Publications

Gijbels, A., Erdos, B., Trouwborst, I., Jardon, K. M., Adriaens, M. E., Goossens, G. H., Blaak, E. E., Feskens, E. J. M., & Afman, L. A. (2024). Hepatic insulin resistance and muscle insulin resistance are characterized by distinct postprandial plasma metabolite profiles: a cross-sectional study. Cardiovascular Diabetology, 23(1), Article 97. Advance online publication. https://doi.org/10.1186/s12933-024-02188-0

Esposito, M., Valente, G., Plasencia-Calaña, Y., Dumontier, M., Giordano, B. L., & Formisano, E. (2024). Bridging auditory perception and natural language processing with semantically informed deep neural networks. Scientific Reports, 14(1), Article 20994. https://doi.org/10.1038/s41598-024-71693-9

Cheng, S. L., Hedges, M., Keski-Rahkonen, P., Chatziioannou, A. C., Scalbert, A., Chung, K. F., Sinharay, R., Green, D. C., de Kok, T. M. C. M., Vlaanderen, J., Kyrtopoulos, S. A., Kelly, F., Portengen, L., Vineis, P., Vermeulen, R. C. H., Chadeau-Hyam, M., & Dagnino, S. (2024). Multiomic Signatures of Traffic-Related Air Pollution in London Reveal Potential Short-Term Perturbations in Gut Microbiome-Related Pathways (vol 58, pg 8771, 2024). Environmental Science & Technology. https://doi.org/10.1021/acs.est.4c09132

DeBenedictis, J. N., Murrell, C., Hauser, D., van Herwijnen, M., Elen, B., de Kok, T. M., & van Breda, S. G. (2024). Effects of Different Combinations of Phytochemical-Rich Fruits and Vegetables on Chronic Disease Risk Markers and Gene Expression Changes: Insights from the MiBLEND Study, a Randomized Trial. Antioxidants, 13(8), Article 915. https://doi.org/10.3390/antiox13080915

Bahram Sangani, N., Koetsier, J., Mélius, J., Kutmon, M., Ehrhart, F., Evelo, C. T., Curfs, L. M. G., Reutelingsperger, C. P., & Eijssen, L. M. T. (2024). A novel insight into neurological disorders through HDAC6 protein-protein interactions. Scientific Reports, 14(1), Article 14666. https://doi.org/10.1038/s41598-024-65094-1

Calcini, N., da Silva Lantyer, A., Zeldenrust, F., & Celikel, T. (2024). Nonlinear super-resolution signal processing allows intracellular tracking of calcium dynamics. Journal of neural engineering, 21(3), Article 036008. https://doi.org/10.1088/1741-2552/ad417c

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

Erdos, B., O'Donovan, S. D., Adriaens, M. E., Gijbels, A., Trouwborst, I., Jardon, K. M., Goossens, G. H., Afman, L. A., Blaak, E. E., van Riel, N. A. W., & Arts, I. C. W. (2024). Leveraging continuous glucose monitoring for personalized modeling of insulin-regulated glucose metabolism. Scientific Reports, 14(1), 8037. Article 8037. https://doi.org/10.1038/s41598-024-58703-6

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

Chojnacki, M., Kulesz, K., Michelon, I., Azaryan, N., Barbero, E., Crepieux, B., Lica, R., Murawski, Ziemba, M., Piersa-Siłkowska, M., Vitulova, K., Korgul, A., Jolivet, R. B., Prokopowicz, R., Köster, U., & Kowalska, M. (2024). Production of ^129mXe and ^131mXe via neutron activation of ¹²⁸Xe and ¹³⁰Xe at ILL-RHF and NCBJ-MARIA high-flux reactors. Applied Radiation and Isotopes, 205, Article 111174. https://doi.org/10.1016/j.apradiso.2024.111174

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

Delfin, C., Dragan, I., Kuznetsov, D., Tajes, J. F., Smit, F., Coral, D. E., Farzaneh, A., Haugg, A., Hungele, A., Niknejad, A., Hall, C., Jacobs, D., Marek, D., Fraser, D. P., Thuillier, D., Ahmadizar, F., Mehl, F., Pattou, F., Burdet, F., ... Ibberson, M. (2024). A Federated Database for Obesity Research: An IMI-SOPHIA Study. Life, 14(2), Article 262. https://doi.org/10.3390/life14020262

Kulesz, K., Engel, R. Y., Jolivet, R. B., & Kowalska, M. (2024). A numerical study of the anisotropic distribution of γ-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), Article 425. 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