Lienhard, M., van den Beucken, T., Timmermann, B., Hochradel, M., Boerno, S., Caiment, F., Vingron, M., & Herwig, R. (2023). IsoTools: a flexible workflow for long-read transcriptome sequencing analysis. Bioinformatics, 39(6), Article btad364. https://doi.org/10.1093/bioinformatics/btad364
Riemens, R. J. M., Kenis, G., & van den Beucken, T. (2020). Human-induced pluripotent stem cells as a model for studying sporadic Alzheimer's disease. Neurobiology of Learning and Memory, 175, Article 107318. https://doi.org/10.1016/j.nlm.2020.107318
Caiment, F., Wolters, J., Smit, E., Schrooders, Y., Kleinjans, J., & van den Beucken, T. (2020). Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression. Archives of Toxicology, 94(10), 3463-3473. https://doi.org/10.1007/s00204-020-02835-x
Caiment, F., Wolters, J., Smit, E., Schrooders, Y., Kleinjans, J. C. S., & van den Beucken, T. (2019). Identification of key transcription factor networks mediating valproic acid-induced mitochondrial dysfunctioning in primary human hepatocytes. Toxicology Letters, 314, S162-S162.
Smit, E., Kleinjans, J. C. S., & van den Beucken, T. (2019). Phosphorylation of eIF2α promotes cell survival in response to benzo[a]pyrene exposure. Toxicology in Vitro, 54, 330-337. https://doi.org/10.1016/j.tiv.2018.10.015
Smit, E., Caiment, F., Piepers, J., Kleinjans, J. C. S., & van den Beucken, T. (2018). Translational regulation is a key determinant of the cellular response to benzo[a]pyrene. Toxicology Letters, 295, 144-152. https://doi.org/10.1016/j.toxlet.2018.06.009
Briede, J. J., Deferme, L., Wolters, J. E. J., Claessen, S. M. H., van den Beucken, T., Wagner, R. J., van Breda, S. G., & Kleinjans, J. C. S. (2018). A cross-omics approach to investigate temporal gene expression regulation by 5-hydroxymethylcytosine via TBH-derived oxidative stress showed involvement of different regulatory kinases. Toxicology in Vitro, 48, 318-328. https://doi.org/10.1016/j.tiv.2018.02.006
Smit, E., Souza, T., Jennen, D. G. J., Kleinjans, J. C. S., & van den Beucken, T. (2017). Identification of essential transcription factors for adequate DNA damage response after benzo(a)pyrene and aflatoxin B1 exposure by combining transcriptomics with functional genomics. Toxicology, 390, 74-82. https://doi.org/10.1016/j.tox.2017.09.002
Souza, T. M., van den Beucken, T., Kleinjans, J. C. S., & Jennen, D. G. J. (2017). Inferring transcription factor activity from microarray data reveals novel targets for toxicological investigations. Toxicology, 389, 101-107. https://doi.org/10.1016/j.tox.2017.07.008