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Gardiner, J. (2025). Engineering chromatin and transcriptome regulation in plants: Strategies, challenges, and outlook. Current Opinion in Plant Biology, 88, Article 102810.

Oki, K., Enoki, A., Yokota, Y., Kurihara, T., Shimizu, T., Saburi, W., Tohge, T., Mori, H., Van den Ackerveken, G., Kitaoka, N., & Matsuura, H. (2025). AtGH3.10 and JAR1 Produce 12-Hydroxyjasmonoyl-l-isoleucine from 12-Hydroxyjasmonic Acid in Arabidopsis thaliana. ChemBioChem, 26(19), Article e202500151.

de Vries, R. P., Wiebenga, A., Aguilar Osorio, G., Aguilar Pontes, M. V., Battaglia, E., Benocci, T., Benoit Gelber, I., Bouzid, O., Casado Lopez, S., Coconi Linares, N., Debets, A. J. M., de Jong, J. F. J., Drula, E., Falkoski, D., Grijpstra, J., Gruben, B. S., Klaubauf, S., Khosravi, C., Kowalczyk, J. E., ... Robert, V. (2025). The FUNG-GROWTH database: linking fungal phenotype to genome. Microbiology Resource Announcements, 14(9), Article e0037825.

Anton-Sales, C., van den Bergh, E. S., Thérèse-Navarro, A., Severing, E., Moñino-López, D., DiPalma, J., Proveniers, M., McClung, C. R., Jeuken, M., & Bonnema, G. (2025). Breeding for delayed bolting decelerated the circadian clock in cultivated lettuce. The New phytologist, (4). Advance online publication.

Dijkhuizen, R., van Eijnatten, A. L., Mehrem, S. L., van den Bergh, E., van Lieshout, J., Spaninks, K., Kaandorp, S., Offringa, R., Proveniers, M., van den Ackerveken, G., & Snoek, B. L. (2025). From aerial drone to quantitative trait locus: leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa. Plant Journal, 123(3), Article e70405.

Aguirre, M., Loperfido, D., & Ezquer, I. (2025). Decoding hybridization barriers: the molecular and genetic orchestration of the triploid block in Arabidopsis thaliana. BMC Plant Biology, 25(1), Article 913.

Doval, R. L., Müller, A., Brown, D. W., Johnson, D., Quandt, C. A., Barry, K., Clum, A., Hundley, H., LaButti, K., Lipzen, A., Mondo, S. J., Ohm, R. A., Pangilinan, J. L., Riley, R. W., Steindorff, A. S., Wang, M., Drula, E., Henrissat, B., Bushley, K., ... de Vries, R. P. (2025). A Comparison of the Biotechnological Potential of Marine and Terrestrial Species of Two Orders of Sordariomycete Fungi. Marine Biotechnology, 27(4), Article 103.

Escobar-Bravo, R., Schimmel, B. C. J., & Erb, M. (2025). Volatiles from Low R: FR-Treated Maize Plants Increase the Emission of Herbivore-Induced Plant Volatiles in their Neighbors. Journal of Chemical Ecology, 51(4), Article 69.

Almeida, L. F., Machado, S. G., Rodrigues, R. C., do Carmo Gouveia Peluzio, M., de Oliveira Mendes, T. A., Guimarães, V. M., de Vries, R., & Maitan-Alfenas, G. P. (2025). Biotechnology approach for conversion of agro-industrial wastes into emerging source of xylooligosaccharides. Biomass Conversion and Biorefinery , 15(12), 19391-19404.

Beijen, E. P. W., van Maanen, M. H., van den Bergh, E. S., Brouns, R., Marian, I. M., de Vries, T. J., Vonk, P. J., & Ohm, R. A. (2025). Transcription factors Fst8, Ftr3 and Gat1 are regulators of the immune system of the mushroom Schizophyllum commune. Fungal Genetics and Biology, 179, Article 103987.

Mendel, M., Zuijdgeest, X. C. L., van den Berg, F., van der Meer, L., Elberse, J., Skiadas, P., Seidl, M. F., Van den Ackerveken, G., & de Jonge, R. (2025). Exploiting Pseudomonas syringae Type 3 Secretion to Study Effector Contribution to Disease in Spinach. Molecular Plant-Microbe Interactions. Advance online publication.

do Carmo, M. R. A., Manassero, A., Ventorim, R. Z., Peng, M., Morgan, T., LaButti, K., Lipzen, A., Ahrendt, S., Grigoriev, I. V., Ng, V., Koriabine, M., Bauer, D., Drula, E., Henrissat, B., Alfenas, R. F., de Vries, R. P., & Maitan-Alfenas, G. P. (2025). Whole genome sequence, CAZyme repertoire and sugar metabolic model of the phytopathogenic fungus Kretzschmaria zonata GFP 132. Molecular Genetics and Genomics, 300(1), Article 47.

Bellinazzo, F., Manders, I., Heidemann, B., Bolanos, M. A., Stouten, E., Busscher, J., Abarca, D., van der Wal, F., Dornelas, M. C., Angenent, G. C., Proveniers, M., Nijveen, H., & Immink, R. G. H. (2025). Differential growth and flowering capacity of tulip bulbs and the potential involvement of PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBPs). Biology Direct, 20(1), Article 29.

Rogowska-van der Molen, M. A., Manzano-Marin, A., Postma, J. L., Coolen, S., van Alen, T., Jansen, R. S., & Welte, C. U. (2025). From eggs to guts: Symbiotic association of Sodalis nezarae sp. nov. with the Southern green shield bug Nezara viridula. FEMS Microbiology Ecology, 101(3), Article fiaf017.

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.

Chroumpi, T., Müller, A., Peng, M., Cubertorer Navarro, M., Kuijpers, R., Terebieniec, A., Li, J., Markillie, L. M., Mitchell, H. D., Nicora, C. D., Hutchinson, C. M., Paurus, V., Purvine, S. O., Clendinen, C. S., Orr, G., Baker, S. E., Mäkelä, M. R., & de Vries, R. P. (2025). Metabolic engineering reveals the relative importance of different sugar catabolic pathways during consumption of plant biomass by Aspergillus niger. Current Research in Microbial Sciences, 9, Article 100454.

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, 130, 123-157.

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 ľ¹Ï¸£ÀûÓ°ÊÓ.

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 ľ¹Ï¸£ÀûÓ°ÊÓ.

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.

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.

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.

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 ľ¹Ï¸£ÀûÓ°ÊÓ.

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.

Dijkhuizen, R. F., van Eijnatten, A. L., Mehrem, S. L., van den Bergh, E. S., van Lieshout, J., Spaninks, K., Kaandorp, S., Offringa, R., Proveniers, M., van den Ackerveken, G., & Snoek, B. L. (2024). From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa. bioRxiv.

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.

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.

Rogowska-van der Molen, M. A., Manzano-Marín, A., Postma, J. L., Coolen, S., van Alen, T., Jansen, R. S., & Welte, C. U. (2024). From Eggs to Guts: Symbiotic Association of Sodalis nezarae sp. nov. with the Southern Green Shield Bug Nezara viridula. bioRxiv.

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.

Liu, D. (2024). Exploring the potential of Aspergillus vadensis and Penicillium subrubescens as enzyme cell factories. Utrecht ľ¹Ï¸£ÀûÓ°ÊÓ.

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.

Shokrian Hajibehzad, S. (2024). From compact greens to ascending stems: elucidating the role of ATH1 in regulating internode growth dynamics in Arabidopsis thaliana. Utrecht ľ¹Ï¸£ÀûÓ°ÊÓ.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Mueller, A., Xu, L., Heine, C., Flach, T., Mäkelä, M. R., & de Vries, R. P. (2023). Genome Mining Reveals a Surprising Number of Sugar Reductases in Aspergillus niger. Journal of Fungi, 9(12), Article 1138.

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 ľ¹Ï¸£ÀûÓ°ÊÓ.