Publications

A full list of our publications can be found here. Below are some of our key publications.

Publications-Research-group-Cellular-Disease-Modelling

Key Publications

ACE-tRNAs are a platform technology for suppressing nonsense mutations that cause cystic fibrosis Wooree Ko, Joseph J Porter, Sacha Spelier, Emily G Sorensen, Priyanka Bhatt, Jeffrey T Gabell, Isabelle van der Windt, Tyler Couch, Kevin Coote, Martin Mense, Jeffrey M Beekman, John D Lueck Nucleic Acids Research, Volume 53, Issue 13, 22 July 2025
Active mesh and neural network pipeline for cell aggregate segmentation. Smith MB, Sparks H, Almagro J, et al. Biophys J. 2023;122(9):1586-1599.
CFTR and colorectal cancer susceptibility: an urgent need for further studies S. Spelier, S. Derksen, R. Hofland, J.M. Beekman, B. Yetkin-Arik Trends in Cancer, Volume 10, Issue 10, p876-879, October 2024
High-throughput functional assay in cystic fibrosis patient-derived organoids allows drug repurposing Sacha Spelier, Eyleen de Poel, Georgia N. Ithakisiou, Sylvia W.F. Suen, Marne C. Hagemeijer, Danya Muilwijk, Annelotte M. Vonk, Jesse E. Brunsveld, Evelien Kruisselbrink, Cornelis K. van der Ent, Jeffrey M. Beekman ERJ Open Research 2023 9(1): 00495-2022
Organoid-guided synergistic treatment of minimal function CFTR mutations with CFTR modulators, roflumilast and simvastatin: a personalised approach Sacha Spelier, Karin de Winter-de Groot, Natascha Keijzer-Nieuwenhuijze, Yves Liem, Kors van der Ent, Jeffrey Beekman, Lieke S. Kamphuis European Respiratory Journal 2024 63(1): 2300770
OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion. Lefferts JW, Kroes S, Smith MB, et al. Commun Biol. 2024;7(1):319.
Readthrough compounds for nonsense mutations: bridging the translational gap Sacha Spelier, Eveline P.M. van Doorn, Cornelis K. van der Ent, Jeffrey M. Beekman, Martijn A.J. Koppens Trends in Molecular Medicine, volume 29, Issue 4, p297-314, April 2023
Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue. Kuijk, E. et al. (2022). Nat Commun 13, 5915.
Early divergence of mutational processes in human fetal tissues Kuijk, E. et al. (2019). Sci. Adv. 5, eaaw1271.
Human colon stem cells are the predominant epithelial responders to bacterial antigens. de Vries, M. et al. (2025). Front. Immunol. Volume 16 - 2025
The genome-wide mutational consequences of DNA hypomethylation. Besselink, N. et al.(2023). Sci Rep 13, 6874.
The mutational impact of culturing human pluripotent and adult stem cells. Kuijk, E. et al. (2020). Nat Commun 11, 2493.
The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos. Kuijk, E.W. et al. (2012). Development 139, 871–882.
TTC7A missense variants in intestinal disease can be classified by molecular and cellular phenotypes Shojaei Jeshvaghani, Z. et al. (2025). HMG 34, 313–326.