Egon Willighagen

Assistant professor, Maastricht University.

2025-04-08

egon.willighagen@maastrichtuniversity.nl

0000-0001-7542-0286 - chem-bla-ics.linkedchemistry.info -
egonw - egon-willighagen - egonw - @egonw.ap.brid.gy

Education

2002-2008 Ph.D., Chemistry, Representation of Molecules and Molecular Systems in Data Analysis and Modeling, Radboud University, Nijmegen, The Netherlands. isbn:9789090228068

1993-2001 M.Sc., Chemistry, University of Nijmegen, Nijmegen, The Netherlands

Experience

2024-present Assistant Professor, Department of Translational Genomics, Institute NUTRIM for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.

2014-2024 Assistant Professor, Department of Bioinformatics, Maastricht University, Maastricht, The Netherlands.

2012-2014 Postdoc, Department of Bioinformatics, Maastricht University, Maastricht, The Netherlands.

2011 Postdoc, Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.

2010 Postdoc, Unilever Center for Molecular Molecular Informatics, University of Cambridge, Cambridge, United Kingdom.

2008-2010 Postdoc, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.

2007-2008 Postdoc, Plant Research International, Wageningen University & Research Centre, Wageningen, The Netherlands.

2006-2007 Postdoc, Cologne University Bioinformatics Centre, Cologne University, Cologne, Germany.

Publications

Google Scholar u8SjMZ0AAAAJ. H-index: 52.

Web of Science H-index: 41. Citations: 7,505 (without self: 7,149). Highly Cited Papers: 8. Citations per article: 51.04

NIH iCite: Mean RCR: 3.26. Articles in NIH Top 1%: 5, Top 10%: 16

Journal articles

Scientific publications in international journals with a referee system.

2025 Kienhuis, A., Krul, C., van Engelen, J., Evelo, C., Hessel, E., Hoekman, J., Kramer, N., Krop, E., Masereeuw, R., Moors, E., Negro, S., Piersma, A., 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. (2024). ALTEX. doi:10.14573/altex.2407211

2024 Agrawal, A., Balcı, 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. (2023). WikiPathways 2024: next generation pathway database. Nucleic Acids Research, 52(D1), D679–D689. doi:10.1093/nar/gkad960

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. doi:10.1039/d3su00148b

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. doi:10.1038/s41596-024-00993-1

Niarakis, A., Ostaszewski, M., Mazein, A., Kuperstein, I., Kutmon, M., Gillespie, M. E., Funahashi, A., Acencio, M. L., Hemedan, A., Aichem, M., Klein, K., Czauderna, T., Burtscher, F., Yamada, T. G., Hiki, Y., Hiroi, N. F., Hu, F., Pham, N., Ehrhart, F., … Schneider, R. (2024). Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology, 14. doi:10.3389/fimmu.2023.1282859

Ammar, A., Evelo, C., & Willighagen, E. (2024). FAIR assessment of nanosafety data reusability with community standards. Scientific Data, 11(1). doi:10.1038/s41597-024-03324-x

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. doi:10.1039/d3dd00069a

Van Rijn, J. P. M., Martens, M., Ammar, A., Cimpan, M. R., Fessard, V., Hoet, P., Jeliazkova, N., Murugadoss, S., Vinković Vrček, 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). doi:10.1186/s13321-024-00833-0

Bernabé, C. H., Thielemans, L., Kaliyaperumal, R., Carta, C., Zhang, S., van Gelder, C. W. G., Benis, N., da Silva Santos, L. O. B., Cornet, R., dos Santos Vieira, B., Lalout, N., Henriques, I., Ballesteros, A. C., Burger, K., Kersloot, M. G., Ehrhart, F., van Enckevort, E., Evelo, C. T., Gray, A. J. G., …, Willighagen E. L., Jansen, M., Mons, B., Roos, M., Jacobsen, A. (2024). Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution. Data Intelligence, 6(2), 429–456. doi:10.1162/dint_a_00236

Murugadoss, S., Vinković Vrček, I., Schaffert, A., Paparella, M., Pem, B., Sosnowska, A., Stępnik, M., Martens, M., Willighagen, E. L., Puzyn, T., Roxana Cimpan, M., Lemaire, F., Mertens, B., Dusinska, M., Fessard, V., Hoet, P.H.. Linking nanomaterial-induced mitochondrial dysfunction to existing adverse outcome pathways for chemicals. (2024). ALTEX, 41(1). doi:10.14573/altex.2305011

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, 100513. doi:10.1016/j.impact.2024.100513

2023 Martens, M., Stierum, R., Schymanski, E. L., Evelo, C. T., Aalizadeh, R., Aladjov, H., Arturi, K., Audouze, K., Babica, P., Berka, K., Bessems, J., Blaha, L., Bolton, E. E., Cases, M., Damalas, D. Ε., Dave, K., Dilger, M., Exner, T., Geerke, D. P., … Willighagen, E. L. (2023). ELIXIR and Toxicology: a community in development. F1000Research, 10, 1129. doi:10.12688/f1000research.74502.2

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., … Medema, M. H. (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery, 22(11), 895–916. doi:10.1038/s41573-023-00774-7

Furxhi, I., Willighagen, E., Evelo, C., Costa, A., Gardini, D., & Ammar, A. (2023). A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability. NanoImpact, 31, 100475. doi:10.1016/j.impact.2023.100475

Ammar, A., Cavill, R., Evelo, C., & Willighagen, E. (2023). PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. Journal of Cheminformatics, 15(1). doi:10.1186/s13321-023-00701-3

Willighagen, E. (2023). Two years of explicit CiTO annotations. Journal of Cheminformatics, 15(1). doi:10.1186/s13321-023-00683-2

Rocca-Serra, P., Gu, W., Ioannidis, V., Abbassi-Daloii, T., Capella-Gutierrez, S., Chandramouliswaran, I., Splendiani, A., Burdett, T., Giessmann, R. T., Henderson, D., Batista, D., Emam, I., Gadiya, Y., Giovanni, L., Willighagen, E., Evelo, C., Gray, A. J. G., Gribbon, P., Juty, N., … Sansone, S.-A. (2023). The FAIR Cookbook - the essential resource for and by FAIR doers. Scientific Data, 10(1). doi:10.1038/s41597-023-02166-3

Slenter, D. N., Hemel, I. M. G. M., Evelo, C. T., Bierau, J., Willighagen, E. L., & Steinbusch, L. K. M. (2023). Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations. Orphanet Journal of Rare Diseases, 18(1). doi:10.1186/s13023-023-02683-9

2022 Ammar, A., Cavill, R., Evelo, C., & Willighagen, E. (2022). PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow. Journal of Cheminformatics, 14(1). doi:10.1186/s13321-021-00573-5

Hoyt, C. T., Balk, M., Callahan, T. J., Domingo-Fernández, D., Haendel, M. A., Hegde, H. B., Himmelstein, D. S., Karis, K., Kunze, J., Lubiana, T., Matentzoglu, N., McMurry, J., Moxon, S., Mungall, C. J., Rutz, A., Unni, D. R., Willighagen, E., Winston, D., & Gyori, B. M. (2022). Unifying the identification of biomedical entities with the Bioregistry. Scientific Data, 9(1). doi:10.1038/s41597-022-01807-3

Mohammed Taha, H., Aalizadeh, R., Alygizakis, N., Antignac, J.-P., Arp, H. P. H., Bade, R., Baker, N., Belova, L., Bijlsma, L., Bolton, E. E., Brack, W., Celma, A., Chen, W.-L., Cheng, T., Chirsir, P., Čirka, Ľ., D’Agostino, L. A., Djoumbou Feunang, Y., Dulio, V., … Schymanski, E. L. (2022). The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environmental Sciences Europe, 34(1). doi:10.1186/s12302-022-00680-6

Sinclair, G., Thillainadarajah, I., Meyer, B., Samano, V., Sivasupramaniam, S., Adams, L., Willighagen, E. L., Richard, A. M., Walker, M., & Williams, A. J. (2022). Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. Journal of Chemical Information and Modeling, 62(20), 4888–4905. doi:10.1021/acs.jcim.2c00886

Jacobs, A., Williams, D., Hickey, K., Patrick, N., Williams, A. J., Chalk, S., McEwen, L., Willighagen, E., Walker, M., Bolton, E., Sinclair, G., & Sanford, A. (2022). CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. Journal of Chemical Information and Modeling, 62(11), 2737–2743. doi:10.1021/acs.jcim.2c00268

Krans, N. A., Ammar, A., Nymark, P., Willighagen, E. L., Bakker, M. I., & Quik, J. T. K. (2022). FAIR assessment tools: evaluating use and performance. NanoImpact, 27, 100402. doi:10.1016/j.impact.2022.100402

Miller, R. A., Kutmon, M., Bohler, A., Waagmeester, A., Evelo, C. T., & Willighagen, E. L. (2022). Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. PLOS ONE, 17(4), e0263057. doi:10.1371/journal.pone.0263057

Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondrášek, J., Steinbeck, C., Pauli, G. F., Wolfender, J.-L., Bisson, J., & Allard, P.-M. (2022). The LOTUS initiative for open knowledge management in natural products research. eLife, 11. doi:10.7554/elife.70780

Van Rijn, J., Afantitis, A., Culha, M., Dusinska, M., Exner, T. E., Jeliazkova, N., Longhin, E. M., Lynch, I., Melagraki, G., Nymark, P., Papadiamantis, A. G., Winkler, D. A., Yilmaz, H., & Willighagen, E. (2022). European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials. Journal of Cheminformatics, 14(1). doi:10.1186/s13321-022-00614-7

Martens, M., Evelo, C. T., & Willighagen, E. L. (2022). Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. Applied In Vitro Toxicology, 8(1), 2–13. doi:10.1089/aivt.2021.0010

Mortensen, H. M., Martens, M., Senn, J., Levey, T., Evelo, C. T., Willighagen, E. L., & Exner, T. (2022). The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. Frontiers in Toxicology, 4. doi:10.3389/ftox.2022.803983

Ni, Z., Wölk, M., Jukes, G., Mendivelso Espinosa, K., Ahrends, R., Aimo, L., Alvarez-Jarreta, J., Andrews, S., Andrews, R., Bridge, A., Clair, G. C., Conroy, M. J., Fahy, E., Gaud, C., Goracci, L., Hartler, J., Hoffmann, N., Kopczyinki, D., Korf, A., … Fedorova, M. (2022). Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods, 20(2), 193–204. doi:10.1038/s41592-022-01710-0

Sochorová, M., Vávrová, K., Fedorova, M., Ni, Z., Slenter, D., Kutmon, M., Willighagen, E. L., Letsiou, S., Töröcsik, D., Marchetti-Deschmann, M., Zoratto, S., Kremslehner, C., & Gruber, F. (2022). Research Techniques Made Simple: Lipidomic Analysis in Skin Research. Journal of Investigative Dermatology, 142(1), 4-11.e1. doi:10.1016/j.jid.2021.09.017

2021 Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta‐Resendiz, A., Singh, V., Aghamiri, S. S., Acencio, M. L., Glaab, E., Ruepp, A., Fobo, G., Montrone, C., Brauner, B., Frishman, G., Monraz Gómez, L. C., Somers, J., Hoch, M., Kumar Gupta, S., … Schneider, R. (2021). COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms. Molecular Systems Biology, 17(12). doi:10.15252/msb.202110851

Meldal, B. H. M., Perfetto, L., Combe, C., Lubiana, T., Ferreira Cavalcante, J. V., Bye-A-Jee, H., Waagmeester, A., del-Toro, N., Shrivastava, A., Barrera, E., Wong, E., Mlecnik, B., Bindea, G., Panneerselvam, K., Willighagen, E., Rappsilber, J., Porras, P., Hermjakob, H., & Orchard, S. (2021). Complex Portal 2022: new curation frontiers. Nucleic Acids Research, 50(D1), D578–D586. doi:10.1093/nar/gkab991

Hanspers, K., Kutmon, M., Coort, S. L., Digles, D., Dupuis, L. J., Ehrhart, F., Hu, F., Lopes, E. N., Martens, M., Pham, N., Shin, W., Slenter, D. N., Waagmeester, A., Willighagen, E. L., Winckers, L. A., Evelo, C. T., & Pico, A. R. (2021). Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLOS Computational Biology, 17(8), e1009226. doi:10.1371/journal.pcbi.1009226

Kyle, J. E., Aimo, L., Bridge, A. J., Clair, G., Fedorova, M., Helms, J. B., Molenaar, M. R., Ni, Z., Orešič, M., Slenter, D., Willighagen, E., & Webb-Robertson, B.-J. M. (2021). Interpreting the lipidome: bioinformatic approaches to embrace the complexity. Metabolomics, 17(6). doi:10.1007/s11306-021-01802-6

Willighagen, E. (2021). Bacting: a next generation, command line version of Bioclipse. Journal of Open Source Software, 6(62), 2558. doi:10.21105/joss.02558

Winckers, L. A., Evelo, C. T., Willighagen, E. L., & Kutmon, M. (2021). Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. International Journal of Molecular Sciences, 22(17), 9432. doi:10.3390/ijms22179432

Ehrhart, F., Jacobsen, A., Rigau, M., Bosio, M., Kaliyaperumal, R., Laros, J. F. J., Willighagen, E. L., Valencia, A., Roos, M., Capella-Gutierrez, S., Curfs, L. M. G., & Evelo, C. T. (2021). A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration. Scientific Data, 8(1). doi:10.1038/s41597-020-00794-7

Ehrhart, F., Willighagen, E. L., Kutmon, M., van Hoften, M., Curfs, L. M. G., & Evelo, C. T. (2021). A resource to explore the discovery of rare diseases and their causative genes. Scientific Data, 8(1). doi:10.1038/s41597-021-00905-y

Murugadoss, S. (2021). A strategy towards the generation of testable adverse outcome pathways for nanomaterials. ALTEX. doi:10.14573/altex.2102191

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. (2021). A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. BMC Biology, 19(1). doi:10.1186/s12915-020-00940-y

2020 Ammar, A., Bonaretti, S., Winckers, L., Quik, J., Bakker, M., Maier, D., Lynch, I., van Rijn, J., & Willighagen, E. (2020). A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. Nanomaterials, 10(10), 2068. doi:10.3390/nano10102068

Lynch, I., Afantitis, A., Exner, T., Himly, M., Lobaskin, V., Doganis, P., Maier, D., Sanabria, N., Papadiamantis, A. G., Rybinska-Fryca, A., Gromelski, M., Puzyn, T., Willighagen, E., Johnston, B. D., Gulumian, M., Matzke, M., Green Etxabe, A., Bossa, N., Serra, A., … Melagraki, G. (2020). Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? Nanomaterials, 10(12), 2493. doi:10.3390/nano10122493

Martens, M., Ammar, A., Riutta, A., Waagmeester, A., Slenter, D. N., Hanspers, K., A. Miller, R., Digles, D., Lopes, E. N., Ehrhart, F., Dupuis, L. J., Winckers, L. A., Coort, S. L., Willighagen, E. L., Evelo, C. T., Pico, A. R., & Kutmon, M. (2020). WikiPathways: connecting communities. Nucleic Acids Research, 49(D1), D613–D621. doi:10.1093/nar/gkaa1024

Afantitis, A., Melagraki, G., Isigonis, P., Tsoumanis, A., Varsou, D. D., Valsami-Jones, E., Papadiamantis, A., Ellis, L.-J. A., Sarimveis, H., Doganis, P., Karatzas, P., Tsiros, P., Liampa, I., Lobaskin, V., Greco, D., Serra, A., Kinaret, P. A. S., Saarimäki, L. A., Grafström, R., … Lynch, I. (2020). NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Computational and Structural Biotechnology Journal, 18, 583–602. doi:10.1016/j.csbj.2020.02.023

Jacobsen, A., de Miranda Azevedo, R., Juty, N., Batista, D., Coles, S., Cornet, R., Courtot, M., Crosas, M., Dumontier, M., Evelo, C. T., Goble, C., Guizzardi, G., Hansen, K. K., Hasnain, A., Hettne, K., Heringa, J., Hooft, R. W. W., Imming, M., Jeffery, K. G., … Schultes, E. (2020). FAIR Principles: Interpretations and Implementation Considerations. Data Intelligence, 2(1–2), 10–29. doi:10.1162/dint_r_00024

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-Resendiz, A., Messina, F., … Schneider, R. (2020). COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data, 7(1). doi:10.1038/s41597-020-0477-8

Waagmeester, A., Stupp, G., Burgstaller-Muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-Rosinach, N., … Su, A. I. (2020). Wikidata as a knowledge graph for the life sciences. eLife, 9. doi:10.7554/elife.52614

2019 Stanstrup, J., Broeckling, C., Helmus, R., Hoffmann, N., Mathé, E., Naake, T., Nicolotti, L., Peters, K., Rainer, J., Salek, R., Schulze, T., Schymanski, E., Stravs, M., Thévenot, E., Treutler, H., Weber, R., Willighagen, E., Witting, M., & Neumann, S. (2019). The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites, 9(10), 200. doi:10.3390/metabo9100200

Kutmon, M., Ehrhart, F., Willighagen, E. L., Evelo, C. T., & Coort, S. L. (2019). CyTargetLinker app update: A flexible solution for network extension in Cytoscape. F1000Research, 7, 743. doi:10.12688/f1000research.14613.2

Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., Yu, T., Kang, J., Jeon, M., Wolfinger, R., Nguyen, T., Zaslavskiy, M., Abante, J., Abecassis, B. S., Aben, N., Aghamirzaie, D., Aittokallio, T., Akhtari, F. S., Al-lazikani, B., … Saez-Rodriguez, J. (2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications, 10(1). doi:10.1038/s41467-019-09799-2

2018 Miller, R. A., Ehrhart, F., Eijssen, L. M. T., Slenter, D. N., Curfs, L. M. G., Evelo, C. T., Willighagen, E. L., & Kutmon, M. (2019). Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome. Frontiers in Genetics, 10. doi:10.3389/fgene.2019.00059

Townend, G. S., Ehrhart, F., van Kranen, H. J., Wilkinson, M., Jacobsen, A., Roos, M., Willighagen, E. L., van Enckevort, D., Evelo, C. T., & Curfs, L. M. G. (2018). MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. Human Mutation, 39(7), 914–924. doi:10.1002/humu.23542

Martens, M., Verbruggen, T., Nymark, P., Grafström, R., Burgoon, L. D., Aladjov, H., Torres Andón, F., Evelo, C. T., & Willighagen, E. L. (2018). Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. Frontiers in Genetics, 9. doi:10.3389/fgene.2018.00661

Miller, R. A., Woollard, P., Willighagen, E. L., Digles, D., Kutmon, M., Loizou, A., Waagmeester, A., Senger, S., & Evelo, C. T. (2018). Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform. F1000Research, 7, 75. doi:10.12688/f1000research.13197.2

Slenter, D. N., Kutmon, M., Hanspers, K., Riutta, A., Windsor, J., Nunes, N., Mélius, J., Cirillo, E., Coort, S. L., Digles, D., Ehrhart, F., Giesbertz, P., Kalafati, M., Martens, M., Miller, R., Nishida, K., Rieswijk, L., Waagmeester, A., Eijssen, L. M. T., … Willighagen, E. L. (2017). WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research, 46(D1), D661–D667. doi:10.1093/nar/gkx1064

Karcher, S., Willighagen, E. L., Rumble, J., Ehrhart, F., Evelo, C. T., Fritts, M., Gaheen, S., Harper, S. L., Hoover, M. D., Jeliazkova, N., Lewinski, N., Marchese Robinson, R. L., Mills, K. C., Mustad, A. P., Thomas, D. G., Tsiliki, G., & Hendren, C. O. (2018). Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. NanoImpact, 9, 85–101. doi:10.1016/j.impact.2017.11.002

2017 Lampa, S., Willighagen, E., Kohonen, P., King, A., Vrandečić, D., Grafström, R., & Spjuth, O. (2017). RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. Journal of Biomedical Semantics, 8(1). doi:10.1186/s13326-017-0136-y

Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., … Hengstler, J. G. (2017). Adverse outcome pathways: opportunities, limitations and open questions. Archives of Toxicology, 91(11), 3477–3505. doi:10.1007/s00204-017-2045-3

Nymark, P., Rieswijk, L., Ehrhart, F., Jeliazkova, N., Tsiliki, G., Sarimveis, H., Evelo, C. T., Hongisto, V., Kohonen, P., Willighagen, E., & Grafström, R. C. (2017). A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicological Sciences, 162(1), 264–275. doi:10.1093/toxsci/kfx252

van Rijswijk, M., Beirnaert, C., Caron, C., Cascante, M., Dominguez, V., Dunn, W. B., Ebbels, T. M. D., Giacomoni, F., Gonzalez-Beltran, A., Hankemeier, T., Haug, K., Izquierdo-Garcia, J. L., Jimenez, R. C., Jourdan, F., Kale, N., Klapa, M. I., Kohlbacher, O., Koort, K., Kultima, K., … Steinbeck, C. (2017). The future of metabolomics in ELIXIR. F1000Research, 6, 1649. doi:10.12688/f1000research.12342.2

Kohonen, P., Parkkinen, J. A., Willighagen, E. L., Ceder, R., Wennerberg, K., Kaski, S., & Grafström, R. C. (2017). A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nature Communications, 8(1). doi:10.1038/ncomms15932

Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Chertó, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R., & Steinbeck, C. (2017). The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics, 9(1). doi:10.1186/s13321-017-0220-4

2016 Wohlgemuth, G., Mehta, S. S., Mejia, R. F., Neumann, S., Pedrosa, D., Pluskal, T., Schymanski, E. L., Willighagen, E. L., Wilson, M., Wishart, D. S., Arita, M., Dorrestein, P. C., Bandeira, N., Wang, M., Schulze, T., Salek, R. M., Steinbeck, C., Nainala, V. C., Mistrik, R., … Fiehn, O. (2016). SPLASH, a hashed identifier for mass spectra. Nature Biotechnology, 34(11), 1099–1101. doi:10.1038/nbt.3689

Spjuth, O., Rydberg, P., Willighagen, E. L., Evelo, C. T., & Jeliazkova, N. (2016). XMetDB: an open access database for xenobiotic metabolism. Journal of Cheminformatics, 8(1). doi:10.1186/s13321-016-0161-3

Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E. L., Evelo, C. T., & Pico, A. R. (2016). Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLOS Computational Biology, 12(6), e1004989. doi:10.1371/journal.pcbi.1004989

2015 Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Mélius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T., & Pico, A. R. (2015). WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research, 44(D1), D488–D494. doi:10.1093/nar/gkv1024

Tsiliki, G., Munteanu, C. R., Seoane, J. A., Fernandez-Lozano, C., Sarimveis, H., & Willighagen, E. L. (2015). RRegrs: an R package for computer-aided model selection with multiple regression models. Journal of Cheminformatics, 7(1). doi:10.1186/s13321-015-0094-2

Bohler, A., Eijssen, L. M. T., van Iersel, M. P., Leemans, C., Willighagen, E. L., Kutmon, M., Jaillard, M., & Evelo, C. T. (2015). Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. BMC Bioinformatics, 16(1). doi:10.1186/s12859-015-0708-8

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Willighagen, E., & Bolton, E. (2015). PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. Journal of Cheminformatics, 7(1). doi:10.1186/s13321-015-0084-4

Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C. R., Steinbeck, C., & Willighagen, E. (2015). eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. Journal of Biomedical Semantics, 6(1). doi:10.1186/s13326-015-0005-5

Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafström, R., Hardy, B., Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D., & Willighagen, E. (2015). The eNanoMapper database for nanomaterial safety information. Beilstein Journal of Nanotechnology, 6, 1609–1634. doi:10.3762/bjnano.6.165

2014 Grafström, R. C., Nymark, P., Hongisto, V., Spjuth, O., Ceder, R., Willighagen, E., Hardy, B., Kaski, S., & Kohonen, P. (2015). Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of “Omics” Data from Human Cell Cultures. Alternatives to Laboratory Animals, 43(5), 325–332. doi:10.1177/02611929150430050

2013 Spjuth, O., Berg, A., Adams, S., & Willighagen, E. L. (2013). Applications of the InChI in cheminformatics with the CDK and Bioclipse. Journal of Cheminformatics, 5(1). doi:10.1186/1758-2946-5-14

Willighagen, E. L., Waagmeester, A., Spjuth, O., Ansell, P., Williams, A. J., Tkachenko, V., Hastings, J., Chen, B., & Wild, D. J. (2013). The ChEMBL database as linked open data. Journal of Cheminformatics, 5(1). doi:10.1186/1758-2946-5-23

2012 Spjuth, O., Georgiev, V., Carlsson, L., Alvarsson, J., Berg, A., Willighagen, E., Wikberg, J. E. S., & Eklund, M. (2012). Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics, 29(2), 286–289. doi:10.1093/bioinformatics/bts681

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., & Hardy, B. (2013). The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics, 32(1), 47–63. doi:10.1002/minf.201200114

Marshall, M. S., Boyce, R., Deus, H. F., Zhao, J., Willighagen, E. L., Samwald, M., Pichler, E., Hajagos, J., Prud’hommeaux, E., & Stephens, S. (2012). Emerging practices for mapping and linking life sciences data using RDF — A case series. Journal of Web Semantics, 14, 2–13. doi:10.1016/j.websem.2012.02.003

Guha, R., & Willighagen, E. (2012). A Survey of Quantitative Descriptions of Molecular Structure. Current Topics in Medicinal Chemistry, 12(18), 1946–1956. doi:10.2174/156802612804910278

Neylon, C., Aerts, J., Brown, C. T., Coles, S. J., Hatton, L., Lemire, D., Millman, K. J., Murray-Rust, P., Perez, F., Saunders, N., Shah, N., Smith, A., Varoquaux, G., & Willighagen, E. (2012). Changing computational research. The challenges ahead. Source Code for Biology and Medicine, 7(1). doi:10.1186/1751-0473-7-2

Williams, A. J., Ekins, S., Spjuth, O., & Willighagen, E. L. (2012). Accessing, Using, and Creating Chemical Property Databases for Computational Toxicology Modeling. In Methods in Molecular Biology (pp. 221–241). Humana Press. doi:10.1007/978-1-62703-050-2_10

Spjuth, O., Carlsson, L., Alvarsson, J., Georgiev, V., Willighagen, E., & Eklund, M. (2012). Open Source Drug Discovery with Bioclipse. Current Topics in Medicinal Chemistry, 12(18), 1980–1986. doi:10.2174/156802612804910287

Wegner, J. K., Sterling, A., Guha, R., Bender, A., Faulon, J.-L., Hastings, J., O’Boyle, N., Overington, J., Van Vlijmen, H., & Willighagen, E. (2012). Cheminformatics. Communications of the ACM, 55(11), 65–75. doi:10.1145/2366316.2366334

Williams, A. J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E. L., Evelo, C. T., Blomberg, N., Ecker, G., Goble, C., & Mons, B. (2012). Open PHACTS: semantic interoperability for drug discovery. Drug Discovery Today, 17(21–22), 1188–1198. doi:10.1016/j.drudis.2012.05.016

2011 Hastings, J., Chepelev, L., Willighagen, E., Adams, N., Steinbeck, C., & Dumontier, M. (2011). The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web. PLoS ONE, 6(10), e25513. doi:10.1371/journal.pone.0025513

Rojas-Chertó, M., Kasper, P. T., Willighagen, E. L., Vreeken, R. J., Hankemeier, T., & Reijmers, T. H. (2011). Elemental composition determination based on MSn. Bioinformatics, 27(17), 2376–2383. doi:10.1093/bioinformatics/btr409

Samwald, M., Jentzsch, A., Bouton, C., Kallesøe, C. S., Willighagen, E., Hajagos, J., Marshall, M. S., Prud’hommeaux, E., Hassanzadeh, O., Pichler, E., & Stephens, S. (2011). Linked open drug data for pharmaceutical research and development. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-19

Truszkowski, A., Neumann, S., Zielesny, A., Willighagen, E., & Steinbeck, C. (2011). CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution. Journal of Cheminformatics, 3(S1). doi:10.1186/1758-2946-3-s1-p5

Willighagen, E. L., Jeliazkova, N., Hardy, B., Grafström, R. C., & Spjuth, O. (2011). Computational toxicology using the OpenTox application programming interface and Bioclipse. BMC Research Notes, 4(1). doi:10.1186/1756-0500-4-487

Jessop, D. M., Adams, S. E., Willighagen, E. L., Hawizy, L., & Murray-Rust, P. (2011). OSCAR4: a flexible architecture for chemical text-mining. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-41

O’Boyle, N. M., Guha, R., Willighagen, E. L., Adams, S. E., Alvarsson, J., Bradley, J.-C., Filippov, I. V., Hanson, R. M., Hanwell, M. D., Hutchison, G. R., James, C. A., Jeliazkova, N., Lang, A. S., Langner, K. M., Lonie, D. C., Lowe, D. M., Pansanel, J., Pavlov, D., Spjuth, O., … Murray-Rust, P. (2011). Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-37

Truszkowski, A., Jayaseelan, K. V., Neumann, S., Willighagen, E. L., Zielesny, A., & Steinbeck, C. (2011). New developments on the cheminformatics open workflow environment CDK-Taverna. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-54

Willighagen, E. L., Alvarsson, J., Andersson, A., Eklund, M., Lampa, S., Lapins, M., Spjuth, O., & Wikberg, J. E. (2011). Linking the Resource Description Framework to cheminformatics and proteochemometrics. Journal of Biomedical Semantics, 2(Suppl 1), S6. doi:10.1186/2041-1480-2-s1-s6

Willighagen, E. L., & Brändle, M. P. (2011). Resource description framework technologies in chemistry. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-15

2010 Kuhn, T., Willighagen, E. L., Zielesny, A., & Steinbeck, C. (2010). CDK-Taverna: an open workflow environment for cheminformatics. BMC Bioinformatics, 11(1). doi:10.1186/1471-2105-11-159

Spjuth, O., Willighagen, E. L., Guha, R., Eklund, M., & Wikberg, J. E. (2010). Towards interoperable and reproducible QSAR analyses: Exchange of datasets. Journal of Cheminformatics, 2(1). doi:10.1186/1758-2946-2-5

Wohlgemuth, G., Haldiya, P. K., Willighagen, E., Kind, T., & Fiehn, O. (2010). The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports. Bioinformatics, 26(20), 2647–2648. doi:10.1093/bioinformatics/btq476

2009 Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., & Wikberg, J. E. (2009). Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics, 10(1). doi:10.1186/1471-2105-10-397

Wagener, J., Spjuth, O., Willighagen, E. L., & Wikberg, J. E. (2009). XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. BMC Bioinformatics, 10(1). doi:10.1186/1471-2105-10-279

2007 Willighagen, E. L., Wehrens, R., Melssen, W., de Gelder, R., & Buydens, L. M. C. (2007). Supervised Self-Organizing Maps in Crystal Property and Structure Prediction. Crystal Growth & Design, 7(9), 1738–1745. doi:10.1021/cg060872y

Willighagen, E. L., O’Boyle, N. M., Gopalakrishnan, H., Jiao, D., Guha, R., Steinbeck, C., & Wild, D. J. (2007). Userscripts for the Life Sciences. BMC Bioinformatics, 8(1). doi:10.1186/1471-2105-8-487

Kuhn, S., Helmus, T., Lancashire, R. J., Murray-Rust, P., Rzepa, H. S., Steinbeck, C., & Willighagen, E. L. (2007). Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data. Journal of Chemical Information and Modeling, 47(6), 2015–2034. doi:10.1021/ci600531a

Spjuth, O., Helmus, T., Willighagen, E. L., Kuhn, S., Eklund, M., Wagener, J., Murray-Rust, P., Steinbeck, C., & Wikberg, J. E. (2007). Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics, 8(1). doi:10.1186/1471-2105-8-59

2006 Guha, R., Howard, M. T., Hutchison, G. R., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. L. (2006). The Blue Obelisk—Interoperability in Chemical Informatics. Journal of Chemical Information and Modeling, 46(3), 991–998. doi:10.1021/ci050400b

Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., & Willighagen, E. (2006). Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Current Pharmaceutical Design, 12(17), 2111–2120. doi:10.2174/138161206777585274

Willighagen, E. L., Denissen, H. M. G. W., Wehrens, R., & Buydens, L. M. C. (2006). On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors. Journal of Chemical Information and Modeling, 46(2), 487–494. doi:10.1021/ci050282s

Willighagen, E. L., Wehrens, R., & Buydens, L. M. C. (2006). Molecular Chemometrics. Critical Reviews in Analytical Chemistry, 36(3–4), 189–198. doi:10.1080/10408340600969601

2005 Willighagen, E. L., Wehrens, R., Verwer, P., de Gelder, R., & Buydens, L. M. C. (2005). Method for the computational comparison of crystal structures. Acta Crystallographica Section B Structural Science, 61(1), 29–36. doi:10.1107/s0108768104028344

2004 Murray-Rust, P., Rzepa, H. S., Williamson, M. J., & Willighagen, E. L. (2004). Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators. Journal of Chemical Information and Computer Sciences, 44(2), 462–469. doi:10.1021/ci034244p

2003 Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003). The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. Journal of Chemical Information and Computer Sciences, 43(2), 493–500. doi:10.1021/ci025584y

2002 Buijnsters, P. J. J. A., García Rodríguez, C. L., Willighagen, E. L., Sommerdijk, N. A. J. M., Kremer, A., Camilleri, P., Feiters, M. C., Nolte, R. J. M., & Zwanenburg, B. (2002). Cationic Gemini Surfactants Based on Tartaric Acid: Synthesis, Aggregation, Monolayer Behaviour, and Interaction with DNA. European Journal of Organic Chemistry, 2002(8), 1397–1406. doi:10.1002/1099-0690(200204)2002:8<1397::aid-ejoc1397>3.0.co;2-6

2001 Willighagen, E., (2001). Processing CML Conventions in Java, Internet Journal of Chemistry, 4.

2000 Krause, S., Willighagen, E., & Steinbeck, C. (2000). JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures. Molecules, 5(1), 93–98. doi:10.3390/50100093

Books and chapters

Scientific publication as a book or as a contribution to a book including proceedings.

Books

Addshore, D. Mietchen, E. Willighagen, Wikidata Queries around the SARS-CoV-2 virus and pandemic. 2020 (free ebook). doi:10.5281/zenodo.3977414

E. Willighagen, Groovy Cheminformatics with the Chemistry Development Kit, Lulu.com, 2011 (now as free and open access ebook).

J. Wikberg, M. Eklund, E. Willighagen, O. Spjuth, M. Lapins, O. Engkvist, J. Alvarsson, Introduction to Pharmaceutical Bioinformatics. Oakleaf Academic, Stockholm, Sweden. ISBN: 9-789-19794030-6, 2010.

Conference proceedings

Kuhn, T., Banda, J. M., Willighagen, E., Ehrhart, F., Evelo, C., Malas, T. B., Dumontier, M., Merono-Penuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Centeno Ortiz, E., Furlong, L. I., Queralt-Rosinach, N., & Chichester, C. (2018). Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. 2018 IEEE 14th International Conference on E-Science (e-Science), 83–92. doi:10.1109/escience.2018.00024

T. Kuhn, E. Willighagen, C. Evelo, N. Queralt-Rosinach, E. Centeno, L.I. Furlong LI. Reliable Granular References to Changing Linked Data. In: d’Amato C, Fernandez M, Tamma V, Lecue F, Cudré-Mauroux P, Sequeda J, et al., editors. The Semantic Web – ISWC 2017. Cham: Springer International Publishing; 2017. p. 436–51. doi:10.1007/978-3-319-68288-4_26

Nielsen, F. Å., Mietchen, D., & Willighagen, E. (2017). Scholia, Scientometrics and Wikidata. In Lecture Notes in Computer Science (pp. 237–259). Springer International Publishing. doi:10.1007/978-3-319-70407-4_36

C. Batchelor, C. Brenninkmeijer, C. Chichester, M. Davies, D. Digles, I. Dunlop, C. Evelo, A. Gaulton, C. Goble, A. Gray, P. Groth, L. Harland, K. Karapetyan, A. Loizou, J. Overington, S. Pettifer, J. Steele, R. Stevens, V. Tkachenko, A. Waag- meester, A. Williams, E. Willighagen, Scientific lenses to support multiple views over linked chemistry data. In: Mika, P., Tudorache, T., Bernstein, A., Welty, C., Knoblock, C., Vrandečić, D., Groth, P., Noy, N., Janowicz, K., Goble, C. (Eds.), The Semantic Web – ISWC 2014. Vol. 8796 of Lecture Notes in Computer Science. Springer International Publishing, Cham, Ch. 7, pp. 98-113, 2014. doi:10.1007/978-3-319-11964-9_7

N. Jeliazkova, P. Doganis, B. Fadeel, R. Grafstrom, J. Hastings, V. Jeliazkov, P. Kohonen, C. Munteanu, H. Sarimveis, B. Smeets, G. Tsiliki, D. Vorgrimmler, E. Willighagen, The first eNanoMapper prototype: A substance database to support safe-by-design. In: Bioinformatics and Biomedicine (BIBM), 2014 IEEE Interna- tional Conference on. IEEE, pp. 1-9. doi:10.1109/bibm.2014.6999367, 2014.

J. Hastings, E. Willighagen, G. Owen, N. Jeliazkova, The eNanoMapper Consortium, C. Steinbeck, eNanoMapper: Opportunities and challenges in using ontologies to enable data integration for nanomaterial risk assessment. In: Proceedings of the 17th Annual Bio-Ontologies Meeting. pp. 18-21, 2014.

C. Goble, A. Gray, L. Harland, K. Karapetyan, A. Loizou, I. Mikhailov, Y. Rankka, S. Senger, V. Tkachenko, A. Williams, E. Willighagen, Incorporating commercial and private data into an open linked data platform for drug discovery. In: The Semantic Web – ISWC, Lecture Notes in Computer Science. Vol 8219. pp. 65-80. doi:10.1007/978-3-642-41338-4_5, 2013.

C. Brenninkmeijer, C. Evelo, C. Goble, A. Gray, P. Groth, S. Pettifer, R. Stevens, A. William, E. Willighagen, Scientific Lenses over Linked Data: An Approach to Support Task Specific Views of the Data. A Vision. In: Linked Science 2012 - Tackling Big Data, 2012.

E.L. Willighagen, J.E.S. Wikberg, Linking Open Drug Data to Cheminformatics and Proteochemometrics, CEUR Workshop Proceedings In SWAT4LS-2009 - Semantic Web Applications and Tools for Life Sciences, Vol. 559, 2010.

Zhang, Y., Murray-Rust, P., Dove, M., Glen, R.C., Rzepa, H.S., Townsend, J.A., Tyrell, S., Wakelin, J., Willighagen, E.L., 2004. Jumbo - an XML infrastructure for eScience. In: Proceedings of UK e-Science All Hands Meeting 2004. Vol. 1. pp. 930-933, 2004.

Murray-Rust, P., Glen, R.C., Rzepa, H.S., Stewart, J.J.P., Townsend, J.A., Willighagen, E.L., Yong, Z., A semantic grid for molecular science. In: Proceedings of the 2003 UK e-Science All Hands Meeting, 2003.

Book chapters

D.N. Slenter, M. Kutmon, E.L. Willighagen, WikiPathways: Integrating Pathway Knowledge with Clinical Data, in: N. Blau, C. Dionisi Vici, C.R. Ferreira, C. Vianey-Saban, C.D.M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, Springer International Publishing, UK, Ch. 73, 2022. doi:10.1007/978-3-030-67727-5_73

A.J. Williams, S. Ekins, O. Spjuth, E. Willighagen, Acessing, Using, and Creating Chemical Property Databases for Computational Toxicology Modeling, In: Computational Toxicology (Vol. 929), Springer Science+Business Media, Ch. 10, 2012.

E. Willighagen, R. Affentranger, R. Grafström, B. Hardy, N. Jeliazkova, O. Spjuth, Interactive Predictive Toxicology with Bioclipse and OpenTox, In: Open Source Software in Life Science Research: Practical Solutions to Common Challenges in the Pharmaceutical Industry and Beyond, Ed. L. Harland, M. Forster, Biohealthcare Publishing Ltd, Oxford, UK, Ch. 2, ISBN: 1-907-568972, 2012. doi:10.1533/9781908818249.35

B. Hardy, A. Affentranger, E. Benfenati, N. Jeliazkova, V. Jeliazkov, G. My- att, J. Wiseman, G. Stacey, R. Grafström, E. Willighagen, C. Helma, ToxBank: Supporting Integrated Data Analysis and Servicing of Alternative Testing Methods in Toxicology, In: Towards the Replacement of in vivo Repeated Dose Systemic Toxicity Testing, SEURAT-1, 2011.

R. Guha, O. Spjuth, E. Willighagen, Collaborative Cheminformatics Applications, In Collaborative Computational Technologies for Biomedical Research, Ed. S. Ekins, M.A.Z. Hupcey, and A.J. Williams, John Wiley & Sons, Inc., Hoboken, USA, ISBN: 9-780-470-63803-3, 2011. doi:10.1002/9781118026038.ch24

E. Willighagen, 3D Molecular Representations, In Handbook of Cheminformatics Algorithms, Ed. Faulon, J-P. and Bender, A., CRC Press, New York, US, Ch. 3. ISBN: 1-420-08292-2, 2010. doi:10.1201/9781420082999-c3

J-C. Bradley, R. Guha, A. Lang, P. Lindenbaum, C. Neylon, A. Williams, E. Willighagen, Beautifying Data in the Real World. In: Beautiful Data - The Stories Behind Elegant Data Solutions, O’Reilly Media, Inc., Sebastopol, US, Ch. 16, ISBN: 0-596-15711-8, 2009.

Editorials

Guha, R., Willighagen, E., Zdrazil, B., & Jeliazkova, N. (2021). What is the role of cheminformatics in a pandemic? Journal of Cheminformatics, 13(1). doi:10.1186/s13321-021-00491-6

Guha, R., Jeliazkova, N., Willighagen, E., & Zdrazil, B. (2021). Reply to “FAIR chemical structure in the Journal of Cheminformatics.” Journal of Cheminformatics, 13(1). doi:10.1186/s13321-021-00521-3

Guha, R., & Willighagen, E. (2020). Learning cheminformatics. Journal of Cheminformatics, 12(1). doi:10.1186/s13321-019-0406-z

Willighagen, E. (2020). Adoption of the Citation Typing Ontology by the Journal of Cheminformatics. Journal of Cheminformatics, 12(1). doi:10.1186/s13321-020-00448-1

Willighagen, E., Jeliazkova, N., & Guha, R. (2019). Journal of Cheminformatics, ORCID, and GitHub. Journal of Cheminformatics, 11(1). doi:10.1186/s13321-019-0365-4

Guha, R., & Willighagen, E. (2017). Helping to improve the practice of cheminformatics. Journal of Cheminformatics, 9(1). doi:10.1186/s13321-017-0217-z

Willighagen, E. L., & Brändle, M. P. (2011). Resource description framework technologies in chemistry. Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-15

Teaching experience

C-roles

2013-present Course coordinator, PRA3006: Programming in the Life Sciences. Maastricht University

2018-2020 Block coordinator, MBS1015: Scientific Programming. Maastricht University

2017-2018 Block coordinator, BMS1004: Biomedical Approaches. Development. Maastricht University

2012-2018 Track coordinator, BMW2007: Bioinformatics and Systems Biology. Maastricht University

B-roles

2016-2024 Course planning group, HZuyd Bioinformatics. Hoge School Zuyd.

2016-2022 Block planning group member, BBS1001: Building Blocks of Life. Maastricht University

2015-2016 Block planning group member, BMW1006: Experts Collaborate. Maastricht University

2007 Teacher, Homology Modelling. CUBIC, Cologne University

A-roles

2021-present Workshop assistant, BBS1001: Building Blocks of Life. Maastricht University

2020-present Lecturer, MBS1101: Advanced Principles of Genetics & Genomics. Maastricht University

2018-present Lecturer, MSB: Systems Biology. Maastricht University

2018-present Assessor, BBS3006: Thesis Bachelor Biomedical Sciences. Maastricht University

2020-2021 Lecturer, BBS3011: Global differences in diseases and treatment. Maastricht University

2016-present BBS-MEN: Mentor Bachelor Biomedical Sciences. Maastricht University

2015-2016 Mentor Year 1, Biomedical Sciences. Maastricht University

2014-2018 Tutor Problem-based Learning (PBL) Biomedical Sciences, BBS1001 and others. Maastricht University

Thesis promotorship and supervision

Ph.D. co-promotor

2017-2024 Denise Slenter, Maastricht University. 10.26481/dis.20240624ds

2017-2024 Marvin Martens, Maastricht University. 10.26481/dis.20240129mm

2019-2024 Andra Waagmeester, Maastricht University. 10.26481/dis.20240116aw

2018-2023 Ryan Miller, Maastricht University. 10.26481/dis.20221206rm

Ph.D. supervision

2024-present Sidra Adil, Maastricht University.

2022-present Jente Houweling, Maastricht University.

2022-present Javier Millán Acosta, Maastricht University.

2020-2025 Ammar Ammar, Maastricht University.

Awards and honors

2021 Runner Up Prize, Open Initiatives Trophies From the jury-report: “Egon is someone with high standards who really tries to hold himself accountable to these as well. He is not afraid to point his finger at the elephant in the room. We need people like Egon as a long time driving force for cultural change.”

2013 Royal Society of Chemistry eScience Hero Award For the contributions open source cheminformatics, in particular the Chemistry Development Kit, $2500. press release

2007 Blue Obelisk Award For achievements in promoting Open Data, Open Source, and Open Standards in cheminformatics.

Grants and funding

= grant, UM = Maastricht University

Research grants

2025-present FAIR4ChemNL: Accelerating the adoption of universal data standards in chemistry Dutch Research Council (NWO) / TDCC-NES. Sum: 400 k€, Person: ?? k€. Sole PI.

2025-present FAIRify your metabolomics data: achieving convergence on standards for reuse-ready data and workflows (FAIRify) Dutch Research Council (NWO) / TDCC-LSH. Sum: ? k€, Person: ?? k€. Sole PI.

2024-present INTOXICOM Implementation Study. ELIXIR Europe. Sum: 59 k€, Person: ?? k€. Co-PI with Marvin Martens

2023-present TGX-MAP: Transcriptomics in Risk Assessment. EFSA. Sum: ?? k€, UM: 276 k€. Co-PI with Tooba Abbassi-Daloii and Marvin Martens.

2022-present The Virtual Human Platform for Safety Assessment (VHP4Safety). Dutch Research Council (NWO), NWA 1292.19.272. Sum: 10.4 M€, UM: 1.38 M€. Co-PI with Chris Evelo.

2024-2025 Chemistry Development Kit 2024. Dutch Research Council (NWO). Sum: 50 k€, Person: 25 k€. Sole PI. doi:10.3897/rio.10.e124884

2022-2023 Lipid Pathway Curation. ELIXIR Europe. Sum: ?? k€, UM: 5.7 k€. Co-PI with Denise Slenter.

2022-2023 BridgeDb and Wikidata: a powerful combination generating interoperable open research, Dutch Research Council (NWO), 203.001.121. Sum: 50 k€, UM: 50 k€. Sole PI. doi:10.3897/rio.8.e83031

2020-2024 Computing infrastructure for the definition, performance testing and implementation of safe-by-design approaches in nanotechnology supply chains (SbD4nano), European Commission H2020. 862195. Sum: 5.98 M€, UM: 343 k€. Sole PI.

2019-2021 Scholia, Alfred P. Sloan Foundation. G-2019-11458. Sum: 496 k€, UM: 75 k€. Sole PI. doi:[10.3897/rio.5.e35820]https://doi.org/10.3897/rio.5.e35820)

2019-2023 Risk Governance of Nanotechnology (RiskGONE), European Commission H2020. 814425. Sum: 5.00 M€, UM: 221 k€. Sole PI.

2019-2023 Innovative Nanoinformatics models and tools: towards a Solid, verified and Integrated Approach to Predictive (eco)Toxicology (NanoSolveIT), European Commission H2020. 814572. Sum: 7.49 M€, UM: 407 k€. Sole PI.

2018-2022 The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons), European Commission H2020. 731032. Sum: 5.59 M€, UM: 291 k€. Sole PI.

2014-2017 eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment, European Commission FP7. 604134. Sum: 4.98 M€, UM: 843 k€. Sole PI.

Talks

Keynotes

2022 OpenTox Virtual Conference 2022. Online.

2015 International Conference on Biomedical Ontology. Lisbon, Portugal

Invited talks

2023 University of Groningen. Open Science Community Groningen Summer Event. Groningen, The Netherlands

OECD. OECD “FAIR research output for nanosafety” meeting. Paris, France

2019 Beilstein Open Science 2019. Rüdesheim, Germany

2017 AgreenSkills+ Annual Meeting. Paris, France

2015 System Biology in Nanosafety Research. Stockholm, Sweden

2014 Royal Society of Chemistry. What’s in a Name?. London, UK

2009 GDCh-Wissenschafts-forum Chemie 2009. Frankfurt, Germany

2007 GDCh-Wissenschaftsforum Chemie 2007. Ulm, Germany

Memberships

1993-???,???-present KNCV

2023-2024 American Chemical Society

Professional service

Scientific committees

2024-present Titular Member, International Union of Pure and Applied Chemistry, CPCDS

2023-present Advisor Board Member, The Netherlands Reproducibility Network

2022-present Advisory Board Member, NFDI4Chem

2022-present Founder of the Open Science Community Maastricht

2014-present Board Member, Stichting Chemische Congressen 6

2020-2022 Scientific Advisor, International Advisory Board of the NanoFabNet Project

2018-2024 Working Group Chair, Database Working Group, EU NanoSafety Cluster

2013-2026 Working Group Chair, Database Working Group, EU NanoSafety Cluster

Editorial Boards

2025-present Guest-editor, Journal of Cheminformatics (Springer Nature. Top10 journal)

2016-2021 Editor-in-Chief, Journal of Cheminformatics (Springer Nature. Top10 journal)

2010 Guest-editor, Journal of Cheminformatics (Springer Nature. Top10 journal)

2009-2016 Invited Expert, World Wide Web Consortium (W3C)

2009-2011 CINF Programming Committee Member, American Chemical Society

2007-2011 Advisor, ChemSpider.com Advisory Group

Media

Opinions

2020 Caspar van Lissa c.s. Overheid wees transparant in strijd tegen het coronavirus. NRC (2020) https://www.nrc.nl/nieuws/2020/04/27/overheid-wees-transparant-in-strijd-tegen-het-coronavirus-a3997982

2019 Egon Willighagen. Universiteiten mogen hun rol in de samenleving niet uitbesteden. ScienceGuide (2019) https://www.scienceguide.nl/2019/11/universiteiten-mogen-hun-rol-in-de-samenleving-niet-uitbesteden/

Interviews

2019 Laura Howes. Chemistry data should be FAIR, proponents say. But getting there will be a long road, C&EN (2019) https://cen.acs.org/policy/publishing/Chemistry-data-should-FAIR-proponents/97/i35

Sicco de Knecht. So what about editor compensation?, ScienceGuide (2019) https://www.scienceguide.nl/2019/04/so-what-about-editor-compensation/

2018 “Als je geen open access wilt, zeg dat dan gewoon hardop!” ScienceGuide (2018) https://www.scienceguide.nl/2018/12/als-je-geen-open-access-wilt-zeg-dat-dan-gewoon-hardop/

Arjen Dijkgraag. Open accessstress. C2W (2018), https://www.sciencelink.net/nieuws-and-verdieping/open-accessstress/8374.article

2017 Puck Moll. Focus op software, C2W (2017), https://www.sciencelink.net/nieuws-and-verdieping/focus-op-software/5919.article

News

2021 Maurice Timmermans, Twee UM’ers ontvangen NWO-beurzen voor open science, Observant (2021) https://www.observantonline.nl/Home/Artikelen/id/57779/twee-um-ers-ontvangen-nwo-beurzen-voor%C2%A0open-science

2020 Cleo Freriks, UM researchers: corona is given high priority, Observant (2020) https://www.observantonline.nl/english/Home/Articles/id/43066

2019 Andrea Widener. Societies and scientists react to open access Plan S, C&EN (2019) https://cen.acs.org/policy/publishing/Societies-scientists-react-open-access/97/web/2019/02

Sicco de Knecht. Germans to close “transformative” deal with SpringerNature, ScienceGuide (2019) https://www.scienceguide.nl/2019/08/germans-to-close-transformative-deal-with-springernature/

2018 Puck Moll. Nieuwe generatie, C2W (2017), https://www.sciencelink.net/nieuws-and-verdieping/nieuwe-generatie/6551.article

2014 Wendy Degens, Cleo Freriks, Maurice Timmermans, “I see bright researchers leaving the university”, Observant (2014) https://www.observantonline.nl/english/Home-old/Articles/articleType/ArticleView/articleId/2111/I-see-bright-researchers-leaving-the-university

International Newsletters

2022 ELIXIR launches new Toxicology Community, ELIXIR Europe News (2022) https://elixir-europe.org/news/new-toxicology-community

2021 Niets afschaffen, wel verbreden, NWO Magazine (2021) https://www.nwo.nl/niets-afschaffen-wel-verbreden

Languages

Native: Dutch

Advanced: English

Basic: German

Last updated: May 2025