Publications

Below you will find preprints and peer-reviewed publications as part of our IMAGINE! project.

(Are you working on a new manuscript? Here a quick link how to cite IMAGINE!)

Preprints (awaiting peer-review)

Patterned illumination enables denser deep-learning based single-molecule localization microscopy (2025). Cnossen J et al. bioRxiv Preprint. DOI: https://doi.org/10.1101/2025.03.09.642203

SSNA1 organizes the distal luminal centriolar network and promotes ciliogenesis without microtubule association (2025). Huang Yi-Chi et al. bioRxiv Preprint. DOI: 10.1101/2025.04.28.648957. URL: https://doi.org/10.1101/2025.04.28.648957

Outcome-Driven Microscopy: Closed-Loop Optogenetic Control of Cell Biology (2024). Passmore Josiah B. et al. bioRxiv Preprint. DOI: 10.1101/2024.12.12.628240. URL: https://doi.org/10.1101/2024.12.12.628240

Small molecule-directed differentiation of submerged-cultured human nasal airway epithelia for respiratory disease modelling (2024). Dreyer Henriette H.M. et al. bioRxiv Preprint. DOI: 10.1101/2024.10.17.618953. URL: https://doi.org/10.1101/2024.10.17.618953

Intestinal LKB1 loss drives a pre-malignant program along the serrated cancer pathway (2023). Plugge S.F. et al. bioRxiv Preprint. DOI: 10.1101/2023.07.17.548873. URL: https://doi.org/10.1101/2023.07.17.548873

Publications

2026

Cell surface interactome analysis identifies TSPAN4 as a negative regulator of PD‐L1 in melanoma (2026) G. A. Franken et al. Molecular Oncology. DOI: 10.1002/1878-0261.70182. URL: https://doi.org/10.1002/1878-0261.70182

2025

Closed-loop optogenetic control of cell biology enables outcome-driven microscopy (2025) Passmore JB et al. Nat Commun. 2025;17:1087.DOI: 10.1038/s41467-025-67848-5

Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body (2025). Berrevoets Enya S. et al. Nat Commun 16, 10689 URL: https://doi.org/10.1038/s41467-025-65723-x

Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients (2025). Buissant des Amorie et al. Nature communications. DOI: 10.1038/s41467-025-61878-9. https://doi.org/10.1038/s41467-025-61878-9

Resolution in super-resolution microscopy – facts, artifacts, technological advancements and biological applications. (2025) Prakash K, Baddeley D, Eggeling C, Fiolka R, Heintzmann R, Manley S, Radenovic A, Shroff H, Smith C, Schermelleh L. J Cell Sci. 2025;138:jcs263567. DOI:https://doi.org/10.1242/jcs.263567

Strategies for overcoming ABC‑transporter‑mediated drug resistance (2025). de Groot et al. AJP Cell Physiol. DOI: 10.1152/ajpcell.00412.2025. URL: https://doi.org/10.1152/ajpcell.00412.2025

Optogenetic and chemical genetic tools for rapid repositioning of vimentin intermediate filaments (2025). Pasolli Milena et al. J Cell Biol. DOI: 10.1083/jcb.202504004. URL:
https://doi.org/10.1083/jcb.202504004

CD151 interacts with integrin beta 2 in B cell lymphomas (2025). Hagemann Philipp M. et al. Cellular and Molecular Life Sciences. DOI: 10.1007/s00018-025-05747-0. URL: https://doi.org/10.1007/s00018-025-05747-0

An algorithmic perspective on deciphering cell–cell interactions with spatial omics data (2025). van Santvoort Maxime, Eduati Federica. Briefings in Bioinformatics. DOI: 10.1093/bib/bbaf236. URL: https://doi.org/10.1093/bib/bbaf236

Mathematically mapping the network of cells in the tumor microenvironment (2025). van Santvoort Maxime et al. Cell Reports Methods. DOI: 10.1016/j.crmeth.2025.100985. URL: https://doi.org/10.1016/j.crmeth.2025.100985

Diversity of microtubule arrays in animal cells at a glance (2025). Van Grinsven, Emma J. and Akhmanova, Anna Journal of Cell Science. DOI: 10.1242/jcs.263476. URL: https://doi.org/10.1242/jcs.263476

The oestrous cycle stage affects mammary tumour sensitivity to chemotherapy (2025). Bornes, Laura et al, Nature. DOI: 10.1038/s41586-024-08276-1. URL: https://doi.org/10.1038/s41586-024-08276-1

2024

Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study (2024). Lapuente-Santana Óscar, Kant Joan, Eduati Federica. npj Precision Oncology. DOI: 10.1038/s41698-024-00749-w. URL: https://doi.org/10.1038/s41698-024-00749-w

A Photocaged Microtubule‐Stabilising Epothilone Allows Spatiotemporal Control of Cytoskeletal Dynamics (2024). Schmitt Carina et al. Angewandte Chemie International Edition. DOI: 10.1002/anie.202410169. URL: https://doi.org/10.1002/anie.202410169

Oriented Antibody Coupling to an Antifouling Polymer Using Glycan Remodeling for Biosensing by Particle Motion (2024). Linssen, Maud D. M. E. et al, Bioconjugate Chemistry. DOI: 10.1021/acs.bioconjchem.4c00196. URL: https://doi.org/10.1021/acs.bioconjchem.4c00196

Multiphoton fluorescence microscopy for in vivo imaging (2024) Xu C et al. Cell. 187:4458-87. https://doi.org/10.1016/j.cell.2024.07.036

Image scanning microscopy: a vectorial physical optics analysis. (2024) Hung ST, Kalisvaart D, Smith C. Opt Express. 2024;32:1524-39 URL: https://doi.org/10.1364/OE.500957

2023

Bilayer Microfluidic Device for Combinatorial Plug Production (2023). Yelleswarapu Maaruthy et al. Journal of Visualized Experiments. DOI: 10.3791/66154. URL: https://doi.org/10.3791/66154

Acknowledgement

Written acknowledgement text:

This work was supported by the Netherlands Organization for Scientific Research (NWO) Gravitation programme IMAGINE! (project number 24.005.009).