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List of works by Ronald P de Vries

(Post-)genomics approaches in fungal research

scientific article

A broader role for AmyR in Aspergillus niger: regulation of the utilisation of D-glucose or D-galactose containing oligo- and polysaccharides

scientific article published on 27 August 2011

A community-driven reconstruction of the metabolic network

scientific article published on 26 September 2018

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

A genomic survey of proteases in Aspergilli

scientific article

A novel L-arabinose-responsive regulator discovered in the rice-blast fungus Pyricularia oryzae (Magnaporthe oryzae).

scientific article published on 21 January 2016

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

scientific article published on 20 January 2018

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

scientific article published on 12 August 2009

ARA1 regulates not only L-arabinose but also D-galactose catabolism in Trichoderma reesei.

scientific article

Accumulation of recalcitrant xylan in mushroom-compost is due to a lack of xylan substituent removing enzyme activities of Agaricus bisporus

scientific article published on 26 June 2015

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

scientific article

Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales ⬇️

scientific article published on June 30, 2011

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

scientific article published on 24 February 2015

Aspergillus enzymes involved in degradation of plant cell wall polysaccharides

scientific article

Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism

scientific article published on 28 February 2014

Bacillus subtilis attachment to Aspergillus niger hyphae results in mutually altered metabolism

scientific article

Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity

scientific article published on November 2007

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

scientific article published on 22 March 2018

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

scientific article published on 24 January 2020

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

scientific article published on 04 November 2019

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

scientific article

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

scientific article

Carbohydrate-related enzymes of important Phytophthora plant pathogens

scientific article

Characterisation of three fungal glucuronoyl esterases on glucuronic acid ester model compounds.

scientific article

Characterization and biotechnological application of recombinant xylanases from Aspergillus nidulans

scientific article

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

Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger

scientific article

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

scientific article published on 27 September 2019

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

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin

scientific article published on 27 September 2017

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 genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

scientific article

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

scientific article published on 20 March 2012

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

scientific article

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

scientific article

Compatible solutes and fungal development

scientific article

Complementary symbiont contributions to plant decomposition in a fungus-farming termite.

scientific article

Compost Grown Agaricus bisporus Lacks the Ability to Degrade and Consume Highly Substituted Xylan Fragments

scientific article published on 3 August 2015

Construction of a cellulase hyper-expression system in Trichoderma reesei by promoter and enzyme engineering

scientific article (publication date: 8 February 2012)

Control and possible applications of a novel carrot-spoilage basidiomycete, Fibulorhizoctonia psychrophila

scientific article published on 5 January 2008

Cooperation of Aspergillus nidulans enzymes increases plant polysaccharide saccharification

scientific article published on 5 February 2016

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

scientific article published on 22 December 2015

CreA modulates the XlnR-induced expression on xylose of Aspergillus niger genes involved in xylan degradation

article

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

scientific article

Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper.

scientific article published on 31 August 2016

D-Galactose uptake is nonfunctional in the conidiospores of Aspergillus niger

scientific article published on 28 February 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

scientific article

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

scientific article published on 09 April 2019

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

Disruption of photoautotrophic intertidal mats by filamentous fungi.

scientific article published on 28 February 2015

Disruption of the L-arabitol dehydrogenase encoding gene in Aspergillus tubingensis results in increased xylanase production

scientific article published on 26 June 2013

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

scientific article

Draft Genome Sequence of Talaromyces adpressus.

scientific article published on 11 January 2018

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

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

article

Efficient plant biomass degradation by thermophilic fungus Myceliophthora heterothallica

scientific article

Enhancing saccharification of wheat straw by mixing enzymes from genetically-modified Trichoderma reesei and Aspergillus niger

scientific article

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

scientific article published on 08 October 2018

Establishment of compatibility in the Ustilago maydis/maize pathosystem

scientific article published on 01 October 2007

Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

scientific article published on 14 November 2019

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

scientific article

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Expression profiling of pectinolytic genes from Aspergillus niger

scientific article published in October 2002

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

scientific article

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

scientific article

FluG affects secretion in colonies 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 Stress Database (FSD)––a repository of fungal stress physiological data.

scientific article published on 12 February 2018

Fungal enzyme sets for plant polysaccharide degradation

scientific article

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

GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger

scientific article published on 12 October 2012

Generic names in Magnaporthales

scientific article

Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression

scientific article published on 18 November 2015

Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness

publication published on 16 March 2021

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

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

scientific article published on 8 October 2012

Genome sequence of the model mushroom Schizophyllum commune

scientific article

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

scientific article

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

scientific article

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

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

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

scientific article

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

scientific article published on 14 November 2019

Glycerol dehydrogenase, encoded by gldB is essential for osmotolerance in Aspergillus nidulans

scientific article published on July 2003

Growing a circular economy with fungal biotechnology: a white paper

scientific article published on 02 April 2020

Growth and hydrolase profiles can be used as characteristics to distinguish Aspergillus niger and other black aspergilli.

scientific article

Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies

scientific article

High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger

scientific article published on 13 October 2017

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

scientific article

Hydrolytic potential of five fungal supernatants to enhance a commercial enzyme cocktail.

scientific article

Identification of an l-Arabitol Transporter from Aspergillus niger

scientific article published in 2023

Identification of genes encoding microbial glucuronoyl esterases

article

Improving cellulase production by Aspergillus niger using adaptive evolution

scientific article published on 15 February 2016

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

scientific article published on 18 May 2018

In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR.

scientific article published on 6 November 2017

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

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

scientific article published on 28 March 2012

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

scientific article

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

article

Isolation and characterization of two specific regulatory Aspergillus niger mutants shows antagonistic regulation of arabinan and xylan metabolism

scientific article published in May 2003

Localization of protein secretion in fungal colonies using a novel culturing technique; the ring-plate system

scientific article published on 18 January 2007

Mannitol is required for stress tolerance in Aspergillus niger conidiospores

scientific article

Mapping the polysaccharide degradation potential of Aspergillus niger

scientific article

Microbial Interactions

scientific article published on 01 May 2017

Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran

scientific article

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

scientific article published on 25 November 2019

Modern taxonomy of biotechnologically important Aspergillus and Penicillium species

scientific article

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

scientific article published on 16 September 2019

N-acetylglucosamine, the building block of chitin, inhibits growth of Neurospora crassa.

scientific article published on 20 July 2017

Nutritional physiology of a rock-inhabiting, model microcolonial fungus from an ancestral lineage of the Chaetothyriales (Ascomycetes).

scientific article

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

scientific article

On the origin of vanillyl alcohol oxidases.

scientific article published on 4 April 2018

Overexpression, purification and characterisation of homologous α-L-arabinofuranosidase and endo-1,4-β-D-glucanase in Aspergillus vadensis

scientific article

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

Phylogenetic analysis and substrate specificity of GH2 β-mannosidases from Aspergillus species

scientific article published on 07 September 2013

Physiological and molecular aspects of degradation of plant polysaccharides by fungi: what have we learned from Aspergillus?

scientific article

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

scientific article published on 31 August 2018

Plant biomass degradation by fungi

article

Plant biomass degradation by fungi

scientific article

Plant-polysaccharide-degrading enzymes from Basidiomycetes

scientific article

Post-genomic approaches to understanding interactions between fungi and their environment.

scientific article

Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

scientific article published on March 2009

Prevalence of transcription factors in ascomycete and basidiomycete fungi

scientific article

Protease and lipase activities of fungal and bacterial strains derived from an artisanal raw ewe's milk cheese.

scientific article

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

Regulation of pentose utilisation by AraR, but not XlnR, differs in Aspergillus nidulans and Aspergillus niger

scientific article

Regulation of plant biomass utilization in Aspergillus

scientific article

Regulation of the feruloyl esterase (faeA) gene from Aspergillus niger.

scientific article

Regulators of plant biomass degradation in ascomycetous fungi.

scientific article

Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae).

scientific article

Secondary metabolite profiling, growth profiles and other tools for species recognition and important Aspergillus mycotoxins.

scientific article published in January 2007

Secretion of small proteins is species-specific within Aspergillus sp.

scientific article

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

scientific article published on 25 January 2018

Sexual crossing of thermophilic fungus Myceliophthora heterothallica improved enzymatic degradation of sugar beet pulp

scientific article published on 20 February 2016

Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi.

scientific article

Spatial and developmental differentiation of mannitol dehydrogenase and mannitol-1-phosphate dehydrogenase in Aspergillus niger

scientific article

Spatial differentiation in the vegetative mycelium of Aspergillus niger

scientific article published on 19 October 2007

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization.

scientific article published on 28 August 2015

Stability of feruloyl esterases from Aspergillus ⬇️

scientific article published on 01 May 1998

Sugar catabolism in Aspergillus and other fungi related to the utilization of plant biomass

scientific article published on 12 November 2014

Synergistic effect of Aspergillus niger and Trichoderma reesei enzyme sets on the saccharification of wheat straw and sugarcane bagasse

scientific article

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

scientific article published on 01 March 2018

Technical advance in fungal biotechnology: development of a miniaturized culture method and an automated high-throughput screening.

scientific article

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 2008 update of the Aspergillus nidulans genome annotation: a community effort

scientific article

The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds

scientific article published on April 2002

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

scientific article published on 25 August 2021

The Hypocrea jecorina (syn. Trichoderma reesei) lxr1 gene encodes a D-mannitol dehydrogenase and is not involved in L-arabinose catabolism

scientific article published on 21 March 2009

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

scientific article

The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

scientific article

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

The amsterdam declaration on fungal nomenclature.

scientific article

The beta-1,4-endogalactanase A gene from Aspergillus niger is specifically induced on arabinose and galacturonic acid and plays an important role in the degradation of pectic hairy regions

scientific article

The distinctive regulatory roles of PrtT in the cell metabolism of Penicillium oxalicum

scientific article

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 genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

scientific article

The genome sequence of the model ascomycete fungus Podospora anserina

scientific article

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

scientific article

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

scientific article published on 01 September 2018

The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse

scientific article published on 26 July 2013

The influence of pretreatment methods on saccharification of sugarcane bagasse by an enzyme extract from Chrysoporthe cubensis and commercial cocktails: A comparative study

scientific article published on 14 June 2015

The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger

scientific article published on 27 June 2015

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 obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet

article

The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger.

scientific article published on 18 April 2017

The pentose catabolic pathway of the rice-blast fungus Magnaporthe oryzae involves a novel pentose reductase restricted to few fungal species

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

The secretome of the maize pathogen Ustilago maydis

scientific article published on 31 March 2008

The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin

scientific article published on 13 May 2016

The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger.

scientific article published on October 1998

The transcriptional activators AraR and XlnR from Aspergillus niger regulate expression of pentose catabolic and pentose phosphate pathway genes

scientific article

The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115).

scientific article published on 26 March 2011

Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse

scientific article published on 18 October 2011

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

scientific article published on 14 November 2019

Two glucuronoyl esterases of Phanerochaete chrysosporium

scientific article

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

scientific article published on 28 June 2015

Unique regulatory mechanism for D-galactose utilization in Aspergillus nidulans

scientific article published on 05 August 2011

Volatile compound profiling of Turkish Divle Cave cheese during production and ripening.

scientific article

Xlr1 is involved in the transcriptional control of the pentose catabolic pathway, but not hemi-cellulolytic enzymes in Magnaporthe oryzae

scientific article published on 27 June 2013

aguA , the Gene Encoding an Extracellular α-Glucuronidase from Aspergillus tubingensis , Is Specifically Induced on Xylose and Not on Glucuronic Acid ⬇️

scientific article published on January 1, 1998

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

scientific article published on 26 November 2018

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