Publications

O'Donovan, S. D., Rundle, M., Thomas, E. L., Bell, J. D., Frost, G., Jacobs, D. M., Wanders, A., de Vries, R., Mariman, E. C. M., van Baak, M. A., Sterkman, L., Nieuwdorp, M., Groen, A. K., Arts, I. C. W., van Riel, N. A. W., & Afman, L. A. (2024). Quantifying the effect of nutritional interventions on metabolic resilience using personalized computational models. iScience, 27(4), Article 109362. https://doi.org/10.1016/j.isci.2024.109362

Krauskopf, J., Eggermont, K., Caiment, F., Verfaillie, C., & de Kok, T. M. (2024). Molecular insights into PCB neurotoxicity: Comparing transcriptomic responses across dopaminergic neurons, population blood cells, and Parkinson's disease pathology. Environment International, 186, Article 108642. https://doi.org/10.1016/j.envint.2024.108642

He, Y., DeBenedictis, J. N., Caiment, F., van Breda, S. G. J., & de Kok, T. M. C. M. (2024). Author Correction: Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx (Scientific Reports, (2023), 13, 1, (18281), 10.1038/s41598-023-45582-6). Scientific Reports, 14(1), Article 5096. https://doi.org/10.1038/s41598-024-53927-y

Kulesz, K., Engel, R. Y., Jolivet, R. B., & Kowalska, M. (2024). A numerical study of the anisotropic distribution of ?-ray emission from oriented ^{129m,131m,133m}Xe. Measurement Science & Technology, 35(2), Article 025027. https://doi.org/10.1088/1361-6501/acfe30

Izquierdo, P., Jolivet, R. B., Attwell, D., & Madry, C. (2024). Amyloid plaques and normal ageing have differential effects on microglial Ca²⁺ activity in the mouse brain. Pflugers Archiv-European Journal of Physiology, 476(2), 257-270. https://doi.org/10.1007/s00424-023-02871-3

DeBenedictis, J. N., Baars, E., Ochoteco-Asensio, J., van Breda, S. G., & de Kok, T. M. (2024). Genetic Variability Impacts Genotoxic and Transcriptome Responses in the Human Colon after the Consumption of Processed Red Meat Products and Those with Added Phytochemical Extracts. Nutrients, 16(3). https://doi.org/10.3390/nu16030425

Slenter, D., Kutmon, M., Evelo, C. T., & Willighagen, E. L. (2024). Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool. Digital Discovery, 3(1), 81-98. https://doi.org/10.1039/d3dd00069a

Agrawal, A., Balci, H., Hanspers, K., Coort, S. L., Martens, M., Slenter, D. N., Ehrhart, F., Digles, D., Waagmeester, A., Wassink, I., Abbassi-Daloii, T., Lopes, E. N., Iyer, A., Acosta, J. M., Willighagen, L. G., Nishida, K., Riutta, A., Basaric, H., Evelo, C. T., ... Pico, A. R. (2024). WikiPathways 2024: next generation pathway database. Nucleic acids research, 52(D1), D679–D689. https://doi.org/10.1093/nar/gkad960

Donovan, S. D. O., Cavill, R., Wimmenauer, F., Lukas, A., Stumm, T., Smirnov, E., Lenz, M., Ertaylan, G., Jennen, D. G. J., van Riel, N. A. W., Driessens, K., Peeters, R. L. M., & de Kok, T. M. C. M. (2023). Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data. PLOS ONE, 18(11), Article e0292030. https://doi.org/10.1371/journal.pone.0292030

Waagmeester, A., Willighagen, E. L., Su, A. I., Kutmon, M., Gayo, J. E. L., Fernández-Álvarez, D., Groom, Q., Schaap, P. J., Verhagen, L. M., & Koehorst, J. J. (2023). Author Correction: A protocol for adding knowledge to Wikidata. Bmc Biology, 21(1), Article 261. https://doi.org/10.1186/s12915-023-01764-2

Cvetkovic, J., Jacobi, R. H. J., Miranda-Bedate, A., Pham, N., Kutmon, M., Groot, J., van de Garde, M. D. B., & Pinelli, E. (2023). Human monocytes exposed to SARS-CoV-2 display features of innate immune memory producing high levels of CXCL10 upon restimulation. Journal of Innate Immunity, 15(1), 911-924. https://doi.org/10.1159/000535120

Jiang, J., van Ertvelde, J., Ertaylan, G., Peeters, R., Jennen, D., de Kok, T. M., & Vinken, M. (2023). Unraveling the mechanisms underlying drug-induced cholestatic liver injury: identifying key genes using machine learning techniques on human in vitro data sets. Archives of Toxicology, 97(11), 2969-2981. https://doi.org/10.1007/s00204-023-03583-4

Bischoff, N. S., Proquin, H., Jetten, M. J., Schrooders, Y., Jonkhout, M. C. M., Briedé, J. J., van Breda, S. G., Jennen, D. G. J., Medina-Reyes, E. I., Delgado-Buenrostro, N. L., Chirino, Y. I., van Loveren, H., & de Kok, T. M. (2023). Correction: Bischoff et al. The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer. Nanomaterials 2022, 12, 1256. Nanomaterials, 13(21), Article 2888. https://doi.org/10.3390/nano13212888

Heynckes, M., Hoffmann, K., Formisano, E., De Martino, F., & De Weerd, P. (2023). Predictability awareness rather than mere predictability enhances the perceptual benefits for targets in auditory rhythms over targets following temporal cues. PLOS ONE, 18(10), Article e0284755. https://doi.org/10.1371/journal.pone.0284755

Canna, A., Cantone, E., Roefs, A., Franssen, S., Prinster, A., Formisano, E., Di Salle, F., & Esposito, F. (2023). Functional MRI activation of the nucleus tractus solitarius after taste stimuli at ultra-high field: a proof-of-concept single-subject study. Frontiers in nutrition, 10, Article 1173316. https://doi.org/10.3389/fnut.2023.1173316

He, Y., De Benedictis, J. N., Caiment, F., van Breda, S. G. J., & de Kok, T. M. C. M. (2023). Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx. Scientific Reports, 13(1), Article 18281. https://doi.org/10.1038/s41598-023-45582-6

Shin, W., Kutmon, M., Mina, E., van Amelsvoort, T., Evelo, C. T., & Ehrhart, F. (2023). Exploring pathway interactions to detect molecular mechanisms of disease: 22q11.2 deletion syndrome. Orphanet Journal of Rare Diseases, 18(1), Article 335. https://doi.org/10.1186/s13023-023-02953-6

Catala, P., Vivensang, F., van Beek, D., Adriaens, M. E., Dickman, M. M., LaPointe, V. L. S., & Kutmon, M. (2023). Elucidating the Corneal Endothelial Cell Proliferation Capacity through an Interspecies Transcriptome Comparison. Advanced Biology, 7(10), Article 2300065. https://doi.org/10.1002/adbi.202300065

Erdős, B., Van sloun, B., Goossens, G. H., O’donovan, S. D., De galan, B. E., Van greevenbroek, M. M. J., Stehouwer, C. D. A., Schram, M. T., Blaak, E. E., Adriaens, M. E., Van riel, N. A. W., & Arts, I. C. W. (2023). Quantifying postprandial glucose responses using a hybrid modeling approach: Combining mechanistic and data-driven models in The Maastricht Study. PLOS ONE, 18(7), Article e0285820. https://doi.org/10.1371/journal.pone.0285820

DeBenedictis, J. N., de Kok, T. M., & van Breda, S. G. (2023). Impact of Processing Method and Storage Time on Phytochemical Concentrations in an Antioxidant-Rich Food Mixture. Antioxidants, 12(6), Article 1252. https://doi.org/10.3390/antiox12061252