H., Gaudenz, K., Hermanson, S., Ekker, S.C., O'Connor, M.B., and Marsh, J.L. (2001) Twisted gastrulation is a conserved extracellular BMP antagonist. Nature. 410(6827):479-483

Royo, J.L., Hidalgo, C., Roncero, Y., Seda, M.A., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2011) Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One. 6(9):e24824

Sabel, J.L., d'Alençon, C., O'Brien, E.K., Otterloo, E.V., Lutz, K., Cuykendall, T.N., Schutte, B.C., Houston, D.W., and Cornell, R.A. (2009) Maternal Interferon Regulatory Factor 6 is required for the differentiation of primary superficial epithelia in Danio and Xenopus embryos. Developmental Biology. 325(1):249-262

Santos, M.E., Braasch, I., Boileau, N., Meyer, B.S., Sauteur, L., Böhne, A., Belting, H.G., Affolter, M., Salzburger, W. (2014) The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature communications. 5:5149

Schafer, M., Kinzel, D., and Winkler, C. (2007) Discontinuous organization and specification of the lateral floor plate in zebrafish. Developmental Biology. 301(1):117-129

Schötz, E.M., Burdine, R.D., Jülicher, F., Steinberg, M.S., Heisenberg, C.P., and Foty, R.A. (2008) Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2(1):42-56

Shah, M.H., Tabanera, N., Krishnadas, S.R., Pillai, M.R., Bovolenta, P., Sundaresan, P. (2017) Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma.. Molecular genetics & genomic medicine. 5:323-335

Shao, M., Wang, M., Liu, Y.Y., Ge, Y.W., Zhang, Y.J., Shi, D.L. (2017) Vegetally localised Vrtn functions as a novel repressor to modulate bmp2b transcription during dorsoventral patterning in zebrafish.. Development (Cambridge, England). 144:3361-3374

Shao, T., Zhu, L.Y., Nie, L., Shi, W., Dong, W.R., Xiang, L.X., Shao, J.Z. (2015) Characterization of surface phenotypic molecules of teleost dendritic cells. Developmental and comparative immunology. 49:38-43

Shen, L., Zhu, J., Chen, F., Lin, W., Cai, J., Zhong, J., Zhong, H. (2015) RUNX1-Evi-1 fusion gene inhibited differentiation and apoptosis in myelopoiesis: an in vivo study. BMC cancer. 15:970

Shi, G., Cui, Q., Pan, Y., Sheng, N., Guo, Y., Dai, J. (2017) 6:2 fluorotelomer carboxylic acid (6:2 FTCA) exposure induces developmental toxicity and inhibits the formation of erythrocytes during zebrafish embryogenesis. Aquatic toxicology (Amsterdam, Netherlands). 190:53-61

Shimizu, T., Bae, Y.K., Muraoka, O., and Hibi, M. (2005) Interaction of Wnt and caudal-related genes in zebrafish posterior body formation. Developmental Biology. 279(1):125-141

Shin, M., Yin, H.M., Shih, Y.H., Nozaki, T., Portman, D., Toles, B., Kolb, A., Luk, K., Isogai, S., Ishida, K., Hanasaka, T., Parsons, M.J., Wolfe, S.A., Burns, C.E., Burns, C.G., Lawson, N.D. (2023) Generation and application of endogenously floxed alleles for cell-specific knockout in zebrafish. Developmental Cell. 58(22):2614-2626.e7

Spieler, D., Kaffe, M., Knauf, F., Bessa, J., Tena, J.J., Giesert, F., Schormair, B., Tilch, E., Lee, H., Horsch, M., Czamara, D., Karbalai, N., von Toerne, C., Waldenberger, M., Gieger, C., Lichtner, P., Claussnitzer, M., Naumann, R., Müller-Myhsok, B., Torres, M., Garrett, L., Rozman, J., Klingenspor, M., Gailus-Durner, V., Fuchs, H., Hrabě de Angelis, M., Beckers, J., Holter, S.M., Meitinger, T., Hauck, S.M., Laumen, H., Wurst, W., Casares, F., Gómez-Skarmeta, J.L., Winkelmann, J. (2014) Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon. Genome research. 24:592-603

Steed, E., Faggianelli, N., Roth, S., Ramspacher, C., Concordet, J.P., Vermot, J. (2016) klf2a couples mechanotransduction and zebrafish valve morphogenesis through fibronectin synthesis. Nature communications. 7:11646

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Sun, H., Wang, Y., Zhang, J., Chen, Y., Liu, Y., Lin, Z., Liu, M., Sheng, K., Liao, H., Tsang, K.S., Zhang, X., Jiang, X., Xu, W., Mao, M., Chan, H.C. (2018) CFTR mutation enhances Dishevelled degradation and results in impairment of Wnt-dependent hematopoiesis. Cell Death & Disease. 9:275

Svoboda, O., Stachura, D.L., Machonova, O., Zon, L.I., Traver, D., Bartunek, P. (2016) Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature Protocols. 11:1007-1020

Takeuchi, M., Fuse, Y., Watanabe, M., Andrea, C.S., Takeuchi, M., Nakajima, H., Ohashi, K., Kaneko, H., Kobayashi-Osaki, M., Yamamoto, M., Kobayashi, M. (2015) LSD1/KDM1A promotes hematopoietic commitment of hemangioblasts through downregulation of Etv2. Proceedings of the National Academy of Sciences of the United States of America. 112(45):13922-7

Tena, J.J., Alonso, M.E., de la Calle-Mustienes, E., Splinter, E., de Laat, W., Manzanares, M., and Gómez-Skarmeta, J.L. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nature communications. 2:310

Thompson, M.A., Ransom, D.G., Pratt, S.J., MacLennan, H., Kieran, M.W., Detrich,III, H.W., Vail, B., Huber, T.L., Paw, B., Brownlie, A.J., Oates, A.C., Fritz, A., Gates, MA., Amores, A., Bahary, N., Talbot, W.S., Her, H., Beier, D.R., Postlethwait, J.H., and Zon, L.I. (1998) The cloche and spadetail genes differentially affect hematopoiesis and vasculogenesis. Developmental Biology. 197:248-269

Tse, W.K., Eisenhaber, B., Ho, S.H., Ng, Q., Eisenhaber, F., and Jiang, Y.J. (2009) Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. BMC Genomics. 10:637

Tuazon, F.B., Wang, X., Andrade, J.L., Umulis, D., Mullins, M.C. (2020) Proteolytic Restriction of Chordin Range Underlies BMP Gradient Formation. Cell Reports. 32:108039

Vermot, J., Forouhar, A.S., Liebling, M., Wu, D., Plummer, D., Gharib, M., and Fraser, S.E. (2009) Reversing blood flows act through klf2a to ensure normal valvulogenesis in the developing heart. PLoS Biology. 7(11):e1000246

Wang, H., Lapek, J., Fujimura, K., Strnadel, J., Liu, B., Gonzalez, D.J., Zhang, W., Watson, F., Yu, V., Liu, C., Melo, C.M., Miller, Y.I., Elliott, K.C., Cheresh, D.A., Klemke, R.L. (2018) Pseudopodium-enriched atypical kinase 1 mediates angiogenesis by modulating GATA2-dependent VEGFR2 transcription. Cell discovery. 4:26

Wang, L., Shang, N., Feng, H., Guo, Q., and Dai, H. (2013) Molecular cloning of grass carp (Ctenopharyngodon idellus) T-bet and GATA-3, and their expression profiles with IFN-γ in response to grass carp reovirus (GCRV) infection. Fish physiology and biochemistry. 39(4):793-805

Wang, Y.S., Chen, Y.T., Wu, C.Y. (2023) Functional characterization of stap2b in zebrafish vascular development. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 37:e23053e23053

Wei, S., Shang, H., Cao, Y., Wang, Q. (2016) The coiled-coil domain containing protein Ccdc136b antagonizes maternal Wnt/β-catenin activity during zebrafish dorsoventral axial patterning. Journal of genetics and genomics = Yi chuan xue bao. 43(7):431-8

Wen, L., Wei, W., Gu, W., Huang, P., Ren, X., Zhang, Z., Zhu, Z., Lin, S., and Zhang, B. (2008) Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Developmental Biology. 314(1):84-92

Wong, K.S., Proulx, K., Rost, M.S., and Sumanas, S. (2009) Identification of vasculature-specific genes by microarray analysis of etsrp/etv2 overexpressing zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(7):1836-1850

Xie, J., and Fisher, S. (2005) Twisted gastrulation enhances BMP signaling through chordin dependent and independent mechanisms. Development (Cambridge, England). 132(2):383-391

Xie, X.W., Liu, J.X., Hu, B., and Xiao, W. (2011) Zebrafish foxo3b Negatively Regulates Canonical Wnt Signaling to Affect Early Embryogenesis. PLoS One. 6(9):e24469

Xiong, B., Rui, Y., Zhang, M., Shi, K., Jia, S., Tian, T., Yin, K., Huang, H., Lin, S., Zhao, X., Chen, Y., Chen, Y.G., Lin, S.C., and Meng, A. (2006) Tob1 controls dorsal development of zebrafish embryos by antagonizing maternal beta-catenin transcriptional activity. Developmental Cell. 11(2):225-238

Yamauchi, H., Hotta, Y., Konishi, M., Miyake, A., Kawahara, A., and Itoh, N. (2006) Fgf21 is essential for haematopoiesis in zebrafish. EMBO reports. 7(6):649-654

Yan, Y., Ning, G., Li, L., Liu, J., Yang, S., Cao, Y., Wang, Q. (2019) The BMP ligand Pinhead together with Admp supports the robustness of embryonic patterning. Science advances. 5:eaau6455

Yang, L., Rastegar, S., and Strähle, U. (2010) Regulatory interactions specifying Kolmer-Agduhr interneurons. Development (Cambridge, England). 137(16):2713-2722

Ye, D., Yang, Q., Li, Y., Huang, X., Hu, J., Qian, S., Tan, Z., and Song, P. (2011) G{alpha}(13) is closely related to hematopoiesis in zebrafish. Molecular biology reports. 38(4):2685-2694

Young, S.R., Mumaw, C., Marrs, J.A., and Skalnik, D.G. (2006) Antisense targeting of CXXC finger protein 1 inhibits genomic cytosine methylation and primitive hematopoiesis in zebrafish. The Journal of biological chemistry. 281(48):37034-37044

Yu, S.R., Burkhardt, M., Nowak, M., Ries, J., Petrášek, Z., Scholpp, S., Schwille, P., and Brand, M. (2009) Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules. Nature. 461(7263):533-536

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

Zhang, Z., Qin, Z. (2018) Characterization of Midkine in tongue sole (Cynoglossus semilaevis)and its role on the germ layer genesis in zebrafish (Danio rerio). Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology. 226:64-72

Zhou, X., Xiao, C., Li, Y., Shang, Y., Yin, D., Li, S., Xiang, B., Lu, R., Ji, Y., Wu, Y., Meng, W., Zhu, H., Liu, J., Hu, H., Mo, X., Xu, H. (2018) Mid1ip1b modulates apical reorientation of non-centrosomal microtubule organizing center in epithelial cells. Journal of genetics and genomics = Yi chuan xue bao. 45(8):433-442

Zhu, L., Wang, C., Jiang, H., Zhang, L., Mao, L., Zhang, Y., Qi, S., Liu, X. (2022) Quizalofop-P-ethyl induced developmental toxicity and cardiotoxicity in early life stage of zebrafish (Danio rerio). Ecotoxicology and environmental safety. 238:113596

Mai, J., Yang, L., Wang, M., Deng, J.M., Min, M., Xie, H.J., Jiang, Y.M., Sun, H.Q., Liu, X.J. (2025) Elevated Serum Homocysteine Levels Impair Embryonic Neurodevelopment by Dysregulating the Heat Shock Proteins. Developmental Neurobiology. 85:e22958e22958

D'haene, E., López-Soriano, V., Martínez-García, P.M., Kalayanamontri, S., Rey, A.D., Sousa-Ortega, A., Naranjo, S., Van de Sompele, S., Vantomme, L., Mahieu, Q., Vergult, S., Neto, A., Gómez-Skarmeta, J.L., Martínez-Morales, J.R., Bauwens, M., Tena, J.J., De Baere, E. (2024) Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci. Genome biology. 25:123123

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

England, S.J., Rusnock, A.K., Mujcic, A., Kowalchuk, A., de Jager, S., Hilinski, W.C., Juárez-Morales, J.L., Smith, M.E., Grieb, G., Banerjee, S., Lewis, K.E. (2023) Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Development. 18:88

Kondo, M., Kimura, K., Kobayashi-Sun, J., Yamamori, S., Taniguchi, M., Traver, D., Kobayashi, I. (2023) The sinusoidal hematopoietic niche is formed by Jam1a via Notch signaling in the zebrafish kidney. iScience. 26:106508106508

Liu, X., Zhou, L., Li, W., Wu, J., Wang, D. (2023) Gata2a Mutation Causes Progressive Microphthalmia and Blindness in Nile Tilapia. International Journal of Molecular Sciences. 24(4):

Prendergast, A.E., Jim, K.K., Marnas, H., Desban, L., Quan, F.B., Djenoune, L., Laghi, V., Hocquemiller, A., Lunsford, E.T., Roussel, J., Keiser, L., Lejeune, F.X., Dhanasekar, M., Bardet, P.L., Levraud, J.P., van de Beek, D., Vandenbroucke-Grauls, C.M.J.E., Wyart, C. (2023) CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection. Current biology : CB. 33(5):940-956.e10

Wang, Y.S., Chen, Y.T., Wu, C.Y. (2023) Functional characterization of stap2b in zebrafish vascular development. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 37:e23053e23053

Begeman, I.J., Emery, B., Kurth, A., Kang, J. (2022) Regeneration and developmental enhancers are differentially compatible with minimal promoters. Developmental Biology. 492:47-58

Fan, C., Ouyang, Y., Yuan, X., Wang, J. (2022) An enhancer trap zebrafish line for lateral line development and regulation of six2b expression. Gene expression patterns : GEP. 43:119231

Li, L., Chen, M., Liu, W., Tai, P., Liu, X., Liu, J.X. (2022) Zebrafish cox17 modulates primitive erythropoiesis via regulation of mitochondrial metabolism to facilitate hypoxia tolerance. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 36:e22596

Shao, T., Ji, J.F., Zheng, J.Y., Li, C., Zhu, L.Y., Fan, D.D., Lin, A.F., Xiang, L.X., Shao, J.Z. (2022) Zbtb46 Controls Dendritic Cell Activation by Reprogramming Epigenetic Regulation of cd80/86 and cd40 Costimulatory Signals in a Zebrafish Model. Journal of immunology (Baltimore, Md. : 1950). 208(12):2686-2701

Wang, R., Guo, S., Yang, L. (2022) Tal2 is required for generation of GABAergic neurons in the zebrafish midbrain. Developmental Dynamics : an official publication of the American Association of Anatomists. 252(2):263-275

Zhu, L., Wang, C., Jiang, H., Zhang, L., Mao, L., Zhang, Y., Qi, S., Liu, X. (2022) Quizalofop-P-ethyl induced developmental toxicity and cardiotoxicity in early life stage of zebrafish (Danio rerio). Ecotoxicology and environmental safety. 238:113596

Bengani, H., Grozeva, D., Moyon, L., Bhatia, S., Louros, S.R., Hope, J., Jackson, A., Prendergast, J.G., Owen, L.J., Naville, M., Rainger, J., Grimes, G., Halachev, M., Murphy, L.C., Spasic-Boskovic, O., van Heyningen, V., Kind, P., Abbott, C.M., Osterweil, E., Raymond, F.L., Roest Crollius, H., FitzPatrick, D.R. (2021) Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability. PLoS One. 16:e0256181

Fan, X., Yang, H., Hu, L., Wang, D., Wang, R., Hao, A., Chen, X. (2021) Propofol impairs specification of retinal cell types in zebrafish by inhibiting Zisp-mediated Noggin-1 palmitoylation and trafficking. Stem Cell Research & Therapy. 12:195

Gioacchino, E., Koyunlar, C., Zink, J., de Looper, H., de Jong, M., Dobrzycki, T., Mahony, C.B., Hoogenboezem, R., Bosch, D., van Strien, P.M.H., van Royen, M.E., French, P.J., Bindels, E., Gussinklo, K.J., Monteiro, R., Touw, I.P., de Pater, E. (2021) Essential role for Gata2 in modulating lineage output from hematopoietic stem cells in zebrafish. Blood advances. 5:2687-2700

Moreno-Mármol, T., Ledesma-Terrón, M., Tabanera, N., Martin-Bermejo, M.J., Cardozo, M.J., Cavodeassi, F., Bovolenta, P. (2021) Stretching of the retinal pigment epithelium contributes to zebrafish optic cup morphogenesis. eLIFE. 10:

Peña, O.A., Lubin, A., Rowell, J., Hoade, Y., Khokhar, N., Lemmik, H., Mahony, C., Dace, P., Umamahesan, C., Payne, E.M. (2021) Differential Requirement of Gata2a and Gata2b for Primitive and Definitive Myeloid Development in Zebrafish. Frontiers in cell and developmental biology. 9:708113

Amorim, J.P., Gali-Macedo, A., Marcelino, H., Bordeira-Carriço, R., Naranjo, S., Rivero-Gil, S., Teixeira, J., Galhardo, M., Marques, J., Bessa, J. (2020) A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. Cell Reports. 32:107862

Bridoux, L., Zarrineh, P., Mallen, J., Phuycharoen, M., Latorre, V., Ladam, F., Losa, M., Baker, S.M., Sagerstrom, C., Mace, K.A., Rattray, M., Bobola, N. (2020) HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genetics. 16:e1009162

Gallardo-Fuentes, L., Santos-Pereira, J.M., Tena, J.J. (2020) Functional Conservation of Divergent p63-Bound cis-Regulatory Elements. Frontiers in genetics. 11:339

Hsieh, J.Y., Ulrich, B.N., Issa, F.A., Lin, M.A., Brown, B., Papazian, D.M. (2020) Infant and adult SCA13 mutations differentially affect Purkinje cell excitability, maturation, and viability in vivo. eLIFE. 9:

Ji, J.F., Hu, C.B., Shao, T., Fan, D.D., Zhang, N., Lin, A.F., Xiang, L.X., Shao, J.Z. (2020) Differential immune responses of immunoglobulin Z subclass members in antibacterial immunity in a zebrafish model. Immunology. 162(1):105-120

Murat El Houdigui, S., Adam-Guillermin, C., Armant, O. (2020) Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish. International Journal of Molecular Sciences. 21(11)

Pang, S., Gao, Y., Li, A., Yao, X., Qu, G., Hu, L., Liang, Y., Song, M., Jiang, G. (2020) Tetrabromobisphenol A perturbs erythropoiesis and impairs blood circulation in zebrafish embryos. Environmental science & technology. 54(20):12998-13007

Schauer, A., Pinheiro, D., Hauschild, R., Heisenberg, C.P. (2020) Zebrafish embryonic explants undergo genetically encoded self-assembly. eLIFE. 9:

Wong, E.S., Zheng, D., Tan, S.Z., Bower, N.L., Garside, V., Vanwalleghem, G., Gaiti, F., Scott, E., Hogan, B.M., Kikuchi, K., McGlinn, E., Francois, M., Degnan, B.M. (2020) Deep conservation of the enhancer regulatory code in animals. Science (New York, N.Y.). 370(6517):

Chan, S., Shen, D., Sang, Y., Wang, S., Wang, Y., Chen, C., Gao, B., Song, C. (2019) Development of enhancer-trapping and -detection vectors mediated by the Tol2 transposon in zebrafish. PeerJ. 7:e6862

Gálvez-Santisteban, M., Chen, D., Zhang, R., Serrano, R., Nguyen, C., Zhao, L., Nerb, L., Masutani, E.M., Vermot, J., Burns, C.G., Burns, C.E., Del Álamo, J.C., Chi, N.C. (2019) Hemodynamic-mediated endocardial signaling controls in vivo myocardial reprogramming. eLIFE. 8:

Lombardo, V.A., Heise, M., Moghtadaei, M., Bornhorst, D., Männer, J., Abdelilah-Seyfried, S. (2019) Morphogenetic control of zebrafish cardiac looping by Bmp signaling. Development (Cambridge, England). 146(22):

Prummel, K.D., Hess, C., Nieuwenhuize, S., Parker, H.J., Rogers, K.W., Kozmikova, I., Racioppi, C., Brombacher, E.C., Czarkwiani, A., Knapp, D., Burger, S., Chiavacci, E., Shah, G., Burger, A., Huisken, J., Yun, M.H., Christiaen, L., Kozmik, Z., Müller, P., Bronner, M., Krumlauf, R., Mosimann, C. (2019) A conserved regulatory program initiates lateral plate mesoderm emergence across chordates. Nature communications. 10:3857

Shin, M., Nozaki, T., Idrizi, F., Isogai, S., Ogasawara, K., Ishida, K., Yuge, S., Roscoe, B., Wolfe, S.A., Fukuhara, S., Mochizuki, N., Deguchi, T., Lawson, N.D. (2019) Valves Are a Conserved Feature of the Zebrafish Lymphatic System. Developmental Cell. 51(3):374-386.e5

Andrzejczuk, L.A., Banerjee, S., England, S.J., Voufo, C., Kamara, K., Lewis, K.E. (2018) Tal1, Gata2a, and Gata3 Have Distinct Functions in the Development of V2b and Cerebrospinal Fluid-Contacting KA Spinal Neurons. Frontiers in neuroscience. 12:170

Farrell, J.A., Wang, Y., Riesenfeld, S.J., Shekhar, K., Regev, A., Schier, A.F. (2018) Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science (New York, N.Y.). 360(6392)

Jang, H., Oakley, E., Forbes-Osborne, M., Kesler, M., Norcross, R., Morris, A.C., Galperin, E. (2018) Hematopoietic and neural crest defects in zebrafish shoc2 mutants: a novel vertebrate model for Noonan-like syndrome. Human molecular genetics. 28(3):501-514

Letelier, J., de la Calle-Mustienes, E., Pieretti, J., Naranjo, S., Maeso, I., Nakamura, T., Pascual-Anaya, J., Shubin, N.H., Schneider, I., Martinez-Morales, J.R., Gómez-Skarmeta, J.L. (2018) A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins. Nature Genetics. 50(4):504-509

Marlétaz, F., Firbas, P.N., Maeso, I., Tena, J.J., Bogdanovic, O., Perry, M., Wyatt, C.D.R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R.D., van Heeringen, S.J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I., Permanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon, A., Subirana, L., Balwierz, P.J., Duckett, P.E., Farahani, E., Aury, J.M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutiérrez, È., Cañestro, C., Castro, F., D'Aniello, S., Ferrier, D.E.K., Huang, S., Laudet, V., Marais, G.A.B., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I., Takahashi, T., Mirabeau, O., Xu, A., Yu, J.K., Carninci, P., Martinez-Morales, J.R., Crollius, H.R., Kozmik, Z., Weirauch, M.T., Garcia-Fernàndez, J., Lister, R., Lenhard, B., Holland, P.W.H., Escriva, H., Gómez-Skarmeta, J.L., Irimia, M. (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 564:64-70

Shen, D., Xue, S., Chan, S., Sang, Y., Wang, S., Wang, Y., Chen, C., Gao, B., Mueller, F., Song, C. (2018) Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes. 9(12)

Torbey, P., Thierion, E., Collombet, S., de Cian, A., Desmarquet-Trin-Dinh, C., Dura, M., Concordet, J.P., Charnay, P., Gilardi-Hebenstreit, P. (2018) Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation. PLoS Genetics. 14:e1007581

Yan, L., Chen, J., Zhu, X., Sun, J., Wu, X., Shen, W., Zhang, W., Tao, Q., Meng, A. (2018) Maternal Huluwa dictates the embryonic body axis through β-catenin in vertebrates. Science (New York, N.Y.). 362(6417)

Zhang, Z., Qin, Z. (2018) Characterization of Midkine in tongue sole (Cynoglossus semilaevis)and its role on the germ layer genesis in zebrafish (Danio rerio). Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology. 226:64-72

Chiang, I.K., Fritzsche, M., Pichol-Thievend, C., Neal, A., Holmes, K., Lagendijk, A., Overman, J., D'Angelo, D., Omini, A., Hermkens, D., Lesieur, E., Liu, K., Ratnayaka, I., Corada, M., Bou-Gharios, G., Carroll, J., Dejana, E., Schulte-Merker, S., Hogan, B., Beltrame, M., De Val, S., Francois, M. (2017) SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development. Development (Cambridge, England). 144(14):2629-2639

Kulkeaw, K., Inoue, T., Ishitani, T., Nakanishi, Y., Zon, L.I., Sugiyama, D. (2017) Purification of zebrafish erythrocytes as a means of identifying a novel regulator of haematopoiesis. British journal of haematology. 180(3):420-431

Liu, H., Leslie, E.J., Carlson, J.C., Beaty, T.H., Marazita, M.L., Lidral, A.C., Cornell, R.A. (2017) Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting. Nature communications. 8:14759

Lu, Y., Xie, S., Zhang, W., Zhang, C., Gao, C., Sun, Q., Cai, Y., Xu, Z., Xiao, M., Xu, Y., Huang, X., Wu, X., Liu, W., Wang, F., Kang, Y., Zhou, T. (2017) Twa1/Gid8 is a β-catenin nuclear retention factor in Wnt signaling and colorectal tumorigenesis. Cell Research. 27(12):1422-1440

Shah, M.H., Tabanera, N., Krishnadas, S.R., Pillai, M.R., Bovolenta, P., Sundaresan, P. (2017) Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma.. Molecular genetics & genomic medicine. 5:323-335

Shi, G., Cui, Q., Pan, Y., Sheng, N., Guo, Y., Dai, J. (2017) 6:2 fluorotelomer carboxylic acid (6:2 FTCA) exposure induces developmental toxicity and inhibits the formation of erythrocytes during zebrafish embryogenesis. Aquatic toxicology (Amsterdam, Netherlands). 190:53-61

Antosova, B., Smolikova, J., Klimova, L., Lachova, J., Bendova, M., Kozmikova, I., Machon, O., Kozmik, Z. (2016) The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6. PLoS Genetics. 12:e1006441

Becker, P.W., Sacilotto, N., Nornes, S., Neal, A., Thomas, M., Liu, K., Preece, C., Ratnayaka, I., Davies, B., Bou-Gharios, G., De Val, S. (2016) Intronic Flk1 Enhancer Directs Arterial-Specific Expression via RBPJ-Mediated Venous Repression. Arteriosclerosis, Thrombosis, and Vascular Biology. 36(6):1209-19

Cardoso, J.C., Bergqvist, C.A., Felix, R.C., Larhammar, D. (2016) Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages. Journal of molecular endocrinology. 57(1):73-86

Davey, C.F., Mathewson, A.W., Moens, C.B. (2016) PCP Signaling between Migrating Neurons and their Planar-Polarized Neuroepithelial Environment Controls Filopodial Dynamics and Directional Migration. PLoS Genetics. 12:e1005934

Guo, L., Yamashita, H., Kou, I., Takimoto, A., Meguro-Horike, M., Horike, S.I., Sakuma, T., Miura, S., Adachi, T., Yamamoto, T., Ikegawa, S., Hiraki, Y., Shukunami, C. (2016) Functional Investigation of a Non-coding Variant Associated with Adolescent Idiopathic Scoliosis in Zebrafish: Elevated Expression of the Ladybird Homeobox Gene Causes Body Axis Deformation. PLoS Genetics. 12:e1005802

Khatri, D., Zizioli, D., Tiso, N., Facchinello, N., Vezzoli, S., Gianoncelli, A., Memo, M., Monti, E., Borsani, G., Finazzi, D. (2016) Down-regulation of coasy, the gene associated with NBIA-VI, reduces Bmp signaling, perturbs dorso-ventral patterning and alters neuronal development in zebrafish. Scientific Reports. 6:37660

Langdon, Y.G., Fuentes, R., Zhang, H., Abrams, E.W., Marlow, F.L., Mullins, M.C. (2016) Split top: A maternal cathepsin B that regulates dorsoventral patterning and morphogenesis. Development (Cambridge, England). 143(6):1016-28

Macaulay, I.C., Svensson, V., Labalette, C., Ferreira, L., Hamey, F., Voet, T., Teichmann, S.A., Cvejic, A. (2016) Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. Cell Reports. 14(4):966-77

Monteiro, R., Pinheiro, P., Joseph, N., Peterkin, T., Koth, J., Repapi, E., Bonkhofer, F., Kirmizitas, A., Patient, R. (2016) Transforming Growth Factor β Drives Hemogenic Endothelium Programming and the Transition to Hematopoietic Stem Cells. Developmental Cell. 38(4):358-70

Steed, E., Faggianelli, N., Roth, S., Ramspacher, C., Concordet, J.P., Vermot, J. (2016) klf2a couples mechanotransduction and zebrafish valve morphogenesis through fibronectin synthesis. Nature communications. 7:11646

Wei, S., Shang, H., Cao, Y., Wang, Q. (2016) The coiled-coil domain containing protein Ccdc136b antagonizes maternal Wnt/β-catenin activity during zebrafish dorsoventral axial patterning. Journal of genetics and genomics = Yi chuan xue bao. 43(7):431-8

Butko, E., Distel, M., Pouget, C., Weijts, B., Kobayashi, I., Ng, K., Mosimann, C., Poulain, F.E., McPherson, A., Ni, C.W., Stachura, D.L., Del Cid, N., Espín-Palazón, R., Lawson, N.D., Dorsky, R., Clements, W.K., Traver, D. (2015) Gata2b is a restricted early regulator of hemogenic endothelium in the zebrafish embryo. Development (Cambridge, England). 142:1050-61

Diotel, N., Viales, R.R., Armant, O., März, M., Ferg, M., Rastegar, S., Strähle, U. (2015) Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. The Journal of comparative neurology. 523(8):1202-21

Ernest, S., Rosa, F.M. (2015) A genomic region encompassing a newly identified exon provides enhancing activity sufficient for normal myo7aa expression in zebrafish sensory hair cells. Developmental Neurobiology. 75(9):961-83

Gago-Rodrigues, I., Fernández-Miñán, A., Letelier, J., Naranjo, S., Tena, J.J., Gómez-Skarmeta, J.L., Martinez-Morales, J.R. (2015) Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis. Nature communications. 6:7054

Heckel, E., Boselli, F., Roth, S., Krudewig, A., Belting, H. G., Charvin, G., Vermot, J. (2015) Oscillatory Flow Modulates Mechanosensitive klf2a Expression through trpv4 and trpp2 during Heart Valve Development. Current biology : CB. 25(10):1354-1361

Kok, F.O., Shin, M., Ni, C., Gupta, A., Grosse, A.S., van Impel, A., Kirchmaier, B.C., Peterson-Maduro, J., Kourkoulis, G., Male, I., DeSantis, D.F., Sheppard-Tindell, S., Ebarasi, L., Betsholtz, C., Schulte-Merker, S., Wolfe, S.A., Lawson, N.D. (2015) Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish. Developmental Cell. 32(1):97-108

May, M., Hwang, K.S., Miles, J., Williams, C., Niranjan, T., Kahler, S.G., Chiurazzi, P., Steindl, K., van der Spek, P.J., Swagemakers, S., Mueller, J., Stefl, S., Alexov, E., Ryu, J.I., Choi, J.H., Kim, H.T., Tarpey, P., Neri, G., Holloway, L., Skinner, C., Stevenson, R.E., Dorsky, R.I., Wang, T., Schwartz, C.E., Kim, C.H. (2015) ZC4H2, an XLID Gene, is Required for the Generation of a Specific Subset of CNS Interneurons. Human molecular genetics. 24(17):4848-61

Patil, P., Uechi, T., Kenmochi, N. (2015) Incomplete splicing of neutrophil-specific genes affects neutrophil development in a zebrafish model of poikiloderma with neutropenia. RNA Biology. 12:426-434

Samsa, L.A., Givens, C., Tzima, E., Stainier, D.Y., Qian, L., Liu, J. (2015) Cardiac contraction activates endocardial Notch signaling to modulate chamber maturation in zebrafish. Development (Cambridge, England). 142:4080-91

Shao, T., Zhu, L.Y., Nie, L., Shi, W., Dong, W.R., Xiang, L.X., Shao, J.Z. (2015) Characterization of surface phenotypic molecules of teleost dendritic cells. Developmental and comparative immunology. 49:38-43

Shi, X., He, B.L., Ma, A.C., Guo, Y., Chi, Y., Man, C.H., Zhang, W., Zhang, Y., Wen, Z., Cheng, T., Leung, A.Y. (2015) Functions of idh1 and its mutation in the regulation of developmental hematopoiesis in zebrafish. Blood. 125(19):2974-84

Wang, C., Chen, X., Shi, W., Wang, F., Du, Z., Li, X., Yao, Y., Liu, T., Shao, T., Li, G., Hao, A. (2015) 2-bromopalmitate impairs neural stem/progenitor cell proliferation, promotes cell apoptosis and induces malformation in zebrafish embryonic brain. Neurotoxicology and teratology. 50:53-63

Auer, T.O., Duroure, K., Concordet, J.P., Del Bene, F. (2014) CRISPR/Cas9-mediated conversion of eGFP- into Gal4-transgenic lines in zebrafish. Nature Protocols. 9:2823-2840

Bhatia, S., Monahan, J., Ravi, V., Gautier, P., Murdoch, E., Brenner, S., van Heyningen, V., Venkatesh, B., and Kleinjan, D.A. (2014) A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos. Developmental Biology. 387(2):214-228

Dietrich, A.C., Lombardo, V.A., Abdelilah-Seyfried, S. (2014) Blood Flow and Bmp Signaling Control Endocardial Chamber Morphogenesis. Developmental Cell. 30:367-377

Hu, B., Zhang, W., Feng, X., Ji, W., Xie, X., and Xiao, W. (2014) Zebrafish eaf1 suppresses foxo3b expression to modulate transcriptional activity of gata1 and spi1 in primitive hematopoiesis. Developmental Biology. 388(1):81-93

Mommaerts, H., Esguerra, C.V., Hartmann, U., Luyten, F.P., Tylzanowski, P. (2014) Smoc2 modulates embryonic myelopoiesis during zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 243(11):1375-90

Spieler, D., Kaffe, M., Knauf, F., Bessa, J., Tena, J.J., Giesert, F., Schormair, B., Tilch, E., Lee, H., Horsch, M., Czamara, D., Karbalai, N., von Toerne, C., Waldenberger, M., Gieger, C., Lichtner, P., Claussnitzer, M., Naumann, R., Müller-Myhsok, B., Torres, M., Garrett, L., Rozman, J., Klingenspor, M., Gailus-Durner, V., Fuchs, H., Hrabě de Angelis, M., Beckers, J., Holter, S.M., Meitinger, T., Hauck, S.M., Laumen, H., Wurst, W., Casares, F., Gómez-Skarmeta, J.L., Winkelmann, J. (2014) Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon. Genome research. 24:592-603

Zhu, L.Y., Lin, A.F., Shao, T., Nie, L., Dong, W.R., Xiang, L.X., and Shao, J.Z. (2014) B cells in teleost fish act as pivotal initiating APCs in priming adaptive immunity: an evolutionary perspective on the origin of the B-1 cell subset and B7 molecules. Journal of immunology (Baltimore, Md. : 1950). 192(6):2699-2714

Chen, S.Y., Shih, H.Y., Lin, S.J., Hsiao, C.D., Li, Z.C., and Cheng, Y.C. (2013) Etv5a regulates the proliferation of ventral mesoderm cells and the formation of hemato-vascular derivatives. Journal of Cell Science. 126(Pt 24):5626-34

Costa, A.M., Pereira-Castro, I., Ricardo, E., Spencer, F., Fisher, S., and da Costa, L.T. (2013) GRG5/AES Interacts with T-Cell Factor 4 (TCF4) and Downregulates Wnt Signaling in Human Cells and Zebrafish Embryos. PLoS One. 8(7):e67694

Fang, Y., Gupta, V., Karra, R., Holdway, J.E., Kikuchi, K., and Poss, K.D. (2013) Translational profiling of cardiomyocytes identifies an early Jak1/Stat3 injury response required for zebrafish heart regeneration. Proceedings of the National Academy of Sciences of the United States of America. 110(33):13416-13421

Law, S.H., and Sargent, T.D. (2013) Maternal pak4 Expression is Required for Primitive Myelopoiesis in Zebrafish. Mechanisms of Development. 130(2-3):181-194

Liu, X., Xiong, C., Jia, S., Zhang, Y., Chen, Y.G., Wang, Q., and Meng, A. (2013) Araf kinase antagonizes Nodal-Smad2 activity in mesendoderm development by directly phosphorylating the Smad2 linker region. Nature communications. 4:1728

Moore, J.C., Sheppard, S., Shestopalov, I.A., Chen, J.K., and Lawson, N. (2013) Post-transcriptional mechanisms contribute to Etv2 repression during vascular development. Developmental Biology. 384(1):128-40

Peralta, M., Steed, E., Harlepp, S., González-Rosa, J.M., Monduc, F., Ariza-Cosano, A., Cortés, A., Rayón, T., Gómez-Skarmeta, J.L., Zapata, A., Vermot, J., and Mercader, N. (2013) Heartbeat-Driven Pericardiac Fluid Forces Contribute to Epicardium Morphogenesis. Current biology : CB. 23(18):1726-35

Regadas, I., Matos, M.R., Monteiro, F.A., Gomez-Skarmeta, J.L., Lima, D., Bessa, J., Casares, F., and Reguenga, C. (2013) Several Cis-regulatory Elements Control mRNA Stability, Translation Efficiency, and Expression Pattern of Prrxl1 (Paired Related Homeobox Protein-like 1). The Journal of biological chemistry. 288(51):36285-301

Wang, L., Liu, T., Xu, L., Gao, Y., Wei, Y., Duan, C., Chen, G.Q., Lin, S., Patient, R., Zhang, B., Hong, D., and Liu, F. (2013) Fev regulates hematopoietic stem cell development via ERK signaling. Blood. 122(3):367-75

Bogdanovic, O., Fernandez-Minan, A., Tena, J.J., de Lacalle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S.J., Veenstra, G.J., and Gomez-Skarmeta, J.L. (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome research. 22(10):2043-2053

Coolen, M., Thieffry, D., Drivenes, O., Becker, T.S., and Bally-Cuif, L. (2012) miR-9 Controls the Timing of Neurogenesis through the Direct Inhibition of Antagonistic Factors. Developmental Cell. 22(5):1052-1064

Djiotsa, J., Verbruggen, V., Giacomotto, J., Ishibashi, M., Manning, E., Rinkwitz, S., Manfroid, I., Lvoz, M., and Peers, B. (2012) Pax4 is not essential for beta-cell differentiation in zebrafish embryos but modulates alpha-cell generation by repressing arx gene expression. BMC Developmental Biology. 12(1):37

Folgueira, M., Bayley, P., Navratilova, P., Becker, T.S., Wilson, S.W., and Clarke, J.D. (2012) Morphogenesis underlying the development of the everted teleost telencephalon. Neural Development. 7(1):32

Irimia, M., Royo, J.L., Burguera, D., Maeso, I., Gómez-Skarmeta, J.L., and Garcia-Fernandez, J. (2012) Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. Scientific Reports. 2:433

Jia, S., Dai, F., Wu, D., Lin, X., Xing, C., Xue, Y., Wang, Y., Xiao, M., Wu, W., Feng, X.H., and Meng, A. (2012) Protein Phosphatase 4 Cooperates with Smads to Promote BMP Signaling in Dorsoventral Patterning of Zebrafish Embryos. Developmental Cell. 22(5):1065-1078

Lim, S., Kumari, P., Gilligan, P., Quach, H.N., Mathavan, S., and Sampath, K. (2012) Dorsal activity of maternal squint is mediated by a non-coding function of the RNA. Development (Cambridge, England). 139(16):2903-2915

Lobo, G.P., Isken, A., Hoff, S., Babino, D., and von Lintig, J. (2012) BCDO2 acts as a carotenoid scavenger and gatekeeper for the mitochondrial apoptotic pathway. Development (Cambridge, England). 139(16):2966-2977

Quiroz, Y., Lopez, M., Mavropoulos, A., Motte, P., Martial, J.A., Hammerschmidt, M., and Muller, M. (2012) The HMG-Box Transcription Factor Sox4b Is Required for Pituitary Expression of gata2a and Specification of Thyrotrope and Gonadotrope Cells in Zebrafish. Molecular endocrinology (Baltimore, Md.). 26(6):1014-1027

Stengel, R., Rivera-Milla, E., Sahoo, N., Ebert, C., Bollig, F., Heinemann, S.H., Schonherr, R., and Englert, C. (2012) Kcnh1 voltage-gated potassium channels are essential for early zebrafish development. The Journal of biological chemistry. 287(42):35565-35575

Veldman, M.B., and Lin, S. (2012) Etsrp/Etv2 Is Directly Regulated by Foxc1a/b in the Zebrafish Angioblast. Circulation research. 110(2):220-229

Belting, H.G., Wendik, B., Lunde, K., Leichsenring, M., Mössner, R., Driever, W., and Onichtchouk, D. (2011) Pou5f1 contributes to dorsoventral patterning by positive regulation of vox and modulation of fgf8a expression. Developmental Biology. 356(2):323-36

Cui, Y., He, S., Xing, C., Lu, K., Wang, J., Xing, G., Meng, A., Jia, S., He, F., and Zhang, L. (2011) SCF(FBXL15) regulates BMP signalling by directing the degradation of HECT‐type ubiquitin ligase Smurf1. The EMBO journal. 30(13):2675-89

Issa, F.A., Mazzochi, C., Mock, A.F., and Papazian, D.M. (2011) Spinocerebellar ataxia type 13 mutant potassium channel alters neuronal excitability and causes locomotor deficits in zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31(18):6831-6841

McGrail, M., Hatler, J.M., Kuang, X., Liao, H.K., Nannapaneni, K., Noack Watt, K.E., Uhl, J.D., Largaespada, D.A., Vollbrecht, E., Scheetz, T.E., Dupuy, A.J., Hostetter, J.M., and Essner, J.J. (2011) Somatic mutagenesis with a sleeping beauty transposon system leads to solid tumor formation in zebrafish. PLoS One. 6(4):e18826

Royo, J.L., Hidalgo, C., Roncero, Y., Seda, M.A., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2011) Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One. 6(9):e24824

Taneda, T., Zhu, W., Cao, Q., Watanabe, H., Yamaguchi, Y., Handa, H., and Wada, T. (2011) Erythropoiesis is regulated by the transcription elongation factor Foggy/Spt5 through gata1 gene regulation. Genes to cells : devoted to molecular & cellular mechanisms. 16(2):231-242

Xie, X.W., Liu, J.X., Hu, B., and Xiao, W. (2011) Zebrafish foxo3b Negatively Regulates Canonical Wnt Signaling to Affect Early Embryogenesis. PLoS One. 6(9):e24469

Zhu, C., Smith, T., McNulty, J., Rayla, A.L., Lakshmanan, A., Siekmann, A.F., Buffardi, M., Meng, X., Shin, J., Padmanabhan, A., Cifuentes, D., Giraldez, A.J., Look, A.T., Epstein, J.A., Lawson, N.D., and Wolfe, S.A. (2011) Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development (Cambridge, England). 138(20):4555-4564

Branam, A.M., Hoffman, G.G., Pelegri, F., and Greenspan, D.S. (2010) Zebrafish Chordin-like and Chordin Are Functionally Redundant in Regulating Patterning of the Dorsoventral Axis. Developmental Biology. 341(2):444-458

Dong, X., Navratilova, P., Fredman, D., Drivenes, Ø., Becker, T.S., and Lenhard, B. (2010) Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic acids research. 38(4):1071-1085

Harvey, S.A., Tümpel, S., Dubrulle, J., Schier, A.F., and Smith, J.C. (2010) no tail integrates two modes of mesoderm induction. Development (Cambridge, England). 137(7):1127-1135

Kobayashi, I., Ono, H., Moritomo, T., Kano, K., Nakanishi, T., and Suda, T. (2010) Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells. Blood. 115(2):e1-e9

Naranjo, S., Voesenek, K., de la Calle-Mustienes, E., Robert-Moreno, A., Kokotas, H., Grigoriadou, M., Economides, J., Van Camp, G., Hilgert, N., Moreno, F., Alsina, B., Petersen, M.B., Kremer, H., and Gómez-Skarmeta, J.L. (2010) Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing. Human genetics. 128(4):411-419

Okuda, Y., Ogura, E., Kondoh, H., and Kamachi, Y. (2010) B1 SOX coordinate cell specification with patterning and morphogenesis in the early zebrafish embryo. PLoS Genetics. 6:e1000936

Ragvin, A., Moro, E., Fredman, D., Navratilova, P., Drivenes, O., Engström, P.G., Alonso, M.E., Mustienes, E.D., Gomez Skarmeta, J.L., Tavares, M.J., Casares, F., Manzanares, M., van Heyningen, V., Molven, A., Njølstad, P.R., Argenton, F., Lenhard, B., and Becker, T.S. (2010) Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proceedings of the National Academy of Sciences of the United States of America. 107(2):775-780

Zhong, H., Xin, S., Zhao, Y., Lu, J., Li, S., Gong, J., Yang, Z., and Lin, S. (2010) Genetic approach to evaluate specificity of small molecule drug candidates inhibiting PLK1 using zebrafish. Molecular Biosystems. 6(8):1463-1468

Amsterdam, A., Lai, K., Komisarczuk, A.Z., Becker, T.S., Bronson, R.T., Hopkins, N., and Lees, J.A. (2009) Zebrafish Hagoromo Mutants Up-Regulate fgf8 Postembryonically and Develop Neuroblastoma. Molecular cancer research : MCR. 7(6):841-850

Bessa, J., Tena, J.J., de la Calle-Mustienes, E., Fernández-Miñán, A., Naranjo, S., Fernández, A., Montoliu, L., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2009) Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(9):2409-2417

Gillis, W.Q., St John, J., Bowerman, B., and Schneider, S.Q. (2009) Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family. BMC Evolutionary Biology. 9:207

Kumari, J., Bogwald, J., and Dalmo, R.A. (2009) Transcription factor GATA-3 in Atlantic salmon (Salmo salar): molecular characterization, promoter activity and expression analysis. Molecular immunology. 46(15):3099-3107

Little, S.C., and Mullins, M.C. (2009) Bone morphogenetic protein heterodimers assemble heteromeric type I receptor complexes to pattern the dorsoventral axis. Nature cell biology. 11(5):637-643

Mei, W., Lee, K.W., Marlow, F.L., Miller, A.L., and Mullins, M.C. (2009) hnRNP I is required to generate the Ca2+ signal that causes egg activation in zebrafish. Development (Cambridge, England). 136(17):3007-3017

Navratilova, P., Fredman, D., Hawkins, T.A., Turner, K., Lenhard, B., and Becker, T.S. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Developmental Biology. 327(2):526-540

Pase, L., Layton, J.E., Kloosterman, W.P., Carradice, D., Waterhouse, P.M., and Lieschke, G.J. (2009) miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2. Blood. 113(8):1794-1804

Sabel, J.L., d'Alençon, C., O'Brien, E.K., Otterloo, E.V., Lutz, K., Cuykendall, T.N., Schutte, B.C., Houston, D.W., and Cornell, R.A. (2009) Maternal Interferon Regulatory Factor 6 is required for the differentiation of primary superficial epithelia in Danio and Xenopus embryos. Developmental Biology. 325(1):249-262

Tse, W.K., Eisenhaber, B., Ho, S.H., Ng, Q., Eisenhaber, F., and Jiang, Y.J. (2009) Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. BMC Genomics. 10:637

Wong, K.S., Proulx, K., Rost, M.S., and Sumanas, S. (2009) Identification of vasculature-specific genes by microarray analysis of etsrp/etv2 overexpressing zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(7):1836-1850

Zhang, Y., Li, X., Qi, J., Wang, J., Liu, X., Zhang, H., Lin, S.C., and Meng, A. (2009) Rock2 controls TGFβ signaling and inhibits mesoderm induction in zebrafish embryos. Journal of Cell Science. 122(Pt 13):2197-2207

Cermenati, S., Moleri, S., Cimbro, S., Corti, P., Del Giacco, L., Amodeo, R., Dejana, E., Koopman, P., Cotelli, F., and Beltrame, M. (2008) Sox18 and Sox7 play redundant roles in vascular development. Blood. 111(5):2657-2666

Dee, C.T., Hirst, C.S., Shih, Y.H., Tripathi, V.B., Patient, R.K., and Scotting, P.J. (2008) Sox3 regulates both neural fate and differentiation in the zebrafish ectoderm. Developmental Biology. 320(1):289-301

Imamura, S., Uchiyama, J., Koshimizu, E., Hanai, J., Raftopoulou, C., Murphey, R.D., Bayliss, P.E., Imai, Y., Burns, C.E., Masutomi, K., Gagos, S., Zon, L.I., Roberts, T.M., and Kishi, S. (2008) A non-canonical function of zebrafish telomerase reverse transcriptase is required for developmental hematopoiesis. PLoS One. 3(10):e3364

Komisarczuk, A.Z., Topp, S., Stigloher, C., Kapsimali, M., Bally-Cuif, L., and Becker, T.S. (2008) Enhancer detection and developmental expression of zebrafish sprouty1, a member of the fgf8 synexpression group. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(9):2594-2603

Krieg, M., Arboleda-Estudillo, Y., Puech, P.H., Käfer, J., Graner, F., Müller, D.J., and Heisenberg, C.P. (2008) Tensile forces govern germ-layer organization in zebrafish. Nature cell biology. 10(4):429-436

Punnamoottil, B., Kikuta, H., Pezeron, G., Erceg, J., Becker, T.S., and Rinkwitz, S. (2008) Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(8):2195-2208

Sultana, N., Nag, K., Hoshijima, K., Laird, D.W., Kawakami, A., and Hirose, S. (2008) Zebrafish early cardiac connexin, Cx36.7/Ecx, regulates myofibril orientation and heart morphogenesis by establishing Nkx2.5 expression. Proceedings of the National Academy of Sciences of the United States of America. 105(12):4763-4768

Chun, C.Z., and Chen, T.T. (2007) Microinjecting recombinant rainbow trout Ea4-peptide of pro-IGF-I into zebrafish embryos causes abnormal development in heart, red blood cells, and vasculature. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 145(1):39-44

Gardiner, M.R., Gongora, M.M., Grimmond, S.M., and Perkins, A.C. (2007) A global role for zebrafish klf4 in embryonic erythropoiesis. Mechanisms of Development. 124(9-10):762-774

Horsfield, J.A., Anagnostou, S.H., Hu, J.K., Cho, K.H., Geisler, R., Lieschke, G., Crosier, K.E., and Crosier, P.S. (2007) Cohesin-dependent regulation of Runx genes. Development (Cambridge, England). 134(14):2639-2649

Londin, E.R., Mentzer, L., and Sirotkin, H.I. (2007) Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling. BMC Developmental Biology. 7(1):120

North, T.E., Goessling, W., Walkley, C.R., Lengerke, C., Kopani, K.R., Lord, A.M., Weber, G.J., Bowman, T.V., Jang, I.H., Grosser, T., Fitzgerald, G.A., Daley, G.Q., Orkin, S.H., and Zon, L.I. (2007) Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature. 447(7147):1007-1011

Pei, W., Noushmehr, H., Costa, J., Ouspenskaia, M.V., Elkahloun, A.G., and Feldman, B. (2007) An early requirement for maternal FoxH1 during zebrafish gastrulation. Developmental Biology. 310(1):10-22

Rui, Y., Xu, Z., Xiong, B., Cao, Y., Lin, S., Zhang, M., Chan, S.C., Luo, W., Han, Y., Lu, Z., Ye, Z., Zhou, H.M., Han, J., Meng, A., and Lin, S.C. (2007) A beta-Catenin-Independent Dorsalization Pathway Activated by Axin/JNK Signaling and Antagonized by Aida. Developmental Cell. 13(2):268-282

Shankaran, S.S., Sieger, D., Schroter, C., Czepe, C., Pauly, M.C., Laplante, M.A., Becker, T.S., Oates, A.C., and Gajewski, M. (2007) Completing the set of h/E(spl) cyclic genes in zebrafish: her12 and her15 reveal novel modes of expression and contribute to the segmentation clock. Developmental Biology. 304(2):615-632

Chun, C.Z., Tsai, H.J., and Chen, T.T. (2006) Trout Ea4- or human Eb-peptide of pro-IGF-I disrupts heart, red blood cell, and vasculature development in zebrafish embryos. Molecular reproduction and development. 73(9):1112-1121

Hadrys, T., Punnamoottil, B., Pieper, M., Kikuta, H., Pezeron, G., Becker, T.S., Prince, V., Baker, R., and Rinkwitz, S. (2006) Conserved co-regulation and promoter sharing of hoxb3a and hoxb4a in zebrafish. Developmental Biology. 297(1):26-43

Leskow, F.C., Holloway, B.A., Wang, H., Mullins, M.C., and Kazanietz, M.G. (2006) The zebrafish homologue of mammalian chimerin Rac-GAPs is implicated in epiboly progression during development. Proceedings of the National Academy of Sciences of the United States of America. 103(14):5373-5378

Lucas, M.E., Muller, F., Rudiger, R., Henion, P.D., and Rohrer, H. (2006) The bHLH transcription factor hand2 is essential for noradrenergic differentiation of sympathetic neurons. Development (Cambridge, England). 133(20):4015-4024

Pineda, R.H., Svoboda, K.R., Wright, M.A., Taylor, A.D., Novak, A.E., Gamse, J.T., Eisen, J.S., and Ribera, A.B. (2006) Knockdown of Nav1.6a Na+ channels affects zebrafish motoneuron development. Development (Cambridge, England). 133(19):3827-3836

Rentzsch, F., Zhang, J., Kramer, C., Sebald, W., and Hammerschmidt, M. (2006) Crossveinless 2 is an essential positive feedback regulator of Bmp signaling during zebrafish gastrulation. Development (Cambridge, England). 133(5):801-811

Yamauchi, H., Hotta, Y., Konishi, M., Miyake, A., Kawahara, A., and Itoh, N. (2006) Fgf21 is essential for haematopoiesis in zebrafish. EMBO reports. 7(6):649-654

Bakkers, J., Camacho-Carvajal, M., Nowak, M., Kramer, C., Danger, B., and Hammerschmidt, M. (2005) Destabilization of DeltaNp63alpha by Nedd4-Mediated Ubiquitination and Ubc9-Mediated Sumoylation, and Its Implications on Dorsoventral Patterning of the Zebrafish Embryo. Cell cycle (Georgetown, Tex.). 4(6):790-800

Craven, S.E., French, D., Ye, W., de Sauvage, F., and Rosenthal, A. (2005) Loss of hspa9b in zebrafish recapitulates the ineffective hematopoiesis of the myelodysplastic syndromes. Blood. 105(9):3528-3534

Ellingsen, S., Laplante, M.A., Konig, M., Kikuta, H., Furmanek, T., Hoivik, E.A., and Becker, T.S. (2005) Large-scale enhancer detection in the zebrafish genome. Development (Cambridge, England). 132(17):3799-3811

Heicklen-Klein, A., McReynolds, L.J., and Evans, T. (2005) Using the zebrafish model to study GATA transcription factors. Seminars in cell & developmental biology. 16(1):95-106

Juarez, M.A., Su, F., Chun, S., Kiel, M.J., and Lyons, S.E. (2005) Distinct roles for Scl in erythroid specification and maturation in zebrafish. The Journal of biological chemistry. 280(50):41636-41644

Lyman Gingerich, J., Westfall, T.A., Slusarski, D.C., and Pelegri, F. (2005) hecate, a zebrafish maternal effect gene, affects dorsal organizer induction and intracellular calcium transient frequency. Developmental Biology. 286(2):427-439

Oren, T., Torregroza, I., and Evans, T. (2005) An Oct-1 binding site mediates activation of the gata2 promoter by BMP signaling. Nucleic acids research. 33(13):4357-4367

Shimizu, T., Bae, Y.K., Muraoka, O., and Hibi, M. (2005) Interaction of Wnt and caudal-related genes in zebrafish posterior body formation. Developmental Biology. 279(1):125-141

Xie, J., and Fisher, S. (2005) Twisted gastrulation enhances BMP signaling through chordin dependent and independent mechanisms. Development (Cambridge, England). 132(2):383-391

Cao, Y., Zhao, J., Sun, Z., Zhao, Z., Postlethwait, J., and Meng, A. (2004) fgf17b, a novel member of Fgf family, helps patterning zebrafish embryos. Developmental Biology. 271(1):130-143

Davidson, A.J., and Zon, L.I. (2004) The 'definitive' (and 'primitive') guide to zebrafish hematopoiesis. Oncogene. 23(43):7233-7246

Marlow, F., Gonzalez, E.M., Yin, C., Rojo, C., and Solnica-Krezel, L. (2004) No tail co-operates with non-canonical Wnt signaling to regulate posterior body morphogenesis in zebrafish. Development (Cambridge, England). 131(1):203-216

Penberthy, W.T., Zhao, C., Zhang, Y., Jessen, J.R., Yang, Z., Bricaud, O., Collazo, A., Meng, A., and Lin, S. (2004) Pur alpha and Sp8 as opposing regulators of neural gata2 expression. Developmental Biology. 275(1):225-234

Ransom, D.G., Bahary, N., Niss, K., Traver, D., Burns, C., Trede, N.S., Paffett-Lugassy, N., Saganic, W.J., Lim, C.A., Hersey, C., Zhou, Y., Barut, B.A., Lin, S., Kingsley, P.D., Palis, J., Orkin, S.H., and Zon, L.I. (2004) The Zebrafish moonshine Gene Encodes Transcriptional Intermediary Factor 1gamma, an Essential Regulator of Hematopoiesis. PLoS Biology. 2(8):E237

Rohde, L.A., Oates, A.C., and Ho, R.K. (2004) A Crucial Interaction between Embryonic Red Blood Cell Progenitors and Paraxial Mesoderm Revealed in spadetail Embryos. Developmental Cell. 7(2):251-262

Itoh, M., Kudoh, T., Dedekian, M., Kim, C.-H., and Chitnis, A.J. (2002) A role for iro1 and iro7 in the establishment of an anteroposterior compartment of the ectoderm adjacent to the midbrain-hindbrain boundary. Development (Cambridge, England). 129(10):2317-2327

Roman, B.L., Pham, V., Lawson, N.D., Kulik, M., Childs, S., Lekven, A.C., Garrity, D.M., Moon, R.T., Fishman, M.C., Lechleider, R.J., and Weinstein, B.M. (2002) Disruption of acvrl1 increases endothelial cell number in zebrafish cranial vessels. Development (Cambridge, England). 129(12):3009-3019

Szeto, D.P., Griffin, K.J.P., and Kimelman, D. (2002) hrT is required for cardiovascular development in zebrafish. Development (Cambridge, England). 129(21):5903-5101

Imai,Y. and Talbot, W.S. (2001) Morpholino phenocopies of the bmp2b/swirl and bmp7/snailhouse mutations. Genesis (New York, N.Y. : 2000). 30(3):160-163

Mintzer, K.A., Lee, M.A., Runke, G., Trout, J., Whitman, M., and Mullins, M.C. (2001) lost-a-fin encodes a type I BMP receptor, Alk8, acting maternally and zygotically in dorsoventral pattern formation. Development (Cambridge, England). 128(6):859-869

Ross, J.J., Shimmi, O., Vilmos, P., Petryk, A., Kim, H., Gaudenz, K., Hermanson, S., Ekker, S.C., O'Connor, M.B., and Marsh, J.L. (2001) Twisted gastrulation is a conserved extracellular BMP antagonist. Nature. 410(6827):479-483

Fekany-Lee, K., Gonzalez, E., Miller-Bertoglio, V., and Solnica-Krezel, L. (2000) The homeobox gene bozozok promotes anterior neuroectoderm formation in zebrafish through negative regulation of BMP2/4 and Wnt pathways. Development (Cambridge, England). 127(11):2333-2345

Kelly, C., Chin, A.J., Leatherman, J.L., Kozlowski, D.J., and Weinberg, E.S. (2000) Maternally controlled ß-catenin-mediated signaling is required for organizer formation in the zebrafish. Development (Cambridge, England). 127(18):3899-3911

Barth, K.A., Kishimoto, Y., Rohr, K.B., Seydler, C., Schulte-Merker, S., and Wilson, S.W. (1999) Bmp activity establishes a gradient of positional information throughout the entire neural plate. Development (Cambridge, England). 126(22):4977-4987

Parichy, D.M., Rawls, J.F., Pratt, S.J., Whitfield, T.T., and Johnson, S.L. (1999) Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development. Development (Cambridge, England). 126(15):3425-3436

Gering, M., Rodaway, A.R.F., Göttgens, B., Patient, R.K., and Green, A.R. (1998) The SCL gene specifies haemangioblast development from early mesoderm. The EMBO journal. 17:4029-4045

Jessen, J.R., Meng, A., McFarlane, R.J., Paw, B.H., Zon, L.I., Smith, G.R., and Lin, S. (1998) Modification of bacterial artificial chromosomes through Chi-stimulated homologous recombination and its application in zebrafish transgenesis. Proceedings of the National Academy of Sciences of the United States of America. 95:5121-5126

Nasevicius, A., Hyatt, T., Kim, H., Guttman, J., Walsh, E., Sumanas, S., Wang, Y.S., and Ekker, S.C. (1998) Evidence for a fizzled-mediated wnt pathway required for zebrafish dorsal mesoderm formation. Development (Cambridge, England). 125:4283-4292

Postlethwait, J.H, Yan, Y.-L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.-S., Larhammar, D., Rosa, F., Westerfield, M., Zon, L.I., Johnson, S.L., and Talbot, W.S. (1998) Vertebrate genome evolution and the zebrafish gene map. Nature Genetics. 18:345-349

Abdelilah, S. and Driever, W. (1997) Pattern formation in janus-mutant zebrafish embryos. Developmental Biology. 184(1):70-84

Meng, A., Tang, H., Ong, B.A., Farrell, M.J., and Lin, S. (1997) Promoter analysis in living zebrafish embryos identifies a cis-acting motif required for neuronal expression of GATA-2. Proceedings of the National Academy of Sciences of the United States of America. 94(12):6267-6272

Hammerschmidt, M., Pelegri, F., Mullins, M.C., Kane, D.A., van Eeden, F.J., Granato, M., Brand, M., Furutani-Seiki, M., Haffter, P., Heisenberg, C.P., Jiang, Y.J., Kelsh, R.N., Odenthal, J., Warga, R.M., and Nüsslein-Volhard, C. (1996) dino and mercedes, two genes regulating dorsal development in the zebrafish embryo. Development (Cambridge, England). 123:95-102

Detrich, H.W. III., Kieran, M.W., Chan, F.Y., Barone, L.M., Yee, K., Rundstadler, J.A., Pratt, S., Ransom, D., and Zon, L.I. (1995) Intraembryonic hematopoietic cell migration during vertebrate development. Proceedings of the National Academy of Sciences of the United States of America. 92:10713-10717