List of works - Miia R. Mäkelä

A comparative genomics study of 23 Aspergillus species from section Flavi

scientific article published on 27 February 2020

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

article

Agaricus bisporus and related Agaricus species on lignocellulose: production of manganese peroxidase and multicopper oxidases

scientific article published on 21 February 2013

An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates

scientific article

Applicability of Recombinant Laccases From the White-Rot Fungus <i>Obba rivulosa</i> for Mediator-Promoted Oxidation of Biorefinery Lignin at Low pH

scientific article published on 17 December 2020

Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

scientific article published on 24 February 2015

Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox.

scientific article

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

scientific article

Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion.

scientific article published on January 2014

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.

scientific article published on 26 April 2018

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

scientific article

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

scientific article published on 06 January 2020

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

scientific article published on 10 August 2017

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

scientific article

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

scientific article published on 03 March 2021

Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis

scientific article

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

scientific article published on 27 February 2019

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

scientific article published on 18 October 2018

Discovery and functional analysis of a salicylic acid hydroxylase from <i>Aspergillus niger</i>

scientific article published on 04 January 2021

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 02 May 2019

Effect of copper, nutrient nitrogen, and wood-supplement on the production of lignin-modifying enzymes by the white-rot fungus Phlebia radiata

scientific article published on 13 December 2012

Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates

scientific article published on 01 January 2018

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

scientific article

Expression and molecular properties of a new laccase of the white rot fungus Phlebia radiata grown on wood

scientific article published on 23 August 2006

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

scientific article

Functional diversity in Dichomitus squalens monokaryons

scientific article published on 8 March 2017

Fungal Ligninolytic Enzymes and Their Applications.

scientific article published on December 2016

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

scientific article published on 10 March 2020

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

scientific article

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

scientific article published on 16 October 2017

GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans

scientific article published on 25 February 2022

Genetic transformation of the white-rot fungus Dichomitus squalens using a new commercial protoplasting cocktail.

scientific article published on 4 October 2017

Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735.

scientific article

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

scientific article published on 13 December 2018

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

scientific article published on 01 September 2018

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

scientific article published on 14 November 2019

Heterologous expression and structural characterization of two low pH laccases from a biopulping white-rot fungus Physisporinus rivulosus.

scientific article

Identification of an l-Arabitol Transporter from Aspergillus niger

scientific article published in 2023

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

scientific article published on 18 May 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

scientific article published in 2018

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

article

Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota).

scientific article published on 19 October 2015

Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events

scientific article

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

scientific article published on 25 November 2019

Occurrence and function of enzymes for lignocellulose degradation in commercial Agaricus bisporus cultivation

scientific article

Oxalate decarboxylase of the white-rot fungus Dichomitus squalens demonstrates a novel enzyme primary structure and non-induced expression on wood and in liquid cultures.

scientific article published on 23 April 2009

Oxalate decarboxylase: biotechnological update and prevalence of the enzyme in filamentous fungi.

scientific article published on 13 May 2010

Oxalate-metabolising genes of the white-rot fungus Dichomitus squalens are differentially induced on wood and at high proton concentration

scientific article

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification

scientific article

Plant biomass degradation by fungi

scientific article

Plant biomass degradation by fungi

article

Plant-polysaccharide-degrading enzymes from Basidiomycetes

scientific article

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

scientific article published on 08 March 2021

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

scientific article published on 11 October 2019

Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity

scientific article published on 05 March 2021

Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens

scientific article published on 14 December 2015

Selective Cleavage of Lignin β--4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus

scientific article published on 25 January 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.

scientific article

The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp

scientific article published on 25 August 2021

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

The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds

scientific article published on 20 September 2019

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 22 December 2017

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

scientific article published on 20 February 2019

Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose.

scientific article published on 3 January 2014

Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle.

scientific article published on 28 June 2015

List of works by Miia R. Mäkelä

A comparative genomics study of 23 Aspergillus species from section Flavi

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

Agaricus bisporus and related Agaricus species on lignocellulose: production of manganese peroxidase and multicopper oxidases

An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates

Applicability of Recombinant Laccases From the White-Rot Fungus <i>Obba rivulosa</i> for Mediator-Promoted Oxidation of Biorefinery Lignin at Low pH

Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox.

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion.

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.

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

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

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

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

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis

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

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

Discovery and functional analysis of a salicylic acid hydroxylase from <i>Aspergillus niger</i>

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

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

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

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

Effect of copper, nutrient nitrogen, and wood-supplement on the production of lignin-modifying enzymes by the white-rot fungus Phlebia radiata

Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates

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

Expression and molecular properties of a new laccase of the white rot fungus Phlebia radiata grown on wood

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

Functional diversity in Dichomitus squalens monokaryons

Fungal Ligninolytic Enzymes and Their Applications.

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

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

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

GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans

Genetic transformation of the white-rot fungus Dichomitus squalens using a new commercial protoplasting cocktail.

Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735.

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

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

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

Heterologous expression and structural characterization of two low pH laccases from a biopulping white-rot fungus Physisporinus rivulosus.

Identification of an l-Arabitol Transporter from Aspergillus niger

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

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

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

Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota).

Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events

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

Occurrence and function of enzymes for lignocellulose degradation in commercial Agaricus bisporus cultivation

Oxalate decarboxylase of the white-rot fungus Dichomitus squalens demonstrates a novel enzyme primary structure and non-induced expression on wood and in liquid cultures.

Oxalate decarboxylase: biotechnological update and prevalence of the enzyme in filamentous fungi.

Oxalate-metabolising genes of the white-rot fungus Dichomitus squalens are differentially induced on wood and at high proton concentration

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification

Plant biomass degradation by fungi

Plant biomass degradation by fungi

Plant-polysaccharide-degrading enzymes from Basidiomycetes

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

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

Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity

Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens

Selective Cleavage of Lignin β--4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus

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.

The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp

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

The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds

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

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

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

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

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

Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose.

Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle.