Publications

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

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. Advance online publication. 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), 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), 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). 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), 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, 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). 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

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, 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), 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

Reddy, S. K., & de Vries, R. (2023). Mycoproteins and yeast proteins in food industry. In Our Future Proteins (pp. 179-187). VU University Press. https://www.scribd.com/document/641363074/Future-Proteins

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

Jochems, P. G. M., Heming, B., Lapin, D., Moonen, N. E. L., Van den Ackerveken, G., & Masereeuw, R. (2022). Bioengineered intestinal tubules as a tool to test intestinal biological efficacy of lettuce species. npj Science of Food, 6(1), 1-8. Article 58. https://doi.org/10.1038/s41538-022-00175-x

Schoonbeek, H. J., Yalcin, H. A., Burns, R., Taylor, R. E., Casey, A., Holt, S., Van den Ackerveken, G., Wells, R., & Ridout, C. J. (2022). Necrosis and ethylene-inducing-like peptide patterns from crop pathogens induce differential responses within seven brassicaceous species. Plant Pathology, 71(9), 2004-2016. https://doi.org/10.1111/ppa.13615

Kun, R. S. (2022). Harnessing the CRISPR/Cas9 system to study the regulatory network of plant biomass degradation in Aspergillus niger. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/745

Venegas, F. A., Koutaniemi, S., Langeveld, S. M. J., Bellemare, A., Chong, S. L., Dilokpimol, A., Lowden, M. J., Hilden, K. S., Leyva-Illades, J. F., Mäkelä, M. R., My Pham, T. T., Peng, M., Hancock, M. A., Zheng, Y., Tsang, A., Tenkanen, M., Powlowski, J., & de Vries, R. P. (2022). Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity. New Biotechnology, 70, 28-38. https://doi.org/10.1016/j.nbt.2022.04.003

Li, X., Kouzounis, D., Kabel, M. A., & de Vries, R. P. (2022). GH10 and GH11 endoxylanases in Penicillium subrubescens: Comparative characterization and synergy with GH51, GH54, GH62 α-L-arabinofuranosidases from the same fungus. New Biotechnology, 70, 84-92. https://doi.org/10.1016/j.nbt.2022.05.004

Marinovíc, M., Di Falco, M., Aguilar Pontes, M. V., Gorzsás, A., Tsang, A., de Vries, R. P., Mäkelä, M. R., & Hildén, K. (2022). Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora. Biomolecules, 12(8), Article 1017. https://doi.org/10.3390/biom12081017

Dilokpimol, A., Verkerk, B., Li, X., Bellemare, A., Lavallee, M., Frommhagen, M., Underlin, E. N., Kabel, M. A., Powlowski, J., Tsang, A., & de Vries, R. P. (2022). Screening of novel fungal Carbohydrate Esterase family 1 enzymes identifies three novel dual feruloyl/acetyl xylan esterases. FEBS Letters, 596(15), 1932-1943. https://doi.org/10.1002/1873-3468.14322