Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation

Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes

(2016) Donghwan Shim et al.   JOURNAL OF BIOTECHNOLOGY

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

Fungal enzymes for environmental management

(2015) Ursula Kües   CURRENT OPINION IN BIOTECHNOLOGY

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

(2015) Annegret Kohler et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Grouping of multicopper oxidases in Lentinula edodes by sequence similarities and expression patterns

(2015) Yuichi Sakamoto et al.   AMB Express

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Improvement of yield of the edible and medicinal mushroom Lentinula edodes on wheat straw by use of supplemented spawn

(2014) Rigoberto Gaitán-Hernández et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes

(2014) Wen-Bing Gong et al.   Fungal Biology

Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation

(2014) Young-Jin Park et al.   PLoS One

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

Cultivation of oyster mushroom Pleurotus ostreatus on date-palm leaves mixed with other agro-wastes in Saudi Arabia

(2014) Kholoud M. Alananbeh et al.   SAUDI JOURNAL OF BIOLOGICAL SCIENCES

Cloning of the Lentinula edodes B mating-type locus and identification of the genetic structure controlling B mating

(2013) Lin Wu et al.   GENE

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Composition and Expression of Genes Encoding Carbohydrate-Active Enzymes in the Straw-Degrading Mushroom Volvariella volvacea

(2013) Bingzhi Chen et al.   PLoS One

Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome

(2013) Dapeng Bao et al.   PLoS One

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

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

(2012) E. Morin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) D. Floudas et al.   SCIENCE

Genome sequence of the model medicinal mushroom Ganoderma lucidum

(2012) Shilin Chen et al.   Nature Communications

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

Biodegradation of dyes and polyaromatic hydrocarbons by two allelic forms of Lentinula edodes laccase expressed from Pichia pastoris

(2011) Kin-Sing Wong et al.   BIORESOURCE TECHNOLOGY

Differential effects of shiitake- and white button mushroom-supplemented diets on hepatic steatosis in C57BL/6 mice

(2011) Lawrance C. Chandra et al.   FOOD AND CHEMICAL TOXICOLOGY

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

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

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

Genome sequence of the model mushroom Schizophyllum commune

(2010) Robin A Ohm et al.   NATURE BIOTECHNOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

(2010) J. E. Stajich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and Secretome Analyses of Phanerochaete chrysosporium Reveal Complex Patterns of Gene Expression

(2009) A. Vanden Wymelenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The effects of whole mushrooms during inflammation

(2009) Sanhong Yu et al.   BMC IMMUNOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors

(2008) J. Park et al.   BIOINFORMATICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Isolation and transcript analysis of two-component histidine kinase gene Le.nik1 in Shiitake mushroom, Lentinula edodes

(2007) Carol Y.Y. Szeto et al.