ZFIN ID: ZDB-PERS-970314-3
Oates, Andrew
Email: andrew.oates@epfl.ch
URL: https://oateslab.epfl.ch/
Affiliation: Oates Lab
Address: École Polytechnique Fédérale de Lausanne (EPFL) SV IBI UPOATES Station 19 CH-1015 Lausanne Switzerland
Country: Switzerland
Phone: +41 (0)21 693 26 38


Ernst, A., Piragyte, I., Mp, A.M., Le, N.D., Grandgirard, D., Leib, S.L., Oates, A., Mercader, N. (2023) Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform. Scientific Reports. 13:1703717037
Özelçi, E., Mailand, E., Rüegg, M., Oates, A.C., Sakar, M.S. (2022) Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation. Nature communications. 13:79347934
Naganathan, S.R., Oates, A.C. (2022) Preparation of Single-Somite Explants from Zebrafish Embryos. Journal of visualized experiments : JoVE. (184)
Naganathan, S.R., Popović, M., Oates, A.C. (2022) Left-right symmetry of zebrafish embryos requires somite surface tension. Nature. 605(7910):516-521
Uriu, K., Liao, B.K., Oates, A.C., Morelli, L.G. (2021) From local resynchronization to global pattern recovery in the zebrafish segmentation clock. eLIFE. 10:
Naganathan, S.R., Oates, A.C. (2020) Patterning and mechanics of somite boundaries in zebrafish embryos. Seminars in cell & developmental biology. 107:170-178
Venzin, O.F., Oates, A.C. (2019) What are you synching about? Emerging complexity of notch signaling in the segmentation clock. Developmental Biology. 460(1):40-54
Narayanan, R., Oates, A.C. (2019) Detection of mRNA by Whole Mount in situ Hybridization and DNA Extraction for Genotyping of Zebrafish Embryos. Bio-protocol. 9:e3193
LLeras Forero, L., Narayanan, R., Huitema, L.F.A., VanBergen, M., Apschner, A., Peterson-Maduro, J., Logister, I., Valentin, G., Morelli, L.G., Oates, A., Schulte-Merker, S. (2018) Segmentation of the zebrafish axial skeleton relies on notochord sheath cells and not on the segmentation clock. eLIFE. 7
Richter, S., Schulze, U., Tomançak, P., Oates, A.C. (2017) Small molecule screen in embryonic zebrafish using modular variations to target segmentation. Nature communications. 8:1901
Uriu, K., Bhavna, R., Oates, A.C., Morelli, L.G. (2017) A framework for quantification and physical modeling of cell mixing applied to oscillator synchronization in vertebrate somitogenesis. Biology Open. 6(8):1235-1244
Bhavna, R., Uriu, K., Valentin, G., Tinevez, J.Y., Oates, A.C (2016) Object Segmentation and Ground Truth in 3D Embryonic Imaging. PLoS One. 11:e0150853
Liao, B.K., Jörg, D.J., Oates, A.C. (2016) Faster embryonic segmentation through elevated Delta-Notch signalling. Nature communications. 7:11861
Webb, A.B., Lengyel, I.M., Jörg, D.J., Valentin, G., Jülicher, F., Morelli, L.G., Oates, A.C. (2016) Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock. eLIFE. 5
Jörg, D.J., Morelli, L.G., Soroldoni, D., Oates, A.C., Jülicher, F. (2015) Continuum theory of gene expression waves during vertebrate segmentation. New journal of physics. 17:093042
Windner, S.E., Doris, R.A., Ferguson, C.M., Nelson, A.C., Valentin, G., Tan, H., Oates, A.C., Wardle, F.C., Devoto, S.H. (2015) Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish. Development (Cambridge, England). 142(6):1159-68
Lengyel, I.M., Soroldoni, D., Oates, A.C., Morelli, L.G. (2014) Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations. Papers in physics. 6:
Uriu, K., Morelli, L.G., Oates, A.C. (2014) Interplay between intercellular signaling and cell movement in development. Seminars in cell & developmental biology. 35C:66-72
Rost, F., Eugster, C., Schröter, C., Oates, A.C., Brusch, L. (2014) Chevron formation of the zebrafish muscle segments. The Journal of experimental biology. 217(Pt 21):3870-82
Webb, A.B., Soroldoni, D., Oswald, A., Schindelin, J., Oates, A.C. (2014) Generation of Dispersed Presomitic Mesoderm Cell Cultures for Imaging of the Zebrafish Segmentation Clock in Single Cells. Journal of visualized experiments : JoVE. (89)
Soroldoni, D., Jörg, D.J., Morelli, L.G., Richmond, D.L., Schindelin, J., Jülicher, F., Oates, A.C. (2014) Genetic oscillations. A Doppler effect in embryonic pattern formation. Science (New York, N.Y.). 345:222-5
Bajard, L., Morelli, L.G., Ares, S., Pécréaux, J., Jülicher, F., Oates, A.C. (2014) Wnt-regulated dynamics of positional information in zebrafish somitogenesis. Development (Cambridge, England). 141:1381-91
Schröter, C., Ares, S., Morelli, L.G., Isakova, A., Hens, K., Soroldoni, D., Gajewski, M., Jülicher, F., Maerkl, S.J., Deplancke, B., and Oates, A.C. (2012) Topology and dynamics of the zebrafish segmentation clock core circuit. PLoS Biology. 10(7):e1001364
Krol, A.J., Roellig, D., Dequéant, M.L., Tassy, O., Glynn, E., Hattem, G., Mushegian, A., Oates, A.C., and Pourquié, O. (2011) Evolutionary plasticity of segmentation clock networks. Development (Cambridge, England). 138(13):2783-2792
Schröter, C., and Oates, A.C. (2010) Segment Number and Axial Identity in a Segmentation Clock Period Mutant. Current biology : CB. 20(14):1254-1258
Herrgen, L., Ares, S., Morelli, L.G., Schröter, C., Jülicher, F., and Oates, A.C. (2010) Intercellular Coupling Regulates the Period of the Segmentation Clock. Current biology : CB. 20(14):1244-1253
Strzelecka, M., Trowitzsch, S., Weber, G., Lührmann, R., Oates, A.C., and Neugebauer, K.M. (2010) Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis. Nature structural & molecular biology. 17(4):403-409
Strzelecka, M., Oates, A.C., and Neugebauer, K.M. (2010) Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus (Austin, Tex.). 1(1):96-108
Soroldoni, D., Hogan, B.M., and Oates, A.C. (2009) Simple and efficient transgenesis with meganuclease constructs in zebrafish. Methods in molecular biology (Clifton, N.J.). 546:117-130
Picker, A., Roellig, D., Pourquié, O., Oates, A.C., and Brand, M. (2009) Tissue micromanipulation in zebrafish embryos. Methods in molecular biology (Clifton, N.J.). 546:153-172
Herrgen, L., Schröter, C., Bajard, L., and Oates, A.C. (2009) Multiple embryo time-lapse imaging of zebrafish development. Methods in molecular biology (Clifton, N.J.). 546:243-254
Schröter, C., Herrgen, L., Cardona, A., Brouhard, G.J., Feldman, B., and Oates, A.C. (2008) Dynamics of zebrafish somitogenesis. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(3):545-553
Riedel-Kruse, I.H., Müller, C., and Oates, A.C. (2007) Synchrony Dynamics During Initiation, Failure, and Rescue of the Segmentation Clock. Science (New York, N.Y.). 317(5846):1911-1915
Kikuta, H., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstrom, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., Ghislain, J., Pezeron, G., Mourrain, P., Ellingsen, S., Oates, A.C., Thisse, C., Thisse, B., Foucher, I., Adolf, B., Geling, A., Lenhard, B., and Becker, T.S. (2007) Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome research. 17(5):545-555
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
Echeverri, K., and Oates, A.C. (2007) Coordination of symmetric cyclic gene expression during somitogenesis by Suppressor of Hairless involves regulation of retinoic acid catabolism. Developmental Biology. 301(2):388-403
Tucker, B., Hepperle, C., Kortschak, D., Rainbird, B., Wells, S., Oates, A.C., and Lardelli, M. (2007) Zebrafish Angiotensin II Receptor-like 1a (agtrl1a) is expressed in migrating hypoblast, vasculature, and in multiple embryonic epithelia. Gene expression patterns : GEP. 7(3):258-265
Langenberg, T., Dracz, T., Oates, A.C., Heisenberg, C.P., and Brand, M. (2006) Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(4):928-933
Oates, A.C., Rohde, L.A., and Ho, R.K. (2005) Generation of segment polarity in the paraxial mesoderm of the zebrafish through a T-box-dependent inductive event. Developmental Biology. 283(1):204-214
Oates, A.C., Mueller, C., and Ho, R.K. (2005) Cooperative function of deltaC and her7 in anterior segment formation. Developmental Biology. 280(1):133-149
Hogan, B.M., Hunter, M.P., Oates, A.C., Crowhurst, M.O., Hall, N.E., Heath, J.K., Prince, V.E., and Lieschke, G.J. (2004) Zebrafish gcm2 is required for gill filament budding from pharyngeal ectoderm. Developmental Biology. 276(2):508-522
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
Brownlie, A., Hersey, C., Oates, A.C., Paw, B.H., Falick, A.M., Witkowska, H.E., Flint,J., Higgs, D., Jessen, J., Bahary, N., Zhu, H., Lin, S. and Zon, L. (2003) Characterization of embryonic globin genes of the zebrafish. Developmental Biology. 255(1):48-61
Oates, A.C. and Ho, R.K. (2002) Redundancy between components of the segmentation oscillator and the Delta/Notch pathway protects the anterior somites of zebrafish from genetic perturbation. Developmental Biology. 247(2):516
Lieschke, G.J., Oates, A.C., Paw, B.H., Thompson, M.A., Hall, N.E., Ward, A.C., Ho, R.K., Zon, L.I., and Layton, J.E. (2002) Zebrafish SPI-1 (PU.1) marks a site of myeloid development independent of primitive erythropoiesis: implications for axial patterning. Developmental Biology. 246(2):274-295
Oates, A.C. and Ho, R.K. (2002) Hairy/E(spl)-related (Her) genes are central components of the segmentation oscillator and display redundancy with the Delta/Notch signaling pathway in the formation of anterior segmental boundaries in the zebrafish. Development (Cambridge, England). 129(12):2929-2946
Coulthard, M.G., Duffy, S., Down, M., Evans, B., Power, M., Smith, F., Stylianou, C., Kleikamp, S., Oates, A., Lackmann, M., Burns, G.F., and Boyd, A.W. (2002) The role of the Eph-ephrin signalling system in the regulation of developmental patterning. The International journal of developmental biology. 46(4):375-384
Lyons, S.E., Shue, B.C., Lei, L., Oates, A.C., Zon, L.I., and Liu, P.P. (2001) Molecular cloning, genetic mapping, and expression analysis of four zebrafish c/ebp genes. Gene. 281(1-2):43-51
Lieschke, G.J., Oates, A.C., Crowhurst, M.O., Ward, A.C., and Layton, J.E. (2001) Morphologic and functional characterization of granulocytes and macrophages in embryonic and adult zebrafish. Blood. 98(10):3087-3096
Oates, A.C., Pratt, S.J., Vail, B., Yan, Y.-L., Ho, R.K., Johnson, S.L., Postlethwait, J.H., and Zon, L.I. (2001) The zebrafish klf gene family. Blood. 98(6):1792-1801
Prince, V.E., Holley, S.A., Bally-Cuif, L., Prabhakaran, B., Oates, A.C., Ho, R.K., and Vogt, T.F. (2001) Zebrafish lunatic fringe demarcates segmental boundaries. Mechanisms of Development. 105(1-2):175-180
Lyons, S.E., Shue, B.C., Oates, A.C., Zon, L.I., and Liu, P.P. (2001) A novel myeloid-restricted zebrafish CCAAT/enhancer-binding protein with a potent transcriptional activation domain. Blood. 97(9):2611-2617
Bruce, A.E., Oates, A.C., Prince, V.E., and Ho, R.K. (2001) Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes. Evolution & development. 3(3):127-144
Blake, T., Adya, N., Kim, C.H., Oates, A.C., Zon, L., Chitnis, A., Weinstein, B.M., and Liu, P.P. (2000) Zebrafish homolog of the leukemia gene CBFB: its expression during embryogenesis and its relationship to scl and gata-1 in hematopoiesis. Blood. 96(13):4178-4184
Lyons, S.E., Shue, B.C., Oates, A.C., Zon, L.I., and Liu, P.P. (2000) A novel myeloid-restricted zebrafish C/EBP with a potent transcriptional activation domain. Blood. 96(11):2877
Oates, A.C., Bruce, A.E., and Ho, R.K. (2000) Too much interference: injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. Developmental Biology. 224(1):20-28
Ahn, D., Ruvinsky, I., Oates, A.C., Silver, L.M., and Ho, R.K. (2000) tbx20, a new vertebrate T-box gene expressed in the cranial motor neurons and developing cardiovascular structures in zebrafish. Mechanisms of Development. 95(1-2):253-258
Ruvinsky, I., Oates, A.C., Silver, L.M., and Ho, R.K. (2000) The evolution of paired appendages in vertebrates: T-box genes in the zebrafish. Development genes and evolution. 210(2):82-91
Oates, A.C., Brownlie, A., Pratt, S.J., Irvine, D.V., Liao, E.C., Paw, B.H., Dorian, K.J., Johnson, S.L., Postlethwait, J.H., Zon, L.I., and Wilks, A.F. (1999) Gene duplication of zebrafish JAK2 homologs is accompanied by divergent embryonic expresssion patterns: only jak2a is expressed during erythropoiesis. Blood. 94(8):2622-2636
Oates, A.C., Wollberg, P., Pratt, S.J., Paw, B.H., Johnson, S.L., Ho, R.K., Postlethwait, J.H., Zon, L.I., and Wilks, A.F. (1999) Zebrafish stat3 is expressed in restricted tissues during embryogenesis and stat1 rescues cytokine signaling in a STAT1-deficient human cell line. Developmental Dynamics : an official publication of the American Association of Anatomists. 215(4):352-370
Oates, A.C., Lackmann, M., Power, M.A., Brennan, C., Smith, F.M., Do, C., Evans, B., Holder, N., and Boyd, A.W. (1999) An early developmental role for Eph-ephrin interaction during vertebrate gastrulation. Mechanisms of Development. 83(1-2):77-94
Brownlie, A., Donovan, A., Pratt, S.J., Paw, B.H., Oates, A.C., Brugnara, C., Witkowska, H.E., Sassa, S., and Zon, L.I. (1998) Positional cloning of the zebrafish sauternes gene: a model for congenital sideroblastic anaemia. Nature Genetics. 20:244-250
Lackmann, M., Oates, A.C., Dottori, M., Smith, F.M., Do, C., Power, M., Kravets, L., and Boyd, A.W. (1998) Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization. The Journal of biological chemistry. 273:20228-20237
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
Liao, E.C., Paw, B.H., Oates, A.C., Pratt, S.J., Postlethwait, J.H., and Zon, L.I. (1998) SCL/Tal-1 transcription factor acts downstream of cloche to specify hematopoietic and vascular progenitors in zebrafish. Genes & Development. 12:621-626