PUBLICATIONS
2025
A conserved disruption of nucleocytoplasmic compartmentalization in meiosis is controlled by a kinase-phosphatase pair in Saccharomyces cerevisiae.
Walsh ME, Chetlapalli K, Styler BS, Upadhyayula S, King GA, Ünal E.
Mol Biol Cell. 2025 Dec 1;36(12):ar147. doi: 10.1091/mbc.E25-05-0229. Epub 2025 Oct 8.PMID: 41060786
Mesoscale volumetric fluorescence imaging at nanoscale resolution by photochemical sectioning.
Wang W, Ruan X, Liu G, Milkie DE, Li W, Betzig E, Upadhyayula S, Gao R.
Science. 2025 Oct 16;390(6770):eadr9109. doi: 10.1126/science.adr9109. Epub 2025 Oct 16.PMID: 41100598
Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens.
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.
Nat Methods. 2025 Oct;22(10):2171-2179. doi: 10.1038/s41592-025-02844-7. Epub 2025 Oct 1.PMID: 41034611
Visualizing PIEZO1 localization and activity in hiPSC-derived single cells and organoids with HaloTag technology.
Bertaccini GA, Casanellas I, Evans EL, Nourse JL, Dickinson GD, Liu G, Seal S, Ly AT, Holt JR, Wijerathne TD, Yan S, Hui EE, Lacroix JJ, Panicker MM, Upadhyayula S, Parker I, Pathak MM.
Nat Commun. 2025 Jul 1;16(1):5556. doi: 10.1038/s41467-025-59150-1.PMID: 40593468
A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms.
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.
bioRxiv [Preprint]. 2025 Jun 3:2025.06.02.657494. doi: 10.1101/2025.06.02.657494.PMID: 40661351
A Cell Observatory to reveal the subcellular foundations of life.
Betzig E.
Nat Methods. 2025 Apr;22(4):646-649. doi: 10.1038/s41592-024-02379-3.PMID: 39112799
Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens
T Alshaabi, D Milkie, G Liu, C Shirazinejad, J Hong, K Achour, F Gorlitz, …
Research Square, rs. 3. rs-6273247
BPS2025-PIEZO1-HaloTag hiPSCs to visualize channel localization, motility, and activity in cells and tissue
GA Bertaccini, I Casanellas, EL Evans, JL Nourse, GD Dickinson, G Liu, …
Biophysical Journal 124 (3), 265a
Multicilia dynamically transduce Sonic Hedgehog signaling to regulate choroid plexus functions.
Mao S, Song R, Jin S, Pang S, Jovanovic A, Zimmerman A, Li P, Wu X, Wendland MF, Lin K, Chen WC, Choksi SP, Chen G, Holtzman MJ, Reiter JF, Wan Y, Xuan Z, Xiang YK, Xu CS, Upadhyayula S, Hess HF, He L.
Cell Rep. 2025 Mar 25;44(3):115383. doi: 10.1016/j.celrep.2025.115383. Epub 2025 Mar 8.PMID: 40057957
2024
How to build the virtual cell with artificial intelligence: Priorities and opportunities.
Bunne C, Roohani Y, Rosen Y, Gupta A, Zhang X, Roed M, Alexandrov T, AlQuraishi M, Brennan P, Burkhardt DB, Califano A, Cool J, Dernburg AF, Ewing K, Fox EB, Haury M, Herr AE, Horvitz E, Hsu PD, Jain V, Johnson GR, Kalil T, Kelley DR, Kelley SO, Kreshuk A, Mitchison T, Otte S, Shendure J, Sofroniew NJ, Theis F, Theodoris CV, Upadhyayula S, Valer M, Wang B, Xing E, Yeung-Levy S, Zitnik M, Karaletsos T, Regev A, Lundberg E, Leskovec J, Quake SR.
Cell. 2024 Dec 12;187(25):7045-7063. doi: 10.1016/j.cell.2024.11.015.PMID: 39672099
Neural space-time model for dynamic multi-shot imaging.
Cao R, Divekar NS, Nuñez JK, Upadhyayula S, Waller L.
Nat Methods. 2024 Dec;21(12):2336-2341. doi: 10.1038/s41592-024-02417-0. Epub 2024 Sep 24.PMID: 39317729
Molecularly Distinct Clathrin-Coated Pits Differentially Impact EGFR Fate and Signaling (vol 27, pg 3049, 2019)
R Pascolutti, V Algisi, A Conte, A Raimondi, M Pasham, S Upadhyayula, …
CELL REPORTS 43 (11)
Molecularly Distinct Clathrin-Coated Pits Differentially Impact EGFR Fate and Signaling
R Pascolutti, V Algisi, A Conte, A Raimondi, M Pasham, S Upadhyayula, …
Image processing tools for petabyte-scale light sheet microscopy data.
Ruan X, Mueller M, Liu G, Görlitz F, Fu TM, Milkie DE, Lillvis JL, Kuhn A, Gan Chong J, Hong JL, Herr CYA, Hercule W, Nienhaus M, Killilea AN, Betzig E, Upadhyayula S.
Nat Methods. 2024 Dec;21(12):2342-2352. doi: 10.1038/s41592-024-02475-4. Epub 2024 Oct 17.PMID: 39420143
A Cell Observatory to reveal the subcellular foundations of life
E Betzig
Nature Methods, 1-4
PIEZO1-halotag hiPSC lines: A new tool to assay PIEZO1 localization and activity from single cells to tissue organoids
GA Bertaccini, E Evans, JL Nourse, GD Dickinson, G Liu, I Casanellas, …
Biophysical Journal 123 (3), 242a-243a
Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems
R Cao, N Divekar, J Nuñez, S Upadhyayula, L Waller
bioRxiv, 2024.01. 16.575950
Nanoscale volumetric fluorescence imaging via photochemical sectioning
W Wang, X Ruan, G Liu, DE Milkie, W Li, E Betzig, S Upadhyayula, R Gao
bioRxiv, 2024.08. 01.605857
2023
Characterization, comparison, and optimization of lattice light sheets.
Liu G, Ruan X, Milkie DE, Görlitz F, Mueller M, Hercule W, Killilea A, Betzig E, Upadhyayula S.
Sci Adv. 2023 Mar 31;9(13):eade6623. doi: 10.1126/sciadv.ade6623. Epub 2023 Mar 31.PMID: 37000868
Origin of wiring specificity in an olfactory map revealed by neuron type-specific, time-lapse imaging of dendrite targeting
Wong KKL, Li T, Fu TM, Liu G, Lyu C, Kohani S, Xie Q, Luginbuhl DJ, Upadhyayula S, Betzig E, Luo L.
Elife. 2023 Mar 28;12:e85521. doi: 10.7554/eLife.85521.PMID: 36975203
2022
Image-to-image regression with distribution-free uncertainty quantification and applications in imaging
AN Angelopoulos, AP Kohli, S Bates, M Jordan, J Malik, T Alshaabi, …
International Conference on Machine Learning, 717-730
A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling
Mondal C, Gacha-Garay MJ, Larkin KA, Adikes RC, Di Martino JS, Chien CC, Fraser M, Eni-Aganga I, Agullo-Pascual E, Cialowicz K, Ozbek U, Naba A, Gaitas A, Fu TM, Upadhyayula S, Betzig E, Matus DQ, Martin BL, Bravo-Cordero JJ.
Cell Rep. 2022 Sep 20;40(12):111358. doi: 10.1016/j.celrep.2022.111358.PMID: 3613048
A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility.
Sheu SH, Upadhyayula S, Dupuy V, Pang S, Deng F, Wan J, Walpita D, Pasolli HA, Houser J, Sanchez-Martinez S, Brauchi SE, Banala S, Freeman M, Xu CS, Kirchhausen T, Hess HF, Lavis L, Li Y, Chaumont-Dubel S, Clapham DE.
Cell. 2022 Sep 1;185(18):3390-3407.e18. doi: 10.1016/j.cell.2022.07.026.
PMID: 36055200
Branched actin networks are organized for asymmetric force production during clathrin-mediated endocytosis in mammalian cells.
Jin M, Shirazinejad C, Wang B, Yan A, Schöneberg J, Upadhyayula S, Xu K, Drubin DG.
Nat Commun. 2022 Jun 22;13(1):3578. doi: 10.1038/s41467-022-31207-5.PMID: 3573285
2021
Adaptive wavelet distillation from neural networks through interpretations
Ha W, Singh C, Lanusse F, Upadhyayula S, Yu B
Advances in Neural Information Processing Systems 34, 20669-20682
A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy.
Gao R, Yu CJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES.
Nat Nanotechnol. 2021 Jun;16(6):698-707. doi: 10.1038/s41565-021-00875-7. Epub 2021 Mar 29.PMID: 33782587
Cellular bases of olfactory circuit assembly revealed by systematic time-lapse imaging
T Li, TM Fu, KKL Wong, H Li, Q Xie, DJ Luginbuhl, MJ Wagner, E Betzig, …
Cell 184 (20), 5107-5121. e14
2020
Design and Validation of a Human Brain Endothelial Microvessel-on-a-Chip Open Microfluidic Model Enabling Advanced Optical Imaging.
Salman MM, Marsh G, Kusters I, Delincé M, Di Caprio G, Upadhyayula S, de Nola G, Hunt R, Ohashi KG, Gray T, Shimizu F, Sano Y, Kanda T, Obermeier B, Kirchhausen T.
Front Bioeng Biotechnol. 2020 Sep 28;8:573775. doi: 10.3389/fbioe.2020.573775. eCollection 2020.
PMID: 33117784
3D ATAC-PALM: super-resolution imaging of the accessible genome.
Xie L, Dong P, Chen X, Hsieh TS, Banala S, De Marzio M, English BP, Qi Y, Jung SK, Kieffer-Kwon KR, Legant WR, Hansen AS, Schulmann A, Casellas R, Zhang B, Betzig E, Lavis LD, Chang HY, Tjian R, Liu Z.
Nat Methods. 2020 Apr;17(4):430-436. doi: 10.1038/s41592-020-0775-2. Epub 2020 Mar 16.
PMID: 32203384
Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells.
Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang CL, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, Betzig E, Hess HF.
Science. 2020 Jan 17;367(6475):eaaz5357. doi: 10.1126/science.aaz5357.
PMID: 31949053
2019
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.
Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E.
Science. 2019 Jan 18;363(6424):eaau8302. doi: 10.1126/science.aau8302.
PMID: 30655415
Microscopy with adaptive optics
E Betzig, N Ji
2018
Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure
Swinburne IA, Mosaliganti KR, Upadhyayula S, Liu TL, Hildebrand DGC, Tsai TY, Chen A, Al-Obeidi E, Fass AK, Malhotra S, Engert F, Lichtman JW, Kirchhausen T, Betzig E, Megason SG.
Elife. 2018 Jun 19;7:e37131. doi: 10.7554/eLife.37131.PMID: 29916365
Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms
Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E.
Science. 2018 Apr 20;360(6386):eaaq1392. doi: 10.1126/science.aaq1392.PMID: 29674564