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2025
Suarez-Gomez D, Perez-Rosas NC, Miranda-Contreras GI, Colom-Braña SR, Zhang W, Mim MSahir, Tan S, Gazzo D, Tepole ABuganza, Deng Q et al..  2025.  CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals. bioRxiv.
Alshaabi T, Milkie D, Liu G, Shirazinejad C, Hong J, Achour K, Görlitz F, Milunovic-Jevtic A, Simmons C, Abuzahriyeh I et al..  2025.  Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens. Research Square.
Mao S, Song R, Jin S, Pang S, Jovanovic A, Zimmerman A, Li P, Wu X, Wendland MF, Lin K et al..  2025.  Multicilia dynamically transduce Sonic Hedgehog signaling to regulate choroid plexus functions. Cell Reports.
Fu T-M, Liu G, Milkie DE, Ruan X, Görlitz F, Shi Y, Ferro V, Divekar NS, Wang W, York HM et al..  2025.  A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms. bioRxiv.
2024
Updegrove TB, Delerue T, Anantharaman V., Cho H, Chan C, Nipper T, Choo-Wosoba H, Jenkins L, Zhang L, Su Y et al..  2024.  Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity. Sci Adv. 10(42):eadq0791.
De Niz M, García REscobedo, Ramirez CTerán, Pakowski Y, Abonza Y, Bialy N, Orr VL, Olivera A, Abonza V, Alleva K et al..  2024.  Building momentum through networks: Bioimaging across the Americas. Journal of Microscopy. n/a
Chareyre S, Li X, Anjuwon-Foster BR, Updegrove TB, Clifford S, Brogan AP, Su Y, Zhang L, Chen J, Shroff H et al..  2024.  Cell division machinery drives cell-specific gene activation during differentiation in .. Proc Natl Acad Sci U S A. 121(13):e2400584121.
Udeshi ND, Xu C, Jiang Z, Gao SMax, Yin Q, Luo W, Carr SA, Davis MM, Li J.  2024.  Cell-surface Milieu Remodeling in Human Dendritic Cell Activation.. J Immunol.
Nern A, Loesche F, Takemura S-ya, Burnett LE, Dreher M, Gruntman E, Hoeller J, Huang GB, Januszewski M, Klapoetke NC et al..  2024.  Connectome-driven neural inventory of a complete visual system. Nature.
Rivlin PK, Januszewski M, Longden KD, Neace E, Scheffer LK, Ordish C, Clements J, Phillips E, Smith N, Takemura S et al..  2024.  Connectomic Analysis of Mitochondria in the Central Brain of Drosophila. bioRxiv.
Yaguchi K, Saito D, Menon T, Matsura A, Mizutani T, Kotani T, Nair S, Uehara R.  2024.  Haploidy-linked cell proliferation defects limit larval growth in Zebrafish. Open Biol.. 14(10):240126.
Ruan X, Mueller M, Liu G, Görlitz F, Fu T-M, Milkie DE, Lillvis J, Killilea A, Betzig E, Upadhyayula S.  2024.  Image processing tools for petabyte-scale light sheet microscopy data.. Nat. Methods.
Xu C, Li Z, Lyu C, Hu Y, McLaughlin CN, Wong KKin Lam, Xie Q, Luginbuhl DJ, Li H, Udeshi ND et al..  2024.  Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching.. Cell.
Wang W, Ruan X, Liu G, Milkie DE, Li W, Betzig E, Upadhyayula S, Gao R.  2024.  Nanoscale volumetric fluorescence imaging via photochemical sectioning. bioRxiv.
2023
Liu G, Ruan X, Milkie DE, Görlitz F, Mueller M, Hercule W, Kililea A, Betzig E, Upadhyayula S.  2023.  Characterization, Comparison, and Optimization of Lattice Light Sheets. Science Advances.
Takemura S-ya, Hayworth KJ, Huang GB, Januszewski M, Lu Z, Marin EC, Preibisch S, C Xu S, Bogovic J, Champion AS et al..  2023.  A Connectome of the Male Drosophila Ventral Nerve Cord. bioRxiv.
Usama SMuhammad, Marker SC, Li D-H, Caldwell DR, Stroet M, Patel NL, Tebo AG, Hernot S, Kalen JD, Schnermann M.  2023.  Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging.. Journal of the American Chemical Society. 145(27):14647–14659.
Wong KKin Lam, Li T, Fu T-M, Liu G, Lyu C, Kohani S, Xie Q, Luginbuhl DJ, Upadhyayula S, Betzig E et al..  2023.  Origin of wiring specificity in an olfactory map revealed by neuron type-specific, time-lapse imaging of dendrite targeting.. eLife. 12
2022
Beatty ZG, Muthusamy AK, Unger EK, Dougherty DA, Tian L, Looger LL, Shivange AV, Bera K, Lester HA, Nichols AL.  2022.  Fluorescence Screens for Identifying Central Nervous System-Acting Drug-Biosensor Pairs for Subcellular and Supracellular Pharmacokinetics.. Bio-Protocol. 12(22)
S Shuster A, Li J, Chon UR, Sinantha-Hu MC, Luginbuhl DJ, Udeshi ND, Carey DKiki, Takeo YH, Xie Q, Xu C et al..  2022.  In situ cell-type-specific cell-surface proteomic profiling in mice.. Neuron.
Li J, Zaslavsky M, Su Y, Guo J, Sikora MJ, van Unen V, Christophersen A, Chiou S-H, Chen L, Li J et al..  2022.  KIRCD8 T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.. Science. 376(6590):eabi9591.
Plaza SM, Clements J, Dolafi T, Umayam L, Neubarth NN, Scheffer LK, Berg S.  2022.  neuPrint: An open access tool for EM connectomics.. Frontiers in Neuroinformatics. 16:896292.
Kim S, Kim Y-E, Song I, Ujihara Y, Kim N, Jiang Y-H, Yin HH, Lee T-H, Kim IHwan.  2022.  Neural circuit pathology driven by Shank3 mutation disrupts social behaviors.. Cell Reports. 39(10):110906.
Mondal C, Gacha-Garay MJ, Larkin KA, Adikes RC, Di Martino JS, Chien C-C, Fraser M, Eni-Aganga I, Agullo-Pascual E, Cialowicz K et al..  2022.  A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling.. Cell Reports. 40(12):111358.
Sheu S-H, Upadhyayula S, Dupuy V, Pang S, Lemire AL, Walpita D, H. Pasolli A, Deng F, Wan J, Wang L et al..  2022.  A serotonergic axon-cilium synapse drives nuclear signaling to maintain chromatin accessibility. Cell. 185(18):3390-3407.