Publications
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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. Advance online publication. https://doi.org/10.1038/s41596-024-00993-1More 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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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
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Abbassi-Daloii, T., Mallon, S. D., Abdellaoui, S. E., Voortman, L. M., & Raz, V. (2024). High-throughput Analysis of Capillary Density in Skeletal Muscle Cross Sections. Bio-protocol, 14(2), Article 4922. https://doi.org/10.21769/BioProtoc.4922More information about this publication
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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/d3dd00069aMore information about this publication
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Murugadoss, S., Vinkovic Vrcek, I., Schaffert, A., Paparella, M., Pem, B., Sosnowska, A., Stepnik, M., Martens, M., Willighagen, E. L., Puzyn, T., Roxana Cimpan, M., Lemaire, F., Mertens, B., Dusinska, M., Fessard, V., & Hoet, P. H. (2024). Linking nanomaterial-induced mitochondrial dysfunction to existing adverse outcome pathways for chemicals. ALTEX, 41(1), 76-90. https://doi.org/10.14573/altex.2305011More information about this publication
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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/gkad960More information about this publication
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Martens, M. T. L. J. (2024). Adverse outcome pathways coming to life: exploring new ways to support risk assessments. [Doctoral Thesis, Maastricht University]. Maastricht University. https://doi.org/10.26481/dis.20240129mmMore information about this publication
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Waagmeester, A. S. (2024). Biological pathway abstractions: from two-dimensional drawings to multidimensional linked data. [Doctoral Thesis, Maastricht University]. Maastricht University. https://doi.org/10.26481/dis.20240116awMore information about this publication
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Ehrhart, F., Silva, A., Amelsvoort, T. V., vonScheibler, E., Evelo, C., & Linden, D. E. J. (2024). Copy number variant risk loci for schizophrenia converge on the BDNF pathway. World Journal of Biological Psychiatry, 25(4), 222-232. https://doi.org/10.1080/15622975.2024.2327027More information about this publication
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Koole, L., Martinez-Martinez, P., Amelsvoort, T. V., Evelo, C. T., & Ehrhart, F. (2024). Interactive neuroinflammation pathways and transcriptomics-based identification of drugs and chemical compounds for schizophrenia. World Journal of Biological Psychiatry, 25(2), 116-129. https://doi.org/10.1080/15622975.2023.2281514More information about this publication
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Wittwehr, C., Clerbaux, L.-A., Edwards, S., Angrish, M., Mortensen, H., Carusi, A., Gromelski, M., Lekka, E., Virvilis, V., Martens, M., Bonino da Silva Santos, L. O., & Nymark, P. (2024). Why adverse outcome pathways need to be FAIR. ALTEX, 40(4), 50-56. https://doi.org/10.14573/altex.2307131More information about this publication
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Hosseini beghaeiraveri, S. A., Labra gayo, J. E., Waagmeester, A., Ammar, A., Gonzalez, C., Slenter, D., Ul-Hasan, S., Willighagen, E., Mcneill, F., Gray, A. J. G., Kaffee, L.-A. (Ed.), Razniewski, S. (Ed.), & Vougiouklis, P. (Ed.) (2023). Wikidata subsetting: Approaches, tools, and evaluation. Semantic web, 1-27. Advance online publication. https://doi.org/10.3233/SW-233491More information about this publication
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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/s12915-023-01764-2More information about this publication
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Maier, D., Exner, T. E., Papadiamantis, A. G., Ammar, A., Tsoumanis, A., Doganis, P., Rouse, I., Slater, L. T., Gkoutos, G. V., Jeliazkova, N., Ilgenfritz, H., Ziegler, M., Gerhard, B., Kopetsky, S., Joshi, D., Walker, L., Svendsen, C., Sarimveis, H., Lobaskin, V., ... Lynch, I. (2023). Harmonising knowledge for safer materials via the "NanoCommons" Knowledge Base. Frontiers in Physics, 11, Article 1271842. https://doi.org/10.3389/fphy.2023.1271842More information about this publication
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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/10.1159/000535120More information about this publication
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Mullowney, M. W., Duncan, K. R., Elsayed, S. S., Garg, N., van der Hooft, J. J. J., Martin, N. I., Meijer, D., Terlouw, B. R., Biermann, F., Blin, K., Durairaj, J., Gorostiola González, M., Helfrich, E. J. N., Huber, F., Leopold-Messer, S., Rajan, K., de Rond, T., van Santen, J. A., Sorokina, M., ... van Westen, G. J. P. (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery, 22(11), 895–916. https://doi.org/10.1038/s41573-023-00774-7More information about this publication