Publications

Rohde LA, Bercowsky-Rama A, Negrete J Jr, Valentin G, Naganathan SR, Desai RA, Strnad P, Soroldoni D, Jülicher F, Oates AC. Cell-autonomous generation of the wave pattern within the vertebrate segmentation clock. BioRxiv. May 30, 2021. Doi https://doi.org/10.1101/2021.05.29.446196.

Fantner GE, Oates AC. Instruments of change for academic tool development. 2021. Nature Physics, Volume 17, Issue 4, p.421-424.

Negrete J Jr, Oates AC. Towards a physical understanding of developmental patterning. Nat Rev Genet. 2021 May 10. Doi: 10.1038/s41576-021-00355-7. Online ahead of print. PMID: 33972772 Review.

Uriu K, Liao BK, Oates AC, Morelli LG. From local resynchronization to global pattern recovery in the zebrafish segmentation clock. Elife. 2021 Feb 15;10:e61358. doi: 10.7554/eLife.61358. PMID: 33587039 Free PMC article.

Negrete J Jr, Lengyel IM, Rohde LA, Desai RA, Oates AC, Jülicher F, Theory of time delayed genetic oscillations with external noisy regulation, New Journal of Physics, 2021.

Naganathan SR, Oates AC. Patterning and mechanics of somite boundaries in zebrafish embryos, Seminars in Cell & Developmental Biology, Elsevier, November 2020, Volume 107, 170-178.

Naganathan SR, Popovic M, Oates AC. Somite deformations buffer imprecise segment lengths to ensure left-right symmetry. BioRxiv. August 14, 2020.
doi. https://doi.org/10.1101/2020.08.14.251645.

Oates AC. Waiting on the Fringe: cell autonomy and signaling delays in segmentation clocks. Curr Opin Genet Dev. 2020 Aug;63:61-70. doi: 10.1016/j.gde.2020.04.008. Epub 2020 Jun 5. PMID: 32505051 Free article. Review.

Venzin OF, Oates AC. What are you synching about? Emerging complexity of Notch signaling in the segmentation clock. Dev Biol. 2020 Apr 1;460(1):40-54.

Narayanan R, Oates AC. Detection of mRNA by Whole Mount in situ Hybridization and DNA Extraction for Genotyping of Zebrafish Embryos Bio-Protocol. 2019. 9 (6), e3193.

Negrete J Jr, Oates AC. Embryonic lateral inhibition as optical modes: An analytical framework for mesoscopic pattern formation. Physical Review E. 2019. 99 (4), 042417.

Lleras Forero L, Narayanan R, Huitema LF, VanBergen M, Apschner A, Peterson-Maduro J, Logister I, Valentin G, Morelli LG, Oates AC, Schulte-Merker S. Segmentation of the zebrafish axial skeleton relies on notochord sheath cells and not on the segmentation clock. Elife. 2018 Apr 6;7.

Richter S, Schulze U, Tomançak P, Oates AC. Small molecule screen in embryonic zebrafish using modular variations to target segmentation. Nat Commun. 2017 Dec. 1;8(1):1901.

Naganathan SR, Oates AC. Mechanochemical coupling and developmental pattern formation, Current Opinion in Systems Biology, Elsevier, October 2017, Volume 5, 104-111.

Uriu K, Bhavna R, Oates AC, Morelli LG. A framework for quantification and physical modeling of cell mixing applied to oscillator synchronization in vertebrate somitogenesis. Biol Open. 2017 Aug. 15;6(8):1235-1244.

Liao BK, Oates AC. Delta-Notch signalling in segmentation. Arthropod Struct Dev. 2017 May. 46(3):429-447.

Naganathan SR, Qian C, Oates AC. Emergence of bilaterally symmetric somites. Mechanisms Of Development, 2017, 145, S68-S68.

Naganathan SR, Oates AC. The Sweetness of Embryonic Elongation and Differentiation. Developmental Cell. 2017 Feb 27, 40(4):323-324.

Jörg DJ, Oates AC, Jülicher F. Sequential Pattern Formation Governed by Signaling Gradients. Physical Biology. 2016 13, 05LT03.

Liao BK, Jörg DJ, Oates AC. Faster embryonic segmentation through elevated Delta-Notch signalling. Nature Communications. 2016 Jun 15;7:11861.

Rajasekaran B, Uriu K, Valentin G, Tinevez JY, Oates AC. Object Segmentation and Ground Truth in 3D Embryonic Imaging. PLoS One 2016 Jun 22;11(6): e0150853.

Webb AB, Lengyel IM, Jörg DJ, Valentin G, Jülicher F, Morelli LG, Oates AC. Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock. Elife. 2016 Feb 16;5. pii: e08438.

Webb AB, Oates AC. Timing by rhythms: Daily clocks and developmental rulers. Development Growth and Differentiation. 2016 Jan;58(1):43-58.

Jörg DJ, Morelli LG, Soroldoni D, Oates AC, Jülicher J. Continuum theory of vertebrate segmentation. New Journal of Physics, Sept 2015, 17 (9), 093042.

Bergert M, Erzberger A, Desai RA, Aspalter IM, Oates AC, Charras G, Salbreux G, Paluch EK. Force transmission during adhesion-independent migration. Nature Cell Biology. 2015 Apr;17(4):524-9.

Windner SE, Doris RA, Ferguson CM, Nelson AC, Valentin G, Tan H, Oates AC, Wardle FC, Devoto SH. Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish. Development. 2015 Feb 27. pii: dev.113431.

Lengyel IM, Soroldoni D, Oates AC, Morelli, LG. Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations. Papers in Physics, 6, 2014.

Rost F, Eugster C, Schröter C, Oates AC, Brusch L. Chevron formation of the zebrafish muscle segments. Journal of Experimental Biology. 2014 Sept; 217, 3870-3882.

Soroldoni D, Jörg DJ, Morelli LG, Richmond DL, Schindelin J, Jülicher F, Oates, AC. A Doppler Effect in Embryonic Pattern Formation. Science. 2014 July 11;345, 222-225.

Webb AB, Soroldoni D, Oswald A, Schindelin J, and Oates AC. Generation of dispersed presomitic mesoderm cell cultures for imaging of the zebrafish segmentation clock in single cells. Journal of Visual Experimentation. 2014 (89), e50307.

Uriu K, Morelli LG, Oates AC. Interplay between intercellular signaling and cell movement in development. Seminars in Cell and Developmental Biology. 2014 Jun 2. pii: S1084-9521(14)00157-8.

Bajard L, Morelli LG, Ares S, Pecreaux J, Jülicher F, Andrew C. Oates AC. Wnt-regulated dynamics of positional information in vertebrate segmentation. Development. 2014 Mar;141(6):1381-91.

Uriu K, Ares S, Oates AC, Morelli LG. Dynamics of mobile coupled oscillators. Physical Review E, March 2013, 032911.

Valentin G, Oates AC.  Opening a can of centipedes: new insights into mechanisms of body segmentation BMC Biology 2013 Nov 29;11:116.

Richmond DL, Oates AC. The segmentation clock: inherited trait or universal design principle? Current Opinion in Genetics and Development. 2012, Dec 22:600-606.

Ullner E, Ares, S, Morelli LG, Oates AC, Julicher F, Nicola E, Heussen R, Whitmore D, Blyuss K, Fryett M, Zakharova A, Koseska A, Nene NR, Zaikin A. Noise and oscillations in biological systems: multidisciplinary approach between experimental biology, theoretical modelling and synthetic biology. International Journal of Modern Physics B. 2012 Oct 26(25):1246009.

Schröter C, Ares S, Morelli LG, Isakova A, Hens K, Soroldoni D, Gajewski M, Jülicher F, Maerkl SJ, Deplancke B, Oates AC. Topology and dynamics of the zebrafish segmentation clock core circuit. PLoS Biology. 2012, July 10(7):e1001364.

Synopsis: Weaver, J. A window into the workings of the segmentation clock. PLoS Biology. 2012, 10(7):e1001366.

Research highlight: Stower, H. Segmentation by sequestration. Nature Reviews Genetics. 2012, 13:595.

Morelli LG, Uriu K, Ares S, Oates AC. Computational approaches to developmental patterning. Science. 2012 Apr 13;336(6078):187-91.

Bajard L, Oates AC. Breathe in and straighten your back: Hypoxia, Notch and scoliosis. Cell. 2012 Apr 13;149(2):255-6.

Uriu K, Ares S, Oates AC, Morelli LG. Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions. Physical Biology. 2012 9:036006.

Ares S, Morelli LG, Jörg DJ, Oates AC, Jülicher F. Collective modes of coupled phase oscillators with delayed coupling. Physical Review Letters. 2012 108, 204101.

Oates AC, Morelli LG, Ares S. Patterning embryos with oscillations: structure, function, and dynamics of the vertebrate segmentation clock. Development. 2012 Feb 139:625-639.

Soroldoni D, Oates AC. Live transgenic reporters of the vertebrate embryo’s segmentation clock. Current Opinion in Genetics and Development. 2011 Oct;21(5):600-5.

Krol AJ, Roellig D, Dequeant M-L, Tassy O, Glynn E, Hattem G, Mushegian A, Oates AC, Pourquie O. Evolutionary plasticity of segmentation clock networks. Development. 2011 June 138:2783-2792.

Roellig D, Morelli LG, Ares S, Jülicher F, Oates AC. Snapshot: The Segmentation Clock. Cell. 2011 May 145(5):800-800.e1.

Oswald A, Oates AC. Control of endogenous gene expression timing by introns. Genome Biology. 2011, 12:107.

Oates AC. What’s all the noise about developmental stochasticity? Development. 2011 Feb; 138: 601-607.

Dahmann C, Oates AC, Brand M. Boundary formation and maintenance in tissue development. Nature Reviews Genetics. 2011 Jan;12(1):43-55.

Herrgen L, Schröter C, Morreli L, Ares S, Julicher F, Oates AC. Intercellular coupling regulates the period of the segmentation clock. Current Biology. 2010 15 July 20(14): 1244-1253.

Schröter, C, Oates AC. Segment number and regional identity in a segmentation clock period mutant. Current Biology. 2010 15 July 20(14):1254-1258.

Strzelecka M, Trowitzsch S, Weber G, Luhrmann R, Oates AC, Neugebauer KM. Coilin-dependent snRNP biogenesis is essential for zebrafish embryogenesis. Nature Structural and Molecular Biology. 2010 Apr;17(4):403-9.

Strzelecka M, Oates AC, Neugebauer KM. Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus. 2010 Jan 1(1):96-108.

Herrgen L, Schröter C, Bajard L, Oates AC. Multiple embryo time-lapse imaging of zebrafish development. Methods Mol Biol. 2009 546:243-54

Soroldoni D, Hogan BM and Oates AC. Simple and efficient transgenesis with meganuclease constructs in zebrafish. Methods Mol Biol. 2009 546:117-30.

Picker A, Roellig D, Oates AC and Brand M. Tissue micromanipulation in zebrafish embryos. Methods Mol Biol. 2009;546:153-72.

Oates AC, Gorfinkiel N, González-Gaitán M, Heisenberg CP. Quantitative approaches in developmental biology. Nature Reviews Genetics. 2009 Aug;10(8):517-30.

Morelli L, Ares S, Herrgen L, Schröter C, Jülicher F, Oates AC. Delayed coupling theory of vertebrate segmentation. HFSP Journal, 2009 Feb 3(1):55-66.

Schröter C, Herrgen L, Cardona, A, Brouhard GJ, Feldman B, Oates AC. Dynamics of zebrafish somitogenesis. Developmental Dynamics, 2008 Mar;237(3):545-53.

Riedel-Kruse IH, Müller C, Oates AC. Synchrony dynamics during initiation, failure, and rescue of the segmentation clock. Science, 2007 Sep 28;317:1911-5.

Editor’s choice: BA Purnell, Modeling Developmental Segmentation. Sci. STKE 2007, tw355 (2007).

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engstrom PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007 May;17(5):545-55.

Shankaran SS, Sieger D, Schröter C, Czepe C, Pauly MC, Laplante MA, Becker TS, Oates AC, Gajewski M. 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. Dev Biol. 2007 Apr 15;304(2):615-32.

Echeverri K, Oates AC. Coordination of symmetric cyclic gene expression during somitogenesis by Suppressor of Hairless involves regulation of retinoic acid catabolism. Dev Biol. 2007 Jan 15;301(2):388-403.

Tucker B, Hepperle C, Kortschak D, Rainbird B, Wells S, Oates AC, Lardelli M. Zebrafish Angiotensin II Receptor-like 1a (agtrl1a) is expressed in migrating hypoblast, vasculature, and in multiple embryonic epithelia. Gene Expr Patterns. 2007 Jan; 7(3):258-65.

Langenberg T, Dracz T, Oates AC, Heisenberg CP, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. Dev Dyn. 2006 Apr; 235(4):928-33

Oates AC, Rohde LA, Ho RK. Generation of segment polarity in the paraxial mesoderm of the zebrafish through a T-box-dependent inductive event. Dev Biol. 2005 Jul 1; 283(1):204-14

Oates AC, Müller C, Ho RK. Cooperative function of deltaC and her7 in anterior segment formation.  Dev Biol. 2005 April 1; 280(1):133-149.

Hogan BM, Hunter MP, Oates AC, Crowhurst MO, Hall NE, Heath JK, Prince VE, Lieschke GJ. Zebrafish gcm2 is required for gill filament budding from pharyngeal ectoderm. Dev Biol. 2004 Dec 15;276(2):508-22.

Rohde LA, Oates AC, Ho RK. A Crucial Interaction between Embryonic Red Blood Cell Progenitors and Paraxial Mesoderm Revealed in spadetail Embryos. Dev Cell. 2004 Aug;7(2):251-62.

Brownlie A, Hersey C, Oates AC, Paw BH, Falick AM, Witkowska HE, Flint J, Higgs D, Jessen J, Bahary N, Zhu H, Lin S, Zon L. Characterization of embryonic globin genes of the zebrafish. Dev Biol. 2003 Mar 1;255(1):48-61.

Oates AC, Zon LI. JAK/STATs in zebrafish: conservation of JAK/STAT signaling in vertebrates.  In Signal Transducers and Activators of Transcription (STATs): Activators and Biology.  Eds Segal SB, Levy DE, Hirano T. Kluwer Academic Publishers, Dordrecht, The Netherlands, 2003.

Oates AC, Ho RK.  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. 2002 Jun 15;129(12):2929-2946.

Lieschke GJ*, Oates AC*, Paw BH, Thompson MA, Hall NE, Ward AC, Ho RK, Zon LI, Layton JE.  Zebrafish SPI-1 (PU.1) Marks a Site of Myeloid Development Independent of Primitive Erythropoiesis: Implications for Axial Patterning. Dev Biol. 2002 Jun 15;246(2):274-295. *Equal first authors.

Coulthard MG, Duffy S, Down M, Evans B, Power M, Smith F, Stylianou C, Kleikamp S, Oates AC, Lackmann M, Burns GF, Boyd AW. The role of the Eph-ephrin signalling system in the regulation of developmental patterning. Int J Dev Biol. 2002;46(4):375-84.

Oates AC, Pratt SJ, Vail B, Yan Yl, Ho RK, Johnson SL, Postlethwait JH, Zon LI.  The zebrafish klf gene family. Blood. 2001 Sep 15;98(6):1792-801.

Lieschke GJ, Oates AC, Crowhurst MO, Ward AC, Layton JE.  Morphologic and functional characterization of granulocytes and macrophages in embryonic and adult zebrafish. Blood. 2001 Nov 15;98(10):3087-96.

Bruce AE, Oates AC, Prince VE, Ho RK.  Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes.  Evol Dev. 2001 May-Jun;3(3):127-44.

Lyons SE, Shue BC, Oates AC, Zon LI, Liu PP.  A novel myeloid-restricted zebrafish CCAAT/enhancer-binding protein with a potent transcriptional activation domain. Blood. 2001 May 1;97(9):2611-7.

Lyons SE, Shue BC, Lei L, Oates AC, Zon LI, Liu PP.  Molecular cloning, genetic mapping, and expression analysis of four zebrafish c/ebp genes. Gene. 2001 Dec 27;281(1-2):43-51.

Prince VE, Holley SA, Bally-Cuif L, Prabhakaran B, Oates AC, Ho RK, Vogt TF.  Zebrafish lunatic fringe demarcates segmental boundaries. Mech Dev. 2001 Jul;105(1-2):175-80.

Oates AC, Bruce AE, Ho RK.  Too much interference: injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. Dev Biol. 2000 Aug 1;224(1):20-8.

Editor’s Choice: RNAi: Too Much of a Good Thing? Sci. STKE 2000, tw10 (2000).

Ruvinsky I, Oates AC, Silver LM, Ho RK.  The evolution of paired appendages in vertebrates: T-box genes in the zebrafish. Dev Genes Evol. 2000 Feb;210(2):82-91.

Ahn DG, Ruvinsky I, Oates AC, Silver LM, Ho RK.  tbx20, a new vertebrate T-box gene expressed in the cranial motor neurons and developing cardiovascular structures in zebrafish. Mech Dev. 2000 Jul;95(1-2):253-8.

Blake T, Adya N, Kim CH, Oates AC, Zon L, Chitnis A, Weinstein BM, Liu PP.  Zebrafish homolog of the leukemia gene CBFB: its expression during embryogenesis and its relationship to scl and gata-1 in hematopoiesis. Blood. 2000 Dec 15;96(13):4178-84.

Oates AC, Lackmann M, Power MA, Brennan C, Down LM, Do C, Evans B, Holder N, Boyd AW.  An early developmental role for eph-ephrin interaction during vertebrate gastrulation. Mech Dev. 1999 May;83(1-2):77-94.

Oates AC, Brownlie A, Pratt SJ, Irvine DV, Liao EC, Paw BH, Dorian KJ, Johnson SL, Postlethwait JH, Zon LI, Wilks AF.  Gene duplication of zebrafish JAK2 homologs is accompanied by divergent embryonic expression patterns: only jak2a is expressed during erythropoiesis. Blood. 1999 Oct 15;94(8):2622-36.

Oates AC, Wollberg P, Pratt SJ, Paw BH, Johnson SL, Ho RK, Postlethwait JH, Zon LI, Wilks AF.  Zebrafish stat3 is expressed in restricted tissues during embryogenesis and stat1 rescues cytokine signaling in a STAT1-deficient human cell line. Dev Dyn. 1999 Aug;215(4):352-70.

Halford MM, Oates AC, Hibbs ML, Wilks AF, Stacker SA.  Genomic structure and expression of the mouse growth factor receptor related to tyrosine kinases (Ryk). J Biol Chem. 1999 Mar 12;274(11):7379-90.

Oates AC, Bonkovsky JL, Irvine DV, Kelly LE, Thomas JB, Wilks AF.  Embryonic expression and activity of doughnut, a second RYK homolog in Drosophila. Mech Dev. 1998 Nov;78(1-2):165-9.

Oates AC, Wollberg P, Achen MG, Wilks AF.  Sampling the genomic pool of protein tyrosine kinase genes using the polymerase chain reaction with genomic DNA. Biochem Biophys Res Commun. 1998 Aug 28;249(3):660-7.

Lackmann M, Oates AC, Dottori M, Smith FM, Do C, Power M, Kravets L, Boyd AW.  Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization. J Biol Chem. 1998 Aug 7;273(32):20228-37.

Liao EC, Paw BH, Oates AC, Pratt SJ, Postlethwait JH, Zon LI.  SCL/Tal-1 transcription factor acts downstream of cloche to specify hematopoietic and vascular progenitors in zebrafish. Genes Dev. 1998 Mar 1;12(5):621-6.

Lackmann M, Harpur AG, Oates AC, Mann RJ, Gabriel A, Meutermans W, Alewood PF, Kerr IM, Stark GR, Wilks AF.  Biomolecular interaction analysis of IFN gamma-induced signaling events in whole-cell lysates: prevalence of latent STAT1 in high-molecular weight complexes. Growth Factors. 1998;16(1):39-51.

Brownlie A, Donovan A, Pratt SJ, Paw BH, Oates AC, Brugnara C, Witkowska HE, Sassa S, Zon LI.  Positional cloning of the zebrafish sauternes gene: a model for congenital sideroblastic anaemia. Nat Genet. 1998 Nov;20(3):244-50.

Thompson MA, Ransom DG, Pratt SJ, MacLennan H, Kieran MW, Detrich HW 3rd, Vail B, Huber TL, Paw B, Brownlie AJ, Oates AC, Fritz A, Gates MA, Amores A, Bahary N, Talbot WS, Her H, Beier DR, Postlethwait JH, Zon LI.  The cloche and spadetail genes differentially affect hematopoiesis and vasculogenesis. Dev Biol. 1998 May 15;197(2):248-69.

Ernst M, Oates AC, Dunn AR. Gp130-mediated signal transduction in embryonic stem cells involves activation of Jak and Ras/mitogen-activated protein kinase pathways. J Biol Chem. 1996 Nov 22;271(47):30136-43.

Wilks AF, Oates AC.  The JAK/STAT pathway. Cancer Surv. 1996;27:139-63.

Nicholson SE, Oates AC, Harpur AG, Ziemiecki A, Wilks AF, Layton JE.  Tyrosine kinase JAK1 is associated with the granulocyte-colony-stimulating factor receptor and both become tyrosine-phosphorylated after receptor activation. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2985-8.

Edited books

Lieschke G, Oates AC and Kawakami K. “Zebrafish Methods and Protocols” Methods in Molecular Biology Series, 2009. Humana Press, Springer Protocols, Dordrecht.