Publications

2020

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., Hilden, K. S., Kabel, M. A., Baker, S. E., Makela, M. R. & de Vries, R. P., Jan 2020, In : Environmental Microbiology. 22, 3, p. 1154-1166 13 p.

Research output: Contribution to journalArticleScientificpeer-review

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Fungal Treatment Modifies Kraft Lignin for Lignin- and Cellulose-Based Carbon Fiber Precursors

Mikkila, J., Trogen, M., Koivu, K. A. Y., Kontro, J., Kuuskeri, J., Maltari, R., Dekere, Z., Kemell, M., Makela, M. R., Nousiainen, P. A., Hummel, M., Sipila, J. & Hilden, K., 24 Mar 2020, In : ACS Omega. 5, 11, p. 6130-6140 11 p.

Research output: Contribution to journalArticleScientificpeer-review

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Impacts of holmium and lithium to the growth of selected basidiomycetous fungi and their ability to degrade textile dyes

Kahkonen, M. A., Miettinen, O. & Hilden, K. S., 28 Jul 2020, In : 3 Biotech. 10, 8, 6 p., 357.

Research output: Contribution to journalArticleScientificpeer-review

On the Effect of Hot-Water Pretreatment in Sulfur-Free Pulping of Aspen and Wheat Straw

Hyväkkö, U., Maltari, R., Kakko, T., Kontro, J., Mikkilä, J., Kilpeläinen, P., Enqvist, E., Tikka, P., Hilden, K., Nousiainen, P. & Sipilä, J., 14 Jan 2020, In : ACS Omega. 5, 1, p. 265-273 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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Penicillium subrubescens adapts its enzyme production to the composition of plant biomass

Dilokpimol, A., Peng, M., Di Falco, M., Chin A Woeng, T., Maria Wilhelmina Hegi, R., Granchi, Z., Tsang, A., Hildén, K. S., Mäkelä, M. R. & de Vries, R. P., Sep 2020, In : Bioresource Technology. 311, 9 p., 123477.

Research output: Contribution to journalArticleScientificpeer-review

Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi

Mäkelä, M. R., Hilden, K., Kowalczyk, J. E. & Hatakka, A., 2020, Grand Challenges in Fungal Biotechnology. Nevalainen, H. (ed.). Springer International Publishing , p. 405-438 ( Grand Challenges in Biology and Biotechnology).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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, 27 p., 107396.

Research output: Contribution to journalReview ArticleScientificpeer-review

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., 27 Sep 2019, In : Frontiers in Bioengineering and Biotechnology. 7, 12 p., 249.

Research output: Contribution to journalArticleScientificpeer-review

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

Kun, R., Gomes, A. C. S., Hilden, S. K., Salazar Cerezo, S., Mäkelä, M. R. & de Vries, R., 1 Nov 2019, In : Biotechnology Advances. 37, 6, 16 p., 107361.

Research output: Contribution to journalReview ArticleScientificpeer-review

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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., 2 Dec 2019, In : ACS Sustainable Chemistry & Engineering. 7, 23, p. 19081-19089 19 p.

Research output: Contribution to journalArticleScientificpeer-review

Draft genome sequences of three monokaryotic isolates of the white-rot basidiomycete fungus Dichomitus squalens

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., Hilden, S. K., Mäkelä, M. R. & de Vries, R. P., 2 May 2019, In : Microbiology Resource Announcements. 8, 18, 3 p., e00264-19.

Research output: Contribution to journalArticleScientificpeer-review

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Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

Mäkinen, M., Kuuskeri, J., Laine, P., Smolander, O-P., Kovalchuk, A., Zeng, Z., Asiegbu, F., Paulin, L., Auvinen, P. & Lundell, T., 28 May 2019, In : BMC Genomics. 20, 22 p., 430.

Research output: Contribution to journalArticleScientificpeer-review

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On the role of hot water extraction as a pretreatment method in search for soft pulping methods for modern biorefineries

Sipilä, J., Hyväkkö, U., Maltari, R., Kakko, T-A., Kontro, J., Mikkilä, J. A., Kilpeläinen, P., Enqvist, E., Tikka, P., Hilden, K. & Nousiainen, P. A., 31 Mar 2019. 1 p.

Research output: Conference materialsAbstract

Basidiomycete Genomics

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

Research output: Contribution to journalEditorialScientific

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Biochemical characterization of laccases from the white-rot fungus Obba rivulosa

Kähkönen, M. A., Nousiainen, P. A., Kontro, J. H. S., Marinovic, M., Baig, I., Kamer, P., Sipilä, A. J., Mäkelä, M. R. & Hilden, S. K., 29 Aug 2018, p. 32.

Research output: Conference materialsAbstract

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

Mäkelä, 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 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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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., Hilden, K., Mäkelä, M. R. & de Vries, R. P., Mar 2018, In : Fungal Genetics and Biology. 112, p. 40-46 7 p.

Research output: Contribution to journalArticleScientificpeer-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., Mäkelä, M. R. & 1 others, de Vries, R. P., Nov 2018, In : Environmental Microbiology. 20, 11, p. 4141-4156 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Draft genome sequence of the basidiomycete white-rot fungus Phlebia centrifuga

Mäkelä, M. R., Peng, M., Granchi, Z., Chin-A-Woeng, T., Hegi, R., van Pelt, S., Ahrendt, S., Riley, R., Heinaut, M., Henrissat, B., Grigoriev, I., de Vries, R. & Hilden, S. K., Apr 2018, In : Genome Announcements. 6, 14, 2 p., UNSP e01414-17.

Research output: Contribution to journalArticleScientificpeer-review

Efficient extraction method for high quality fungal RNA from complex lignocellulosic substrates

Mäkelä, M. R. & Hilden, S. K., 2018, Fungal Genomics: methods and protocols. de Vries, R. & Tsang, A. (eds.). 2. ed. New York: Humana press, Vol. 1775. p. 69-73 5 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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

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

Research output: Contribution to journalArticleScientificpeer-review

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

Dilokpimol, A., Makela, M. R., Cerullo, G., Zhou, M., Varriale, S., Gidijala, L., Bras, J. L. A., Jutten, P., Piechot, A., Verhaert, R., Faraco, V., Hilden, K. S. & de Vries, R. P., 25 Jan 2018, In : New Biotechnology. 40, Part B, p. 282-287 6 p.

Research output: Contribution to journalArticleScientificpeer-review

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Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Mäkelä, M. R., Di Falco, M., McDonnell, E., Nguyen, T. T. M., Wiebenga, A., Hilden, S. K., Peng, M., Grigoriev, I. V., Tsang, A. & de Vries, R. P., Sep 2018, In : Studies in Mycology. 91, p. 79-99 21 p.

Research output: Contribution to journalArticleScientificpeer-review

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On the effect of hot-water pretreatment in the chemical pulping of wood and annual plants in microwave reactor

Hyväkkö, U. T., Kakko, T-A., Maltari, R. A., Kontro, J. H. S., Mikkilä, J. A., Kilpeläinen, P., Enqvist, E., Tikka, P., Nousiainen, P. A. & Sipilä, A. J., 2018.

Research output: Conference materialsOther conference material

Puunlahottajat

Lundell, T. & Mäkelä, M., 2018, Sienten biologia. Timonen, S. & Valkonen, J. (eds.). 2. ed. Helsinki: Gaudeamus, p. 259-279

Research output: Chapter in Book/Report/Conference proceedingChapterProfessional

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Role of Fungi in Wood Decay

Hildén, K. & Mäkelä, M. R., 26 Apr 2018, Reference Module in Life Sciences. Roitberg, B. D. (ed.). Elsevier, Vol. 2018.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Open Access

The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates

Pontes, M. V. A., Patyshakuliyeva, A., Post, H., Jurak, E., Hilden, K., Altelaar, M., Heck, A., Kabel, M. A., de Vries, R. P. & Mäkelä, M. R., Mar 2018, In : Fungal Genetics and Biology. 112, p. 12-20 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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The Synthetic Potential of Fungal Feruloyl Esterases: A Correlation with Current Classification Systems and Predicted Structural Properties

Antonopoulou, I., Dilokpimol, A., Iancu, L., Mäkelä, 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., Jun 2018, In : Catalysts. 8, 6, 22 p., 242.

Research output: Contribution to journalArticleScientificpeer-review

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2017

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

de Vries, R. P., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Akemi Uchima, C., Anderluh, G., Asadollahi, M., Askin, M., Barry, K., Battaglia, E., Bayram, Ö., Benocci, T., Braus-Stromeyer, S. A., Caldana, C., Cánovas, D., Cerqueira, G. C., Chen, F., Chen, W., Choi, C. & 97 others, Clum, A., Corrêa dos Santos, R. A., de Lima Damásio, A. R., Diallinas, G., Emri, T., Fekete, E., Flipphi, M., Freyberg, S., Gallo, A., Gournas, C., Habgood, R., Hainaut, M., Harispe, M. L., Henrissat, B., Hilden, S. K., Hope, R., Hossain, A., Karabika, E., Karaffa, L., Karányi, Z., Kraševec, N., Kuo, A., Kusch, H., LaButti, K., Lagendijk, E. L., Lapidus, A., Levasseur, A., Lindquist, E., Lipzen, A., Logrieco, A. F., MacCabe, A., Mäkelä, M. R., Malavazi, I., Melin, P., Meyer, V., Mielnichuk, N., Miskei, M., Molnár, Á. P., Mulé, G., Ngan, C. Y., Orejas, M., Orosz, E., Ouedraogo, J. P., Overkamp, K. M., Park, H-S., Perrone, G., Piumi, F., Punt, P. J., Ram, A. F. J., Ramón, A., Rauscher, S., Record, E., Riaño-Pachón, D. M., Robert, V., Röhrig, J., Ruller, R., Salamov, A., Salih, N. S., Samson, R. A., Sándor, E., Sanguinetti, M., Schütze, T., Sepčić, K., Shelest, E., Sherlock, G., Sophianopoulou, V., Squina, F. M., Sun, H., Susca, A., Todd, R. B., Tsang, A., Unkles, S. E., van de Wiele, N., van Rossen-Uffink, D., Velasco de Castro Oliveira, J., Vesth, T. C., Visser, J., Yu, J-H., Zhou, M., Andersen, M. R., Archer, D. B., Baker, S. E., Benoit, I., Brakhage, A. A., Braus, G. H., Fischer, R., Frisvad, J. C., Goldman, G. H., Houbraken, J., Oakley, B., Pócsi, I., Scazzocchio, C., Seiboth, B., vanKuyk, P. A., Wortman, J., Dyer, P. S. & Grigoriev, I. V., 2017, In : Genome Biology. 18, 28, 45 p.

Research output: Contribution to journalArticleScientificpeer-review

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Engineering towards catalytic use of fungal class-II peroxidases for dye-decolorizing and conversion of lignin model compounds

Lundell, T. K., Bentley, E., Hilden, S. K., Rytioja, J. T., Kuuskeri, J. T., Ufot, U. F., Nousiainen, P. A., Hofrichter, M., Wahlsten, M. P-V., Doyle, W. & Smith, A. T., 2017, In : Current Biotechnology. 6, 2, p. 116-117 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Expanding the feruloyl esterase gene family of Aspergillus niger by characterization of a feruloyl esterase, FaeC

Dilokpimol, A., Mäkelä, M. R., Mansouri, S., Belova, O., Waterstraat, M., Bunzel, M., de Vries, R. P. & Hilden, K. S., 25 Jul 2017, In : New Biotechnology. 37, p. 200-209 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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Functional diversity in Dichomitus squalens monokaryons

Lopez, S. C., Theelen, B., Manserra, S., Issak, T. Y., Rytioja, J., Makelä, M. R. & de Vries, R. P., Jun 2017, In : IMA Fungus. 8, 1, p. 17-25 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes

Mali, T., Kuuskeri, J., Shah, F. & Lundell, T. K., 27 Sep 2017, In : PLoS One. 12, 9, 21 p., e0185171.

Research output: Contribution to journalArticleScientificpeer-review

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Newtonian boreal forest ecology: The Scots pine ecosystem as an example

Hari, P., Aakala, T., Aalto, J., Back, J., Hollmen, J., Jogiste, K., Koupaei, K. K., Kahkonen, M. A., Korpela, M., Kulmala, L., Nikinmaa, E., Pumpanen, J., Salkinoja-Salonen, M., Schiestl-Aalto, P., Simojoki, A. & Havimo, M., 14 Jun 2017, In : PLoS One. 12, 6, 27 p., 0177927.

Research output: Contribution to journalArticleScientificpeer-review

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The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi

Peng, M., Dilokpirnol, A., Mäkelä, M. R., Hilden, K., Bervoets, S., Riley, R., Grigoriev, I. V., Hainaut, M., Henrissat, B., de Vries, R. P. & Granchi, Z., 20 Mar 2017, In : Journal of Biotechnology. 246, p. 1-3 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

Rytioja, J., Hilden, K., Di Falco, M., Zhou, M., Aguilar-Pontes, M. V., Sietiö, O-M., Tsang, A., de Vries, R. & Mäkelä, M. R., 2017, In : Environmental Microbiology. 19, 3, p. 1237-1250 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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2016

Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications

Dilokpimol, A., Mäkelä, M. R., Aguilar-Pontes, M. V., Benoit-Gelber, I., Hilden, S. K. & de Vries, R., 2016, In : Biotechnology for Biofuels. 9, p. 231 18 p., 231.

Research output: Contribution to journalReview ArticleScientificpeer-review

Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

Miettinen, O., Riley, R., Barry, K., Cullen, D., de Vries, R. P., Hainaut, M., Hatakka, A., Henrissat, B., Hildén, K., Kuo, R., LaButti, K., Lipzen, A., Mäkelä, M. R., Sandor, L., Spatafora, J. W., Grigoriev, I. V. & Hibbett, D. S., 2016, In : Genome Announcements. 4, 5, 2 p., e00976-16.

Research output: Contribution to journalArticleScientificpeer-review

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Enzymatic plant cell wall degradation by the white rot fungus Dichomitus squalens

Rytioja, J., 2016, Helsinki: University of Helsinki. 82 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Fungal degradation of plant oligo- and polysaccharides

de Vries, R. P., van den Brink, J., Hilden, K. S., Mäkelä, M. R. & Stålbrand, H., 2016, Handbook of Carbohydrate-Modifying Biocatalysts. Grunwald, P. (ed.). 2. ed. Singapore: Pan Stanford Publishing, p. 809-896 87 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review