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  • Ronald P. de Vries
2020

CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer

Salazar-Cerezo, S., Kun, R. S., de Vries, R. P. & Garrigues, S., Feb 2020, In : Enzyme and microbial technology. 133, p. 109463

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens

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., 20 Jan 2020, In : Journal of Biotechnology. 308, p. 35-39 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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

Coconi Linares, N., Dilokpimol, A., Stålbrand, H., Mäkelä, M. R. & de Vries, R. P., Jan 2020, In : Bioresource Technology. 295, p. 122258

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
2019

A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi

Lubbers, R. J. M., Dilokpimol, A., Visser, J., Makela, M. R., Hilden, K. S. & de Vries, R. P., 15 Nov 2019, In : BIOTECHNOLOGY ADVANCES. 37, 7

Research output: Contribution to journal/periodicalBook/Film/Article reviewScientific

Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger

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, In : Frontiers in bioengineering and biotechnology. 7, p. 249

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Daly, P., Peng, M., Mitchell, H. D., Kim, Y-M., Ansong, C., Brewer, H., de 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. & de Vries, R. P., 25 Dec 2019, In : Environmental Microbiology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass

Benocci, T., Aguilar-Pontes, M. V., Kun, R. S., Lubbers, R. J. M., Lail, K., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V., Seiboth, B., Daly, P. & de Vries, R. P., 09 Apr 2019

Research output: Other contributionScientific

Open Access

Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation

Kun, R. S., Gomes, A. C. S., Hilden, K. S., Cerezo, S. S., Makela, M. R. & de Vries, R. P., 01 Nov 2019, In : BIOTECHNOLOGY ADVANCES. 37, 6

Research output: Contribution to journal/periodicalBook/Film/Article reviewScientific

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

Lubbers, R. J. M., Dilokpimol, A., Peng, M., Visser, J., Makela, M. R., Hilden, K. S. & de Vries, R. P., 02 Dec 2019, In : ACS Sustainable Chemistry & Engineering. 7, 23, p. 19081-19089

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Draft Genome Sequences of Three Monokaryotic Isolates o the White-Rot Basidiomycete Fungus Dichomitus squalens

Lopez, S. C., Peng, M., Daly, P., Andreopoulos, B., Pangilinan, J., Lipzen, A., Riley, R., Ahrendt, S., Ng, V., Barry, K., Daum, C., Grigoriev, I. V., Hilden, K. S., Makela, M. R. & de Vries, R. P., May 2019, In : MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 8, 18

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

Lubbers, R. J. M., Liwanag, A. J., Peng, M., Dilokpimol, A., Benoit-Gelber, I. & de Vries, R. P., 29 Oct 2019, In : Journal of Applied Microbiology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens

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., 01 Dec 2019, In : Applied and Environmental Microbiology. 85, 23

Research output: Contribution to journal/periodicalArticleScientificpeer-review

l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans

Németh, Z., Kulcsár, L., Flipphi, M., Orosz, A., Aguilar-Pontes, M. V., de Vries, R. P., Karaffa, L. & Fekete, E., Feb 2019, In : Fungal Genetics and Biology. 123, p. 53-59 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Macroalgae Derived Fungi Have High Abilities to Degrade Algal Polymers

Patyshakuliyeva, A., Falkoski, D. L., Wiebenga, A., Timmermans, K. & Vries, R. P. D., 26 Dec 2019, In : Microorganisms. 8, 1

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

Dos Santos Gomes, A. C., Falkoski, D., Battaglia, E., Peng, M., Nicolau de Almeida, M., Coconi Linares, N., Meijnen, J-P., Visser, J. & de Vries, R. P., 2019, In : Biotechnology for Biofuels. 12, p. 220

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The current biotechnological status and potential of plant and algal biomass degrading/modifying enzymes from ascomycete fungi.

de Vries, R. P., Patyshakuliyeva, A., Garrigues, S. & Agarwal-Jans, S., 2019, Grand challenges in Fungal Biotechnology. Nevalainen, H. (ed.). Springer Nature, p. 81-120 40 p.

Research output: Chapter in book/volumeChapterScientificpeer-review

The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum

Linares, N. C., Di Falco, M., Benoit-Gelber, I., Gruben, B. S., Peng, M., Tsang, A., Makela, M. R. & de Vries, R. P., 25 Jul 2019, In : New Biotechnology. 51, p. 57-66

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The quest for fungal strains and their co-culture potential to improve enzymatic degradation of Chinese distillers' grain and other agricultural wastes

Ming, C., Dilokpimol, A., Zou, C., Liao, W., Zhao, L., Wang, M., de Vries, R. P. & Kang, Y., Oct 2019, In : International Biodeterioration & Biodegradation. 144

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

Khosravi, C., Kowalczyk, J. E., Chroumpi, T., Battaglia, E., Aguilar Pontes, M-V., Peng, M., Wiebenga, A., Ng, V., Lipzen, A., He, G., Bauer, D., Grigoriev, I. V. & de Vries, R. P., 14 Nov 2019, In : BMC Genomics. 20, 1, p. 853

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
2018

A community-driven reconstruction of the metabolic network

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, In : Fungal Biology and Biotechnology. 5, p. 16

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A senescence-delaying pre-culture medium for transcriptomics of Podospora anserina

Benocci, T., de Vries, R. P. & Daly, P., Mar 2018, In : Journal of Microbiological Methods. 146, p. 33-36

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Basidiomycete Genomics

de Vries, R. P., Makela, M. R., Hilden, K. S. & Kamper, J., Mar 2018, In : Fungal Genetics and Biology. 112, p. 1-1

Research output: Contribution to journal/periodicalEditorial (disabled)Scientific

Open Access

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Khosravi, C., Battaglia, E., Kun, R. S., Dalhuijsen, S., Visser, J., Aguilar-Pontes, M. V., Zhou, M., Heyman, H. M., Kim, Y-M., Ronald, S. E. B. & de Vries, R. P., 22 Mar 2018, In : BMC Genomics. 19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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

Makela, M. R., Dilokpimol, A., Koskela, S. M., Kuuskeri, J., de Vries, R. P. & Hilden, K., Sep 2018, In : Microbial Biotechnology. 11, 5, p. 869-880

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes

Peng, M., Aguilar-Pontes, M. V., Hainaut, M., Henrissat, B., Hildén, K., Mäkelä, M. R. & de Vries, R. P., Mar 2018, In : Fungal Genetics and Biology. p. 40-46

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

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., Maekelae, M. R. & 1 others, de Vries, R. P., Nov 2018, In : Environmental Microbiology. 20, 11, p. 4141-4156

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Draft Genome Sequence of Talaromyces adpressus

Cerullo, G., Houbraken, J., Granchi, Z., Pepe, O., Varriale, S., Ventorino, V., Chin-A-Woeng, T., Meijer, M., de Vries, R. P. & Faraco, V., Jan 2018, In : MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 6, 2, p. e01430-17

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga

Makela, M. R., Peng, M., Granchi, Z., Chin-A-Woeng, T., Hegi, R., van Pelt, S. I., Ahrendt, S., Riley, R., Hainaut, M., Henrissat, B., Grigoriev, I. V., de Vries, R. P. & Hilden, K. S., Apr 2018, In : MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 6, 14

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
Open Access

Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails

Benocci, T., Daly, P., Aguilar-Pontes, M. V., Lail, K., Wang, M., Lipzen, A., Ng, V., Grigoriev, I. V. & de Vries, R. P., 17 Sep 2018, In : Biotechnology Journal. p. e1800185

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Evolutionary Adaptation to Generate Mutants

de Vries, R. P., Lubbers, R., Patyshakuliyeva, A., Wiebenga, A. & Benoit-Gelber, I., 2018, In : Methods in Molecular Biology. 1775, p. 133-137 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies

Dilokpimol, A., Makela, M. R., Varriale, S., Zhou, M., Cerullo, G., Gidijala, L., Hinkka, H., Bras, J. L. A., Juetten, P., Piechot, A., Verhaert, R., Hilden, K. S., Faraco, V. & de Vries, R. P., 25 Mar 2018, In : New Biotechnology. 41, p. 9-14 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Fungal Genomics: Methods and Protocols

de Vries, R. P., Tsang, A. & Grigoriev, I. V., 2018, Springer. (Methods in Molecular Biology)

Research output: Book/ReportBookScientificpeer-review

Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization

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., 25 Jan 2018, In : New Biotechnology. 40, Pt B, p. 282-287 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Fungal Stress Database (FSD)-a repository of fungal stress physiological data

Orosz, E., van de wiele, N., Emri, T., Zhou, M., Robert, V., de Vries, R. P. & Pocsi, I., 12 Feb 2018, In : DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

de Vries, R. P., Makela, M. R., DiFalco, M., McDonnell, E., Hilden, K. S., Peng, M., Grigoriev, I. V. & Tsang, A., 2018, In : Studies in Mycology. 91, p. 79-99

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales)

Urquhart, A. S., Mondo, S. J., Makela, M. R., Hane, J. K., Wiebenga, A., Het, G., Mihaltcheva, S., Pangilinan, J., Lipzen, A., Barry, K., De Vries, R. P., Grigoriev, I. V. & Idnurm, A., 13 Dec 2018, In : Frontiers in Microbiology. 9

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Improved hemicellulase production by genetic modification of carbon catabolite repression and xylanolitic activation in Aspergillus niger

de Vries, R. P., Robl, D., Padilla, G. & da Cruz Pradella, JG., 2018, In : Current Biotechnology. 7, p. 10-18 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens

Lopez, S. C., Peng, M., Issak, T. Y., Daly, P., de Vries, R. P. & Makela, M. R., Jun 2018, In : Applied and Environmental Microbiology. 84, 11

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics

Peng, M., Aguilar-Pontes, M. V., de Vries, R. P. & Makela, M. R., 18 May 2018, In : Frontiers in Microbiology. 9

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Introduction: Overview of Fungal Genomics

de Vries, R. P., Grigoriev, I. V. & Tsang, A., 2018, In : Methods in Molecular Biology. 1775, p. 1-7 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

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., Chen, C. & 19 others, LaButti, K., Haridas, S., Nolan, M., Sandor, L., Kuo, A., Lipzen, A., Hainaut, M., Drula, E., Tsang, A., Magnuson, J. K., Henrissat, B., Wiebenga, A., Simmons, B. A., Makela, M. R., de Vries, R. P., Grigoriev, I. V., Mortensen, U. H., Baker, S. E. & Andersen, M. R., Dec 2018, In : Nature Genetics. 50, 12, p. 1688-+

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

On the origin of vanillyl alcohol oxidases

Gygli, G., de Vries, R. P. & van Berkel, W. J. H., Jul 2018, In : Fungal Genetics and Biology. 116, p. 24-32

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Physiological background of the remarkably high Cd2+ tolerance of the Aspergillus fumigatus Af293 strain

Kurucz, V., Kiss, B., Szigeti, Z. M., Nagy, G., Orosz, E., Hargitai, Z., Harangi, S., Wiebenga, A., de Vries, R. P., Pocsi, I. & Emri, T., Nov 2018, In : Journal of Basic Microbiology. 58, 11, p. 957-967

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Role of microbial cultures and enzymes during cheese production and ripening

de Vries, R. P., 2018, Microbial cultures and enzymes in dairy technology. : Advances in Medical Technologies and Clinical Practice (AMTCP). IGI Global, p. 182-203

Research output: Chapter in book/volumeChapterScientificpeer-review

Selective Cleavage of Lignin beta-O-4 Aryl Ether Bond by beta-Etherase of the White-Rot Fungus Dichomitus squalens

Marinovic, M., Nousiainen, P., Dilokpimol, A., Kontro, J., Moore, R., Sipila, J., de Vries, R. P., Makela, M. R. & Hilden, K., Mar 2018, In : ACS Sustainable Chemistry & Engineering. 6, 3, p. 2878-2882

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion.

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., 27 May 2018, In : Mycologia. p. 316 324 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Temporal microbiota and biochemical profiles during production and ripening of Divle Cave cheese

Ozturkoglu-Budak, S., Aykas, D. P., Kocak, C., Donmez, S., Gursoy, A., De Vries, R. P. & Bron, P. A., Mar 2018, In : International Journal of Dairy Technology. 71, p. 99-106

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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

Marinović, M., Aguilar-Pontes, M. V., Zhou, M., Miettinen, O., de Vries, R. P., Mäkelä, M. R. & Hildén, K., Mar 2018, In : Fungal Genetics and Biology. 112, p. 47-54

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

Makela, M. R., Aguilar-Pontes, M. V., van Rossen-Uffink, D., Peng, M. & de Vries, R. P., 27 Apr 2018, In : Scientific Reports. 8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access