Published in PLoS One on August 08, 2016
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res (2000) 49.22
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
BLAST+: architecture and applications. BMC Bioinformatics (2009) 36.53
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (2014) 28.04
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res (2008) 13.51
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics (2003) 9.53
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One (2012) 9.30
Gene finding in novel genomes. BMC Bioinformatics (2004) 8.64
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res (2007) 6.48
CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res (2012) 6.39
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res (2014) 6.00
Swiss-Prot: juggling between evolution and stability. Brief Bioinform (2004) 5.73
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature (2008) 5.42
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (2012) 4.93
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res (2012) 4.91
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol (2004) 4.85
SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics (2010) 4.76
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res (2008) 4.38
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (2010) 4.18
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res (2005) 4.13
HISAT: a fast spliced aligner with low memory requirements. Nat Methods (2015) 2.83
GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics (2012) 2.72
Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A (2009) 2.71
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science (2011) 2.67
Mushroom nutriceuticals. World J Microbiol Biotechnol (1996) 2.55
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet (2015) 2.51
Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol (2010) 2.44
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics (2008) 1.79
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A (2012) 1.74
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A (2014) 1.70
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One (2012) 1.54
Approaches to Fungal Genome Annotation. Mycology (2011) 1.47
Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. Appl Environ Microbiol (2009) 1.44
Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol (2013) 1.33
Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun (2012) 1.30
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol (2012) 1.26
Bioconversion of agrowastes by Lentinula edodes: the high potential of viticulture residues. Appl Microbiol Biotechnol (2005) 1.10
Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One (2014) 1.08
Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PLoS One (2013) 1.03
Differential effects of shiitake- and white button mushroom-supplemented diets on hepatic steatosis in C57BL/6 mice. Food Chem Toxicol (2011) 0.97
Fungal enzymes for environmental management. Curr Opin Biotechnol (2015) 0.91
The effects of whole mushrooms during inflammation. BMC Immunol (2009) 0.89
Biodegradation of dyes and polyaromatic hydrocarbons by two allelic forms of Lentinula edodes laccase expressed from Pichia pastoris. Bioresour Technol (2011) 0.88
Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood. Appl Environ Microbiol (2015) 0.87
Characterization of the Lentinula edodes exg2 gene encoding a lentinan-degrading exo-beta-1,3-glucanase. Curr Genet (2005) 0.87
Cloning of the Lentinula edodes B mating-type locus and identification of the genetic structure controlling B mating. Gene (2013) 0.87
Composition and expression of genes encoding carbohydrate-active enzymes in the straw-degrading mushroom Volvariella volvacea. PLoS One (2013) 0.86
Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes. Fungal Biol (2014) 0.84
Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol (2016) 0.83
The genetic structure of the A mating-type locus of Lentinula edodes. Gene (2013) 0.83
A novel Lentinula edodes laccase and its comparative enzymology suggest guaiacol-based laccase engineering for bioremediation. PLoS One (2013) 0.82
Grouping of multicopper oxidases in Lentinula edodes by sequence similarities and expression patterns. AMB Express (2015) 0.76
Improvement of yield of the edible and medicinal mushroom Lentinula edodes on wheat straw by use of supplemented spawn. Braz J Microbiol (2014) 0.76
Cultivation of oyster mushroom Pleurotus ostreatus on date-palm leaves mixed with other agro-wastes in Saudi Arabia. Saudi J Biol Sci (2014) 0.76
Isolation and transcript analysis of two-component histidine kinase gene Le.nik1 in Shiitake mushroom, Lentinula edodes. Mycol Res (2007) 0.76
A novel cysteine desulfurase influencing organosulfur compounds in Lentinula edodes. Sci Rep (2015) 0.76