Publications

1. Torres Ortega, L.R., Dietrich, J., Wandy, J., Mol, H., and van der Hooft, J.J.J. (2026). Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles. Nat. Commun. 17. DOI: 10.1038/s41467-026-75038-0.

2. Szenei, J., Burke, A., Liong, A., Korenskaia, A., Lukowski, A.L., Ziemert, N., Nikel, P.I., Leão, P.N., Moore, B.S., Weber, T., and Blin, K. (2026). Computational Pipeline Reveals Nature’s Untapped Reservoir of Halogenating Enzymes. ACS Omega. DOI: 10.1021/acsomega.6c02136.

3. Pecin, G., Gonzalez-Menendez, V., Martin, J., Annang, F., Mackenzie, T.A., Reyes, F., and Genilloud, O. (2026). Discovery of spectabilide A, a new cytotoxic cyclic lipodepsipeptide from Trichothecium spectabile comb. nov. (Ascomycota, Sordariomycetes) revealed by OSMAC-guided metabolomics. IMA Fungus 17, e192814. DOI: 10.3897/imafungus.17.192814.

4. Korenskaia, A., Adamek, M., Szenei, J., Vader, L., Blin, K., Weber, T., and Ziemert, N. (2026). PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes. Bioinformatics. DOI: 10.1093/bioinformatics/btag393.

5. Contreras-Aviles, W., Torres-Ortega, L.R., Heuvelink, E., Marcelis, L.F.M., van der Hooft, J.J.J., and Kappers, I.F. (2026). Characterizing the effect of short wavelengths on the floral flavonoid metabolome of medicinal cannabis using a comparative computational metabolomics workflow. Metabolomics 22. DOI: 10.1007/s11306-026-02500-x.

6. Zdouc, M.M., Blin, K., Louwen, N.L.L., Navarro, J., Loureiro, C., Bader, C.D., Bailey, C.B., Barra, L., Booth, T.J., Bozhuyuk, K.A.J., et al. (2025). MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Res. 53, D678–D690. DOI: 10.1093/nar/gkae1115.

7. Rutz, A., Probst, D., Aguilar, C., Akiyama, D.Y., Alberti, F., Augustijn, H.E., Avalon, N.E., Beemelmanns, C., Barbieri, H.B., Biermann, F., et al. (2025). MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis. Nucleic Acids Res. 54, D635–D642. DOI: 10.1093/nar/gkaf969.

8. Mildau, K., Ehlers, H., Meisenburg, M., Del Pup, E., Koetsier, R.A., Torres Ortega, L.R., de Jonge, N.F., Singh, K.S., Ferreira, D., Othibeng, K., et al. (2025). Effective data visualization strategies in untargeted metabolomics. Nat. Prod. Rep. 42, 982–1019. DOI: 10.1039/d4np00039k.

9. Blin, K., Szenei, J., and Vader, L. (2025). Using antiSMASH. Methods Enzymol. 717, 1–28. DOI: 10.1016/bs.mie.2025.04.006.

10. Blin, K., Shaw, S., Vader, L., Szenei, J., Reitz, Z.L., Augustijn, H.E., Cediel-Becerra, J.D.D., de Crecy-Lagard, V., Koetsier, R.A., Williams, S.E., et al. (2025). antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation. Nucleic Acids Res. 53, W32–W38. DOI: 10.1093/nar/gkaf334.

1. Vader, L., Harvey, C.J.B., Weber, T., and Hon, L.S. (2026). geneML: Gene annotation across diverse fungal species using deep learning. BioRxiv. DOI: 10.64898/2026.05.18.725946.

2. Torres-Ortega, L.R., Charria-Girón, E., Huber, F., Simone, M., Sosio, M., and van der Hooft, J.J.J. (2026). Beyond the Default: Optimizing Molecular Networking with arteMIS. BioRxiv. DOI: 10.64898/2026.08.17.745252.

3. Szenei, J., Burke, A., Liong, A., Korenskaia, A., Lukowski, A.L., Ziemert, N., Nikel, P.I., Leão, P.N., Moore, B.S., Weber, T., and Blin, K. (2026). Computational pipeline reveals nature’s untapped reservoir of halogenating enzymes. BioRxiv. DOI: 10.64898/2026.01.20.700248.

4. Contreras-Avilés, W., Torres-Ortega, L.R., Heuvelink, E., Marcelis, L.F.M., van der Hooft, J.J.J., and Kappers, I.F. (2026). Characterizing the effect of short wavelengths on the floral flavonoid metabolome of medicinal cannabis using a comparative computational metabolomics workflow. BioRxiv. DOI: 10.64898/2026.04.28.721290.

5. Charria-Girón, E., van Ijcken, J., Della Vedova, L., Torres-Ortega, L.R., and van der Hooft, J.J.J. (2026). Quantifying per-match Reliability in Library Matching for Untargeted Metabolomics Workflows. BioRxiv. DOI: 10.64898/2026.07.30.741704.

6. Charria-Girón, E., Torres-Ortega, L.R., Greef, J.M., Felix, Y.M., Caicedo, N.H., Surup, F., Medema, M.H., and van der Hooft, J.J.J. (2026). Hidden molecular relationships are revealed by bootstrap resampling of mass spectral pairs with SpecReBoot. BioRxiv. DOI: 10.64898/2026.02.03.703446.

7. Charria-Girón, E., Torres-Ortega, L.R., Greef, J.M., Felix, Y.M., Caicedo, N.H., Surup, F., Medema, M.H., and van der Hooft, J.J.J. (2026). Bootstrap resampling of mass spectral pairs with SpecReBoot reveals hidden molecular relationships. BioRxiv. DOI: 10.64898/2026.02.03.703446.

8. Torres Ortega, L.R., Dietrich, J., Wandy, J., Mol, H., and van der Hooft, J.J.J. (2025). Large-scale discovery and annotation of hidden substructure patterns in mass spectrometry profiles. BioRxiv. DOI: 10.1101/2025.06.19.659491.

9. Korenskaia, A., Szenei, J., Vader, L., Blin, K., Weber, T., and Ziemert, N. (2025). PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes. BioRxiv. DOI: 10.1101/2025.09.23.677986.

10. Zdouc, M.M., Meijer, D., Biermann, F., Holme, J., Korenskaia, A., Lien, A., Louwen, N.L.L., Navarro-Muñoz, J.C., Nguyen, G.-S., Rutz, A., et al. (2024). The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis. ChemRxiv, DOI: 10.26434/chemrxiv–22024–26478mtl. DOI: 10.26434/chemrxiv-2024-78mtl.