Papers
*Equal contribution
Tschanz, A, Matus, DQ*, Swinburne I*. Systematic comparison of mStayGold and mGold2 variants for live imaging in zebrafish. 2025. microPublication Biology. 10.17912/micropub.biology.001847.
Swinburne, IA, Munjal, A, Kukreja, K, Williams, S, Kawanishi, T, O’Brown, N, Ishimatsu, K, Klein, A, Megason, SG. A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish. bioRxiv 2025.09.30.679639; doi.org/10.1101/2025.09.30.679639 [Biorxiv]
Alshaabi T, Milkie DE, Liu G, Shirazinejad C, Hong JL, Achour K, Görlitz F, Milunovic-Jevtic A, Simmons C, Abuzahriyeh IS, Hong E, Williams SE, Harrison N, Huang E, Bae ES, Killilea AN, Swinburne IA, Drubin DG, Upadhyayula S, Betzig E. Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens. Nat Methods. 2025 Oct;22(10):2171-2179. doi: 10.1038/s41592-025-02844-7. Epub 2025 Oct 1. PMID: 41034611; PMCID: PMC12510882.[NatMethods]
Fu TM, Liu G, Milkie DE, Ruan X, Görlitz F, Shi Y, Ferro V, Divekar NS, Wang W, York HM, Kilic V, Mueller M, Liang Y, Daugird TA, Gacha-Garay MJ, Larkin KA, Adikes RC, Harrison N, Shirazinejad C, Williams S, Nourse JL, Sheu SH, Gao L, Li T, Mondal C, Achour K, Hercule W, Stabley D, Emmerich K, Dong P, Drubin D, Liu ZJ, Clapham D, Mumm JS, Koyama M, Killilea A, Bravo-Cordero JJ, Keene CD, Luo L, Kirchhausen T, Pathak MM, Arumugam S, Nunez JK, Gao R, Matus DQ, Martin BL, Swinburne IA, Betzig E, Legant WR, Upadhyayula S. A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms. bioRxiv [Preprint]. 2025 Jun 3:2025.06.02.657494. doi: 10.1101/2025.06.02.657494. PMID: 40661351; PMCID: PMC12259214. [Biorxiv]
Peterman E, Murphy A, Swinburne IA, Linbo TH, Megason SG, Rasmussen JP. Microtubules regulate tissue-level navigation in skin-resident macrophages. J Cell Sci. 2025 Sep 15;138(18):jcs264101. doi: 10.1242/jcs.264101. Epub 2025 Sep 18. PMID: 40827096; PMCID: PMC12516128. [JCellSci]
Kroll JB, Cha A, Oyler-Yaniv A, Lambert T, Swinburne IA, Murphy A, Megason SG. Tetrahedral serial multiview microscopy and image fusion for improved resolution and extent in stained zebrafish embryos. Dev Dyn. 2024 Jul;253(7):690-704. doi: 10.1002/dvdy.683. Epub 2023 Dec 22. PMID: 38131490; PMCID: PMC11192867.[DevDyn]
Mosaliganti, K.R.*, Swinburne, I.A.*, Chan, C.U.*, Obholzer, N.D., Green, A.A., Tanksale, S., Mahadevan, L., and Megason, S.G. Size control of the inner ear via hydraulic feedback. eLife 8:e39596 (2019); bioRxiv doi.org/10.1101/349381 [eLife]
Swinburne, I.A., Mosaliganti, K.R., Upadhyayula, S., Liu, T-L., Hildebrand, D.G.C., Tsai, T.Y.-C., Chen, A., Al-Obeidi, E., Fass, A.K., Malhotra, S., Engert, F., Lichtman, J.W., Kirchhausen, T., Betzig, E., and Megason, S.G. Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure. eLife 7:e37131 (2018); bioRxiv, doi: doi.org/10.1101/143826 [eLife]
Liu, T.L.*, Upadhyayula, S.*, Milkie, D.E., Singh, V., Wang, K, Swinburne, I.A., Mosaliganti, K.R., Collins, Z.M., Hiscock, T.W., Shea, J., Kohrman, A.Q., Medwig, T.N., Damournet, D., Forster, R., Cunniff, B., Ruan, Y., Yashiro, H., Scholpp, S., Meyerowitz, E.M., Hockemeyer, D, Drubin, D.G., Martin, B.L., Matus, D.Q., Koyama, M., Megason, S.G., Kirchhausen, T., and Betzig, E. Observing the cell in its native state: imaging subcellular dynamics in multicellular organisms. Science 360, eaaq1392 (2018); bioRxiv doi.org/10.1101/243352 (2018) [PUBMED]
Green A.A., Mosaliganti K.R., Swinburne I.A., Obholzer N.D., Megason S.G. Recovery of shape and size in a developing organ pair. Dev Dyn 246(6):451-465 (2017). doi: 10.1002/dvdy.24498. [PUBMED]
Nissim S., Weeks O., Talbot J.C., Hedgepeth J.W., Wucherpfennig J., Schatzman-Bone S., Swinburne I., Cortes M., Alexa K., Megason S., North T.E., Amacher S.L., Goessling W. Iterative use of nuclear receptor Nr5a2 regulates multiple stages of liver and pancreas development. Dev Biol 418(1):108-23 (2016). doi: 10.1016/j.ydbio.2016.07.019. [PUBMED]
Swinburne, I.A., Green, A.A., and Megason S.G. Improved long-term imaging of embryos with genetically encoded α-bungarotoxin. PLoS One 10(8):e0134005 (2015). [PLoS ONE]
Xiong F., Ma W., Hiscock T.W., Mosaliganti K.R., Tentner A.R., Brakke K.A., Rannou N., Gelas A., Souhait L., Swinburne I.A., Obholzer N.D., and Megason S.G. Interplay of cell shape and division orientation promotes robust morphogenesis of developing epithelia. Cell 159(2): 415-27 (2014). [PUBMED] [Cell]
Xiong, F., Tentner, A.R., Huang, P., Gelas, A., Mosaliganti, K.R., Souhait, L., Rannou, N., Swinburne, I.A., Obholzer, N.D., Cowgill, P.D., Schier, A.F., and Megason, S.G. Specified neural progenitors sort to form sharp domains after noisy Shh signaling. Cell 153(3): 550-561 (2013). [PUBMED] [Cell]
Mosaliganti, K.R., Noche, R.R., Xiong F., Swinburne I.A., and Megason S.G. ACME: Automated Cell Morphology Extraction for Comprehensive Reconstruction of Cell Membranes. PLOS Computational Biology 8(12): e1002780 (2012). [PLoS Computation Biology]
Obholzer N*, Swinburne I.A.*, Scwab E, Nechiporuk A.V., Nicolson T, and Megason S.G. Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. Development 139(22): 4280-90 (2012). [Development]
Lin YF, Swinburne, I, and Yelon D. Multiple influences of blood flow on cardiomyocyte hypertrophy in the embryonic zebrafish heart. Developmental Biology 362(2): 242-53 (2012). [PUBMED]
Swinburne, I.A., Miguez, D., Landgraf, D. and Silver, P.A. Intron length increases oscillatory periods of gene expression in animal cells. Genes & Development 22(17): 2342-6 (2008). [Genes & Development]
Swinburne, I.A., and Silver, P.A. Intron delays and transcriptional timing during development. Developmental Cell 14(3): 324-30 (2008). [Developmental Cell]
Cironi, P., Swinburne, I.A. and Silver, P.A. Enhancement of cell-type specificity by quantitative modulation of a chimeric ligand. Journal of Biological Chemistry 283(13): 8469-76 (2008). [JBC]
Swinburne, I.A., Meyer, C.A., Liu, X.S., Silver, P.A., Brodsky, A.S. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Research 16(7): 912-21 (2006). [Genome Research]
Brodsky, A.S., Meyer, C.A., Swinburne, I.A., Hall, G., Keenan, B.J., Liu, X.S., Fox, E.A., Silver, P.A. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biology 6(8): R64. PMID:16086846 (2005). [Genome Biology]
Walsh, E.E., Falsey, A.R., Swinburne, I.A., Formica, M.A. Reverse transcription polymerase chain reaction (RT-PCR) for diagnosis of respiratory syncytial virus infection in adults: use of a single-tube "hanging droplet" nested PCR. Journal of Medical Virology 63: 259-63 (2001). [JMV]