Publications

Tbx16 and mesogenin 1 promote presomitic mesoderm differentiation by repressing the mesodermal progenitor cell state

Zhu, G, Genuth, MG*, Xiao, Y*, Kindberg, AA, Hackett, K, and Holley, SA.

PLoS Genet. 2026. 22(6):e1012176. doi: 10.1371/journal.pgen.1012176.

* Equal Contribution.

Actn4 Links Inactive Integrin α5 With Actin in Zebrafish Somites

Sun, S. and Holley, SA. 

Mol Cell Proteomics. 2026. 101087.doi: 10.1016/j.mcpro.2025.101087. PMCID: PMC12860946

A cadherin-integrin-ECM code for presomitic mesoderm fluidity

Genuth, MG*, Jülich, D*, Ton, AT*, Smith, SJ, Guillon, E., Shattuck, MD, O’Hern, CS, and Holley, SA. 

Development. 2025. 152(21): dev204874.doi: 10.1242/dev.204874. PMCID: PMC12633790 

* Equal Contribution.

A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish

Capon, SJ, Maroufidou, A, Feltes, M, Xu, Y, Matharoo, D, Jülich, D, Holley, SA, Farber, S, Stainier, DYR.

PLoS Genet. 2025. 21(6):e1011747. PMCID: PMC12212883

Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease

Bhattarai, P, Gunasekaran, TI, Reyes-Dumeyer, D, Jülich, D, Tayran, H, Yilmaz, E, Flaherty, D, Lantigua, R, Medrano, M, Rivera, D, Recio, P, Ertekin-Taner, N,  Teich, AF, Dickson, DW, Holley, SA, Mayeux, R, Kizil, D, and Vardarajan, BN.

Acta Neuropathol. 2024 Apr 10;147(1):70. doi: 10.1007/s00401-024-02721-1.

Live imaging of Fibronectin 1a-mNeonGreen and Fibronectin 1b-mCherry knock-in alleles during early zebrafish development

Jülich, D. and Holley SA.

Cell Dev. 2024. Jan 12;177:203900. doi: 10.1016/j.cdev.2024.203900. PMID: 38218338

Highly specific and non-invasive imaging of Piezo1-dependent activity across scales using GenEPi

Yaganoglu, S, Kalyviotis, K, Vagena-Pantoula, C, Jülich, D, Gaub, BM, Welling, M, Lopes, T, Lachowski, D, Tang, SS, Del Rio Hernandez, A, Salem, V, Müller, DJ, Holley, SA, Vermot, J, Shi, J, Helassa, N, Török, K. and Pantazis, P.

Nat Commun. 2023. Jul 19;14(1):4352. doi: 10.1038/s41467-023-40134-y. PMID: 37468521

Automated time-lapse data segmentation reveals in vivo cell state dynamics

Genuth, MA*, Kojima, Y*, Jülich, D, Kiryu, H. and Holley SA.

Sci Adv. 2023. Jun 2;9(22):eadf1814. doi: 10.1126/sciadv.adf1814. Epub 2023 Jun 2. PMID: 37267354

* Equal Contribution.

The roles of inter-tissue adhesion in development and morphological evolution

Smith, SJ, Guillon, E, and Holley SA.

J Cell Sci. 2022. 135:jcs259579. doi: 10.1242/jcs.259579.

The eye tugs and the nose follows: how inter-tissue adhesion directs oflactory development

Smith, SJ, and Holley SA.

EMBO Rep. 2022. 23:e54396. doi: 10.15252/embr.202154396.

Integrin intra-heterodimer affinity inversely correlates with integrin activatability

Sun, G, Guillon, E, and Holley SA.

Cell Rep. 2021. 35: 109230.

Mechanics as a Means of Information Propagation in Development

Genuth, MA and Holley SA.

Bioessays. 2020. doi: 10.1002/bies.202000121.

Fibronectin is a smart adhesive that both influences and responds to the mechanics of early spinal column development

Guillon, E, Das, D, Jülich, D, Abdel-Rahman, H, Geller, H, and Holley, SA.

eLife. 2020. 9: e48964.

Organization of embryonic morphogenesis via mechanical information

Das D*, Jülich J*, Schwendinger-Schreck JK*, Guillon E, Lawton AK, Dray N, Emonet T, O’Hern CS, Shattuck MD and Holley SA.

Dev Cell. 2019. 49: 829-839.

* Equal Contribution.

Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry

Das D, Chatti V, Emonet T, and Holley SA.

Dev Cell. 2017. 42:170-180.

A sawtooth pattern of Cadherin 2 stability mechanically regulates somite morphogenesis.

McMillen P, Chatti V, Jülich D, Holley SA.

Curr Biol. 2016. 26: 542-549.

Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis.

McMillen P, Holley SA.

Curr Opin Cell Biol. 2015. 36:48-53. Review.

Cross-Scale Integrin Regulation Organizes ECM and Tissue Topology.

Jülich D*, Cobb G*, Melo AM, McMillen P, Lawton AK, Mochrie SG, Rhoades E, Holley SA.

Dev Cell. 2015. 34:33-44.

* Equal Contribution.

The tissue mechanics of vertebrate body elongation and segmentation.

McMillen P, Holley SA.

Curr Opin Genet Dev. 2015 Jun;32:106-111. Review.

Fusaric Acid Induces Notochord Malformation in Zebrafish via Copper Chelation.

Yin ES, Rakhmankulova M, Kucera K, de Sena Filho JG, Portero CE, Narvaez-Trujillo A, Holley SA, Strobel, SA.

Biometals. 2015. 28: 783-9.

Modeling the Zebrafish Segmentation Clock’s Gene Regulatory Network Constrained by Expression Data Suggests Evolutionary Transitions Between Oscillating and Non-Oscillating Transcription.

Schwendinger-Schreck J, Kang Y, Holley SA.

Genetics. 2014. 197: 725-738.

Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics.

Dray N, Lawton A, Nandi A, Jülich D, Emonet T, Holley SA.

Curr Biol. 2013 Jul 22;23(14):1335-41.

Regulated tissue fluidity steers zebrafish body elongation.

Lawton AK, Nandi A, Stulberg MJ, Dray N, Sneddon MW, Pontius W, Emonet T, Holley SA.

Development. 2013 Feb;140(3):573-82.

Segmental Assembly of Fibronectin Matrix Requires rap1b and integrin α5.

Lackner S, Schwendinger-Schreck J, Jülich D, Holley SA.

Dev Dyn. 2012 Nov 29. doi: 10.1002/dvdy.23909.

Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud.

Stulberg MJ, Lin A, Zhao H, Holley SA.

Dev Biol. 2012 Sep 15;369(2):298-307.

The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub.

Trofka A, Schwendinger-Schreck J, Brend T, Pontius W, Emonet T, Holley SA.

Development. 2012 Mar;139(5):940-7.

Expression of the oscillating gene her1 is directly regulated by Hairy/Enhancer of Split, T-box, and Suppressor of Hairless proteins in the zebrafish segmentation clock.

Brend T, Holley SA.

Dev Dyn. 2009 Nov;238(11):2745-59.

Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling.

Jülich D, Mould AP, Koper E, Holley SA.

Development. 2009 Sep;136(17):2913-21.

Zebrafish whole mount high-resolution double fluorescent in situ hybridization.

Brend T, Holley SA.

J Vis Exp. 2009 Mar 25;(25). pii: 1229. doi: 10.3791/1229.

Balancing segmentation and laterality during vertebrate development.

Brend T, Holley SA.

Semin Cell Dev Biol. 2009 Jun;20(4):472-8. Review.

Cell cycle progression is required for zebrafish somite morphogenesis but not segmentation clock function.

Zhang L, Kendrick C, Jülich D, Holley SA.

Development. 2008 Jun;135(12):2065-70.

Two deltaC splice-variants have distinct signaling abilities during somitogenesis and midline patterning.

Mara A, Schroeder J, Holley SA.

Dev Biol. 2008 Jun 1;318(1):126-32.

Oscillators and the emergence of tissue organization during zebrafish somitogenesis.

Mara A, Holley SA.

Trends Cell Biol. 2007 Dec;17(12):593-9. Review.

3D cell nuclei segmentation based on gradient flow tracking.

Li G, Liu T, Tarokh A, Nie J, Guo L, Mara A, Holley S, Wong ST.

BMC Cell Biol. 2007 Sep 4;8:40.

Detection of blob objects in microscopic zebrafish images based on gradient vector diffusion.

Li G, Liu T, Nie J, Guo L, Malicki J, Mara A, Holley SA, Xia W, Wong ST.

Cytometry A. 2007 Oct;71(10):835-45.

The genetics and embryology of zebrafish metamerism.

Holley SA.

Dev Dyn. 2007 Jun;236(6):1422-49. Review.

Priming, initiation and synchronization of the segmentation clock by deltaD and deltaC.

Mara A, Schroeder J, Chalouni C, Holley SA.

Nat Cell Biol. 2007 May;9(5):523-30.

A chemical and genetic approach to the mode of action of fumagillin.

Zhang Y, Yeh JR, Mara A, Ju R, Hines JF, Cirone P, Griesbach HL, Schneider I, Slusarski DC, Holley SA, Crews CM.

Chem Biol. 2006 Sep;13(9):1001-9.

Anterior-posterior differences in vertebrate segments: specification of trunk and tail somites in the zebrafish blastula.

Holley SA.

Genes Dev. 2006 Jul 15;20(14):1831-7. Review

Vertebrate segmentation: snail counts the time until morphogenesis.

Holley SA.

Curr Biol. 2006 May 23;16(10):R367-9. Review

beamter/deltaC and the role of Notch ligands in the zebrafish somite segmentation, hindbrain neurogenesis and hypochord differentiation.

Jülich D, Hwee Lim C, Round J, Nicolaije C, Schroeder J, Davies A, Geisler R, Lewis J, Jiang YJ,  Tübingen 2000 Screen Consortium, Holley SA.

Dev Biol. 2005 Oct 15;286(2):391-404.

Integrinalpha5 and delta/notch signaling have complementary spatiotemporal requirements during zebrafish somitogenesis.

Jülich D, Geisler R, Tübingen 2000 Screen Consortium, Holley SA.

Dev Cell. 2005 Apr;8(4):575-86.

Catching a wave: the oscillator and wavefront that create the zebrafish somite.

Holley SA, Takeda H.

Semin Cell Dev Biol. 2002 Dec;13(6):481-8. Review.