Publications
2022
Scholarly publications
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
Coconi Linares, N., Li, X., Dilokpimol, A., & de Vries, R. P. (2022). Comparative characterization of nine novel GH51, GH54 and GH62 α-l-arabinofuranosidases from Penicillium subrubescens. FEBS Letters, 596(3), 360-368. https://doi.org/10.1002/1873-3468.14278
Chroumpi, T., Martínez-Reyes, N., Kun, R. S., Peng, M., Lipzen, A., Ng, V., Tejomurthula, S., Zhang, Y., Grigoriev, I. V., Mäkelä, M. R., de Vries, R. P., & Garrigues, S. (2022). Detailed analysis of the D-galactose catabolic pathways in Aspergillus niger reveals complexity at both metabolic and regulatory level. Fungal Genetics and Biology, 159, Article 103670. https://doi.org/10.1016/j.fgb.2022.103670
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
Meng, J., Németh, Z., Peng, M., Fekete, E., Garrigues, S., Lipzen, A., Ng, V., Savage, E., Zhang, Y., Grigoriev, I. V., Mäkelä, M. R., Karaffa, L., & de Vries, R. P. (2022). GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans. Microbial Biotechnology, 15(6), 1839-1851. https://doi.org/10.1111/1751-7915.14025
Garrigues, S., Kun, R. S., Peng, M., Bauer, D., Keymanesh, K., Lipzen, A., Ng, V., Grigoriev, I. V., & de Vries, R. P. (2022). Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger. iScience, 25(4), Article 104065. https://doi.org/10.1016/j.isci.2022.104065
Cheng, M., Wijayawardene, N. N., Promputtha, I., de Vries, R. P., Lan, Y., Luo, G., Wang, M., Li, Q., Guo, X., Wang, F., Liu, Y., & Kang, Y. (2022). Potential Fungi Isolated From Anti-biodegradable Chinese Medicine Residue to Degrade Lignocellulose. Frontiers in Microbiology, 13, Article 877884. https://doi.org/10.3389/fmicb.2022.877884
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
Meng, J., Chroumpi, T., Mäkelä, M. R., & de Vries, R. P. (2022). Xylitol production from plant biomass by Aspergillus niger through metabolic engineering. Bioresource Technology, 344(Part A), 1-9. Article 126199. https://doi.org/10.1016/j.biortech.2021.126199
Li, X., Dilokpimol, A., Kabel, M. A., & de Vries, R. P. (2022). Fungal xylanolytic enzymes: Diversity and applications. Bioresource Technology, 344(Part B), 1-10. Article 126290. https://doi.org/10.1016/j.biortech.2021.126290
Sun, P., Li, X., Dilokpimol, A., Henrissat, B., de Vries, R. P., Kabel, M. A., & Mäkelä, M. R. (2022). Fungal glycoside hydrolase family 44 xyloglucanases are restricted to the phylum Basidiomycota and show a distinct xyloglucan cleavage pattern. iScience, 25(1), 1-14. Article 103666. https://doi.org/10.1016/j.isci.2021.103666
Li, X., Kouzounis, D., Kabel, M. A., de Vries, R. P., & Dilokpimol, A. (2022). Glycoside Hydrolase family 30 harbors fungal subfamilies with distinct polysaccharide specificities. New Biotechnology, 67, 32-41. https://doi.org/10.1016/j.nbt.2021.12.004
2021
Scholarly publications
Meng, J., Mäkelä, M. R., & de Vries, R. P. (2021). Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. Advances in Applied Microbiology, 114, 73-109. https://doi.org/10.1016/bs.aambs.2020.09.001
Lubbers, R. J. M., Dilokpimol, A., Visser, J., Hildén, K. S., Mäkelä, M. R., & de Vries, R. P. (2021). Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger. Applied and Environmental Microbiology, 87(6), 1-14. Article e02701-20. https://doi.org/10.1128/AEM.02701-20
Garrigues, S., Kun, R. S., & de Vries, R. P. (2021). Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness. Current Genetics, 67(4), 673-684. https://doi.org/10.1007/s00294-021-01164-5
Chroumpi, T., Peng, M., Markillie, L. M., Mitchell, H. D., Nicora, C. D., Hutchinson, C. M., Paurus, V., Tolic, N., Clendinen, C. S., Orr, G., Baker, S. E., Mäkelä, M. R., & de Vries, R. P. (2021). Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates. Frontiers in Bioengineering and Biotechnology, 9, 1-14. Article 644216. https://doi.org/10.3389/fbioe.2021.644216
Chroumpi, T., Peng, M., Aguilar-Pontes, M. V., Müller, A., Wang, M., Yan, J., Lipzen, A., Ng, V., Grigoriev, I. V., Mäkelä, M. R., & de Vries, R. P. (2021). Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity. Microbial Biotechnology, 14(6), 2525-2537. https://doi.org/10.1111/1751-7915.13790
Peng, M., Khosravi, C., Lubbers, R. J. M., Kun, R. S., Aguilar Pontes, M. V., Battaglia, E., Chen, C., Dalhuijsen, S., Daly, P., Lipzen, A., Ng, V., Yan, J., Wang, M., Visser, J., Grigoriev, I. V., Mäkelä, M. R., & de Vries, R. P. (2021). CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner. The Cell Surface, 7, 1-11. Article 100050. https://doi.org/10.1016/j.tcsw.2021.100050
Terebieniec, A., Chroumpi, T., Dilokpimol, A., Aguilar-Pontes, M. V., Mäkelä, M. R., & de Vries, R. P. (2021). Characterization of D-xylose reductase, XyrB, from Aspergillus niger. Biotechnology Reports, 30, 1-8. Article e00610. https://doi.org/10.1016/j.btre.2021.e00610
Lubbers, R. J. M., Dilokpimol, A., Visser, J., & de Vries, R. P. (2021). Aspergillus niger uses the peroxisomal CoA-dependent β-oxidative genes to degrade the hydroxycinnamic acids caffeic acid, ferulic acid, and p-coumaric acid. Applied Microbiology and Biotechnology, 105(10), 4199-4211. https://doi.org/10.1007/s00253-021-11311-0
Kun, R. S., Garrigues, S., Di Falco, M., Tsang, A., & de Vries, R. P. (2021). Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microbial Biotechnology, 14(4), 1683-1698. https://doi.org/10.1111/1751-7915.13835
Lubbers, R. J. M., & de Vries, R. P. (2021). Production of protocatechuic acid from p-hydroxyphenyl (H) units and related aromatic compounds using an aspergillus niger cell factory. mBio, 12(3), 1-13. Article e00391-21. https://doi.org/10.1128/mBio.00391-21
Kun, R. S., Garrigues, S., Di Falco, M., Tsang, A., & de Vries, R. P. (2021). The chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger. Applied Microbiology and Biotechnology, 105(13), 5553-5564. https://doi.org/10.1007/s00253-021-11428-2
Garrigues, S., Kun, R. S., Peng, M., S.Gruben, B., Gelber, I. B., Mäkelä, M., & P.deVries, R. (2021). The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp. Microbiology spectrum, 9(1), 1-17. https://doi.org/10.1128/Spectrum.01064-21
Peng, M., & de Vries, R. P. (2021). Machine learning prediction of novel pectinolytic enzymes in Aspergillus niger through integrating heterogeneous (post-) genomics data. Microbial genomics, 7(12), 1-9. Article 000674. https://doi.org/10.1099/mgen.0.000674
Crous, P. W., Lombard, L., Sandoval-Denis, M., Seifert, K. A., Schroers, H. J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G. H. J., Lamprecht, S. C., Cai, L., Rossman, A. Y., Stadler, M., Summerbell, R. C., Taylor, J. W., Ploch, S., Visagie, C. M., ... Thines, M. (2021). Fusarium: more than a node or a foot-shaped basal cell. Studies in Mycology, 98, 1-184. Article 100116. https://doi.org/10.1016/j.simyco.2021.100116
Daly, P., Cai, F., Kubicek, C. P., Jiang, S., Grujic, M., Rahimi, M. J., Sheteiwy, M. S., Giles, R., Riaz, A., De Vries, R. P., Akcapinar, G. B., Wei, L., & Druzhinina, I. S. (2021). From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnology Advances, 50, 1-16. Article 107770. https://doi.org/10.1016/j.biotechadv.2021.107770
Buijs, V. A., Zuijdgeest, X. C. L., Groenewald, J. Z., Crous, P. W., & De Vries, R. P. (2021). Carbon utilization and growth-inhibition of citrus-colonizing Phyllosticta species. Fungal Biology, 125(10), 815-825. https://doi.org/10.1016/j.funbio.2021.05.003
Lubbers, R. J. M., Dilokpimol, A., Nousiainen, P. A., Cioc, R. C., Visser, J., Bruijnincx, P. C. A., & de Vries, R. P. (2021). Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories. Microbial Cell Factories, 20(1), 1-14. Article 151. https://doi.org/10.1186/s12934-021-01643-x
2020
Scholarly publications
Salazar-cerezo, S., Kun, R. S., De Vries, R. P., & Garrigues, S. (2020). CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer. Enzyme and Microbial Technology, 133, Article 109463. https://doi.org/10.1016/j.enzmictec.2019.109463
Daly, P., Peng, M., Casado López, S., Lipzen, A., Ng, V., Singan, V. R., Wang, M., Grigoriev, I. V., de Vries, R. P., & Mäkelä, M. R. (2020). Corrigendum to “Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens” [J. Biotechnol. 380 (2020) 35–39]. Journal of Biotechnology, 309, 142. https://doi.org/10.1016/j.jbiotec.2020.01.006
Daly, P., Peng, M., Casado López, S., Lipzen, A., Ng, V., Singan, V. R., Wang, M., Grigoriev, I. V., de Vries, R. P., & Mäkelä, M. R. (2020). Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens. Journal of Biotechnology, 308, 35-39. https://doi.org/10.1016/j.jbiotec.2019.11.014
Coconi Linares, N., Dilokpimol, A., Stålbrand, H., Mäkelä, M. R., & De Vries, R. P. (2020). Recombinant production and characterization of six novel GH27 and GH36 α-galactosidases from Penicillium subrubescens and their synergism with a commercial mannanase during the hydrolysis of lignocellulosic biomass. Bioresource Technology, 295, Article 122258. https://doi.org/10.1016/j.biortech.2019.122258
Garrigues, S., Martinez-Reyes, N., & de Vries, R. P. (2020). Genetic engineering for strain improvement in filamentous fungi. In R. de Vries, & M. Mäkelä (Eds.), Reference Module in Life Sciences 2020 Elsevier. https://doi.org/10.1016/B978-0-12-819990-9.00006-8
Li, J., de Vries, R. P., & Peng, M. (2020). Bioinformatics Approaches for Fungal Biotechnology. In R. de Vries, & M. Mäkelä (Eds.), Reference Module in Life Sciences 2020 Elsevier. https://doi.org/10.1016/B978-0-12-819990-9.00012-3
De Vries, R. P., Patyshakuliyeva, A., Garrigues, S., & Agarwal-jans, S. (2020). The Current Biotechnological Status and Potential of Plant and Algal Biomass Degrading/Modifying Enzymes from Ascomycete Fungi. In Grand Challenges in Fungal Biotechnology (pp. 81-120). (Grand Challenges in Fungal Biotechnology). Springer. https://doi.org/10.1007/978-3-030-29541-7_4
Li, X., Griffin, K., Langeveld, S., Frommhagen, M., Underlin, E. N., Kabel, M. A., de Vries, R. P., & Dilokpimol, A. (2020). Functional Validation of Two Fungal Subfamilies in Carbohydrate Esterase Family 1 by Biochemical Characterization of Esterases From Uncharacterized Branches. Frontiers in Bioengineering and Biotechnology, 8, Article 694. https://doi.org/10.3389/fbioe.2020.00694
Kjærbølling, I., Vesth, T., Frisvad, J. C., Nybo, J. L., Theobald, S., Kildgaard, S., Petersen, T. I., Kuo, A., Sato, A., Lyhne, E. K., Kogle, M. E., Wiebenga, A., Kun, R. S., Lubbers, R. J. M., Mäkelä, M. R., Barry, K., Chovatia, M., Clum, A., Daum, C., ... Andersen, M. R. (2020). A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Communications, 11(1), Article 1106. https://doi.org/10.1038/s41467-019-14051-y
Underlin, E. N., Frommhagen, M., Dilokpimol, A., van Erven, G., de Vries, R. P., & Kabel, M. A. (2020). Feruloyl Esterases for Biorefineries: Subfamily Classified Specificity for Natural Substrates. Frontiers in Bioengineering and Biotechnology, 8, Article 332. https://doi.org/10.3389/fbioe.2020.00332
Van Erven, G., Kleijn, A. F., Patyshakuliyeva, A., Di Falco, M., Tsang, A., De Vries, R. P., Van Berkel, W. J. H., & Kabel, M. A. (2020). Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina. Biotechnology for Biofuels, 13(1), Article 75. https://doi.org/10.1186/s13068-020-01713-z
Chroumpi, T., Aguilar-Pontes, M. V., Peng, M., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., Mäkelä, M. R., & de Vries, R. P. (2020). Identification of a gene encoding the last step of the L-rhamnose catabolic pathway in Aspergillus niger revealed the inducer of the pathway regulator. Microbiological Research, 234, Article 126426. https://doi.org/10.1016/j.micres.2020.126426
Kun, R. S., Meng, J., Salazar-cerezo, S., Mäkelä, M. R., De Vries, R. P., & Garrigues, S. (2020). CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass. Enzyme and Microbial Technology, 136, Article 109508. https://doi.org/10.1016/j.enzmictec.2020.109508
Dilokpimol, A., Peng, M., Di Falco, M., Chin A Woeng, T., Hegi, R. M. W., Granchi, Z., Tsang, A., Hildén, K. S., Mäkelä, M. R., & de Vries, R. P. (2020). Penicillium subrubescens adapts its enzyme production to the composition of plant biomass. Bioresource Technology, 311, Article 123477. https://doi.org/10.1016/j.biortech.2020.123477
Chroumpi, T., Mäkelä, M. R., & de Vries, R. P. (2020). Engineering of primary carbon metabolism in filamentous fungi. Biotechnology Advances, 43, Article 107551. https://doi.org/10.1016/j.biotechadv.2020.107551
de Vries, R. P., & Mäkelä, M. R. (2020). Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches. Trends in Microbiology, 28(6), 487-499. https://doi.org/10.1016/j.tim.2020.01.004
Miyauchi, S., Hage, H., Drula, E., Lesage-Meessen, L., Berrin, J-G., Navarro, D., Favel, A., Chaduli, D., Grisel, S., Haon, M., Piumi, F., Levasseur, A., Lomascolo, A., Ahrendt, S., Barry, K., LaButti, K. M., Chevret, D., Daum, C., Mariette, J., ... Rosso, M-N. (2020). Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Research, 27(2), 1-14. https://doi.org/10.1093/dnares/dsaa011
Meyer, V., Basenko, E. Y., Benz, J. P., Braus, G. H., Caddick, M. X., Csukai, M., de Vries, R. P., Endy, D., Frisvad, J. C., Gunde-Cimerman, N., Haarmann, T., Hadar, Y., Hansen, K., Johnson, R. I., Keller, N. P., Kraševec, N., Mortensen, U. H., Perez, R., Ram, A. F. J., ... Wösten, H. A. B. (2020). Growing a circular economy with fungal biotechnology: a white paper. Fungal Biology and Biotechnology, 7, 1-23. Article 5. https://doi.org/10.1186/s40694-020-00095-z
Daly, P., Peng, M., Mitchell, H. D., Kim, Y., Ansong, C., Brewer, H., Gijsel, P., Lipton, M. S., Markillie, L. M., Nicora, C. D., Orr, G., Wiebenga, A., Hildén, K. S., Kabel, M. A., Baker, S. E., Mäkelä, M. R., & Vries, R. P. (2020). Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environmental Microbiology, 22(3), 1154-1166. https://doi.org/10.1111/1462-2920.14907
2019
Scholarly publications
Khosravi, C., Kowalczyk, J. E., Chroumpi, T., Battaglia, E., Aguilar Pontes, M., Peng, M., Wiebenga, A., Ng, V., Lipzen, A., He, G., Bauer, D., Grigoriev, I. V., & De Vries, R. P. (2019). Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. BMC Genomics, 20(1), Article 853. https://doi.org/10.1186/s12864-019-6235-7
Ming, C., Dilokpimol, A., Zou, C., Liao, W., Zhao, L., Wang, M., De Vries, R. P., & Kang, Y. (2019). The quest for fungal strains and their co-culture potential to improve enzymatic degradation of Chinese distillers’ grain and other agricultural wastes. International Biodeterioration & Biodegradation, 144, Article 104765. https://doi.org/10.1016/j.ibiod.2019.104765
Coconi Linares, N., Di Falco, M., Benoit-gelber, I., Gruben, B. S., Peng, M., Tsang, A., Mäkelä, M. R., & De Vries, R. P. (2019). The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum. New Biotechnology, 51, 57-66. https://doi.org/10.1016/j.nbt.2019.02.005
Dos Santos Gomes, A. C., Falkoski, D., Battaglia, E., Peng, M., Nicolau De Almeida, M., Coconi Linares, N., Meijnen, J., Visser, J., & De Vries, R. P. (2019). Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism. Biotechnology for Biofuels, 12(1), Article 220. https://doi.org/10.1186/s13068-019-1556-y
Patyshakuliyeva, A., Falkoski, D. L., Wiebenga, A., Timmermans, K., & De Vries, R. P. (2019). Macroalgae Derived Fungi Have High Abilities to Degrade Algal Polymers. Microorganisms, 8(1). https://doi.org/10.3390/microorganisms8010052
Daly, P., Peng, M., Di Falco, M., Lipzen, A., Wang, M., Ng, V., Grigoriev, I. V., Tsang, A., Mäkelä, M. R., De Vries, R. P., & Druzhinina, I. S. (Ed.) (2019). Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens. Applied and Environmental Microbiology, 85(23). https://doi.org/10.1128/AEM.01828-19
Lubbers, R. J. M., Liwanag, A. J., Peng, M., Dilokpimol, A., Benoit‐gelber, I., & Vries, R. P. (2019). Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance. Journal of Applied Microbiology. https://doi.org/10.1111/jam.14505
Casado López, S., Peng, M., Daly, P., Andreopoulos, B., Pangilinan, J., Lipzen, A., Riley, R., Ahrendt, S., Ng, V., Barry, K., Daum, C., Grigoriev, I. V., Hildén, K. S., Mäkelä, M. R., De Vries, R. P., & Stajich, J. E. (Ed.) (2019). Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens. Microbiology Resource Announcements, 8(18). https://doi.org/10.1128/MRA.00264-19
Lubbers, R. J. M., Dilokpimol, A., Peng, M., Visser, J., Mäkelä, M. R., Hildén, K. S., & De Vries, R. P. (2019). Discovery of Novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the Filamentous Fungus Aspergillus niger. Acs sustainable chemistry & engineering, 7( 23), 19081-19089. https://doi.org/10.1021/acssuschemeng.9b04918
Lubbers, R. J. M., Dilokpimol, A., Navarro, J., Peng, M., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., Visser, J., Hildén, K. S., & De Vries, R. P. (2019). Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger. Frontiers in Bioengineering and Biotechnology, 7. https://doi.org/10.3389/fbioe.2019.00249
Benocci, T., Daly, P., Aguilar-Pontes, M. V., Lail, K., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., & de Vries, R. P. (2019). Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails. Biotechnology Journal, 14(4), Article e1800185. https://doi.org/10.1002/biot.201800185
Németh, Z., Kulcsár, L., Flipphi, M., Orosz, A., Aguilar-Pontes, M. V., de Vries, R. P., Karaffa, L., & Fekete, E. (2019). l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans. Fungal Genetics and Biology, 123, 53-59. https://doi.org/10.1016/j.fgb.2018.11.004
2018
Scholarly publications
Vesth, T. C., Nybo, J. L., Theobald, S., Frisvad, J. C., Larsen, T. O., Nielsen, K. F., Hoof, J. B., Brandl, J., Salamov, A., Riley, R., Gladden, J. M., Phatale, P., Nielsen, M. T., Lyhne, E. K., Kogle, M. E., Strasser, K., McDonnell, E., Barry, K., Clum, A., ... Andersen, M. R. (2018). Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics, 50, 1688-1695. https://doi.org/10.1038/s41588-018-0246-1
López, S. C., Peng, M., Issak, T. Y., Daly, P., de Vries, R. P., & Mäkelä, M. R. (2018). Induction of genes encoding plant cell wall-degrading carbohydrate-active enzymes by lignocellulose-derived monosaccharides and cellobiose in the white-rot fungus Dichomitus squalens. Applied and Environmental Microbiology, 84(11), Article e0043-18. https://doi.org/10.1128/AEM.00403-18
Marinović, M., Nousiainen, P., Dilokpimol, A., Kontro, J., Moore, R., Sipilä, J., De Vries, R. P., Mäkelä, M. R., & Hildén, K. (2018). Selective Cleavage of Lignin β- O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens. ACS Sustainable Chemistry and Engineering, 6(3), 2878-2882. https://doi.org/10.1021/acssuschemeng.7b03619
Marinović, M., Aguilar-Pontes, M. V., Zhou, M., Miettinen, O., de Vries, R. P., Mäkelä, M. R., & Hildén, K. (2018). Temporal transcriptome analysis of the white-rot fungus Obba rivulosa shows expression of a constitutive set of plant cell wall degradation targeted genes during growth on solid spruce wood. Fungal Genetics and Biology, 112, 47-54. https://doi.org/10.1016/j.fgb.2017.07.004
Dilokpimol, A., Mäkelä, M. R., Varriale, S., Zhou, M., Cerullo, G., Gidijala, L., Hinkka, H., Brás, J. L. A., Jütten, P., Piechot, A., Verhaert, R., Hildén, K. S., Faraco, V., & de Vries, R. P. (2018). Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies. New Biotechnology, 41, 9-14. https://doi.org/10.1016/j.nbt.2017.11.004
Dilokpimol, A., Mäkelä, M. R., Cerullo, G., Zhou, M., Varriale, S., Gidijala, L., Brás, J. L. A., Jütten, P., Piechot, A., Verhaert, R., Faraco, V., Hilden, K. S., & de Vries, R. P. (2018). Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization. New Biotechnology, 40(Pt B), 282-287. https://doi.org/10.1016/j.nbt.2017.10.003
Peng, M., Aguilar-Pontes, M. V., Hainaut, M., Henrissat, B., Hilden, K., Makela, M. R., & de Vries, R. P. (2018). Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes. Fungal Genetics and Biology, 112, 40-46. https://doi.org/10.1016/j.fgb.2017.08.001
Ozturkoglu-Budak, S., Aykas, D. P., Kocak, C., Donmez, S., Gursoy, A., De Vries, R. P., & Bron, P. A. (2018). Temporal microbiota and biochemical profiles during production and ripening of Divle Cave cheese. International Journal of Dairy Technology, 71, 99-106. https://doi.org/10.1111/1471-0307.12493
Orosz, E., van de wiele, N., Emri, T., Zhou, M., Robert, V., de Vries, R. P., & Pocsi, I. (2018). Fungal Stress Database (FSD)-a repository of fungal stress physiological data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2018, Article bay009. https://doi.org/10.1093/database/bay009
Benocci, T., Aguilar-Pontes, M. V., Kun, R. S., Seiboth, B., de Vries, R. P., & Daly, P. (2018). ARA1 regulates not only L-arabinose but also D-galactose catabolism in Trichoderma reesei. FEBS Letters, 592(1), 60-70. https://doi.org/10.1002/1873-3468.12932
Benocci, T., de Vries, R. P., & Daly, P. (2018). A senescence-delaying pre-culture medium for transcriptomics of Podospora anserina. Journal of Microbiological Methods, 146, 33-36. https://doi.org/10.1016/j.mimet.2018.01.010
Cerullo, G., Houbraken, J., Granchi, Z., Pepe, O., Varriale, S., Ventorino, V., Chin-A-Woeng, T., Meijer, M., de Vries, R. P., & Faraco, V. (2018). Draft Genome Sequence of Talaromyces adpressus. Genome Announcements, 6(2), Article e01430-17. https://doi.org/10.1128/genomeA.01430-17
Khosravi, C., Battaglia, E., Kun, R. S., Dalhuijsen, S., Visser, J., Aguilar-Pontes, M. V., Zhou, M., Heyman, H. M., Kim, Y. M., Baker, S. E., & de Vries, R. P. (2018). Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans. BMC Genomics, 19(1), Article 214. https://doi.org/10.1186/s12864-018-4609-x
Varriale, S., Houbraken, J., Granchi, Z., Pepe, O., Cerullo, G., Ventorino, V., Chin-A-woeng, T., Meijer, M., Riley, R., Grigoriev, I. V., Henrissat, B., de Vries, R. P., & Faraco, V. (2018). Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded arundo donax with potential abilities in lignocellulose conversion. Mycopathologia, 110(2), 316-324. https://doi.org/10.1080/00275514.2018.1456835
Gygli, G., de Vries, R. P., & van Berkel, W. J. H. (2018). On the origin of vanillyl alcohol oxidases. Fungal Genetics and Biology, 116, 24-32. https://doi.org/10.1016/j.fgb.2018.04.003
Makela, M. R., Dilokpimol, A., Koskela, S. M., Kuuskeri, J., de Vries, R. P., & Hilden, K. (2018). Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database. Microbial Biotechnology, 11(5), 869-880. https://doi.org/10.1111/1751-7915.13273
Makela, M. R., Aguilar-Pontes, M. V., van Rossen-Uffink, D., Peng, M., & de Vries, R. P. (2018). The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA. Scientific Reports, 8, Article 6655. https://doi.org/10.1038/s41598-018-25152-x
Peng, M., Aguilar-Pontes, M. V., de Vries, R. P., & Makela, M. R. (2018). In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics. Frontiers in Microbiology, 9, Article 1045. https://doi.org/10.3389/fmicb.2018.01045
Antonopoulou, I., Dilokpimol, A., Iancu, L., Makela, M. R., Varriale, S., Cerullo, G., Huttner, S., Uthoff, S., Juetten, P., Piechot, A., Steinbuechel, A., Olsson, L., Faraco, V., Hilden, K. S., de Vries, R. P., Rova, U., & Christakopoulos, P. (2018). The Synthetic Potential of Fungal Feruloyl Esterases: A Correlation with Current Classification Systems and Predicted Structural Properties. Catalysts, 8(6), Article 242. https://doi.org/10.3390/catal8060242
Kurucz, V., Kiss, B., Szigeti, Z. M., Nagy, G., Orosz, E., Hargitai, Z., Harangi, S., Wiebenga, A., de Vries, R. P., Pócsi, I., & Emri, T. (2018). Physiological background of the remarkably high Cd2+ tolerance of the Aspergillus fumigatus Af293 strain. Journal of Basic Microbiology, 58(11), 957-967. https://doi.org/10.1002/jobm.201800200
Mäkelä, M. R., DiFalco, M., McDonnell, E., Nguyen, T. T. M., Wiebenga, A., Hildén, K., Peng, M., Grigoriev, I. V., Tsang, A., & de Vries, R. P. (2018). Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Studies in Mycology, 91, 79-99. https://doi.org/10.1016/j.simyco.2018.09.001
Aguilar-Pontes, M. V., Brandl, J., McDonnell, E., Strasser, K., Nguyen, T. T. M., Riley, R., Mondo, S., Salamov, A., Nybo, J. L., Vesth, T. C., Grigoriev, I. V., Andersen, M. R., Tsang, A., & de Vries, R. P. (2018). The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Studies in Mycology, 91, 61-78. https://doi.org/10.1016/j.simyco.2018.10.001
Daly, P., Lopez, S. C., Peng, M., Lancefield, C. S., Purvine, S. O., Kim, Y-M., Zink, E. M., Dohnalkova, A., Singan, V. R., Lipzen, A., Dilworth, D., Wang, M., Ng, V., Robinson, E., Orr, G., Baker, S. E., Bruijnincx, P. C. A., Hilden, K. S., Grigoriev, I. V., ... de Vries, R. P. (2018). Dichomitus squalens partially tailors its molecular responses to the composition of solid wood. Environmental Microbiology, 20(11), 4141-4156. https://doi.org/10.1111/1462-2920.14416
Emri, T., Antal, K., Riley, R., Karanyi, Z., Miskel, M., Orosz, E., Baker, S. E., Wiebenga, A., de Vries, R. P., & Pocsi, I. (2018). Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance. Studies in Mycology, 91, 23-36. https://doi.org/10.1016/j.simyco.2018.10.003
Brandl, J., Aguilar-Pontes, M. V., Schäpe, P., Noerregaard, A., Arvas, M., Ram, A. F. J., Meyer, V., Tsang, A., de Vries, R. P., & Andersen, M. R. (2018). A community-driven reconstruction of the Aspergillus niger metabolic network. Fungal Biology and Biotechnology, 5(16). https://doi.org/10.1186/s40694-018-0060-7
Grum-Grzhimaylo, A. A., Falkoski, D. L., van den Heuvel, J., Valero-Jiménez, C. A., Min, B., Choi, I-G., Lipzen, A., Daum, C. G., Aanen, D. K., Tsang, A., Henrissat, B., Bilanenko, E. N., de Vries, R. P., van Kan, J. A. L., Grigoriev, I. V., & Debets, A. J. M. (2018). The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet. Molecular Ecology, 27(23), 4808-4819. https://doi.org/10.1111/mec.14912
Urquhart, A. S., Mondo, S. J., Mäkelä, M. R., Hane, J. K., Wiebenga, A., He, G., Mihaltcheva, S., Pangilinan, J., Lipzen, A., Barry, K., de Vries, R. P., Grigoriev, I. V., & Idnurm, A. (2018). Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales). Frontiers in Microbiology, 9, Article 3058. https://doi.org/10.3389/fmicb.2018.03058
Pontes, M. V. A., Patyshakuliyeva, A., Post, H., Jurak, E., Hildén, K. S., Altelaar, M., Heck, A., Kabel, M. A., de Vries, R. P., & Mäkelä, M. R. (2018). The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates. Fungal Genetics and Biology, 112, 12-20. https://doi.org/10.1016/j.fgb.2017.12.004
2017
Scholarly publications
Mäkelä, M. R., Bouzid, O., Ruiz-Robleto, J., Post, H., Peng, M., Heck, A., Altelaar, M., & de Vries, R. P. (2017). Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis. New Biotechnology, 37(Part B), 162-171. https://doi.org/10.1016/j.nbt.2017.02.002
Benoit-Gelber, I., Gruntjes, T., Vinck, A., van Veluw, J., Wosten, H., Boeren, S., Vervoort, J. J. M., & de Vries, R. P. (2017). Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran. Fungal Genetics and Biology, 102, 31-37. https://doi.org/10.1016/j.fgb.2017.02.006
2016
Scholarly publications
Corrochano, L. M., Kuo, A., Marcet-Houben, M., Polaino, S., Salamov, A., Villalobos-Escobedo, J. M., Grimwood, J., Álvarez, M. I., Avalos, J., Bauer, D., Benito, E. P., Benoit, I., Burger, G., Camino, L. P., Cánovas, D., Cerdá-Olmedo, E., Cheng, J-F., Domínguez, A., Eliáš, M., ... Grigoriev, I. V. (2016). Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Current Biology, 26(12), 1577-84. https://doi.org/10.1016/j.cub.2016.04.038
Ozturkoglu Budak, S., Figge, M. J., Houbraken, J., & de Vries, R. P. (2016). The diversity and evolution of microbiota in traditional Turkish Divle Cave cheese during ripening. International Dairy Journal, 58, 50-53. https://doi.org/10.1016/j.idairyj.2015.09.011
Jiang, Y., Duarte, A. V., van Den Brink, J., Wiebenga, A., Zou, G., Wang, C., de Vries, R. P., Zhou, Z., & Benoit, I. (2016). Enhancing saccharification of wheat straw by mixing enzymes from genetically-modified Trichoderma reesei and Aspergillus niger. Biotechnology Letters, 38(1), 65–70. https://doi.org/10.1007/s10529-015-1951-9
2015
Scholarly publications
Patyshakuliyeva, A., Harm, P., Zhou, M., Jurak, E., Heck, A. J. R., Hildén, K. S., Kabel, M. A., Mäkelä, M. R., Altelaar, M. A. F., & De Vries, R. P. (2015). Unraveling the abilities of agaricus bisporus to degrade plant biomass throughout its life cycle. Acta Microbiologica et Immunologica Hungarica, 62, 198. https://doi.org/10.1556/030.62.2015
De Vries, R. P. (2015). Novel developments in plant biomass degradation by fungi. Acta Microbiologica et Immunologica Hungarica, 62, 240. https://doi.org/10.1556/030.62.2015
Kowalczyk, J. E., Gruben, B. S., Battaglia, E., Wiebenga, A., Majoor, E., & de Vries, R. P. (2015). Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression. PLoS One, 10(11), Article e0143200. https://doi.org/10.1371/journal.pone.0143200
Niu, J., Homan, T. G., Arentshorst, M., de Vries, R. P., Visser, J., & Ram, A. F. J. (2015). The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger. Fungal Genetics and Biology, 82, 32-42. https://doi.org/10.1016/j.fgb.2015.06.006
Mäkelä, M. R., Marinović, M., Nousiainen, P., Liwanag, A. J. M., Benoit, I., Sipilä, J., Hatakka, A., de Vries, R. P., & Hildén, K. S. (2015). Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass. Advances in Applied Microbiology, 91, 63-137. https://doi.org/10.1016/bs.aambs.2014.12.001
Carreira, C., Staal, M., Falkoski, D., De Vries, R. P., Middelboe, M., & Brussaard, C. P. D. (2015). Disruption of photoautotrophic intertidal mats by filamentous fungi. Environmental Microbiology, 17(8), 2910-2921. https://doi.org/10.1111/1462-2920.12835
Benoit, I., van den Esker, M. H., Patyshakuliyeva, A., Mattern, D. J., Blei, F., Zhou, M., Dijksterhuis, J., Brakhage, A. A., Kuipers, O. P., de Vries, R. P., & Kovács, Á. T. (2015). Bacillus subtilis attachment to Aspergillus niger hyphae results in mutually altered metabolism. Environmental Microbiology, 17(6), 2099-2113. https://doi.org/10.1111/1462-2920.12564
Dhillon, B., Feau, N., Aerts, A. L., Beauseigle, S., Bernier, L., Copeland, A., Foster, A., Gill, N., Henrissat, B., Herath, P., LaButti, K. M., Levasseur, A., Lindquistb, E. A., Majoor, E., Ohm, R. A., Pangilinan, J. L., Pribowo, A., Saddler, J. N., Sakalidis, M. L., ... Hamelin, R. C. (2015). Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proceedings of the National Academy of Sciences of the United States of America, 112(11), 3451-3456. https://doi.org/10.1073/pnas.1424293112
Jurak, E., Patyshakuliyeva, A., Kapsokalyvas, D., Xing, L., Van Zandvoort, M. A. M. J., De Vries, R. P., Gruppen, H., & Kabel, M. A. (2015). Accumulation of recalcitrant xylan in mushroom-compost is due to a lack of xylan substituent removing enzyme activities of Agaricus bisporus. Carbohydr Polym, 132, 359-368. Article 10056. https://doi.org/10.1016/j.carbpol.2015.06.065
Benoit, I., Culleton, H., Zhou, M., DiFalco, M., Aguilar-Osorio, G., Battaglia, E., Bouzid, O., Brouwer, C. P. J. M., El-Bushari, H. B. O., Coutinho, P. M., Gruben, B. S., Hildén, K. S., Houbraken, J., Barboza, L. A. J., Levasseur, A., Majoor, E., Mäkelä, M. R., Narang, H. M., Trejo-Aguilar, B., ... De Vries, R. P. (2015). Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. Biotechnology for Biofuels, 8(1), Article 107. https://doi.org/10.1186/s13068-015-0285-0
Jurak, E., Patyshakuliyeva, A., De Vries, R. P., Gruppen, H., & Kabel, M. A. (2015). Compost grown agaricus bisporus lacks the ability to degrade and consume highly substituted xylan fragments. PLoS One, 10(8), Article 134169. https://doi.org/10.1371/journal.pone.0134169
Maitan-Alfenas, G. P., Visser, E. M., Alfenas, R. F., Nogueira, B. R. G., de Campos, G. G., Milagres, A. F., de Vries, R. P., & Guimarães, V. M. (2015). The influence of pretreatment methods on saccharification of sugarcane bagasse by an enzyme extract from Chrysoporthe cubensis and commercial cocktails: A comparative study. Bioresource Technology, 192, 670-676. https://doi.org/10.1016/j.biortech.2015.05.109
Benoit, I., Zhou, M., Duarte, A. V., Downes, D. J., Todd, R. B., Kloezen, W., Post, H., Heck, A. J. R., Altelaar, A. F. M., & de Vries, R. P. (2015). Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports, 5, Article 13592. https://doi.org/10.1038/srep13592
Patyshakuliyeva, A., Post, H., Zhou, M., Jurak, E., Heck, A. J. R., Hildén, K. S., Kabel, M. A., Mäkelä, M. R., Altelaar, M. A. F., & De Vries, R. P. (2015). Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle. Environmental Microbiology, 17(8), 3098-3109. https://doi.org/10.1111/1462-2920.12967
Wang, F., Krijgsheld, P., Hulsman, M., de Bekker, C., Müller, W. H., Reinders, M., de Vries, R. P., & Wosten, H. (2015). FluG affects secretion in colonies of Aspergillus niger. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 107(1), 225-240. https://doi.org/10.1007/s10482-014-0321-2
2014
Scholarly publications
Todd, R. B., Zhou, M., Ohm, R. A., Leeggangers, H. A. C. F., Visser, L., & de Vries, R. P. (2014). Prevalence of transcription factors in ascomycete and basidiomycete fungi. BMC Genomics, 15(1), Article 214. https://doi.org/10.1186/1471-2164-15-214
Gruben, B. S., Zhou, M., Wiebenga, A., Ballering, J., Overkamp, K. M., Punt, P. J., & De Vries, R. P. (2014). Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism. Applied Microbiology and Biotechnology, 98(12), 5531-5540. https://doi.org/10.1007/s00253-014-5607-9
Levasseur, A., Lomascolo, A., Chabrol, O., Ruiz-Dueñas, F. J., Boukhris-Uzan, E., Piumi, F., Kües, U., Ram, A. F. J., Murat, C., Haon, M., Benoit, I., Arfi, Y., Chevret, D., Drula, E., Kwon, M. J., Gouret, P., Lesage-Meessen, L., Lombard, V., Mariette, J., ... Wosten, H. (2014). The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics, 15, 1-24. Article 486. https://doi.org/10.1186/1471-2164-15-486
Klaubauf, S., Narang, H. M., Post, H., Zhou, M., Brunner, K., Mach-Aigner, A. R., Mach, R. L., Heck, A. J. R., Altelaar, A. F. M., & de Vries, R. P. (2014). Similar is not the same: Differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genetics and Biology, 72, 73-81. https://doi.org/10.1016/j.fgb.2014.07.007
2013
Scholarly publications
Morin, E., Kohler, A., Baker, A. R., Foulongne-Oriol, M., Lombard, V., Nagy, L. G., Ohm, R. A., Patyshakuliyeva, A., Brun, A., Aerts, A. L., Bailey, A. M., Billette, C., Coutinho, P. M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hildén, K., Kües, U., ... Martin, F. (2013). Erratum: Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche (Proceedings of the National Academy of Sciences of the United States of America (2012) 109 (17501-17506) DOI: 10.1073/pnas.1206847109). Proceedings of the National Academy of Sciences of the United States of America, 110(10), 4146. https://doi.org/10.1073/pnas.1300201110
Patyshakuliyeva, A., Jurak, E., Kohler, A., Baker, A., Battaglia, E., de Bruijn, W., Burton, K. S., Challen, M. P., Coutinho, P. M., Eastwood, D. C., Gruben, B. S., Mäkelä, M. R., Nadal, M., van den Brink, J., Wiebenga, L. A., Zhou, M., Henrissat, B., Kabel, M., Gruppen, H., & de Vries, R. P. (2013). Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus. BMC Genomics, 14, 663. https://doi.org/10.1186/1471-2164-14-663
Battaglia, E., Klaubauf, S., Vallet, J., Ribot, C., Lebrun, M. H., & de Vries, R. P. (2013). Xir1 is involved in the transcriptional control of the pentose catabolic pathway, but not hemi-cellulolytic enzymes in magnaporthe oryzae. Fungal Genetics and Biology, 57, 76-84.
de Souza, W. R., Maitan-Alfenas, G. P., Gouvea, P. F., Brown, N. A., Savoldi, M., Battaglia, E., Goldman, M. H., de Vries, R. P., & Goldman, G. H. (2013). The infuence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse. Fungal Genetics and Biology, 60, 29-45.
2012
Scholarly publications
vanKuyk, P. A., Benen, J. A. E., Wosten, H. A. B., Visser, J., & de Vries, R. P. (2012). A broader role for AmyR in Aspergillus niger: regulation of the utilisation of d-glucose or d-galactose containing oligo- and polysaccharides. Applied Microbiology and Biotechnology, 93(1), 285-293. https://doi.org/10.1007/s00253-011-3550-6
Morin, E., Kohler, A., Baker, A. R., Foulogne-Oriol, M., Lombard, V., Nagy, L. G., Ohm, R. A., Patyshakuliyeva, A., Brun, A., Aerts, A. L., Billette, C., Coutinho, P. M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hildén, K., Kües, U., Labutti, K. M., ... Martin, F. (2012). Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences of the United States of America, 109, 17501-17506.
de Vries, R. P., Benoit, I., Doehlemann, G., Kobayashi, T., Magnuson, J. K., Panisko, E. A., Baker, S. E., & Lebrun, M. H. (2012). Post-genomic approaches to understanding interactions between fungi and their environment. Fungal Genetics and Biology, 2, 81-86.
Benoit, I., Coutinho, P. M., Schols, H. A., Gerlach, J. P., Henrissat, B., & de Vries, R. P. (2012). Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics, 13, 321. http://www.ncbi.nlm.nih.gov/pubmed/22812459
Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R. A., Henrissat, B., Martinez, A. T., Otillar, R., Spatafora, J. W., Yadav, J. S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P. M., de Vries, R. P., Ferreira, P., Findley, K., ... Hibbett, D. S. (2012). The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science, 336, 1715-1719.
Gruben, B. S., Zhou, M., & de Vries, R. P. (2012). GalX regulates the d-galactose oxido-reductive pathway in Aspergillus niger. FEBS Letters, 3980-3985.
Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P. M., Cullen, D., Dalman, K., Deflorio, G., Diepen, L. T., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Fossdal, C. G., Hansson, D., ... Stenlid, J. (2012). Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytologist, 194, 1001-1013.
Feteke, E., de Vries, R. P., Seiboth, B., Vankuyk, P. A., Sándor, E., Metz, B., Kubicek, C. P., & Karaffa, L. (2012). d-Galactose uptake is nonfunctional in the conidiospores of Aspergillus niger. FEMS Microbiology Letters, 329, 198-203.
Other output
Wang, F., de Vries, R. P., Nitsche, B. M., Ram, A. F. J., & Wösten, H. A. B. (2012). Involving the whole A. niger mycelium in protein secretion. Poster session presented at Ninth Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout.
Benoit, I., Kovacs, A. T., Wösten, H. A. B., Kuipers, O. P., & de Vries, R. P. (2012). Bacillus subtilis biofilms on Aspergilus niger hyphae. Abstract from Ninth Symposium Kluyver for Genomics of Industrial Fermentation, Noordwijkerhout.
Benoit, I., Kovacs, A. T., Wösten, H. A. B., Kuipers, O. P., & de Vries, R. P. (2012). Bacillus subtilis biofilms on Aspergilus niger hyphae. Poster session presented at Ninth Symposium Kluyver for Genomics of Industrial Fermentation, Noordwijkerhout.
Benoit, I., Culleton, H., Coutinho, A., Aguilar-Osorio, G., Battaglia, E., Brouwer, C. P. J. M., El-Bushari, H. B. O., Gruben, B. S., McKie, V., Narang, H-M., Trejo-Aguilar, B., van den Brink, J., Vankuyk, P. A., Wiebenga, L. A., McCleary, B., Henrissat, B., & de Vries, R. P. (2012). Differences in the utilisation of complex substrates within the genus Aspergillus. Abstract from Ninth Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout.
Wang, F., de Vries, R. P., Nitsche, B. M., Ram, A. F. J., & Wösten, H. A. B. (2012). Involving the whole A. niger mycelium in protein secretion. Abstract from Ninth Symposium Kluyver Centre for Genomics of Industrial Fermentation, Noordwijkerhout.
Benoit, I., Vinck, A., van Veluw, G. J., Wosten, H. A. B., & de Vries, R. P. (2012). Co-cultivations of fungi: microscopic analysis and influence on protein production. Abstract from 11th European Conference on Fungal Genetics, Philipps-Universitaet Marburg, Germany.
Benoit, I., Vinck, A., van Veluw, G. J., Wosten, H. A. B., & de Vries, R. P. (2012). Co-cultivations of fungi: microscopic analysis and influence on protein production. Poster session presented at 11th European Conference on Fungal Genetics, Philipps-Universitaet Marburg, Germany.
Benoit, I., Kovacs, A. T., Wösten, H. A. B., Kuipers, O. P., & de Vries, R. P. (2012). Bacillus subtilis biofims on Aspergilus niger hyphae. Abstract from Ninth Symposium Kluyver for Genomics of Industrial Fermentation, Noordwijkerhout.
2011
Scholarly publications
Vinck, A., de Bekker, C., Ossin, A., Ohm, R. A., de Vries, R. P., & Woesten, H. A. B. (2011). Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies. Environmental Microbiology, 13(1), 216-225. https://doi.org/10.1111/j.1462-2920.2010.02322.x
Hu, H. L., van den Brink, J., Gruben, B. S., Wösten, H. A. B., Gu, J. D., & de Vries, R. P. (2011). Improved enzyme production by co-cultivation of Aspergillus niger and Aspergillus oryzae and with other fungi. International Biodeterioration and Biodegradation, 65(1), 248-252. https://doi.org/10.1016/j.ibiod.2010.11.008
Amselem, J., Cuomo, C. A., Kan, J. A., Viaud, V., Benito, E. P., Couloux, A., Coutinho, P. M., de Vries, R. P., Dyer, P. S., Fillinger, S., Fourneir, E., Gout, L., Hahn, M., Kohn, L., Lapalu, N., Plummer, K. M., Pradier, J. M., Quévillon, E., Sharon, A., ... Dickman, M. (2011). Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, 7(8), e1022230.
Christensen, U., Gruben, B. S., Madrid, S., Mulder, H., Nikolaev, I., & de Vries, R. P. (2011). Unique regulatory mechanism for D-galactose utilization in Aspergillus nidulans. Applied and Environmental Microbiology, 77(19), 7084-7087.
Battaglia, E., Visser, L., Nijssen, A., van Veluw, G. J., Wösten, H. A. B., & de Vries, R. P. (2011). Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales. Studies in Mycology, 69(1), 31-38.
Battaglia, E., Hansen, S. F., Leendertse, A., Mulder, H., Nikolaev, I., & de Vries, R. P. (2011). Regulation of pentose utilisation by AraR, but not XInR, differs in Aspergillus nidulans and Aspergillus niger. Applied Microbiology and Biotechnology, 91, 387-397.
Battaglia, E., Benoit, I., van den Brink, J., Wiebenga, L. A., Coutinho, P. M., Henrissat, B., & de Vries, R. P. (2011). Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depcted at genome level. BMC Genomics, 17(12), 38.
Vinck, A., de Bekker, A. M., Ossin, A., Ohm, R. A., de Vries, R. P., & Wösten, H. A. B. (2011). Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colones. Environmental Microbiology, 13(1), 216-225.
Battaglia, E., Coutinho, P. M., Henrissat, B., Tenkanen, M., de Vries, R. P., & Chong, S. L. (2011). The alpha-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase. Applied Microbiology and Biotechnology, 90(4), 1323-1332.
Meijer, M., Houbraken, J., Dalhuijsen, S., Samson, R. A., & de Vries, R. P. (2011). Growth and hydrolase profiles can be used as characteristics to disginguish Aspergillus niger and otehr black aspergilli. Studies in Mycology, 69(1), 19-30.
Other output
Benoit, I., Hu, H., van den Brink, J., Gruben, B. S., Gu, J. D., de Vries, R. P., & Wösten, H. A. B. (2011). Co-cultivations of fungi improve the production of specific enzymes. Poster session presented at 26th Fungal Genetics Conference Asilomar 2011, Asilomar, USA.
2010
Scholarly publications
Ohm, R. A., De Jong, J. F., Lugones, L. G., Aerts, A., Kothe, E., Stajich, J. E., De Vries, R. P., Record, E., Levasseur, A., Baker, S. E., Bartholomew, K. A., Coutinho, P. M., Erdmann, S., Fowler, T. J., Gathman, A. C., Lombard, V., Henrissat, B., Knabe, N., Kües, U., ... Wösten, H. A. B. (2010). Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology, 28(9), 957-963. https://doi.org/10.1038/nbt.1643
Ohm, R. A., de Jong, J. F., Lugones, L. G., Aerts, A., Kothe, E., Stajich, J. E., de Vries, R. P., Record, E., Levasseur, A., Baker, S. E., Bartolomew, K. A., Coutinho, P. M., Erdmann, S., Fowler, T. J., Gathman, A. C., Lombard, V., Henrissat, B., Knabe, N., Kües, U., ... Wösten, H. A. B. (2010). Genome sequence of the model mushroom Schizophillum commune. Nature Biotechnology, 28(9), 957-963.
Aguilar-Osorio, G., Vankuyk, P. A., Seiboth, B., Solomon, P. S., Vinck, A., Kindt, F., Wösten, H. A. B., & de Vries, R. P. (2010). Spatial and developmental differentiation of mannitol dehydrogenase and mannitol-1-phosphate dehydrogenase in Aspergillus niger. Eukaryotic Cell, 9(9), 1398-1402.
Other output
Battaglia, E., Visser, L., Nijssen, A., van Veluw, G. J., Wösten, H. A. B., & de Vries, R. P. (2010). Analysis of regulation of pentose utilization in Aspergillus niger reveals evolutionary adaptations in the eurotiales. Poster session presented at 10th European Conference on Fungal Genetics, Noordwijkerhout (NH Conference Center Leeuwenhorst).
van Kuyk, P. A., de Vries, R. P., Visser, J., Ram, A., van den Hondel, C. A. M. J. J., Battaglia, E., & Vivas Duarte, D. A. (2010). Novel pentose transporters and uses thereof. PCT/NL2009/050683.
Battaglia, E., Visser, L., Nijssen, A., van Veluw, G. J., Wösten, H. A. B., & de Vries, R. P. (2010). Analysis of regulation of pentose utilization in Aspergillus niger reveals evolutionary adaptations in the eurotiales. Abstract from 10th European Conference on Fungal Genetics, Noordwijkerhout (NH Conference Center Leeuwenhorst).
2009
Scholarly publications
Rutten, L., Ribot, C., Trejo-Aguilar, B., Wösten, H. A. B., & De Vries, R. P. (2009). A single amino acid change (Y318F) in the L-arabitol dehydrogenase (LadA) from Aspergillus niger results in a significant increase in affinity for D-sorbitol. BMC Microbiology, 9, Article 166. https://doi.org/10.1186/1471-2180-9-166
Metz, B., de Vries, R. P., Polak, S., Seidl, V., & Seiboth, B. (2009). The Hypocrea jecorina lxr1 gene encodes a D-mannitol dehydrogenase and is not involved in L-arabinose catabolism. FEBS Letters, 583, 1309-1313.
Rutten, L., Ribot, C., Trejo-Aguilar, B., Pail, M., Wosten, H. A. B., & de Vries, R. P. (2009). A single amino acid change in the L-arabitol dehydrogenase (LadA) from Aspergillus niger broadens its substrate specificity and increases its activity. BMC Microbiology [E], 9, 166.
Coutinho, P. M., Anderson, P. M., Kolenova, K., Vankuyk, P. A., Benoit, I., Gruben, B. S., Trejo-Aguilar, B., Visser, H., van Solingen, P., Pakula, T., Seiboth, N. V., Battaglia, E., Aguilar-Osorio, G., de Jong, J. F., Ohm, R. A., Aguilar, M., Henrissat, B., Nielsen, J., Stalbrand, H., & de Vries, R. P. (2009). Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genetics and Biology, 46, S161-S169.
Wortman, J. R., Gilsenan, J. M., Joardar, V., Deegan, J., Clutterbuck, J., Andersen, M. R., Archer, D., Bencina, M., Braus, G., Coutinho, P., von Doehren, H., Doonan, J., Driessen, A., Durek, P., Espeso, E., Fekete, E., Flipphi, M., Garcia Estrada, C., Geysens, S., ... Turner, G. (2009). The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genetics and Biology, 46, S2-S13.
Wadman, M. W., de Vries, R. P., Kalkhove, S. I. C., Veldink, G. A., & Vliegenthart, J. F. G. (2009). Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger. BMC Microbiology [E], 9, 59.
Duranová, M., Spániková, S., Wösten, H. A. B., Biely, P., & de Vries, R. P. (2009). Two glucuronoyl esterases of Phanerochaete chrysosporium. Archives of Microbiology, 191(2), 133-140.
Alberto, F., Navarro, D., de Vries, R. P., Asther, M., & Record, E. (2009). Technical advance in fungal biotechnology: development of a miniaturized culture method and an automated high-throughput screening. Letters in Applied Microbiology, 49(2), 278-282.
Other output
Benoit, I., Battaglia, E., Coutinho, P. M., Henrissat, B., & de Vries, R. P. (2009). Phycomyces blakesleeanus and Rhizopus oryzae show significant differences in carbon utilization compared to ascomycete and basidiomycete fungi. Poster session presented at 25th Fungal Genetics Conference at Asilomar, Pacific Grove, CA, USA.
2008
Scholarly publications
de Vries, R. P., Lange, E. S., Wösten, H. A. B., & Stalpers, J. A. (2008). Control and possible applications of a novel carrot-spoilage basidiomycete, Fibulorhizoctonia psychrophila. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 93(4), 407-413. https://doi.org/10.1007/s10482-007-9218-7
Doehlemann, G., Wahl, R., Vranes, M., de Vries, R. P., Kämper, J., & Kahmann, R. (2008). Establishment of compatability in the Ustilago maydis/maize pathosystem. Journal of Plant Physiology, 165(1), 29-40.
Benoit, I., Danchin, E. G., Bleichrodt, R., & de Vries, R. P. (2008). Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnology Letters, 30(3), 387-396.
Li, X. L., Spániková, S., de Vries, R. P., & Biely, P. (2008). Identification of genes encoding microbial glucuronoyl esterases. FEBS Letters, 581(21), 4029-4035.
Espagne, E., Lespinet, O., Malagnac, F., Da Silva, C., Jaillon, O., Porcel, B. M., Couloux, A., Aury, J. M., Ségurens, B., Poulain, J., Anthouard, V., Grossetete, S., Khalil, H., Coppin, E., Déquard-Chablat, M., Picard, M., Contamine, V., Arnaise, S., Bourdais, A., ... Silar, P. (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology, 9(5), R77.
de Vries, R. P., de Lange, E. S., Wösten, H. A. B., & Stalpers, J. (2008). Fibulorhizoctonia psychrophila, a spoilage fungus of carrot, is a source of enzymes with high activity at low temperatures. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 93, 407-413.
de Vries, R. P. (2008). A genomic look at physiology and extracellular enzymes of Aspergillus in relation to utilization of plant matter. In J. Varga, & R. A. Samson (Eds.), Aspergillus in the genomic era (pp. 87-107). Wageningen Academic Publishers.
Müller, O., Kahmann, R., Aguilar, G., Trejo-Aguilar, B., Wu, A., & de Vries, R. P. (2008). The secretome of the maize pathogen Ustilago maydis. Fungal Genetics and Biology, 45, S63-S70.
Other output
de Vries, R. P. (2008). Advances in pectinolytic genes and regulation in Aspergillus. Poster session presented at 3rd International Symposium on Pectins and Pectinases, Wageningen, The Netherlands.
de Vries, R. P. (2008). Spatial differentiation of mannitol dehydrogenase and mannitol-1-phosphate dehydrogenase explains the absence of a mannitol cycle in Aspergillus niger. Abstract from 5th International Aspergillus Meeting (Asperfest).
2007
Scholarly publications
Pel, H. J., de Winde, J. H., Archer, D. B., Dyer, P. S., Hofmann, G., Schaap, P. J., Turner, G., de Vries, R. P., Albang, R., Albermann, K., Andersen, M. R., Bendtsen, J. D., Benen, J. A. E., van den Berg, M., Breestraat, S., Caddick, M. X., Contreras, R., Cornell, M., Coutinho, P. M., ... Stam, H. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology, 25(2), 221-231. https://doi.org/10.1038/nbt1282
Wösten, H. A. B., Scholtmeijer, K., & De Vries, R. P. (2007). Hyperproduction of enzymes by fungi. In Food Mycology: A Multifaceted Approach to Fungi and Food (pp. 183-196). CRC Press. https://doi.org/10.1201/9781420020984
Pel, H. J., Winde, H. J., Archer, D. B., Dyer, P. S., Hofmann, G., Schaap, P. J., Turner, G., de Vries, R. P., Albang, R., Albermann, K., Andersen, M. R., Bendtsen, J. D., Benen, J. A. E., van den Berg, M., Breestraat, S., Caddick, M. X., Contreras, R., Cornell, M., Coutinho, P. M., ... Stam, H. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger. Nature Biotechnology, 25(2), 221-231.
Levin Chucrel, A. M., de Vries, R. P., Conesa, A., de Bekker, A. M., Talon, M., Menke, H. H., van Peij, N. N., & Wösten, H. A. B. (2007). Spatial differentiation in the vegetative mycelium of Aspergillus niger. Eukaryotic Cell, 6(12), 2311-2322. https://doi.org/10.1128/EC.00244-07
Levin Chucrel, A. M., de Vries, R. P., & Wösten, H. A. B. (2007). Localization of protein secretion in fungal colonies using a novel culturing technique; the ring-plate system. Journal of Microbiological Methods, 69(2), 399-401.
de Groot, M. J. L., van den Dool, C., Wösten, H. A. B., Levisson, M., Vankuyk, P. A., Ruijter, G. J. G., & de Vries, R. P. (2007). Regulation of pentose catabolic pathway genes of Aspergillus niger. Food Technology and Biotechnology, 45(2), 134-138.
de Vries, R. P., Meijer, M., Houbraken, J., & Samson, R. (2007). Variation in growth and protein profiles among black aspergilli. In Aspergillus systematics in the genomic era; An international workshop; Programme, participants and abstracts (pp. 15-15). CBS Fungal Biodiversity Centre; An institute of the Royal Netherlands Academy of Arts and Sciences.
2006
Scholarly publications
Kamper, J., Kahmann, R., Bolker, M., Ma, L. J., Brefort, T., Saville, B. J., Banuett, F., Kronstad, J. W., Gold, S. E., Muller, O., Perlin, M. H., Wösten, H. A. B., de Vries, R. P., Ruiz-Herrera, J., Reynaga-Pena, C. G., Snetselaar, K., McCann, M., Perez-Martin, J., Feldbrugge, M., ... Birren, B. W. (2006). Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 444, 97-101.
Dijksterhuis, J., & de Vries, R. P. (2006). Compatible solutes and fungal development. Biochemical Journal, 399, e3-e5.
Other output
Wadman, M. W., Veldink, G. A., Vliegenthart, J. F. G., Wösten, H. A. B., & de Vries, R. P. (2006). Oxygenase from Aspergillus niger and their influence on sporulation and development. Poster session presented at 8th European Conference on Fungal Genetics, Vienna, Austria.
Vinck, A., Wu, A., de Vries, R. P., & Wösten, H. A. B. (2006). Transport of mRNA and proteins from a fungal mycelium to spore-forming aerial structures?. S36-S36. Abstract from Voorjaarsvergadering van de Nederlandse Vereniging voor Medische Microbiologie (NVMM) en de Nederlandse Vereniging voor Microbiologie (NVvM), Arnhem (Papendal).
2005
Scholarly publications
de Vries, R. P., van Grieken, C., vanKuyk, P. A., & Wösten, H. A. B. (2005). The value of genome sequences in the rapid identification of novel genes encoding specific plant cell wall degrading enzymes. Current Genomics, 6(3), 157-187. https://doi.org/10.2174/1389202053971974
de Vries, R. P., van Grieken, C., Vankuyk, P. A., & Wösten, H. A. B. (2005). The value of genomic sequences in the rapid identification of genes encoding specific plant cell wall degrading enzymes. Current Genomics, 6, 157-187.
de Vries, R. P., Frisvad, J. C., van de Vondervoort, P. J., Burgers, K., Kuijpers, A., Samson, R. A., & Visser, J. (2005). Aspergillus vadensis, a new species of the group of black aspergilli. antonie van leeuwenhoek, 87, 195-203.
2004
Scholarly publications
de Vries, R. P., Burgers, K., van de Vondervoort, P. J., Frisvad, J. C., Samson, R. A., & Visser, J. (2004). A new black Aspergillus species, A. vadensis, is a promising host for homologous and heterologous protein production. Applied and Environmental Microbiology, 70, 3954-3959.
Other output
Levin Chucrel, A. M., de Vries, R. P., & Wösten, H. A. B. (2004). Differential protein secretion in Aspergillus niger. Abstract from 7th European Conference on Fungal Genetics Copenhagen, Kopenhagen.
2003
Scholarly publications
de Vries, R. P. (2003). Regulation of Aspergillus genes encoding plant cell wall polysaccharide-degrading enzymes; relevance for industrial production. Applied Microbiology and Biotechnology, 61, 10-20.
Other output
Levin Chucrel, A. M., de Vries, R. P., & Wösten, H. A. B. (2003). Differential protein secretion in Aspergillus niger. Abstract from Voorjaarsvergadering NVMM/NVvM, Papendal.
van Kuyk, P. A., Visser, J., Levin Chucrel, A. M., Wösten, H. A. B., & de Vries, R. P. (2003). The influence of AmyR on extracellular enzyme production by A. niger is not limited to enzmyes involved in starch degradation. Abstract from 22nd Fungal Genetics Conference, Asilomar, California, United States.
2002
Scholarly publications
de Vries, R. P., Jansen, J., Aguilar, G., Parenicova, L., Joosten, V., & Wulfert, F. (2002). Expression profiling of pectinolytic genes from Aspergillus niger. FEBS Letters, 530(1-3), 41-47.
de Vries, R. P., van de Vondervoort, P. J., Hendriks, L., van de Belt, M., & Visser, J. (2002). Regulation of the alpha-glucuronidase-encoding gene (aguA) from Aspergillus niger. Molecular Genetics and Genomics, 268(1), 96-102.
Other output
de Vries, R. P., van Kuyk, P., de Groot, M., & Visser, J. (2002). Regulation of the beta-galactosidase encoding gene (lacA) from Aspergillus niger. Abstract from Unknown event, Asilomar, USA.
2001
Scholarly publications
de Vries, R. P., Benen, J. A. E., de Graaff, L. H., & Visser, J. (2001). Plant cell wall degrading enzymes produced by Aspergillus. In H. D. Osiewacz (Ed.), Industrial Applications, The Mycota vol. X (pp. 263-279). Springer.
de Vries, R. P., & Visser, J. (2001). Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiology and Molecular Biology Reviews, 65, 497-522.
Fillinger, S., Chaveroche, M-K., van Dijck, P. F. F. M., de Vries, R. P., Ruijter, G., Thevelein, J., & d' Enfert, C. (2001). Characterization of the trehalose-6-phosphate synthase gene in the filamentous fungus Aspergillus nidulans: physiological roles of trehalose-6-phosphate and trehalose. Microbiology, 147, 1851-1862.
Ademark, P., de Vries, R. P., Hägglund, P., Stalbrand, H., & Visser, J. (2001). Cloning and characterization of genes encoding a ß-mannosidase and an a-galactosidase from Aspergillus niger involved in galactomannan degradation. European Journal of Biochemistry, 268, 2982-2990.