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

Climate, decay, and the death of the coal forests

(2016) David Hibbett et al.   CURRENT BIOLOGY

Delayed fungal evolution did not cause the Paleozoic peak in coal production

(2016) Matthew P. Nelsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

(2015) Premsagar Korripally et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Thermal and moisture habitat preferences do not maximize jumping performance in frogs

(2015) Allegra Mitchell et al.   FUNCTIONAL ECOLOGY

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

(2015) Dimitrios Floudas et al.   FUNGAL GENETICS AND BIOLOGY

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities

(2015) László G. Nagy et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Annegret Kohler et al.   NATURE GENETICS

Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium

(2014) Jill Gaskell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

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

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

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

(2014) László G. Nagy et al.   Nature Communications

Finding the true $1000 genome

(2013) Jeffrey Perkel   BIOTECHNIQUES

Carbohydrate-binding modules (CBMs) revisited: reduced amount of water counterbalances the need for CBMs

(2013) Anikó Várnai et al.   Biotechnology for Biofuels

MycoCosm portal: gearing up for 1000 fungal genomes

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

Detection of Genomic Idiosyncrasies Using Fuzzy Phylogenetic Profiles

(2013) Fotis E. Psomopoulos et al.   PLoS One

Combining Phylogenetic Profiling-Based and Machine Learning-Based Techniques to Predict Functional Related Proteins

(2013) Tzu-Wen Lin et al.   PLoS One

Diversification of Fungal Specific Class A Glutathione Transferases in Saprotrophic Fungi

(2013) Yann Mathieu et al.   PLoS One

Xenomic networks variability and adaptation traits in wood decaying fungi

(2013) Mélanie Morel et al.   Microbial Biotechnology

Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling

(2012) Martin Simonsen et al.   BIOINFORMATICS

Novel enzymes for the degradation of cellulose

(2012) Svein Horn et al.   Biotechnology for Biofuels

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

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

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

(2012) Yi-Chieh Wu et al.   SYSTEMATIC BIOLOGY

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

(2011) D. C. Eastwood et al.   SCIENCE

Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium

(2010) A. Vanden Wymelenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New and classic families of secreted fungal heme peroxidases

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

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

(2010) Mukul S Bansal et al.   BMC BIOINFORMATICS

The fungal glutathione S-transferase system. Evidence of new classes in the wood-degrading basidiomycete Phanerochaete chrysosporium

(2009) Mélanie Morel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Phylogenetic analysis, genomic organization, and expression analysis of multi-copper oxidases in the ectomycorrhizal basidiomycete Laccaria bicolor

(2009) P. E. Courty et al.   NEW PHYTOLOGIST

Genome, transcriptome, and secretome analysis of wood decay fungusPostia placentasupports unique mechanisms of lignocellulose conversion

(2009) Diego Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial degradation of lignin: how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this

(2009) Francisco J. Ruiz-Dueñas et al.   Microbial Biotechnology

Complex phylogenetic profiling reveals fundamental genotype–phenotype associations

(2008) Alexey V. Antonov et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Dealing with incongruence in phylogenomic analyses

(2008) N. Galtier et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE