Publications
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Domínguez-Romero, E., Mazurenko, S., Scheringer, M., Martins Dos Santos, V. A. P., Evelo, C. T., Anton, M., Hancock, J. M., Županic, A., & Suarez-Diez, M. (2025). Response to Letter to Editor by A. Derbalah et al: the role of automation in enhancing reproducibility and interoperability of PBPK models. Briefings in bioinformatics, 26(1), Article bbaf060. https://doi.org/10.1093/bib/bbaf060More information about this publication
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Kienhuis, A., Krul, C., van Engelen, J., Evelo, C. T., Hessel, E., Hoekman, J., Kramer, N., Krop, E., Masereeuw, R., Moors, E., Negro, S. O., Piersma, A. H., Pieters, R., Teunis, M., Willighagen, E., & Legler, J. (2025). The Virtual Human Platform for Safety Assessment (VHP4Safety) project: Next generation chemical safety assessment based on human data. ALTEX, 42(1), 111-120. https://doi.org/10.14573/altex.2407211More information about this publication
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Bayjanov, J. R., Doornbos, C., Ozisik, O., Shin, W., Queralt-Rosinach, N., Wijnbergen, D., Saulnier-Blache, J. S., Schanstra, J. P., Buffin-Meyer, B., Klein, J., Fernández, J. M., Kaliyaperumal, R., Baudot, A., ’t Hoen, P. A. C., & Ehrhart, F. (2024). Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Scientific Reports, 14(1), Article 20731. https://doi.org/10.1038/s41598-024-71721-8More information about this publication
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Sangani, N. B., Koetsier, J., Gomes, A. R., Diogo, M. M., Fernandes, T. G., Bouwman, F. G., Mariman, E. C. M., Ghazvini, M., Gribnau, J., Curfs, L. M. G., Reutelingsperger, C. P., & Eijssen, L. M. T. (2024). Involvement of extracellular vesicle microRNA clusters in developing healthy and Rett syndrome brain organoids. Cellular and Molecular Life Sciences, 81(1), Article 410. https://doi.org/10.1007/s00018-024-05409-7More information about this publication
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Dominguez-Romero, E., Mazurenko, S., Scheringer, M., dos Santos, V. A. P. M., Evelo, C. T., Anton, M., Hancock, J. M., Zupanic, A., & Suarez-Diez, M. (2024). Making PBPK models more reproducible in practice. Briefings in Bioinformatics, 25(6), Article bbae569. https://doi.org/10.1093/bib/bbae569More information about this publication
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Koetsier, J., Cavill, R., Reijnders, R., Harvey, J., Homann, J., Kouhsar, M., Deckers, K., Köhler, S., Eijssen, L. M. T., van den Hove, D. L. A., Demuth, I., Düzel, S., Smith, R. G., Smith, A. R., Burrage, J., Walker, E. M., Shireby, G., Hannon, E., Dempster, E., ... Pishva, E. (2024). Blood-based multivariate methylation risk score for cognitive impairment and dementia. Alzheimer's & Dementia, 20(10), 6682-6698. https://doi.org/10.1002/alz.14061More information about this publication
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Sener, D. D., Ogul, H., & Basak, S. (2024). Text-based experiment retrieval in genomic databases. Journal of Information Science, 50(5), 1334-1344. https://doi.org/10.1177/01655515221118670More information about this publication
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Jeliazkova, N., Longhin, E., El yamani, N., Rundén-Pran, E., Moschini, E., Serchi, T., Vrček, I. V., Burgum, M. J., Doak, S. H., Cimpan, M. R., Rios-Mondragon, I., Cimpan, E., Battistelli, C. L., Bossa, C., Tsekovska, R., Drobne, D., Novak, S., Repar, N., Ammar, A., ... Dusinska, M. (2024). A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nature Protocols, 19(9), 2642-2684. https://doi.org/10.1038/s41596-024-00993-1More information about this publication
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Fuchs, C., 't Hoen, P. A. C., Mueller, A. R., Ehrhart, F., & Van Karnebeek, C. D. M. (2024). Drug repurposing in Rett and Rett-like syndromes: a promising yet underrated opportunity? Frontiers in medicine, 11, Article 1425038. https://doi.org/10.3389/fmed.2024.1425038More information about this publication
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Groenewold, M., Bleeker, E. A. J., Noorlander, C. W., Sips, A. J. A. M., van der Zee, M., Aitken, R. J., Baker, J. H., Bakker, M. I., Bouman, E. A., Doak, S. H., Drobne, D., Dumit, V. I., Florin, M.-V., Fransman, W., Gonzalez, M. M., Heunisch, E., Isigonis, P., Jeliazkova, N., Jensen, K. A., ... Scott-Fordsmand, J. J. (2024). Governance of advanced materials: Shaping a safe and sustainable future. NanoImpact, 35, Article 100513. https://doi.org/10.1016/j.impact.2024.100513More information about this publication
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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/s41598-024-65094-1More information about this publication
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Ahmed, Z. T., Zain Al-Abeden, M. S., Al Abdin, M. G., Muqresh, M. A., Al Jowf, G. I., Eijssen, L. M. T., & Haider, K. H. (2024). Dose-response relationship of MSCs as living Bio-drugs in HFrEF patients: a systematic review and meta-analysis of RCTs. Stem Cell Research & Therapy, 15(1), Article 165. https://doi.org/10.1186/s13287-024-03713-4More information about this publication
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Mortensen, H. M., Amos, J. D., Exner, T. E., Flores, K., Harper, S., Jarabek, A. M., Klaessig, F., Lobaskin, V., Lynch, I., Marcum, C. S., Martens, M., Brough, B., Spadola, Q., & Bjorkland, R. (2024). NNI nanoinformatics conference 2023: Movement toward a common infrastructure for federal nanoEHS data computational toxicology: Short communication. Computational Toxicology, 30, Article 100316. https://doi.org/10.1016/j.comtox.2024.100316More information about this publication
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Eischen-Loges, M., Tahmasebi birgani, Z., Alaoui selsouli, Y., Eijssen, L., Rho, H., Sthijns, M., Van griensven, M., Lapointe, V., & Habibović, P. (2024). A roadmap of osteogenic differentiation in human mesenchymal stem cells assessed by protein multiplex analysis. European Cells and Materials, 47, 170-189. https://doi.org/10.22203/eCM.v047a12More information about this publication
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Ammar, A., Evelo, C., & Willighagen, E. (2024). FAIR assessment of nanosafety data reusability with community standards. Scientific data, 11(1), Article 503. https://doi.org/10.1038/s41597-024-03324-xMore information about this publication
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Bernabé, C. H., Thielemans, L., Kaliyaperumal, R., Carta, C., Zhang, S., van Gelder, C. W. G., Benis, N., Santos, L. B. D. S., Cornet, R., dos Santos Vieira, B., Lalout , N., Henriques, I., Cámara Ballesteros, A., Burger, K., Kersloot, M. G., Ehrhart, F., Van Enckevort, E., Evelo, C., Gray, A., ... Jacobsen, A. (2024). Building expertise on FAIR through evolving Bring Your Own Data (BYOD) workshops: describing the data, software, and managementfocused approaches and their evolution. (pp. 429-456). Data Intelligence. https://doi.org/10.1162/dint_a_00236More information about this publication
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van Rijn, J. P. M., Martens, M., Ammar, A., Cimpan, M. R., Fessard, V., Hoet, P., Jeliazkova, N., Murugadoss, S., Vinkovic Vrcek, I., & Willighagen, E. L. (2024). From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials. Journal of Cheminformatics, 16(1), Article 49. https://doi.org/10.1186/s13321-024-00833-0More information about this publication
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Willighagen, E., Teunis, M., & De haan, A. (2024). The Chemistry Development Kit in 2024: improving cheminformatics research. Research Ideas and Outcomes, 10, Article e124884. https://doi.org/10.3897/rio.10.e124884More information about this publication
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van der Meer, D., Cheng, W., Rokicki, J., Fernandez-Cabello, S., Shadrin, A., Smeland, O. B., Ehrhart, F., Gülöksüz, S., Pries, L.-K., Lin, B., Rutten, B. P. F., van Os, J., O'Donovan, M., Richards, A. L., Steen, N. E., Djurovic, S., Westlye, L. T., Andreassen, O. A., Kaufmann, T., ... European Network of National Schizophrenia Networks Studying Gene-Environment Interactions Work Package 6 (EU-GEI WP6) Group (2024). Clustering Schizophrenia Genes by Their Temporal Expression Patterns Aids Functional Interpretation. Schizophrenia Bulletin, 50(2), 327-338. Article sbad140. https://doi.org/10.1093/schbul/sbad140More information about this publication
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Serrano, B. A., Gheorghe, L. C., Exner, T. E., Resch, S., Wolf, C., Himly, M., Falk, A., Bossa, N., Vazquez, S., Papadiamantis, A. G., Afantitis, A., Melagraki, G., Maier, D., Saramveis, H., Willighagen, E., Lobaskin, V., Oldfield, J. D., & Lynch, I. (2024). The role of FAIR nanosafety data and nanoinformatics in achieving the UN sustainable development goals: the NanoCommons experience. RSC Sustainability, 2(5), 1378-1399. https://doi.org/10.1039/d3su00148bMore information about this publication