Quantitative Morphogenesis Laboratory

University of Toronto


Find all of our recent publications on PubMed


Ly M, Schimmer C, Hawkins R, Rothenberg KE*, Fernandez-Gonzalez R*. Integrin-based adhesions promote cell-cell junction and cytoskeletal remodelling to drive embryonic wound healing. J Cell Sci. 2024 Mar 1;137(5):jcs261138. doi: 10.1242/jcs.261138. PMID: 37970744.

Tokamov SA, Buiter S, Ullyot A, Scepanovic G, Williams AM, Fernandez-Gonzalez R, Horne-Badovinac S, Fehon R. Cortical tension promotes Kibra degradation via Par-1. Mol Biol Cell. 2024 Jan 1;35(1):ar2. doi: 10.1091/mbc.E23-06-0246. PMID: 37903240.

Scepanovic G, Fernandez-Gonzalez R. Should I shrink or should I grow: cell size changes in tissue morphogenesis. Genome. 2024 Jan 1. doi: 10.1139/gen-2023-0091. PMID: 38198661.


Balaghi N, Erdemci-Tandogan G, McFaul CM, Fernandez-Gonzalez R. Myosin waves and a mechanical asymmetry guide the oscillatory migration of Drosophila cardiac progenitors. Dev Cell. 2023 Jul 24;58(14):1299-1313. PMID: 37295436.

Rothenberg KE,  Chen Y, McDonald JA, Fernandez-Gonzalez R. Rap1 coordinates cell-cell adhesion and cytoskeletal reorganization to drive collective cell migration in vivo. Current Biology. 2023 Jul 10;33(13):2587-2601. PMID: 37244252.
Recommended by Faculty Opinions: Interesting Hypothesis, New finding.
Dispatch: Wound repair: two distinct Rap1 pathways close the gap.

Fernandez-Gonzalez R, Harris TJC. Contractile and expansive actin networks in Drosophila: Developmental cell biology controlled by network polarization and higher-order interactions. Current Topics in Developmental Biology. 2023;154:99-129. Pubmed PMID: 37100525.

Sheppard L, Green DG, Lerchbaumer G, Rothenberg KE, Fernandez-Gonzalez R, Tepass U. The α-Catenin mechanosensing M region is required for cell adhesion during tissue morphogenesis. J Cell Biol. 2023 Feb 6;222(2):e202108091. Pubmed PMID: 36520419.


De O, Rice C, Zulueta-Coarasa T, Fernandez-Gonzalez R, Ward RE 4th. Septate junction proteins are required for cell shape changes, actomyosin reorganization and cell adhesion during dorsal closure in Drosophila. Front Cell Dev Biol. 2022 Sep 27;10:947444. Pubmed PMID: 36238688.

Simões S, Lerchbaumer G, Pellikka M, Giannatou P, Lam T, Kim D, Yu J, Ter Stal D, Al Kakouni K, Fernandez-Gonzalez R, Tepass U. Crumbs complex-directed apical membrane dynamics in epithelial cell ingression. J Cell Biol. 2022 Jul 4;221(7):e202108076. Pubmed PMID: 35588693.

Fernandez-Gonzalez R, Peifer M. Powering morphogenesis: multiscale challenges at the interface of cell adhesion and the cytoskeleton. Mol Biol Cell. 2022 Jul 1; 33(8):pe4. Pubmed PMID: 35696393.


Scepanovic G, Hunter MV, Kafri R, Fernandez-Gonzalez R. p38-mediated cell growth and survival drive rapid embryonic wound repair. Cell Reports. 2021 Oct 19; 37(3): 109874. 

Fernandez-Gonzalez R, Balaghi N, Wang K, Hawkins R, Rothenberg K, McFaul C, Schimmer C, Ly M, do Carmo AM, Scepanovic G, Erdemci-Tandogan G, Castle V. PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images. Bioinformatics. 2021 Aug 13: btab589. Pubmed PMID: 34390579.
Free access link.

Yu JC*, Balaghi N*, Erdemci-Tandogan G, Castle V, Fernandez-Gonzalez R. Myosin cables control the timing of tissue internalization in the Drosophila embryo. Cells Dev. 2021 July 13:203721. Pubmed PMID: 34271226.
Accepted manuscript.

Biehler C, Rothenberg KE, Jette A, Gaude HM, Fernandez-Gonzalez R, Laprise P. Pak1 and PP2A antagonize aPKC function to support cortical tension induced by the Crumbs-Yurt complex. Elife. 2021 July 2; 10:e67999. Pubmed PMID: 34212861.

Willoughby PM, Allen M, Yu J, Korytnikov R, Chen T, Liu Y, So I, Macpherson N, Mitchell JA, Fernandez-Gonzalez R, Bruce AEE. The recycling endosome protein Rab25 coordinates collective cell movements in the zebrafish surface epithelium. Elife. 2021 Mar 23; 10:e66060. Pubmed PMID: 33755014.

Scepanovic G, Florea A, Fernandez-Gonzalez R. Multiscale In Vivo Imaging of Collective Cell Migration in Drosophila Embryos. Methods Mol Biol. 2021; 2179:199-224. Pubmed PMID: 32939723.


Ngai D, Lino M, Rothenberg KE, Simmons CA, Fernandez-Gonzalez R, Bendeck MP. DDR1 (Discoidin Domain Receptor-1)-RhoA Axis Senses Matrix Stiffness to Promote Vascular Calcification. Arterioscler Thromb Vasc Biol. 2020 Jul; 40(7):1763-1776. Pubmed PMID: 32493168.

Lee SH, Hadipour-Lakmehsari S, Murthy HR, Gibb N, Miyake T, Teng ACT, Cosme J, Yu JC, Moon M, Lim S, Wong V, Liu P, Billia F, Fernandez-Gonzalez R, Stagljar I, Sharma P, Kislinger T, Scott IC, Gramolini AO. REEP5 depletion causes sarco-endoplasmic reticulum vacuolization and cardiac functional defects. Nat Commun. 2020 Feb 19; 1(1):965. Pubmed PMID: 32075961.


Sarpal R, Yan V, Kazakova L, Sheppard L, Yu JC, Fernandez-Gonzalez R, Tepass U. Role of α-Catenin and its mechanosensing properties in regulating Hippo/YAP-dependent tissue growth. PLoS Genet. 2019 Nov 7; 15(11): e1008454. Pubmed PMID: 31697683.

Kobb AB*, Rothenberg KE*, Fernandez-Gonzalez R. Actin and myosin dynamics are independent during Drosophila embryonic wound repair. Mol Biol Cell. 2019 Oct 31; 30(23): 2859-2942. Pubmed PMID: 31553671.

Spracklen AJ, Thornton-Kolbe EM, Bonner AN, Florea A, Compton PJ, Fernandez-Gonzalez R, Peifer M. The Crk adapter protein is essential for Drosophila embryogenesis, where it regulates multiple actin-dependent morphogenic events. Mol Biol Cell. 2019 Aug 15; 30(18): 2349-2434. Pubmed PMID: 31318326.

Rothenberg KE, Fernandez-Gonzalez R. Forceful closure: cytoskeletal networks in embryonic wound repair. Mol Biol Cell. 2019 June 1; 30(12): 1353-1358. Pubmed PMID: 31145669.


Scepanovic G, Fernandez-Gonzalez R. Oriented cell division: the pull of the pole. Dev Cell. 2018 Dec 17;47(6):686-687. Pubmed PMID: 30562509.

Ishiyama N, Sarpal R, Wood MN, Barrick SK, Nishikawa T, Hayashi H, Kobb AB, Flozak AS, Yemelyanov A, Fernandez-Gonzalez R, Yonemura S, Leckband DE, Gottardi CJ, Tepass U, Ikura M. Force-dependent allostery of the α-catenin actin-binding domain controls adherens junction dynamics and functions. Nat Commun 2018 Nov 30;9(1):5121. Pubmed PMID: 30504777.

Hunter MV, Willoughby PM, Bruce AEE, Fernandez-Gonzalez R. Oxidative stress orchestrates cell polarity to promote embryonic wound healing. Dev Cell. 2018 Nov 5;47(3):377-387. Pubmed PMID: 30399336.

Siang LC, Fernandez-Gonzalez R, Feng JJ. Modeling cell intercalation during Drosophila axis elongation. Phys Biol. 2018 Sep 6;15(6):066008. doi: 10.1088/1478-3975/aad865. Pubmed PMID: 30080681.

Zulueta-Coarasa T, Fernandez-Gonzalez R. Dynamic force patterns promote collective cell movements during embryonic wound repair. Nat Phys. 2018 Jul 1;14(7):750-758. doi:10.1038/s41567-018-0111-2.
News & views: Cellular diversity heals.

Zhang Y, Yu JC, Jiang T, Fernandez-Gonzalez R, Harris TJC. Collision of expanding actin caps with actomyosin borders for cortical bending and mitotic rounding in a syncytium. Dev Cell. 2018 Jun 4;45(5):551-564. doi:10.1016/j.devcel.2018.04.024. Pubmed PMID: 29804877.


Wang MFZ, Fernandez-Gonzalez R. (Machine-)Learning to analyze in vivo microscopy: Support vector machines. Biochim Biophys Acta. 2017 Nov;1865(11 Pt B):1719-1727. doi: 10.1016/j.bbapap.2017.09.013. Pubmed PMID: 28974388.

Tewary M, Ostblom J, Prochazka L, Zulueta-Coarasa T, Shakiba N, Fernandez-Gonzalez R, Zandstra PW. A stepwise model of Reaction-Diffusion and Positional-Information governs self-organized human peri-gastrulation-like patterning. Development. 2017 Sep 4. pii: dev.149658. doi: 10.1242/dev.149658. Pubmed PMID: 28870989. 

West JJ, Zulueta-Coarasa T, Maier JA, Lee DM, Bruce AEE, Fernandez-Gonzalez R, Harris TJC. An Actomyosin-Arf-GEF Negative Feedback Loop for Tissue Elongation under Stress. Curr Biol. 2017 Aug 7;27(15):2260-2270.e5. doi: 10.1016/j.cub.2017.06.038. Pubmed PMID: 28736167.

Hunter MV, Fernandez-Gonzalez R. Coordinating cell movements in vivo: junctional and cytoskeletal dynamics lead the way. Curr Opin Cell Biology. 2017 Jun 13; 48:54-62; doi: 10.1016/j.ceb.2017.05.005. Pubmed PMID: 28622576.

McFaul CM, Fernandez-Gonzalez R. Shape of my heart: cell-cell adhesion and cytoskeletal dynamics during Drosophila cardiac morphogenesis. Exp Cell Res. 2017 Apr 4. pii: S0014-4827(17)30184-2. doi: 10.1016/j.yexcr.2017.03.057. Pubmed PMID: 28389210.

Simoes S, Oh Y, Wang MF, Fernandez-Gonzalez R, Tepass U. Myosin II promotes the anisotropic loss of the apical domain during Drosophila neuroblast ingression. J Cell Biol. 2017 Mar 31. pii: jcb.201608038. doi: 10.1083/jcb.201608038. Pubmed PMID: 28363972.

Goodwin K, Lostchuck EE, Cramb KM, Zulueta-Coarasa T, Fernandez-Gonzalez R, Tanentzapf G. Cell-cell and cell-ECM adhesions cooperate to organize actomyosin networks and maintain force transmission during Dorsal Closure. Mol Biol Cell. 2017 Mar 22. pii: mbc.E17-01-0033. doi: 10.1091/mbc.E17-01-0033. Pubmed PMID: 28331071.

Wang MFZ, Hunter MV, Wang G, McFaul C, Yip CM, Fernandez-Gonzalez R. Automated cell tracking identifies mechanically-oriented cell divisions during Drosophila axis elongation. Development. 2017 Feb 17;pii: dev.141473. doi:10.1242/dev.141473. Pubmed PMID: 28213553.

Kobb AB, Zulueta-Coarasa T, Fernandez-Gonzalez R. Tension regulates myosin dynamics during Drosophila embryonic wound repair. J Cell Sci. 2017 Feb 15;130:689-696; doi:10.1242/jcs.196139. Pubmed PMID: 28202603.
Highlighted article: Tension reduces myosin turnover at wound repair sites.


Zulueta-Coarasa T, Fernandez-Gonzalez R. Tension (re)builds: Biophysical mechanisms of embryonic wound repair. Mech Dev. 2016 Dec 15. pii: S0925-4773(16)30063-6. doi:10.1016/j.mod.2016.11.004. Pubmed PMID: 27989746.

Goodwin K, Ellis SJ, Lostchuck E, Zulueta-Coarasa T, Fernandez-Gonzalez R, Tanentzapf G. Basal cell-extraellular matrix adhesion regulates force transmission during tissue morphogenesis. Dev Cell 2016 Dec 5;39(5):611-625. doi:10.1016/j.devcell.2016.11.003. Pubmed PMID: 27923121.

Yu JC, Fernandez-Gonzalez R. Quantitative modelling of epithelial morphogenesis: integrating cell mechanics and molecular dynamics.Semin Cell Dev Biol 2016 Jul 29. doi:10.1016/j.semcdb.2016.07.030. Pubmed PMID: 27481581.

Yu JC, Fernandez-Gonzalez R. Local mechanical forces promote polarized junctional assembly and axis elongation in Drosophila. eLife 2016 Jan 9;5. pii: e10757.doi: 10.7554/eLife.10757. Pubmed PMID: 26747941.


Lan H, Wang Q, Fernandez-Gonzalez R, Feng JJ. A biomechanical model for cell polarization and intercalation during Drosophilagermband extension. Phys Biol. 2015 Sep 10;12(5):056011.doi: 10.1088/1478-3975/12/5/056011. Pubmed PMID: 26356256.

Zulueta-Coarasa T, Fernandez-Gonzalez R. Laser ablation to investigate cell and tissue mechanics in vivo. Integrative Mechanobiology: Micro- and Nano- Techniques in Cell Mechanobiology (edited by Y Sun, DH Kim and C Simmons). Cambridge University Press. 2015.

Hunter MV, Lee DM, Harris TJC, Fernandez-Gonzalez R. Polarized E-cadherin endocytosis directs actomyosin remodeling during embryonic wound repair. J Cell Biol. 2015 Aug 31;210(5):801-16. doi: 10.1083/jcb.201501076. Epub 2015 Aug 24. Pubmed PMID: 26304727.
Recommended by F1000: New finding.

Lau K, Tao H, Liu H, Wen J, Sturgeon K, Sorfazlian N, Lazic S, Burrows JT, Wong MD, Li D, Deimling S, Ciruna B, Scott I, Simmons C, Henkelman RM, Williams T, Hadjantonakis AK, Fernandez-Gonzalez R, Sun Y, Hopyan S. Anisotropic stress orients remodelling of mammalian limb bud ectoderm. Nat Cell Biol. 2015 May;17(5):569-79. doi: 10.1038/ncb3156. Epub 2015 Apr 20. Pubmed PMID: 25893915.

Javaherian S, D’Arcangelo E, Slater B, Zulueta-Coarasa T, Fernandez-Gonzalez R, McGuigan AP. An in vitro model of tissue boundary formation for dissecting the contribution of different boundary forming mechanisms. Integr Biol. 2015 Mar 9;7(3):298-312. doi: 10.1039/C4IB00272E. Epub 2015 Jan 14. Pubmed PMID: 25609037. 

Leung CY, Fernandez-Gonzalez R. Quantitative image analysis of cell behavior and molecular dynamics during tissue morphogenesis. Methods Mol Biol. 2015;1189:99-113. doi: 10.1007/978-1-4939-1164-6_7. Pubmed PMID: 25245689.


Hunter MV, Fernandez-Gonzalez R. Cell migration: a force to be reckoned with. Nat Phys. 2014 Sep 10(9):626-7. doi: 10.1038/nphys.3074. Epub 2014 Aug 03.

Zulueta-Coarasa T, Tamada M, Lee EJ, Fernandez-Gonzalez R. Automated multidimensional image analysis reveals a role for Abl in embryonic wound repair. Development. 2014 Jul;141(14):2901-11. doi: 10.1242/dev.106898. Epub 2014 Jun 19. PubMed PMID: 24948602.


Hunter MV, Fernandez-Gonzalez R. Gastrulation: cell polarity comes full circle. Curr Biol. 2013 Sep 23;23(18):R845-8. doi: 10.1016/j.cub.2013.08.003. PubMed PMID: 24070446.

Fernandez-Gonzalez R, Zallen JA. Wounded cells drive rapid epidermal repair in the early Drosophila embryo. Mol Biol Cell. 2013 Oct;24(20):3227-37. doi: 10.1091/mbc.E13-05-0228. Epub 2013 Aug 28. PubMed PMID: 23985320; PubMed Central PMCID: PMC3806660.


Fernandez-Gonzalez R, Zallen JA. Feeling the squeeze: live-cell extrusion limits cell density in epithelia. Cell. 2012 May 25;149(5):965-7. doi:10.1016/j.cell.2012.05.006. PubMed PMID: 22632965.


Fernandez-Gonzalez R, Zallen JA. Oscillatory behaviors and hierarchical assembly of contractile structures in intercalating cells. Phys Biol. 2011 Aug;8(4):045005. doi: 10.1088/1478-3975/8/4/045005. Epub 2011 Jul 12. PubMed PMID: 21750365.


Arganda-Carreras I, Fernandez-Gonzalez R, Muñoz-Barrutia A, Ortiz-De-Solorzano C. 3D reconstruction of histological sections: Application to mammary gland tissue. Microsc Res Tech. 2010 Oct;73(11):1019-29. doi: 10.1002/jemt.20829. PubMed PMID: 20232465.

Simões Sde M, Blankenship JT, Weitz O, Farrell DL, Tamada M, Fernandez-Gonzalez R, Zallen JA. Rho-kinase directs Bazooka/Par-3 planar polarity during Drosophila axis elongation. Dev Cell. 2010 Sep 14;19(3):377-88. doi: 10.1016/j.devcel.2010.08.011. PubMed PMID: 20833361; PubMed Central PMCID: PMC3131216.

Martin AC, Gelbart M, Fernandez-Gonzalez R, Kaschube M, Wieschaus EF. Integration of contractile forces during tissue invagination. J Cell Biol. 2010 Mar 8;188(5):735-49. doi: 10.1083/jcb.200910099. Epub 2010 Mar 1. PubMed PMID: 20194639; PubMed Central PMCID: PMC2835944.

Shelton DN, Fernandez-Gonzalez R, Illa-Bochaca I, Ortiz-de-Solorzano C, Barcellos-Hoff MH, Welm BE. Use of stem cell markers in dissociated mammary populations. Methods Mol Biol. 2010;621:49-55. doi: 10.1007/978-1-60761-063-2_3.  PubMed PMID: 20405358.

Illa-Bochaca I, Fernandez-Gonzalez R, Shelton DN, Welm BE, Ortiz-de-Solorzano C, Barcellos-Hoff MH. Limiting-dilution transplantation assays in mammary stem cell studies. Methods Mol Biol. 2010;621:29-47. doi: 10.1007/978-1-60761-063-2_2. PubMed PMID: 20405357.

Fernandez-Gonzalez R, Illa-Bochaca I, Shelton DN, Welm BE, Barcellos-Hoff MH, Ortiz-de-Solorzano C. In situ analysis of cell populations: long-term label-retaining cells. Methods Mol Biol. 2010;621:1-28. doi: 10.1007/978-1-60761-063-2_1. PubMed PMID: 20405356.


Marcinkevicius E, Fernandez-Gonzalez R, Zallen JA. Q&A: quantitative approaches to planar polarity and tissue organization. J Biol. 2009;8(12):103. doi: 10.1186/jbiol191. PubMed PMID: 20064196; PubMed Central PMCID: PMC2804277.

Fernandez-Gonzalez R, Zallen JA. Cell mechanics and feedback regulation of actomyosin networks. Sci Signal. 2009 Dec 15;2(101):pe78. doi: 10.1126/scisignal.2101pe78. PubMed PMID: 20009102.

Fernandez-Gonzalez R, Simoes Sde M, Röper JC, Eaton S, Zallen JA. Myosin II dynamics are regulated by tension in intercalating cells.Dev Cell. 2009 Nov;17(5):736-43. doi: 10.1016/j.devcel.2009.09.003. Epub 2009 Oct 29. PubMed PMID: 19879198; PubMed Central PMCID: PMC2854079.

Fernandez-Gonzalez R, Illa-Bochaca I, Welm BE, Fleisch MC, Werb Z, Ortiz-de-Solorzano C, Barcellos-Hoff MH. Mapping mammary gland architecture using multi-scale in situ analysis. Integr Biol (Camb). 2009 Jan;1(1):80-9. doi: 10.1039/b816933k. Epub 2008 Dec 5. PubMed PMID: 20023794; PubMed Central PMCID: PMC2847439.


Fernandez-Gonzalez R, Zallen JA. Epithelial organization: may the force be with you. Curr Biol. 2008 Feb 26;18(4):R163-5. doi: 10.1016/j.cub.2007.12.030. PubMed PMID: 18302918.


Adiga U, Malladi R, Fernandez-Gonzalez R, Ortiz de Solorzano C. High-throughput analysis of multispectral images of breast cancer tissue. IEEE Trans Image Process. 2006 Aug;15(8):2259-68. PubMed PMID: 16900681.

Fernández-González R, Muñoz-Barrutia A, Barcellos-Hoff MH, Ortiz-de-Solorzano C. Quantitative in vivo microscopy: the return from the 'omics'. Curr Opin Biotechnol. 2006 Oct;17(5):501-10. Epub 2006 Aug 8. Review. PubMed PMID: 16899361.


Fernandez-Gonzalez R, Barcellos-Hoff MH, Ortiz-de-Solórzano C. A tool for the quantitative spatial analysis of complex cellular systems.IEEE Trans Image Process. 2005 Sep;14(9):1300-13. PubMed PMID: 16190466.


Fernandez-Gonzalez R, Barcellos-Hoff MH, Ortiz-de-Solorzano C. Quantitative image analysis in mammary gland biology. J Mammary Gland Biol Neoplasia. 2004 Oct;9(4):343-59. Review. PubMed PMID: 15838604.

Fernandez-Gonzalez R, Deschamps T, Idica A, Malladi R, Ortiz-de-Solorzano C. Automatic segmentation of histological structures in mammary gland tissue sections. J Biomed Opt. 2004 May;9(3):444-53. PubMed PMID: 15189081.


Fernandez-Gonzalez R, Jones A, Garcia-Rodriguez E, Chen PY, Idica A, Lockett SJ, Barcellos-Hoff MH, Ortiz-De-Solorzano C. System for combined three-dimensional morphological and molecular analysis of thick tissue specimens. Microsc Res Tech. 2002 Dec 15;59(6):522-30. Review. PubMed PMID: 12467029.