Publications

Müller, A., Meng, J., Kuijpers, R., Mäkelä, M. R., & de Vries, R. P. (2025). Exploring the complexity of xylitol production in the fungal cell factory Aspergillus niger. Enzyme and Microbial Technology, 183, Article 110550. https://doi.org/10.1016/j.enzmictec.2024.110550

Müller, A., Mӓkelӓ, M. R., & de Vries, R. P. (2025). Aldo-keto reductases, short chain dehydrogenases/reductases, and zinc-binding dehydrogenases are key players in fungal carbon metabolism. Advances in Applied Microbiology. Advance online publication. https://doi.org/10.1016/bs.aambs.2024.11.004

Tonn, S. (2024). Advanced plant disease phenotyping methods to track and quantify lettuce downy mildew. [Doctoral thesis 1 (Research UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/2563

Müller, A. (2024). Gene redundancy and metabolic flexibility in Aspergillus niger: Tools to enhance industrial biotechnology. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/2617

Rogowska-Van Der Molen, M. A., Savova, H. V., Janssen, E. A. T., Van Alen, T., Coolen, S., Jansen, R. S., & Welte, C. U. (2024). Unveiling detoxifying symbiosis and dietary influence on the Southern green shield bug microbiota. FEMS Microbiology Ecology, 100(12), Article fiae150. https://doi.org/10.1093/femsec/fiae150

de Wit, J., Tonn, S., Shao, M. R., Van den Ackerveken, G., & Kalkman, J. (2024). Revealing real-time 3D in vivo pathogen dynamics in plants by label-free optical coherence tomography. Nature Communications, 15(1), Article 8353. https://doi.org/10.1038/s41467-024-52594-x

Lubbers, R. J. M., Martínez-Reyes, N., Rhanama, N., Nair, R., Prieto, I., Ihalainen, P., Heikkilä, M., & de Vries, R. P. (2024). Vanillin dehydrogenase (VhdA) from Aspergillus niger is active on depolymerized lignin. Sustainable Chemistry for the Environment, 8, Article 100179. https://doi.org/10.1016/j.scenv.2024.100179

Xu, L. (2024). Diversity of fungal sugar transporters (STs) revealed through integrative omics approaches. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/2574

Pócsi, I., Dijksterhuis, J., Houbraken, J., & de Vries, R. P. (2024). Biotechnological potential of salt tolerant and xerophilic species of Aspergillus. Applied Microbiology and Biotechnology, 108(1), Article 521. https://doi.org/10.1007/s00253-024-13338-5

van Workum, D. J. M., Mehrem, S. L., Snoek, B. L., Alderkamp, M. C., Lapin, D., Mulder, F. F. M., Van den Ackerveken, G., de Ridder, D., Schranz, M. E., & Smit, S. (2024). Lactuca super-pangenome reduces bias towards reference genes in lettuce research. BMC Plant Biology, 24(1), Article 1019. https://doi.org/10.1186/s12870-024-05712-2

Skiadas, P., Vidal, S. R., Dommisse, J., Mendel, M. N., Elberse, J., Van den Ackerveken, G., de Jonge, R., & Seidl, M. F. (2024). Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew. PLoS Genetics, 20(10 October), Article e1011452. https://doi.org/10.1371/journal.pgen.1011452

Liu, D., Garrigues, S., Culleton, H., McKie, V. A., & de Vries, R. P. (2024). Analysis of the molecular basis for the non-amylolytic and non-proteolytic nature of Aspergillus vadensis CBS 113365. New Biotechnology, 82, 25-32. https://doi.org/10.1016/j.nbt.2024.04.003

Liu, D. (2024). Exploring the potential of Aspergillus vadensis and Penicillium subrubescens as enzyme cell factories. Utrecht University. https://doi.org/10.33540/2521

Steindorff, A. S., Aguilar-Pontes, M. V., Robinson, A. J., Andreopoulos, B., LaButti, K., Kuo, A., Mondo, S., Riley, R., Otillar, R., Haridas, S., Lipzen, A., Grimwood, J., Schmutz, J., Clum, A., Reid, I. D., Moisan, M.-C., Butler, G., Nguyen, T. T. M., Dewar, K., ... Grigoriev, I. V. (2024). Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses. Communications Biology, 7(1), Article 1124. https://doi.org/10.1038/s42003-024-06681-w

Shokrian Hajibehzad, S. (2024). From compact greens to ascending stems: elucidating the role of ATH1 in regulating internode growth dynamics in Arabidopsis thaliana. Utrecht University. https://doi.org/10.33540/2418

Goossens, P., Baremans, K., Alderkamp, M., Boshoven, J. C., Van den Ackerveken, G., & Berendsen, R. (2024). Selective enrichment of specific bacterial taxa in downy mildew-affected spinach: Comparative analysis in laboratory and field conditions. bioRxiv. https://doi.org/10.1101/2024.08.23.609345

Liu, D., Xu, L., Peng, M., Lipzen, A., Ng, V., Savage, E., Zhang, Y., Grigoriev, I. V., Garrigues, S., & de Vries, R. P. (2024). AraR plays a more dominant role than XlnR in plant biomass conversion in Penicillium subrubescens. Current Research in Biotechnology, 8, Article 100243. https://doi.org/10.1016/j.crbiot.2024.100243

Theobald, S., Vesth, T. C., Geib, E., Nybo, J. L., Frisvad, J. C., Larsen, T. O., Kuo, A., LaButti, K., Lyhne, E. K., Kjærbølling, I., Ledsgaard, L., Barry, K., Clum, A., Chen, C., Nolan, M., Sandor, L., Lipzen, A., Mondo, S., Pangilinan, J., ... Andersen, M. R. (2024). Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. Journal of Fungi, 10(7), Article 507. https://doi.org/10.3390/jof10070507

Baroncelli, R., Cobo-Díaz, J. F., Benocci, T., Peng, M., Battaglia, E., Haridas, S., Andreopoulos, W., LaButti, K., Pangilinan, J., Lipzen, A., Koriabine, M., Bauer, D., Le Floch, G., Mäkelä, M. R., Drula, E., Henrissat, B., Grigoriev, I. V., Crouch, J. A., de Vries, R. P., ... Thon, M. R. (2024). Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. GigaScience, 13, Article giae036. https://doi.org/10.1093/gigascience/giae036

Coolen, S., Molen, M. A. R. D., Kwakernaak, I., van Pelt, J. A., Postma, J. L., van Alen, T., Jansen, R. S., & Welte, C. U. (2024). Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression. ISME Journal, 18(1), Article wrae097. https://doi.org/10.1093/ismejo/wrae097

Mendel, M., Zuijdgeest, X. C. L., van den Berg, F., van der Meer, L., Elberse, J., Skiadas, P., Seidl, M. F., den Ackerveken, G. V., & de Jonge, R. (2024). Exploiting Pseudomonas syringae Type 3 secretion to study effector contribution to disease in spinach. bioRxiv. https://doi.org/10.1101/2024.06.14.599008

van Butselaar, T., Silva, S., Lapin, D., Bañales Belaunde, I., Tonn, S., van Schie, C., & Van den Ackerveken, G. (2024). The Role of Salicylic Acid in the Expression of RECEPTOR-LIKE PROTEIN 23 and Other Immunity-Related Genes. Phytopathology, 114(5), 1097-1105. https://doi.org/10.1094/PHYTO-10-23-0413-KC

Duran, K., Kohlstedt, M., van Erven, G., Klostermann, C. E., America, A. H. P., Bakx, E., Baars, J. J. P., Gorissen, A., de Visser, R., de Vries, R. P., Wittmann, C., Comans, R. N. J., Kuyper, T. W., & Kabel, M. A. (2024). From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source. Science advances, 10(16), Article eadl3419. https://doi.org/10.1126/sciadv.adl3419

Bodnár, V., Antal, K., de Vries, R. P., Pócsi, I., & Emri, T. (2024). Aspergillus nidulans gfdB, Encoding the Hyperosmotic Stress Protein Glycerol-3-phosphate Dehydrogenase, Disrupts Osmoadaptation in Aspergillus wentii. Journal of Fungi, 10(4), Article 291. https://doi.org/10.3390/jof10040291

Peng, M., Mueller, A., Kowalczyk, J. E., Kun, R. S., & de Vries, R. P. (2024). Discovery of novel plant biomass conversion associated fungal transcription factors using a network-based approach. Current Research in Biotechnology, 8, Article 100230. https://doi.org/10.1016/j.crbiot.2024.100230

Xu, L., Li, J., Gonzalez Ramos, V. M., Lyra, C., Wiebenga, A., Grigoriev, I. V., de Vries, R. P., Mäkelä, M. R., & Peng, M. (2024). Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi. Bioresource Technology, 391(Pt B), Article 130006. https://doi.org/10.1016/j.biortech.2023.130006

Lambou, K., Tag, A., Lassagne, A., Collemare, J., Clergeot, P. H., Barbisan, C., Perret, P., Tharreau, D., Millazo, J., Chartier, E., De Vries, R. P., Hirsch, J., Morel, J. B., Beffa, R., Kroj, T., Thomas, T., & Lebrun, M. H. (2024). The bZIP transcription factor BIP1 of the rice blast fungus is essential for infection and regulates a specific set of appressorium genes. PLoS Pathogens, 20(1), Article e1011945. https://doi.org/10.1371/journal.ppat.1011945

Gonzalez Ramos, V. M., Mueller, A., Peng, M., Pawlowski, M., Lipzen, A., Ng, V., Singan, V., Wang, M., de Vries, R. P., Grigoriev, I. V., Kowalczyk, J. E., & Mäkelä, M. R. (2024). Transcriptional response of the white-rot fungus Dichomitus squalens to polysaccharides reveals a co-expression network of plant biomass conversion related genes. Current Research in Biotechnology, 7, Article 100198. https://doi.org/10.1016/j.crbiot.2024.100198

Bouzid, O., Allouache, A., de Vries, R. P., Zitouni, D., Benoit-Gelber, I., Houbraken, J., & Aziza, M. A. (2024). High potential low-cost crude enzymes from Algerian fungal strains for plant polysaccharides hydrolysis. Biofuels, 15(7), 767-772. https://doi.org/10.1080/17597269.2023.2295661

Ogden, S. C., Nishimura, M. T., & Lapin, D. (2023). Functional diversity of Toll/interleukin-1 receptor domains in flowering plants and its translational potential. Current Opinion in Plant Biology, 76, Article 102481. https://doi.org/10.1016/j.pbi.2023.102481

Goossens, P., Spooren, J., Baremans, K. C. M., Andel, A., Lapin, D., Echobardo, N., Pieterse, C. M. J., Van den Ackerveken, G., & Berendsen, R. L. (2023). Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana. Nature Microbiology, 8(12), 2349-2364. https://doi.org/10.1038/s41564-023-01502-y

Li, J. (2023). Fungi use highly diverse approaches for plant biomass conversion as revealed through bioinformatic analysis. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/1940

Garrigues, S., Peng, M., Kun, R. S., & de Vries, R. P. (2023). Non-homologous end-joining-deficient filamentous fungal strains mitigate the impact of off-target mutations during the application of CRISPR/Cas9. mBio, 14(4), 1-15. Article e0066823. https://doi.org/10.1128/mbio.00668-23

Li, J., Wiebenga, A., Lipzen, A., Ng, V., Tejomurthula, S., Zhang, Y., Grigoriev, I. V., Peng, M., & de Vries, R. P. (2023). Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. Journal of fungi (Basel, Switzerland), 9(8), 1-15. Article 860. https://doi.org/10.3390/jof9080860

Salazar-Cerezo, S., de Vries, R. P., & Garrigues, S. (2023). Strategies for the Development of Industrial Fungal Producing Strains. Journal of fungi (Basel, Switzerland), 9(8), 1-33. Article 834. https://doi.org/10.3390/jof9080834

Shokrian Hajibehzad, S., Silva, S. S., Peeters, N., Stouten, E., Buijs, G., Smeekens, S., & Proveniers, M. (2023). Arabidopsis thaliana rosette habit is controlled by combined light and energy signaling converging on transcriptional control of the TALE homeobox gene ATH1. New Phytologist, 239(3), 1051-1067. https://doi.org/10.1111/nph.19014

Griebel, T., Lapin, D., Locci, F., Kracher, B., Bautor, J., Concia, L., Benhamed, M., & Parker, J. E. (2023). Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity. New Phytologist, 239(4), 1404-1419. https://doi.org/10.1111/nph.19054

Liu, D., Garrigues, S., & de Vries, R. P. (2023). Heterologous protein production in filamentous fungi. Applied Microbiology and Biotechnology, 107(16), 5019-5033. https://doi.org/10.1007/s00253-023-12660-8

Duran, K., Magnin, J., America, A. H. P., Peng, M., Hilgers, R., de Vries, R. P., Baars, J. J. P., van Berkel, W. J. H., Kuyper, T. W., & Kabel, M. A. (2023). The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation. iScience, 26(7), 1-22. Article 107087. https://doi.org/10.1016/j.isci.2023.107087

Butselaar, T. V., Silva, S., Lapin, D., Banales, I., Tonn, S., Schie, C. V., & Ackerveken, G. V. D. (2023). Basal expression of immune receptor genes requires low levels of the phytohormone salicylic acid. bioRxiv. https://doi.org/10.1101/2023.07.14.548351

Lapin, D. (2023). Plant immune receptors can sequester and protect host proteins from pathogen-promoted degradation. Molecular Plant, 16(6), 966-967. https://doi.org/10.1016/j.molp.2023.05.001

Peng, M., Bervoets, S., Chin-A-Woeng, T., Granchi, Z., Hildén, K., Mäkelä, M. R., & de Vries, R. P. (2023). The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiological Research, 270, 1-8. Article 127333. https://doi.org/10.1016/j.micres.2023.127333

Kun, R. S., Salazar-Cerezo, S., Peng, M., Zhang, Y., Savage, E., Lipzen, A., Ng, V., Grigoriev, I. V., de Vries, R. P., & Garrigues, S. (2023). The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. Journal of fungi (Basel, Switzerland), 9(4), 1-14. Article 438. https://doi.org/10.3390/jof9040438

van Butselaar, T. (2023). The Salicylic Acid-Mediated Growth-Immunity Tradeoff in Arabidopsis. [Doctoral thesis 1 (Research UU / Graduation UU), Universiteit Utrecht]. Universiteit Utrecht. https://doi.org/10.33540/1694

Goossens, P., Spooren, J., Baremans, K. C. M., Andel, A., Lapin, D., Echobardo, N., Pieterse, C. M. J., Ackerveken, G. V. D., & Berendsen, R. L. (2023). Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes. bioRxiv. https://doi.org/10.1101/2023.03.14.532520

Reddy, S. K., & de Vries, R. (2023). Mycoproteins and yeast proteins in food industry. In Our Future Proteins (pp. 179-187). VU University Press.

Kun, R. S., Garrigues, S., Peng, M., Keymanesh, K., Lipzen, A., Ng, V., Tejomurthula, S., Grigoriev, I. V., & de Vries, R. P. (2023). The transcriptional activator ClrB is crucial for the degradation of soybean hulls and guar gum in Aspergillus niger. Fungal Genetics and Biology, 165, 1-11. Article 103781. https://doi.org/10.1016/j.fgb.2023.103781

Meng, J., Mäkelä, M. R., & de Vries, R. P. (2023). Identification of an l-Arabitol Transporter from Aspergillus niger. Biomolecules, 13(2), 1-11. Article 188. https://doi.org/10.3390/biom13020188

Johanndrees, O., Baggs, E. L., Uhlmann, C., Locci, F., Läßle, H. L., Melkonian, K., Käufer, K., Dongus, J. A., Nakagami, H., Krasileva, K. V., Parker, J. E., & Lapin, D. (2023). Variation in plant Toll/Interleukin-1 receptor domain protein dependence on ENHANCED DISEASE SUSCEPTIBILITY 1. Plant Physiology, 191(1), 626-642. https://doi.org/10.1093/plphys/kiac480

Li, J., Chroumpi, T., Garrigues, S., Kun, R. S., Meng, J., Salazar-Cerezo, S., Aguilar-Pontes, M. V., Zhang, Y., Tejomurthula, S., Lipzen, A., Ng, V., Clendinen, C. S., Tolić, N., Grigoriev, I. V., Tsang, A., Mäkelä, M. R., Snel, B., Peng, M., & de Vries, R. P. (2022). The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum. Journal of fungi (Basel, Switzerland), 8(12), Article 1315. https://doi.org/10.3390/jof8121315