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

Transcription of lignocellulose-decomposition associated genes, enzyme activities and production of ethanol upon bioconversion of waste substrate by Phlebia radiata

(2018) Mari A. Mäkinen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Processive Degradation of Crystalline Cellulose by a Multimodular Endoglucanase via a Wirewalking Mode

(2018) Kun-Di Zhang et al.   BIOMACROMOLECULES

Multi-genome analysis identifies functional and phylogenetic diversity of basidiomycete adenylate-forming reductases

(2018) Eileen Brandenburger et al.   FUNGAL GENETICS AND BIOLOGY

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

Lytic xylan oxidases from wood-decay fungi unlock biomass degradation

(2018) Marie Couturier et al.   Nature Chemical Biology

The impact of hydrogen peroxide supply on LPMO activity and overall saccharification efficiency of a commercial cellulase cocktail

(2018) Gerdt Müller et al.   Biotechnology for Biofuels

Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass

(2018) Bastien Bissaro et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A revised family-level classification of the Polyporales ( Basidiomycota )

(2017) Alfredo Justo et al.   Fungal Biology

Lignin transformations for high value applications: towards targeted modifications using green chemistry

(2017) S. Gillet et al.   GREEN CHEMISTRY

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus

(2017) Daria Feldman et al.   Scientific Reports

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

(2017) Tuulia Mali et al.   PLoS One

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

(2017) Jana Sperschneider et al.   Scientific Reports

Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana

(2017) Tommaso Raffaello et al.   Scientific Reports

A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness

(2016) Irina S. Druzhinina et al.   Biotechnology for Biofuels

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose

(2016) Jaana Kuuskeri et al.   Biotechnology for Biofuels

Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution

(2016) László G. Nagy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase

(2016) Gaston Courtade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellulose Degradation by Polysaccharide Monooxygenases

(2015) William T. Beeson et al.   Annual Review of Biochemistry

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment

(2015) Patrik Koskinen et al.   BIOINFORMATICS

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus

(2015) Marie Couturier et al.   Biotechnology for Biofuels

Diversity and evolution of ABC proteins in mycorrhiza-forming fungi

(2015) Andriy Kovalchuk et al.   BMC EVOLUTIONARY BIOLOGY

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

(2015) Jaana Kuuskeri et al.   BMC MICROBIOLOGY

Revisiting the taxonomy of Phanerochaete (Polyporales, Basidiomycota) using a four gene dataset and extensive ITS sampling

(2015) Dimitrios Floudas et al.   Fungal Biology

Putative endoglucanase PcGH5 from Phanerochaete chrysosporium is a β-xylosidase that cleaves xylans in synergistic action with endo-xylanase

(2015) Nguyen Duc Huy et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Lytic Polysaccharide Monooxygenases in Biomass Conversion

(2015) Glyn R. Hemsworth et al.   TRENDS IN BIOTECHNOLOGY

Transcriptomic Responses of Phanerochaete chrysosporium to Oak Acetonic Extracts: Focus on a New Glutathione Transferase

(2014) Anne Thuillier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional and Phylogenetic Divergence of Fungal Adenylate-Forming Reductases

(2014) Daniel Kalb et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomics of wood-degrading fungi

(2014) Robin A. Ohm et al.   FUNGAL GENETICS AND BIOLOGY

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

(2014) Johanna Rytioja et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Mitochondrial Genome of Phlebia radiata Is the Second Largest (156 kbp) among Fungi and Features Signs of Genome Flexibility and Recent Recombination Events

(2014) Heikki Salavirta et al.   PLoS One

Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation

(2014) J. W. Agger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

(2014) Chiaki Hori et al.   PLoS Genetics

Evolutionary analysis of hydrophobin gene family in two wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l.

(2013) Anthony C Mgbeahuruike et al.   BMC EVOLUTIONARY BIOLOGY

Diversity and evolution of ABC proteins in basidiomycetes

(2013) Andriy Kovalchuk et al.   MYCOLOGIA

Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay

(2013) Chiaki Hori et al.   MYCOLOGIA

Phylogenetic and phylogenomic overview of the Polyporales

(2013) Manfred Binder et al.   MYCOLOGIA

Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes

(2013) Francisco J. Ruiz-Dueñas et al.   MYCOLOGIA

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Characterization of a Broad-Specificity β-Glucanase Acting on β-(1,3)-, β-(1,4)-, and β-(1,6)-Glucans That Defines a New Glycoside Hydrolase Family

(2012) Mickael Lafond et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Novel enzymes for the degradation of cellulose

(2012) Svein Horn et al.   Biotechnology for Biofuels

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

(2012) Henrik Aspeborg et al.   BMC EVOLUTIONARY BIOLOGY

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

(2012) Hitoshi Suzuki et al.   BMC GENOMICS

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

(2012) Miia R. Mäkelä et al.   Fungal Biology

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

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

(2012) Åke Olson et al.   NEW PHYTOLOGIST

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

(2012) D. Floudas et al.   SCIENCE

Hydrophobins—Unique Fungal Proteins

(2012) Jagadeesh Bayry et al.   PLoS Pathogens

Fungal enzyme sets for plant polysaccharide degradation

(2011) Joost van den Brink et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

New and classic families of secreted fungal heme peroxidases

(2010) Martin Hofrichter et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

(2009) Heather M. Hood et al.   Annual Review of Microbiology

Surface hydrophobin prevents immune recognition of airborne fungal spores

(2009) Vishukumar Aimanianda et al.   NATURE

The search for the fungal tree of life

(2009) David J. McLaughlin et al.   TRENDS IN MICROBIOLOGY

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS