Callegaro, G., Kunnen, S. J., Trairatphisan, P., Grosdidier, S., Niemeijer, M., den Hollander, W., Guney, E., Piñero Gonzalez, J., Furlong, L., Webster, Y. W., Saez-Rodriguez, J., Sutherland, J. J., Mollon, J., Stevens, J. L., & van de Water, B. (2021). The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment. Archives of toxicology, 95(12), 3745–3775.


Callegaro, G., Schimming, J. P., Piñero González, J., Kunnen, S. J., Wijaya, L., Trairatphisan, P., van den Berk, L., Beetsma, K., Furlong, L. I., Sutherland, J. J., Mollon, J., Stevens, J. L., & van de Water, B. (2023). Identifying multiscale translational safety biomarkers using a network-based systems approach. iScience, 26(3), 106094.


Kunnen, S.J., Arnesdotter, E., Willenbockel, C.T., Vinken, M., & van de Water, B. (2024). Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment. ALTEX, 41(2), 213–232.


Kunnen S.J., Callegaro G., Sutherland J.J., Trairatphisan P., van Kessel H.W., Wijaya L.S., Chung G., Pye K., Goldstein K.M., Teague C.R., Fisher C.P., Saez-Rodriguez J., Brown C., Elmore S.A., Heinz-Taheny K.M., Stevens J.L., van de Water B. (2025). Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation. iScience, 28(7):112978 

Wijaya, L.S., Gabor, A., Pot, I. E., van de Have, L., Saez-Rodriguez, J., Stevens, J. L., Le Dévédec, S. E., Callegaro, G., & van de Water, B. (2024). A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury. Toxicological sciences, 198(1), 14–30.


Wijaya L.S., Kunnen S.J., Trairatphisan P., Fisher C.P., Crosby M.E., Schaefer K., Bodié K., Vaughan E.E., Breidenbach L., Reich T., Clausznitzer D., Bonnet S., Zheng S., Pont C., Stevens J.L., Le Dévédec S.E., van de Water B (2025). Spatio-temporal transcriptomic analysis reveals distinct nephrotoxicity, DNA damage, and regeneration response after cisplatin. Cell Biology and Toxicology, 41(1):49.


Vlasveld, M., Callegaro, G., Fisher, C., Eakins, J., Walker, P., Lok, S., van Oost, S., de Jong, B., Pellegrino-Coppola, D., Burger, G., Wink, S., & van de Water, B. (2024). The integrated stress response-related expression of CHOP due to mitochondrial toxicity is a warning sign for DILI liability. Liver international, 44(3), 760–775.


Vrijenhoek, N. G., Wehr, M. M., Kunnen, S. J., Wijaya, L. S., Callegaro, G., Moné, M. J., Escher, S. E., & Van de Water, B. (2022). Application of high-throughput transcriptomics for mechanism-based biological read-across of short-chain carboxylic acid analogues of valproic acid. ALTEX, 39(2), 207–220.

van Kessel H.W., Kunnen S.J., Callegaro G., van de Water B. (2025). Advancing transcriptomics-based mechanistic assessment of nephrotoxicity in vitro using the human RPTEC/TERT1 TXG-MAPr gene co-expression network. Toxicol Sci. 209(1):kfaf159.

Bruns I.B., Li Y, Stevens J.L., van de Water B., Callegaro G. (2025). Cell type heterogeneity in gene co-expression networks: implications for toxicological research. Brief Bioinform. 26(4):bbaf421.